使用 DSPy 进行提示优化
最后更新:2024 年 10 月 3 日

在使用 LLM 构建应用程序时,编写有效的提示是一个漫长而反复试验的过程。通常,如果您更换模型,也需要更改提示。如果能自动化这个过程会怎么样?
这就是 DSPy 的用武之地——一个旨在通过算法优化语言模型提示的框架。通过应用经典的机器学习概念(训练和评估数据、指标、优化),DSPy 为给定的模型和任务生成更好的提示。
在本 notebook 中,我们将了解如何将 DSPy 与 Haystack 管道的稳健性相结合。
- ▶️ 从具有基本提示的 Haystack RAG 管道开始
- 🎯 定义一个目标(在本例中,获得正确且简洁的答案)
- 📊 创建一个 DSPy 程序,定义数据和指标
- ✨ 优化和评估 -> 改进提示
- 🚀 使用优化后的提示构建一个精炼的 Haystack RAG 管道
设置
! pip install haystack-ai datasets dspy-ai sentence-transformers
import os
from getpass import getpass
from rich import print
if "OPENAI_API_KEY" not in os.environ:
os.environ["OPENAI_API_KEY"] = getpass("Enter OpenAI API key:")
加载数据
我们将使用一个标记的 PubMed 数据集的前 1000 行,该数据集包含问题、上下文和答案。
最初,我们将仅使用上下文作为文档并将其写入 Document Store。
(稍后,我们还将使用一小部分数据集中的问题和答案来创建用于优化的训练集和开发集。)
from datasets import load_dataset
from haystack import Document
dataset = load_dataset("vblagoje/PubMedQA_instruction", split="train")
dataset = dataset.select(range(1000))
docs = [Document(content=doc["context"]) for doc in dataset]
/usr/local/lib/python3.10/dist-packages/huggingface_hub/utils/_token.py:81: UserWarning:
Access to the secret `HF_TOKEN` has not been granted on this notebook.
You will not be requested again.
Please restart the session if you want to be prompted again.
warnings.warn(
Downloading readme: 0%| | 0.00/498 [00:00<?, ?B/s]
Downloading data files: 0%| | 0/2 [00:00<?, ?it/s]
Downloading data: 0%| | 0.00/274M [00:00<?, ?B/s]
Downloading data: 0%| | 0.00/986k [00:00<?, ?B/s]
Extracting data files: 0%| | 0/2 [00:00<?, ?it/s]
Generating train split: 0%| | 0/272458 [00:00<?, ? examples/s]
Generating test split: 0%| | 0/1000 [00:00<?, ? examples/s]
from haystack.document_stores.in_memory import InMemoryDocumentStore
document_store = InMemoryDocumentStore()
document_store.write_documents(docs)
1000
document_store.filter_documents()[:5]
[Document(id=f6fde0752a035f7a15860dfa6c45d3ee05380198f18abf43b7b4923ec44c9985, content: 'Chronic rhinosinusitis (CRS) is a heterogeneous disease with an uncertain pathogenesis. Group 2 inna...'),
Document(id=8889ef27dbfe0b3cc5ba24652b393fc9e39cd49d21db1b7dbeb8a79363b4fb12, content: 'Phosphatidylethanolamine N-methyltransferase (PEMT), a liver enriched enzyme, is responsible for app...'),
Document(id=699ac0bd51891960eb58709be9f2ffef41fcbc7ea51f247c7b922e3ad1e358c3, content: 'Psammaplin A (PsA) is a natural product isolated from marine sponges, which has been demonstrated to...'),
Document(id=8c714387bf3999ef9b3e11997d8dc5f894ee2ffc281202db4c1a66faf65e5752, content: 'This study examined links between DNA methylation and birth weight centile (BWC), and explored the i...'),
Document(id=7a59e616dab6b59e767513a13b3cd3551843c52d3349c1fd2a6c827b9885912c, content: 'Tumor microenvironment immunity is associated with breast cancer outcome. A high lymphocytic infiltr...')]
初始 Haystack 管道
让我们在 Haystack 中创建一个简单的 RAG 管道。有关更多信息,请参阅文档。
接下来,我们将介绍如何改进提示。
from haystack.components.retrievers.in_memory import InMemoryBM25Retriever
from haystack.components.generators import OpenAIGenerator
from haystack.components.builders import PromptBuilder
from haystack import Pipeline
retriever = InMemoryBM25Retriever(document_store, top_k=3)
generator = OpenAIGenerator(model="gpt-4o-mini")
template = """
Given the following information, answer the question.
Context:
{% for document in documents %}
{{ document.content }}
{% endfor %}
Question: {{question}}
Answer:
"""
prompt_builder = PromptBuilder(template=template)
rag_pipeline = Pipeline()
rag_pipeline.add_component("retriever", retriever)
rag_pipeline.add_component("prompt_builder", prompt_builder)
rag_pipeline.add_component("llm", generator)
rag_pipeline.connect("retriever", "prompt_builder.documents")
rag_pipeline.connect("prompt_builder", "llm")
<haystack.core.pipeline.pipeline.Pipeline object at 0x7d5a270a8ee0>
🚅 Components
- retriever: InMemoryBM25Retriever
- prompt_builder: PromptBuilder
- llm: OpenAIGenerator
🛤️ Connections
- retriever.documents -> prompt_builder.documents (List[Document])
- prompt_builder.prompt -> llm.prompt (str)
让我们问一些问题……
question = "What effects does ketamine have on rat neural stem cells?"
response = rag_pipeline.run({"retriever": {"query": question}, "prompt_builder": {"question": question}})
print(response["llm"]["replies"][0])
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Ketamine inhibits the proliferation of rat neural stem cells in a dose-dependent manner at concentrations of 200, 500, 800, and 1000µM. Additionally, ketamine decreases intracellular Ca(2+) concentration, suppresses protein kinase C-α (PKCα) activation, and phosphorylation of extracellular signal-regulated kinases 1/2 (ERK1/2) in rat neural stem cells. These effects do not seem to be mediated through caspase-3-dependent apoptosis.
question = "Is the anterior cingulate cortex linked to pain-induced depression?"
response = rag_pipeline.run({"retriever": {"query": question}, "prompt_builder": {"question": question}})
print(response["llm"]["replies"][0])
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Yes, the anterior cingulate cortex (ACC) is linked to pain-induced depression. The first study mentioned in the context compared the role of the ACC and the posterior insular cortex in chronic pain. It was found that lesions in the ACC prevented the anxiodepressive consequences of chronic pain, indicating a connection between the ACC and pain-induced depression. Additionally, optogenetic stimulation of the ACC was able to induce anxiety and depressive-like behaviors in naïve animals.
答案似乎是正确的,但假设我们的用例需要更短的答案。如何在保持正确性的同时调整提示以达到此效果?
DSPy
我们将使用 DSPy 自动优化我们的目标提示:获得正确且简短的答案。
我们将执行几个步骤
- 定义一个用于 RAG 的 DSPy 模块
- 创建训练集和开发集
- 定义一个指标
- 评估未优化的 RAG 模块
- 优化模块
- 评估优化的 RAG
总的来说,这些步骤遵循DSPy 指南中列出的步骤。
import dspy
from dspy.primitives.prediction import Prediction
lm = dspy.OpenAI(model='gpt-4o-mini')
dspy.settings.configure(lm=lm)
DSPy 签名
RAG 模块涉及两个主要任务(较小的模块):检索和生成。
对于生成,我们需要定义一个签名:对 DSPy 模块的输入/输出行为进行声明式规范。特别是,生成模块接收 context 和 question 作为输入,并返回 answer。
在 DSPy 中,文档字符串和字段描述用于创建提示。
class GenerateAnswer(dspy.Signature):
"""Answer questions with short factoid answers."""
context = dspy.InputField(desc="may contain relevant facts")
question = dspy.InputField()
answer = dspy.OutputField(desc="short and precise answer")
DSPy RAG 模块
__init__方法可用于声明子模块。- 模块的逻辑包含在
forward方法中。
ChainOfThought模块通过特定的提示(“让我们一步一步思考”)和示例来鼓励语言模型进行推理。论文- 我们希望重用我们的 Haystack 检索器和已索引的数据,因此我们也定义了一个
retrieve方法。
class RAG(dspy.Module):
def __init__(self):
super().__init__()
self.generate_answer = dspy.ChainOfThought(GenerateAnswer)
# this makes it possible to use the Haystack retriever
def retrieve(self, question):
results = retriever.run(query=question)
passages = [res.content for res in results['documents']]
return Prediction(passages=passages)
def forward(self, question):
context = self.retrieve(question).passages
prediction = self.generate_answer(context=context, question=question)
return dspy.Prediction(context=context, answer=prediction.answer)
创建训练集和开发集
通常,要使用 DSPy 进行提示优化,您需要为您的任务准备一些示例(或使用类似的数据集)。
训练集用于优化,而开发集用于评估。
我们使用原始标记的 PubMed 数据集中的 20 个和 50 个示例(问题和答案)分别创建它们。
trainset, devset=[],[]
for i,ex in enumerate(dataset):
example = dspy.Example(question = ex["instruction"], answer=ex["response"]).with_inputs('question')
if i<20:
trainset.append(example)
elif i<70:
devset.append(example)
else:
break
定义一个指标
定义指标是评估和优化我们提示的关键步骤。
正如我们在本示例中所示,指标可以以非常定制化的方式定义。
在我们的例子中,我们想关注两个方面:答案的正确性和简洁性。
- 对于正确性,我们使用预测答案和真实答案之间的语义相似性(Haystack SASEvaluator)。SAS 分数在 0 到 1 之间变化。
- 为了鼓励简短的答案,我们基于简单的数学公式添加了对长答案的惩罚。惩罚从 0(对于 20 个单词或更少的答案)到 0.5(对于 40 个单词或更多的答案)不等。
from haystack.components.evaluators import SASEvaluator
sas_evaluator = SASEvaluator()
sas_evaluator.warm_up()
def mixed_metric(example, pred, trace=None):
semantic_similarity = sas_evaluator.run(ground_truth_answers=[example.answer], predicted_answers=[pred.answer])["score"]
n_words=len(pred.answer.split())
long_answer_penalty=0
if 20<n_words<40:
long_answer_penalty = 0.025 * (n_words - 20)
elif n_words>=40:
long_answer_penalty = 0.5
return semantic_similarity - long_answer_penalty
/usr/local/lib/python3.10/dist-packages/huggingface_hub/file_download.py:1132: FutureWarning: `resume_download` is deprecated and will be removed in version 1.0.0. Downloads always resume when possible. If you want to force a new download, use `force_download=True`.
warnings.warn(
config.json: 0%| | 0.00/723 [00:00<?, ?B/s]
modules.json: 0%| | 0.00/229 [00:00<?, ?B/s]
config_sentence_transformers.json: 0%| | 0.00/122 [00:00<?, ?B/s]
README.md: 0%| | 0.00/4.13k [00:00<?, ?B/s]
sentence_bert_config.json: 0%| | 0.00/53.0 [00:00<?, ?B/s]
model.safetensors: 0%| | 0.00/1.11G [00:00<?, ?B/s]
tokenizer_config.json: 0%| | 0.00/402 [00:00<?, ?B/s]
sentencepiece.bpe.model: 0%| | 0.00/5.07M [00:00<?, ?B/s]
tokenizer.json: 0%| | 0.00/9.08M [00:00<?, ?B/s]
special_tokens_map.json: 0%| | 0.00/239 [00:00<?, ?B/s]
1_Pooling/config.json: 0%| | 0.00/190 [00:00<?, ?B/s]
评估未优化的 RAG 模块
让我们首先检查未优化的 RAG 模块在开发集上的表现。然后我们将对其进行优化。
uncompiled_rag = RAG()
from dspy.evaluate.evaluate import Evaluate
evaluate = Evaluate(
metric=mixed_metric, devset=devset, num_threads=1, display_progress=True, display_table=5
)
evaluate(uncompiled_rag)
0%| | 0/50 [00:00<?, ?it/s]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 0.7792506217956543 / 1 (77.9): 2%|▏ | 1/50 [00:04<04:03, 4.97s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 0.8678842559456825 / 2 (43.4): 4%|▍ | 2/50 [00:06<02:16, 2.85s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 1.7318382635712624 / 3 (57.7): 6%|▌ | 3/50 [00:08<02:00, 2.57s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 2.391386426985264 / 4 (59.8): 8%|▊ | 4/50 [00:10<01:50, 2.41s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 3.1987738981842995 / 5 (64.0): 10%|█ | 5/50 [00:12<01:40, 2.23s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 3.8259158387780188 / 6 (63.8): 12%|█▏ | 6/50 [00:14<01:36, 2.20s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 4.748057033121586 / 7 (67.8): 14%|█▍ | 7/50 [00:16<01:27, 2.04s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 5.402349318563938 / 8 (67.5): 16%|█▌ | 8/50 [00:18<01:25, 2.03s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 5.476948383450508 / 9 (60.9): 18%|█▊ | 9/50 [00:19<01:13, 1.80s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 5.55394357740879 / 10 (55.5): 20%|██ | 10/50 [00:22<01:21, 2.03s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 6.18200332224369 / 11 (56.2): 22%|██▏ | 11/50 [00:24<01:16, 1.96s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 6.7211928993463514 / 12 (56.0): 24%|██▍ | 12/50 [00:26<01:14, 1.97s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 6.770032941550016 / 13 (52.1): 26%|██▌ | 13/50 [00:27<01:07, 1.82s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 7.499305187910795 / 14 (53.6): 28%|██▊ | 14/50 [00:30<01:11, 1.99s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 8.13342869207263 / 15 (54.2): 30%|███ | 15/50 [00:31<01:03, 1.82s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 8.83576548025012 / 16 (55.2): 32%|███▏ | 16/50 [00:33<01:03, 1.88s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 9.76700830385089 / 17 (57.5): 34%|███▍ | 17/50 [00:35<01:06, 2.01s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 10.354306184500457 / 18 (57.5): 36%|███▌ | 18/50 [00:38<01:07, 2.12s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 10.397395987808705 / 19 (54.7): 38%|███▊ | 19/50 [00:39<01:00, 1.94s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 10.470511642098428 / 20 (52.4): 40%|████ | 20/50 [00:41<00:53, 1.77s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 11.366389837861062 / 21 (54.1): 42%|████▏ | 21/50 [00:43<00:55, 1.92s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 11.44212095141411 / 22 (52.0): 44%|████▍ | 22/50 [00:45<00:59, 2.13s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 11.885303872823716 / 23 (51.7): 46%|████▌ | 23/50 [00:48<01:00, 2.24s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 12.638070541620255 / 24 (52.7): 48%|████▊ | 24/50 [00:50<00:55, 2.12s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 13.284867602586747 / 25 (53.1): 50%|█████ | 25/50 [00:52<00:52, 2.11s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 13.344285535812379 / 26 (51.3): 52%|█████▏ | 26/50 [00:53<00:46, 1.93s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 13.874915313720704 / 27 (51.4): 54%|█████▍ | 27/50 [00:56<00:51, 2.23s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 14.445346760749818 / 28 (51.6): 56%|█████▌ | 28/50 [00:59<00:49, 2.27s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 14.46531408391893 / 29 (49.9): 58%|█████▊ | 29/50 [01:00<00:42, 2.04s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 14.587132939323784 / 30 (48.6): 60%|██████ | 30/50 [01:02<00:37, 1.89s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 14.979336270317436 / 31 (48.3): 62%|██████▏ | 31/50 [01:04<00:39, 2.06s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 15.796318897232414 / 32 (49.4): 64%|██████▍ | 32/50 [01:06<00:38, 2.11s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 16.553095170482994 / 33 (50.2): 66%|██████▌ | 33/50 [01:08<00:34, 2.05s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 16.621720285341144 / 34 (48.9): 68%|██████▊ | 34/50 [01:10<00:29, 1.87s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 17.3888682436198 / 35 (49.7): 70%|███████ | 35/50 [01:12<00:31, 2.09s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 17.926523668691516 / 36 (49.8): 72%|███████▏ | 36/50 [01:15<00:31, 2.22s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 18.750893218442798 / 37 (50.7): 74%|███████▍ | 37/50 [01:17<00:27, 2.09s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 19.441286904737353 / 38 (51.2): 76%|███████▌ | 38/50 [01:19<00:25, 2.15s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 19.763766403123736 / 39 (50.7): 78%|███████▊ | 39/50 [01:22<00:26, 2.41s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 20.659051413461565 / 40 (51.6): 80%|████████ | 40/50 [01:24<00:24, 2.41s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 20.696448824182152 / 41 (50.5): 82%|████████▏ | 41/50 [01:26<00:19, 2.17s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 21.432477793470024 / 42 (51.0): 84%|████████▍ | 42/50 [01:28<00:16, 2.05s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 21.788538274541498 / 43 (50.7): 86%|████████▌ | 43/50 [01:30<00:14, 2.05s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 21.783919956721366 / 44 (49.5): 88%|████████▊ | 44/50 [01:31<00:11, 1.90s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 22.562956538237632 / 45 (50.1): 90%|█████████ | 45/50 [01:33<00:09, 1.94s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 22.630986932851375 / 46 (49.2): 92%|█████████▏| 46/50 [01:35<00:06, 1.75s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 23.399105254746974 / 47 (49.8): 94%|█████████▍| 47/50 [01:37<00:05, 1.86s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 23.46025380138308 / 48 (48.9): 96%|█████████▌| 48/50 [01:38<00:03, 1.75s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 23.981951561011375 / 49 (48.9): 98%|█████████▊| 49/50 [01:40<00:01, 1.84s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 24.406892337836325 / 50 (48.8): 100%|██████████| 50/50 [01:43<00:00, 2.07s/it]
| 问题 | 示例答案 | 上下文 | 预测答案 | 混合指标 | |
|---|---|---|---|---|---|
| 0 | 新辅助放化疗到手术的时间延长是否与食管癌病理完全缓解率的提高相关? | 新辅助放化疗完成与手术之间的时间间隔延长与病理完全缓解率的提高相关,而对手术发病率没有影响。 | ['新辅助放化疗治疗到手术之间的时间间隔已被描述为非食管癌部位对治疗病理反应的重要预测因子。我们... | 是的,新辅助放化疗到手术的时间延长与食管癌病理完全缓解率的提高相关。 | ✔️ [0.7792506217956543] |
| 1 | 癫痫灶定位是否可以基于静息状态的间歇期 MEG 记录进行,而与尖峰是否存在无关? | 我们的初步结果表明,使用无创自发“静息状态”的相对较短持续时间且没有...的记录,可以实现对癫痫灶的准确定位。 | ['为了研究是否可以根据脑磁图 (MEG) 数据的静息状态连接分析来定位癫痫灶。构建了一个多元自回归 (MVAR) 模型... | 是的。 | ✔️ [0.08863363415002823] |
| 2 | 精液幽门螺杆菌治疗是否能改善不育弱精症男性的精子活力? | 幽门螺杆菌治疗可显著提高精液中幽门螺杆菌 IgA 水平升高的不育弱精症男性的精子活力。 | ['为了评估精液幽门螺杆菌治疗对不育弱精症男性的影响。共连续选取了 223 名不育弱精症男性。他们... | 是的,精液幽门螺杆菌治疗可改善不育弱精症男性的精子活力。 | ✔️ [0.8639540076255798] |
| 3 | 迁移的纤毛门是否将轴丝组装位点分隔在果蝇精子细胞中? | 我们的研究结果表明,纤毛门可以从纤毛基部迁移,从而独立于中心粒和...发挥作用。 | ['在大多数细胞中,纤毛在与细胞质分隔的区室内形成。进入纤毛区室受特殊门控... | 是的,迁移的纤毛门将轴丝组装位点分隔在果蝇精子细胞中。 | ✔️ [0.6595481634140015] |
| 4 | 个人公共交通可达性是否与自我报告的积极通勤呈正相关? | 本研究通过考察个人公共交通可达性,扩展了关于通勤使用公共交通的驱动因素的知识。研究结果表明... | ['积极通勤者患慢性病的风险较低。了解公共交通在一定程度上可改变的哪些特征促进其使用是... | 是的,个人公共交通可达性与自我报告的积极通勤呈正相关。 | ✔️ [0.8073874711990356] |
48.81
优化
现在我们可以编译/优化我们创建的 DSPy 程序。
这可以通过使用提示词生成器/优化器来完成,该优化器基于我们的指标和训练集。
特别是,BootstrapFewShot 尝试通过在提示中添加少量示例来改进训练集中的指标。
from dspy.teleprompt import BootstrapFewShot
optimizer = BootstrapFewShot(metric=mixed_metric)
compiled_rag = optimizer.compile(RAG(), trainset=trainset)
0%| | 0/20 [00:00<?, ?it/s]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
5%|▌ | 1/20 [00:04<01:17, 4.06s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
10%|█ | 2/20 [00:09<01:26, 4.80s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
15%|█▌ | 3/20 [00:12<01:10, 4.16s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
20%|██ | 4/20 [00:14<00:59, 3.71s/it]
评估优化的 RAG 模块
现在让我们通过在开发集上评估编译后的 RAG 模块来查看训练是否成功。
evaluate = Evaluate(
metric=mixed_metric, devset=devset, num_threads=1, display_progress=True, display_table=5
)
evaluate(compiled_rag)
0%| | 0/50 [00:00<?, ?it/s]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 0.7792506217956543 / 1 (77.9): 2%|▏ | 1/50 [00:02<02:01, 2.47s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 1.6343245267868043 / 2 (81.7): 4%|▍ | 2/50 [00:05<02:07, 2.66s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 2.5054827690124513 / 3 (83.5): 6%|▌ | 3/50 [00:07<02:04, 2.65s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 3.1650309324264527 / 4 (79.1): 8%|▊ | 4/50 [00:10<01:58, 2.57s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 3.9724184036254884 / 5 (79.4): 10%|█ | 5/50 [00:12<01:50, 2.45s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 4.743226420879364 / 6 (79.1): 12%|█▏ | 6/50 [00:15<01:52, 2.55s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 5.667502892017365 / 7 (81.0): 14%|█▍ | 7/50 [00:17<01:44, 2.42s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 6.321795177459717 / 8 (79.0): 16%|█▌ | 8/50 [00:20<01:48, 2.58s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 6.726730477809906 / 9 (74.7): 18%|█▊ | 9/50 [00:22<01:36, 2.35s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 7.618233811855316 / 10 (76.2): 20%|██ | 10/50 [00:25<01:48, 2.72s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 8.246293556690215 / 11 (75.0): 22%|██▏ | 11/50 [00:27<01:39, 2.56s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 8.786842536926269 / 12 (73.2): 24%|██▍ | 12/50 [00:30<01:38, 2.58s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 9.534724307060241 / 13 (73.3): 26%|██▌ | 13/50 [00:33<01:41, 2.76s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 10.26323206424713 / 14 (73.3): 28%|██▊ | 14/50 [00:36<01:37, 2.70s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 10.897355568408965 / 15 (72.6): 30%|███ | 15/50 [00:38<01:25, 2.45s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 11.573097360134124 / 16 (72.3): 32%|███▏ | 16/50 [00:41<01:30, 2.67s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 12.40762699842453 / 17 (73.0): 34%|███▍ | 17/50 [00:45<01:41, 3.07s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 13.000101816654205 / 18 (72.2): 36%|███▌ | 18/50 [00:48<01:34, 2.96s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 13.781478297710418 / 19 (72.5): 38%|███▊ | 19/50 [00:50<01:28, 2.85s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 14.491218817234039 / 20 (72.5): 40%|████ | 20/50 [00:53<01:24, 2.83s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 15.387097012996673 / 21 (73.3): 42%|████▏ | 21/50 [00:56<01:23, 2.87s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 16.21189798116684 / 22 (73.7): 44%|████▍ | 22/50 [00:59<01:21, 2.92s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 16.994540107250213 / 23 (73.9): 46%|████▌ | 23/50 [01:02<01:16, 2.85s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 17.73131192922592 / 24 (73.9): 48%|████▊ | 24/50 [01:04<01:10, 2.70s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 18.378108990192413 / 25 (73.5): 50%|█████ | 25/50 [01:07<01:07, 2.69s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 18.83699902296066 / 26 (72.4): 52%|█████▏ | 26/50 [01:10<01:07, 2.79s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 19.51262959241867 / 27 (72.3): 54%|█████▍ | 27/50 [01:12<01:03, 2.77s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 20.026981341838834 / 28 (71.5): 56%|█████▌ | 28/50 [01:15<01:00, 2.75s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 20.51759134531021 / 29 (70.8): 58%|█████▊ | 29/50 [01:18<00:55, 2.66s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 21.18675976991653 / 30 (70.6): 60%|██████ | 30/50 [01:21<00:55, 2.76s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 21.72026966810226 / 31 (70.1): 62%|██████▏ | 31/50 [01:25<00:59, 3.13s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 22.53638147115707 / 32 (70.4): 64%|██████▍ | 32/50 [01:28<01:00, 3.34s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 23.25495295524597 / 33 (70.5): 66%|██████▌ | 33/50 [01:31<00:54, 3.19s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 23.510267066955564 / 34 (69.1): 68%|██████▊ | 34/50 [01:36<00:58, 3.65s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 23.84202444553375 / 35 (68.1): 70%|███████ | 35/50 [01:39<00:53, 3.59s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 24.518707108497615 / 36 (68.1): 72%|███████▏ | 36/50 [01:42<00:47, 3.37s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 25.346190285682674 / 37 (68.5): 74%|███████▍ | 37/50 [01:45<00:40, 3.12s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 26.039887082576747 / 38 (68.5): 76%|███████▌ | 38/50 [01:47<00:33, 2.82s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 26.78020550012588 / 39 (68.7): 78%|███████▊ | 39/50 [01:49<00:29, 2.64s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 27.52990843057632 / 40 (68.8): 80%|████████ | 40/50 [01:52<00:25, 2.59s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 28.188934934139247 / 41 (68.8): 82%|████████▏ | 41/50 [01:54<00:22, 2.53s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 28.92496390342712 / 42 (68.9): 84%|████████▍ | 42/50 [01:57<00:20, 2.57s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 29.63569481372833 / 43 (68.9): 86%|████████▌ | 43/50 [01:59<00:17, 2.50s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 30.31016762256622 / 44 (68.9): 88%|████████▊ | 44/50 [02:02<00:15, 2.61s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 31.04774541854858 / 45 (69.0): 90%|█████████ | 45/50 [02:05<00:14, 2.90s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 31.84949089288711 / 46 (69.2): 92%|█████████▏| 46/50 [02:08<00:11, 2.75s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 32.622128200531 / 47 (69.4): 94%|█████████▍| 47/50 [02:11<00:08, 2.72s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 33.349305582046505 / 48 (69.5): 96%|█████████▌| 48/50 [02:13<00:05, 2.76s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 33.87233598232269 / 49 (69.1): 98%|█████████▊| 49/50 [02:19<00:03, 3.77s/it]
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Average Metric: 34.496535253524776 / 50 (69.0): 100%|██████████| 50/50 [02:22<00:00, 2.86s/it]
| 问题 | 示例答案 | 上下文 | 预测答案 | 混合指标 | |
|---|---|---|---|---|---|
| 0 | 新辅助放化疗到手术的时间延长是否与食管癌病理完全缓解率的提高相关? | 新辅助放化疗完成与手术之间的时间间隔延长与病理完全缓解率的提高相关,而对手术发病率没有影响。 | ['新辅助放化疗治疗到手术之间的时间间隔已被描述为非食管癌部位对治疗病理反应的重要预测因子。我们... | 是的,新辅助放化疗到手术的时间延长与食管癌病理完全缓解率的提高相关。 | ✔️ [0.7792506217956543] |
| 1 | 癫痫灶定位是否可以基于静息状态的间歇期 MEG 记录进行,而与尖峰是否存在无关? | 我们的初步结果表明,使用无创自发“静息状态”的相对较短持续时间且没有...的记录,可以实现对癫痫灶的准确定位。 | ['为了研究是否可以根据脑磁图 (MEG) 数据的静息状态连接分析来定位癫痫灶。构建了一个多元自回归 (MVAR) 模型... | 是的,基于静息状态的间歇期 MEG 记录的癫痫灶定位是可行的,而与尖峰是否存在无关。 | ✔️ [0.8550739049911499] |
| 2 | 精液幽门螺杆菌治疗是否能改善不育弱精症男性的精子活力? | 幽门螺杆菌治疗可显著提高精液中幽门螺杆菌 IgA 水平升高的不育弱精症男性的精子活力。 | ['为了评估精液幽门螺杆菌治疗对不育弱精症男性的影响。共连续选取了 223 名不育弱精症男性。他们... | 是的,精液幽门螺杆菌治疗可改善不育弱精症男性的精子活力。 | ✔️ [0.871158242225647] |
| 3 | 迁移的纤毛门是否将轴丝组装位点分隔在果蝇精子细胞中? | 我们的研究结果表明,纤毛门可以从纤毛基部迁移,从而独立于中心粒和...发挥作用。 | ['在大多数细胞中,纤毛在与细胞质分隔的区室内形成。进入纤毛区室受特殊门控... | 是的,迁移的纤毛门将轴丝组装位点分隔在果蝇精子细胞中。 | ✔️ [0.6595481634140015] |
| 4 | 个人公共交通可达性是否与自我报告的积极通勤呈正相关? | 本研究通过考察个人公共交通可达性,扩展了关于通勤使用公共交通的驱动因素的知识。研究结果表明... | ['积极通勤者患慢性病的风险较低。了解公共交通在一定程度上可改变的哪些特征促进其使用是... | 是的,个人公共交通可达性与自我报告的积极通勤呈正相关。 | ✔️ [0.8073874711990356] |
68.99
根据我们的简单指标,我们取得了显著的改进!
检查优化后的提示
让我们来看看那些使我们的结果得到改进的少量示例……
lm.inspect_history(n=1)
Answer questions with short factoid answers.
---
Question: Do tumor-infiltrating immune cell profiles and their change after neoadjuvant chemotherapy predict response and prognosis of breast cancer?
Answer: Breast cancer immune cell subpopulation profiles, determined by immunohistochemistry-based computerized analysis, identify groups of patients characterized by high response (in the pre-treatment setting) and poor prognosis (in the post-treatment setting). Further understanding of the mechanisms underlying the distribution of immune cells and their changes after chemotherapy may contribute to the development of new immune-targeted therapies for breast cancer.
Question: Do large portion sizes increase bite size and eating rate in overweight women?
Answer: Increasing portion size led to a larger bite size and faster eating rate, but a slower reduction in eating speed during the meal. These changes may underlie greater energy intakes with exposure to large portions. Interventions to reduce bite size and slow eating rate may provide individuals with strategies to reduce the risk of overconsumption.
Question: Are secretory phospholipases A2 secreted from ciliated cells and increase mucin and eicosanoid secretion from goblet cells?
Answer: sPLA2 are secreted from ciliated cells and appear to induce mucin and cysLT secretion from goblet cells, strongly suggesting that airway goblet cells are proinflammatory effector cells.
Question: Are reasons why erupted third molars extracted in a public university in Mexico?
Answer: Women and patients 18 to 34 years of age had erupted 3M extracted more frequently, primarily for prosthetic reasons. The age profile indicated a trend in demand for services that differ from those of overall tooth extractions, but not for the trend across gender.
Question: Does increased Syk phosphorylation lead to overexpression of TRAF6 in peripheral B cells of patients with systemic lupus erythematosus?
Answer: Our results suggest that the activated Syk-mediated TRAF6 pathway leads to aberrant activation of B cells in SLE, and also highlight Syk as a potential target for B-cell-mediated processes in SLE.
Question: Are routine preoperative restaging CTs after neoadjuvant chemoradiation for locally advanced rectal cancer low yield : a retrospective case study?
Answer: Because of the financial costs and established risks of intravenous contrast and cumulative radiation exposure, it may be advisable to take a more selective approach to preoperative imaging. Larger, prospective studies may enable identification of an at-risk cohort who would benefit most from restaging CT.
Question: Does the Boston keratoprosthesis provide a wide depth of focus?
Answer: The KPro's wide depth-of-focus makes the visual acuity less dependent on an exact refractive correction at distance and explains the 'pseudoaccomodation' experienced by these patients. This is primarily due to the small pupil diameter of the KPro. The current manufacturing steps in 0.50 dioptre increments appears to be sufficient.
Question: Do obese patients with idiopathic pulmonary fibrosis have a higher 90-day mortality risk with bilateral lung transplantation?
Answer: Our results suggest that obese patients who receive a BLT may be at higher risk of 90-day mortality compared with patients of normal weight. Further study is needed to obtain more detailed information about comorbidities and other risk factors for early death that are not included in the OPTN database.
Question: Is admission hyperglycemia associated with failed reperfusion following fibrinolytic therapy in patients with STEMI : results of a retrospective study?
Answer: In patients with STEMI who undergo FT, admission hyperglycemia is an independent predictor of the failure of fibrinolysis.
Question: Is hidradenitis suppurativa a systemic disease with substantial comorbidity burden : a chart-verified case-control analysis?
Answer: Control subjects were not validated for absence of HS and comorbidity validation was not performed for either group.
Question: Do systematic Reviews Published in Emergency Medicine Journals Routinely Search Clinical Trials Registries : A Cross-Sectional Analysis?
Answer: Systematic reviews published in emergency medicine journals do not routinely include searches of clinical trials registries. By helping authors identify unpublished trial data, the addition of registry searches may improve the validity of systematic reviews.
Question: Does promoter variant rs2301228 on the neural cell adhesion molecule 1 gene confer risk of schizophrenia in Han Chinese?
Answer: Our results provide direct evidence for NCAM1 as a susceptibility gene for schizophrenia, which offers support to a neurodevelopmental model and neuronal connectivity hypothesis in the onset of schizophrenia.
---
Follow the following format.
Context: may contain relevant facts
Question: ${question}
Reasoning: Let's think step by step in order to ${produce the answer}. We ...
Answer: short and precise answer
---
Context:
[1] «Chronic rhinosinusitis (CRS) is a heterogeneous disease with an uncertain pathogenesis. Group 2 innate lymphoid cells (ILC2s) represent a recently discovered cell population which has been implicated in driving Th2 inflammation in CRS; however, their relationship with clinical disease characteristics has yet to be investigated. The aim of this study was to identify ILC2s in sinus mucosa in patients with CRS and controls and compare ILC2s across characteristics of disease. A cross-sectional study of patients with CRS undergoing endoscopic sinus surgery was conducted. Sinus mucosal biopsies were obtained during surgery and control tissue from patients undergoing pituitary tumour resection through transphenoidal approach. ILC2s were identified as CD45(+) Lin(-) CD127(+) CD4(-) CD8(-) CRTH2(CD294)(+) CD161(+) cells in single cell suspensions through flow cytometry. ILC2 frequencies, measured as a percentage of CD45(+) cells, were compared across CRS phenotype, endotype, inflammatory CRS subtype and other disease characteristics including blood eosinophils, serum IgE, asthma status and nasal symptom score. 35 patients (40% female, age 48 ± 17 years) including 13 with eosinophilic CRS (eCRS), 13 with non-eCRS and 9 controls were recruited. ILC2 frequencies were associated with the presence of nasal polyps (P = 0.002) as well as high tissue eosinophilia (P = 0.004) and eosinophil-dominant CRS (P = 0.001) (Mann-Whitney U). They were also associated with increased blood eosinophilia (P = 0.005). There were no significant associations found between ILC2s and serum total IgE and allergic disease. In the CRS with nasal polyps (CRSwNP) population, ILC2s were increased in patients with co-existing asthma (P = 0.03). ILC2s were also correlated with worsening nasal symptom score in CRS (P = 0.04).»
[2] «Allergic airway inflammation is triggered by allergen exposure through several steps including release of IL-33, which promotes cytokine (IL-5, IL-13) production by type 2 innate lymphoid cells (ILC2s). MicroRNA (miR)-155 has recently been described to regulate adaptive responses in allergic inflammation. However, the role of miR-155 in the regulation of ILC2s remains unexplored. We sought to elucidate the contribution of miR-155 in ILC2 expansion using experimental murine models of allergic airway inflammation. To determine the role of miR-155 in the regulation of ILC2s in allergic airway inflammation, miR-155 deficient (miR-155 miR-155 was 10-fold upregulated in WT-derived ILC2s in response to IL-33. Furthermore, miR-155»
[3] «The mechanisms and immune pathways associated with chronic rhinosinusitis (CRS) are not fully understood. Immunological changes during acute exacerbation of CRS may provide valuable clues to the pathogenesis and perpetuation of the disease. To characterize local and systemic immune responses associated with acute worsening of sinonasal symptoms during exacerbation in CRS with nasal polyps (CRSwNP) compared to controls. This was a non-interventional prospective study of individuals with CRSwNP and normal controls. Subjects underwent a baseline visit with collection of nasal secretions, nasal washes, and serum specimens. Within 3 days of acute worsening of sinonasal symptoms, subjects underwent a study visit, followed by a post-visit 2 weeks later. The sinonasal outcome test-22 (SNOT-22) scores and immunological parameters in the specimens were analysed using a novel, unsupervised learning method and by conventional univariate analysis. Both CRSwNP patients and control subjects showed a significant increase in SNOT-22 scores during acute exacerbation. Increased nasal levels of IL-6, IL-5, and eosinophil major basic protein were observed in CRSwNP patients. A network analysis of serum specimens revealed changes in a set of immunological parameters, which are distinctly associated with CRSwNP but not with controls. In particular, systemic increases in VEGF and GM-CSF levels were notable and were validated by a conventional analysis.»
Question: Are group 2 innate lymphoid cells ( ILC2s ) increased in chronic rhinosinusitis with nasal polyps or eosinophilia?
Reasoning: Let's think step by step in order to Answer: Yes, ILC2 frequencies are increased in chronic rhinosinusitis with nasal polyps, high tissue eosinophilia, and eosinophil-dominant CRS. They are also associated with increased blood eosinophilia and worsening nasal symptom scores.
Answer: Yes, ILC2 frequencies are increased in chronic rhinosinusitis with nasal polyps, high tissue eosinophilia, and eosinophil-dominant CRS. They are also associated with increased blood eosinophilia and worsening nasal symptom scores.
---
Context:
[1] «Phosphatidylethanolamine N-methyltransferase (PEMT), a liver enriched enzyme, is responsible for approximately one third of hepatic phosphatidylcholine biosynthesis. When fed a high-fat diet (HFD), Pemt(-/-) mice are protected from HF-induced obesity; however, they develop steatohepatitis. The vagus nerve relays signals between liver and brain that regulate peripheral adiposity and pancreas function. Here we explore a possible role of the hepatic branch of the vagus nerve in the development of diet induced obesity and steatohepatitis in Pemt(-/-) mice. 8-week old Pemt(-/-) and Pemt(+/+) mice were subjected to hepatic vagotomy (HV) or capsaicin treatment, which selectively disrupts afferent nerves, and were compared to sham-operated or vehicle-treatment, respectively. After surgery, mice were fed a HFD for 10 weeks. HV abolished the protection against the HFD-induced obesity and glucose intolerance in Pemt(-/-) mice. HV normalized phospholipid content and prevented steatohepatitis in Pemt(-/-) mice. Moreover, HV increased the hepatic anti-inflammatory cytokine interleukin-10, reduced chemokine monocyte chemotactic protein-1 and the ER stress marker C/EBP homologous protein. Furthermore, HV normalized the expression of mitochondrial electron transport chain proteins and of proteins involved in fatty acid synthesis, acetyl-CoA carboxylase and fatty acid synthase in Pemt(-/-) mice. However, disruption of the hepatic afferent vagus nerve by capsaicin failed to reverse either the protection against the HFD-induced obesity or the development of HF-induced steatohepatitis in Pemt(-/-) mice.»
[2] «Nonalcoholic steatohepatitis (NASH) is associated with cirrhosis and hepatocellular carcinoma. Reactive oxygen species (ROS) and reactive nitrogen species (RNS) play key roles in the development of the disease. However, the therapeutic target of NASH has not been fully defined and new treatments are needed. We investigated the protective effects of the antioxidant indole-derived NecroX-7 in a NASH mouse model using leptin-deficient ob/ob and methionine- and choline-deficient (MCD) diet-fed ob/ob mice. Six-week-old male mice were divided into three groups: ob/+ mice, ob/ob mice treated with vehicle and ob/ob mice treated daily with NecroX-7 (20 mg/kg) for 4 weeks. To study the effects of NecroX-7 in a fibrosis model, NASH was induced by feeding ob/ob mice an MCD diet. The effects of NecroX-7 on NASH progression were evaluated using biochemical, histological and molecular markers. NecroX-7-treated ob/ob mice had a marked decrease in serum aspartate aminotransferase and alanine transaminase compared with vehicle-treated controls. Interestingly, hepatic steatosis and lipid peroxidation were significantly improved by NecroX-7 treatment. NecroX-7 inhibited tert-butylhydroperoxide- and H2 O2 -induced mitochondrial ROS/RNS in primary hepatocytes and attenuated mitochondrial dysfunction in vitro and in vivo. Furthermore, NecroX-7-treated mice exhibited fewer infiltrating macrophages and reduced hepatic tumour necrosis factor-alpha expression. Hepatic fibrosis in MCD-fed ob/ob mice was significantly decreased by NecroX-7 treatment.»
[3] «The ability of a treatment method to interfere with tinnitus-related neural activity patterns, such as cortical gamma rhythms, has been suggested to indicate its potential in relieving tinnitus. Therapeutic modulation of gamma-band oscillations with vagus nerve stimulation has been recently reported in epileptic patients. The aim of this study was to investigate the effects of transcutaneous vagus nerve stimulation (tVNS) on neural oscillatory patterns. We calculated the power spectral density and synchrony of magnetoencephalography recordings during auditory stimulation in seven tinnitus patients and eight normal-hearing control subjects. Comparisons between subject groups were performed to reveal electrophysiological markers of tinnitus. tVNS-specific effects within each group were studied by comparing recording blocks with and without tVNS. We also investigated the correlation of each measure with individual ratings of tinnitus distress, as measured by the tinnitus handicap inventory questionnaire. Tinnitus patients differed from controls in the baseline condition (no tVNS applied), measured by both cortical oscillatory power and synchronization, particularly at beta and gamma frequencies. Importantly, we found tVNS-induced changes in synchrony, correlating strongly with tinnitus handicap inventory scores, at whole-head beta-band (r = -0.857, p = 0.007), whole-head gamma-band (r = -0.952, p = 0.0003), and frontal gamma-band (r = -0.952, p = 0.0003).»
Question: Does vagus nerve contribute to the development of steatohepatitis and obesity in phosphatidylethanolamine N-methyltransferase deficient mice?
Reasoning: Let's think step by step in order to Answer: Yes, the hepatic branch of the vagus nerve plays a role in the development of diet-induced obesity and steatohepatitis in Pemt(-/-) mice. Disruption of the hepatic vagus nerve abolished protection against high-fat diet-induced obesity and glucose intolerance in these mice, while also normalizing phospholipid content and preventing steatohepatitis.
Answer: Yes, the hepatic branch of the vagus nerve plays a role in the development of diet-induced obesity and steatohepatitis in Pemt(-/-) mice.
---
Context:
[1] «Psammaplin A (PsA) is a natural product isolated from marine sponges, which has been demonstrated to have anticancer activity against several human cancer cell lines via the induction of cell cycle arrest and apoptosis. New drugs that are less toxic and more effective against multidrug-resistant cancers are urgently needed. We tested cell proliferation, cell cycle progression and autophagic cell death pathway in doxorubicin-resistant MCF-7 (MCF-7/adr) human breast cancer cells. The potency of PsA was further determined using an in vivo xenograft model.»
[2] «The purpose of this study was to investigate the relationship between huntingtin-associated protein1 (HAP1) gene and radiation therapy of breast cancer cells. HAP1 gene was transfected into breast cancer MCF-7 cells, which was confirmed by quantitative reverse transcription-polymerase chain reaction analysis (qRT-PCR) and Western blot in vitro. The changes of cell radiosensitivity were assessed by colony formation assay. Apoptosis were examined by flow cytometry. The expressions of two radiation-induced genes were evaluated by Western blot. Tumor growth was investigated in nude mice xenograft models in vivo. Our data showed that HAP1 gene expression was significantly increased in HAP1-transfected MCF-7 cells in comparison with the parental cells or negative control cells. The survival rate in MCF-7/HAP1 cells was significantly decreased after irradiation (0, 2, 4, 6, 8Gy), compared to cells in MCF-7 and MCF-7/Pb groups in vitro. HAP1 gene increased apoptosis in MCF-7 cells after irradiation. Additionally, the tumor volume and weight in MCF-7/HAP1+RT group were observably lower than in MCF-7/HAP1 group and MCF-7/Pb+RT group.»
[3] «Due to the chemo resistant nature of cancer cells and adverse effects of current therapies, researchers are looking for the most efficient therapeutic approach which has the lowest side effects and the highest toxicity on cancer cells. The aim of the present study was to investigate the synergic effect of Urtica dioica extract in combination with paclitaxel on cell death and invasion of human breast cancer MDA-MB-468 cell line. To determine the cytotoxic effects of Urtica dioica extract with paclitaxel, MTT assay was performed. The scratch test was exploited to assess the effects of Urtica dioica, Paclitaxel alone and combination on migration of cancer cells. The expression levels of snail-1, ZEB1, ZEB2, twist, Cdc2, cyclin B1 and Wee1 genes were quantified using qRT-PCR and western blot performed for snail-1expression. The effects of plant extract, Paclitaxel alone and combination on different phases of cell cycle was analyzed using flow cytometry. Results of MTT assay showed that Urtica dioica significantly destroyed cancer cells. Interestingly, Concurrent use of Urtica dioica extract with paclitaxel resulted in decreased IC50 dose of paclitaxel. Moreover, findings of scratch assay exhibited the inhibitory effects of Urtica dioica, Paclitaxel alone and combination on migration of MDA-MB-468 cell line. Our findings also demonstrated that the extract substantially decreased the Snail-1 and related gene expression. Ultimately, Cell cycle arrest occurred at G2/M phase post-treatment by deregulating Cdc2 and wee1.»
Question: Does psammaplin A induce Sirtuin 1-dependent autophagic cell death in doxorubicin-resistant MCF-7/adr human breast cancer cells and xenografts?
Reasoning: Let's think step by step in order to produce the answer. We know that psammaplin A has been shown to induce cell cycle arrest and apoptosis in cancer cells. Additionally, the study tested cell proliferation, cell cycle progression, and autophagic cell death pathway in doxorubicin-resistant MCF-7/adr human breast cancer cells.
Answer: Psammaplin A induces Sirtuin 1-dependent autophagic cell death in doxorubicin-resistant MCF-7/adr human breast cancer cells and xenografts.
---
Context:
[1] «This study examined links between DNA methylation and birth weight centile (BWC), and explored the impact of genetic variation. Using HumanMethylation450 arrays, we examined candidate gene-associated CpGs in cord blood from newborns with low (<15th centile), medium (40-60th centile) and high (>85th centile) BWC (n = 12). Candidates were examined in an investigation cohort (n = 110) using pyrosequencing and genotyping for putative methylation-associated polymorphisms performed using standard PCR. Array analysis identified 314 candidate genes associated with BWC extremes, four of which showed ≥ 4 BWC-linked CpGs. Of these, PM20D1 and MI886 suggested genetically determined methylation levels. However, methylation at three CpGs in FGFR2 remained significantly associated with high BWC (p = 0.004-0.027).»
[2] «Studies performed in Andean populations living in high altitude, indicate that the reduced availability of oxygen could be associated to both a fetal growth retardation and a lower birth weight. These variables are predictive of morbidity and mortality during the first year of life. To study perinatal variables of newborns of mothers living at contrasting altitudinal levels, harboring different degrees of Aymara ancestry. Review of medical records of 5,295 women whose deliveries occurred between February 2004 and August 2010. Information was obtained on place of residence, grouped into two categories: coast (150 to 3,000 m) and high plateau (3,000 to 4,300 m), ancestry was estimated using number of Aymara surnames that were homologated to percentages of Amerindian admixture, gestational age, birth weight, height, head circumference and obstetric variables. Gestational age showed a tendency to increase and birth weight, height and head circumference to decrease with altitude of residence. Only weight reached statistical significance. Women with Aymara ancestry gave birth to children with a significantly higher gestational age, weight and cranial circumference.»
[3] «Preterm delivery and sub-optimal fetal growth are associated with each other and affect both mother and infant. Our aim was to determine (i) whether there are detectable differences in DNA methylation between early and late gestation and (ii) whether changes in DNA methylation from entry are associated with spontaneous preterm delivery with and without reduced fetal growth. We conducted a case-control study nested within a large prospective cohort. Gene specific methylation was measured by Methyl-Profiler PCR Array in a Human Breast Cancer Signature Panel of 24 genes from maternal peripheral leukocytes genomic DNA at entry and 3 There was significantly decrease in DNA methylation in 15 of 24 genes during the 3»
Question: Is methylation of the FGFR2 gene associated with high birth weight centile in humans?
Reasoning: Let's think step by step in order to produce the answer. We know that the study identified methylation at three CpGs in the FGFR2 gene that remained significantly associated with high birth weight centile.
Answer: Yes, methylation of the FGFR2 gene is associated with high birth weight centile in humans.
---
Context:
[1] «Minimally invasive retroperitoneoscopic surgery (MIS) for psoas abscess (PA) in patients with thoracolumbar tuberculosis is not well-illustrated and has not reached the status of being fully clinically assessed when we review the English literatures. The aim of this study is to introduce and investigate on efficacy and feasibility of MIS (retroperitoneoscopic technique) for PA in patients with thoracolumbar tuberculosis. From January 2008 to 2013, 39 consecutive patients of the diagnosis of PA with thoracolumbar tuberculosis received the debridement of abscesses and cavity walls of abscesses by the retroperitoneoscopic technique (MIS) in combination with anti-tuberculosis chemotherapy. Medical records and follow-up data were retrospectively studied. CRP and ESR of every patient preoperatively and postoperatively were analyzed Immediate relief in clinical symptoms and signs, and amelioration in imaging and laboratory examinations were obviously observed in all the patients. The follow-up had proceeded for 12-48 (mean 23) months. No complication was observed during the follow-up postoperatively.»
[2] «Current diagnostic tests for gastroesophageal reflux disease (GERD) do not consistently measure chronicity of reflux. Mucosal impedance (MI) is a minimally invasive measurement to assess esophageal conductivity changes due to GERD. We aimed to investigate MI pattern in patients with symptoms of extraesophageal reflux (EER) in a prospective longitudinal cohort study. Patients with potential symptoms of EER undergoing esophagogastroduodenoscopy (EGD) with wireless pH monitoring were studied. Participants included those with erosive esophagitis (E+), normal EGD/abnormal pH (E-/pH+), and normal EGD/normal pH (E-/pH-). MI was measured from the site of injury in patients with E+, as well as at 2, 5, and 10 cm above the squamocolumnar junction (SCJ) in all participants. Forty-one patients with symptoms of EER were studied. MI measurements at 2 cm above the SCJ were significantly (P = 0.04) different among the three groups, with MI lowest for E+ and greatest for E-/pH- patients. Although not statistically significant, there is a graded increase in median (interquartile range) MI axially along the esophagus at 5 cm (P = 0.20) and at 10 cm (P = 0.27) above the SCJ, with those with reflux (E+ and E-/pH+) having a lower MI than those without.»
[3] «We evaluated the current role of minimally invasive surgery (MIS) in children with small bowel obstruction (SBO) at our institution. A retrospective review of patients undergoing MIS for acute SBO was performed from 2008 to 2013. The study population was compared with a historical control including patients from 2001 to 2008. There were 71 patients who met inclusion criteria; 35 were male, and 36 were female. Sixty-two children underwent laparoscopy for their first episode of SBO, and 12 underwent laparoscopy for recurrent SBO, accounting for 74 episodes of SBO managed with MIS. The most common etiology of SBO was adhesions (n=40). Laparoscopy and laparoscopic-assisted procedures were associated with shorter nasogastric tube decompression (1.4±2 days [P<.001] and 1.5±2.7 days [P=.002], respectively) and time to regular diet (3.9±4 days [P=.002] and 4.6±2.8 days [P=.024], respectively) compared with those converted to laparotomy (5.1±4.9 days of nasogastric tube decompressions and 8±4.7 days to regular diet). There was no difference in postoperative morbidity comparing laparoscopy (11%), laparoscopic-assisted (5%), and laparoscopic converted to open procedures (18%) (P=.48).»
Question: Do minimally invasive retroperitoneoscopic surgery for psoas abscess with thoracolumbar tuberculosis?
Reasoning: Let's think step by step in order to Answer: Yes, minimally invasive retroperitoneoscopic surgery for psoas abscess in patients with thoracolumbar tuberculosis is effective and feasible. Immediate relief in clinical symptoms and signs, along with improvement in imaging and laboratory examinations, was observed in all patients who underwent this procedure.
Answer:[32m Yes, minimally invasive retroperitoneoscopic surgery for psoas abscess in patients with thoracolumbar tuberculosis is effective and feasible.[0m
"\n\n\nAnswer questions with short factoid answers.\n\n---\n\nQuestion: Do tumor-infiltrating immune cell profiles and their change after neoadjuvant chemotherapy predict response and prognosis of breast cancer?\nAnswer: Breast cancer immune cell subpopulation profiles, determined by immunohistochemistry-based computerized analysis, identify groups of patients characterized by high response (in the pre-treatment setting) and poor prognosis (in the post-treatment setting). Further understanding of the mechanisms underlying the distribution of immune cells and their changes after chemotherapy may contribute to the development of new immune-targeted therapies for breast cancer.\n\nQuestion: Do large portion sizes increase bite size and eating rate in overweight women?\nAnswer: Increasing portion size led to a larger bite size and faster eating rate, but a slower reduction in eating speed during the meal. These changes may underlie greater energy intakes with exposure to large portions. Interventions to reduce bite size and slow eating rate may provide individuals with strategies to reduce the risk of overconsumption.\n\nQuestion: Are secretory phospholipases A2 secreted from ciliated cells and increase mucin and eicosanoid secretion from goblet cells?\nAnswer: sPLA2 are secreted from ciliated cells and appear to induce mucin and cysLT secretion from goblet cells, strongly suggesting that airway goblet cells are proinflammatory effector cells.\n\nQuestion: Are reasons why erupted third molars extracted in a public university in Mexico?\nAnswer: Women and patients 18 to 34 years of age had erupted 3M extracted more frequently, primarily for prosthetic reasons. The age profile indicated a trend in demand for services that differ from those of overall tooth extractions, but not for the trend across gender.\n\nQuestion: Does increased Syk phosphorylation lead to overexpression of TRAF6 in peripheral B cells of patients with systemic lupus erythematosus?\nAnswer: Our results suggest that the activated Syk-mediated TRAF6 pathway leads to aberrant activation of B cells in SLE, and also highlight Syk as a potential target for B-cell-mediated processes in SLE.\n\nQuestion: Are routine preoperative restaging CTs after neoadjuvant chemoradiation for locally advanced rectal cancer low yield : a retrospective case study?\nAnswer: Because of the financial costs and established risks of intravenous contrast and cumulative radiation exposure, it may be advisable to take a more selective approach to preoperative imaging. Larger, prospective studies may enable identification of an at-risk cohort who would benefit most from restaging CT.\n\nQuestion: Does the Boston keratoprosthesis provide a wide depth of focus?\nAnswer: The KPro's wide depth-of-focus makes the visual acuity less dependent on an exact refractive correction at distance and explains the 'pseudoaccomodation' experienced by these patients. This is primarily due to the small pupil diameter of the KPro. The current manufacturing steps in 0.50 dioptre increments appears to be sufficient.\n\nQuestion: Do obese patients with idiopathic pulmonary fibrosis have a higher 90-day mortality risk with bilateral lung transplantation?\nAnswer: Our results suggest that obese patients who receive a BLT may be at higher risk of 90-day mortality compared with patients of normal weight. Further study is needed to obtain more detailed information about comorbidities and other risk factors for early death that are not included in the OPTN database.\n\nQuestion: Is admission hyperglycemia associated with failed reperfusion following fibrinolytic therapy in patients with STEMI : results of a retrospective study?\nAnswer: In patients with STEMI who undergo FT, admission hyperglycemia is an independent predictor of the failure of fibrinolysis.\n\nQuestion: Is hidradenitis suppurativa a systemic disease with substantial comorbidity burden : a chart-verified case-control analysis?\nAnswer: Control subjects were not validated for absence of HS and comorbidity validation was not performed for either group.\n\nQuestion: Do systematic Reviews Published in Emergency Medicine Journals Routinely Search Clinical Trials Registries : A Cross-Sectional Analysis?\nAnswer: Systematic reviews published in emergency medicine journals do not routinely include searches of clinical trials registries. By helping authors identify unpublished trial data, the addition of registry searches may improve the validity of systematic reviews.\n\nQuestion: Does promoter variant rs2301228 on the neural cell adhesion molecule 1 gene confer risk of schizophrenia in Han Chinese?\nAnswer: Our results provide direct evidence for NCAM1 as a susceptibility gene for schizophrenia, which offers support to a neurodevelopmental model and neuronal connectivity hypothesis in the onset of schizophrenia.\n\n---\n\nFollow the following format.\n\nContext: may contain relevant facts\n\nQuestion: ${question}\n\nReasoning: Let's think step by step in order to ${produce the answer}. We ...\n\nAnswer: short and precise answer\n\n---\n\nContext:\n[1] «Chronic rhinosinusitis (CRS) is a heterogeneous disease with an uncertain pathogenesis. Group 2 innate lymphoid cells (ILC2s) represent a recently discovered cell population which has been implicated in driving Th2 inflammation in CRS; however, their relationship with clinical disease characteristics has yet to be investigated. The aim of this study was to identify ILC2s in sinus mucosa in patients with CRS and controls and compare ILC2s across characteristics of disease. A cross-sectional study of patients with CRS undergoing endoscopic sinus surgery was conducted. Sinus mucosal biopsies were obtained during surgery and control tissue from patients undergoing pituitary tumour resection through transphenoidal approach. ILC2s were identified as CD45(+) Lin(-) CD127(+) CD4(-) CD8(-) CRTH2(CD294)(+) CD161(+) cells in single cell suspensions through flow cytometry. ILC2 frequencies, measured as a percentage of CD45(+) cells, were compared across CRS phenotype, endotype, inflammatory CRS subtype and other disease characteristics including blood eosinophils, serum IgE, asthma status and nasal symptom score. 35 patients (40% female, age 48 ± 17 years) including 13 with eosinophilic CRS (eCRS), 13 with non-eCRS and 9 controls were recruited. ILC2 frequencies were associated with the presence of nasal polyps (P = 0.002) as well as high tissue eosinophilia (P = 0.004) and eosinophil-dominant CRS (P = 0.001) (Mann-Whitney U). They were also associated with increased blood eosinophilia (P = 0.005). There were no significant associations found between ILC2s and serum total IgE and allergic disease. In the CRS with nasal polyps (CRSwNP) population, ILC2s were increased in patients with co-existing asthma (P = 0.03). ILC2s were also correlated with worsening nasal symptom score in CRS (P = 0.04).»\n[2] «Allergic airway inflammation is triggered by allergen exposure through several steps including release of IL-33, which promotes cytokine (IL-5, IL-13) production by type 2 innate lymphoid cells (ILC2s). MicroRNA (miR)-155 has recently been described to regulate adaptive responses in allergic inflammation. However, the role of miR-155 in the regulation of ILC2s remains unexplored. We sought to elucidate the contribution of miR-155 in ILC2 expansion using experimental murine models of allergic airway inflammation. To determine the role of miR-155 in the regulation of ILC2s in allergic airway inflammation, miR-155 deficient (miR-155 miR-155 was 10-fold upregulated in WT-derived ILC2s in response to IL-33. Furthermore, miR-155»\n[3] «The mechanisms and immune pathways associated with chronic rhinosinusitis (CRS) are not fully understood. Immunological changes during acute exacerbation of CRS may provide valuable clues to the pathogenesis and perpetuation of the disease. To characterize local and systemic immune responses associated with acute worsening of sinonasal symptoms during exacerbation in CRS with nasal polyps (CRSwNP) compared to controls. This was a non-interventional prospective study of individuals with CRSwNP and normal controls. Subjects underwent a baseline visit with collection of nasal secretions, nasal washes, and serum specimens. Within 3\xa0days of acute worsening of sinonasal symptoms, subjects underwent a study visit, followed by a post-visit 2\xa0weeks later. The sinonasal outcome test-22 (SNOT-22) scores and immunological parameters in the specimens were analysed using a novel, unsupervised learning method and by conventional univariate analysis. Both CRSwNP patients and control subjects showed a significant increase in SNOT-22 scores during acute exacerbation. Increased nasal levels of IL-6, IL-5, and eosinophil major basic protein were observed in CRSwNP patients. A network analysis of serum specimens revealed changes in a set of immunological parameters, which are distinctly associated with CRSwNP but not with controls. In particular, systemic increases in VEGF and GM-CSF levels were notable and were validated by a conventional analysis.»\n\nQuestion: Are group 2 innate lymphoid cells ( ILC2s ) increased in chronic rhinosinusitis with nasal polyps or eosinophilia?\n\nReasoning: Let's think step by step in order to Answer: Yes, ILC2 frequencies are increased in chronic rhinosinusitis with nasal polyps, high tissue eosinophilia, and eosinophil-dominant CRS. They are also associated with increased blood eosinophilia and worsening nasal symptom scores.\n\nAnswer: Yes, ILC2 frequencies are increased in chronic rhinosinusitis with nasal polyps, high tissue eosinophilia, and eosinophil-dominant CRS. They are also associated with increased blood eosinophilia and worsening nasal symptom scores.\n\n---\n\nContext:\n[1] «Phosphatidylethanolamine N-methyltransferase (PEMT), a liver enriched enzyme, is responsible for approximately one third of hepatic phosphatidylcholine biosynthesis. When fed a high-fat diet (HFD), Pemt(-/-) mice are protected from HF-induced obesity; however, they develop steatohepatitis. The vagus nerve relays signals between liver and brain that regulate peripheral adiposity and pancreas function. Here we explore a possible role of the hepatic branch of the vagus nerve in the development of diet induced obesity and steatohepatitis in Pemt(-/-) mice. 8-week old Pemt(-/-) and Pemt(+/+) mice were subjected to hepatic vagotomy (HV) or capsaicin treatment, which selectively disrupts afferent nerves, and were compared to sham-operated or vehicle-treatment, respectively. After surgery, mice were fed a HFD for 10 weeks. HV abolished the protection against the HFD-induced obesity and glucose intolerance in Pemt(-/-) mice. HV normalized phospholipid content and prevented steatohepatitis in Pemt(-/-) mice. Moreover, HV increased the hepatic anti-inflammatory cytokine interleukin-10, reduced chemokine monocyte chemotactic protein-1 and the ER stress marker C/EBP homologous protein. Furthermore, HV normalized the expression of mitochondrial electron transport chain proteins and of proteins involved in fatty acid synthesis, acetyl-CoA carboxylase and fatty acid synthase in Pemt(-/-) mice. However, disruption of the hepatic afferent vagus nerve by capsaicin failed to reverse either the protection against the HFD-induced obesity or the development of HF-induced steatohepatitis in Pemt(-/-) mice.»\n[2] «Nonalcoholic steatohepatitis (NASH) is associated with cirrhosis and hepatocellular carcinoma. Reactive oxygen species (ROS) and reactive nitrogen species (RNS) play key roles in the development of the disease. However, the therapeutic target of NASH has not been fully defined and new treatments are needed. We investigated the protective effects of the antioxidant indole-derived NecroX-7 in a NASH mouse model using leptin-deficient ob/ob and methionine- and choline-deficient (MCD) diet-fed ob/ob mice. Six-week-old male mice were divided into three groups: ob/+ mice, ob/ob mice treated with vehicle and ob/ob mice treated daily with NecroX-7 (20 mg/kg) for 4 weeks. To study the effects of NecroX-7 in a fibrosis model, NASH was induced by feeding ob/ob mice an MCD diet. The effects of NecroX-7 on NASH progression were evaluated using biochemical, histological and molecular markers. NecroX-7-treated ob/ob mice had a marked decrease in serum aspartate aminotransferase and alanine transaminase compared with vehicle-treated controls. Interestingly, hepatic steatosis and lipid peroxidation were significantly improved by NecroX-7 treatment. NecroX-7 inhibited tert-butylhydroperoxide- and H2 O2 -induced mitochondrial ROS/RNS in primary hepatocytes and attenuated mitochondrial dysfunction in vitro and in vivo. Furthermore, NecroX-7-treated mice exhibited fewer infiltrating macrophages and reduced hepatic tumour necrosis factor-alpha expression. Hepatic fibrosis in MCD-fed ob/ob mice was significantly decreased by NecroX-7 treatment.»\n[3] «The ability of a treatment method to interfere with tinnitus-related neural activity patterns, such as cortical gamma rhythms, has been suggested to indicate its potential in relieving tinnitus. Therapeutic modulation of gamma-band oscillations with vagus nerve stimulation has been recently reported in epileptic patients. The aim of this study was to investigate the effects of transcutaneous vagus nerve stimulation (tVNS) on neural oscillatory patterns. We calculated the power spectral density and synchrony of magnetoencephalography recordings during auditory stimulation in seven tinnitus patients and eight normal-hearing control subjects. Comparisons between subject groups were performed to reveal electrophysiological markers of tinnitus. tVNS-specific effects within each group were studied by comparing recording blocks with and without tVNS. We also investigated the correlation of each measure with individual ratings of tinnitus distress, as measured by the tinnitus handicap inventory questionnaire. Tinnitus patients differed from controls in the baseline condition (no tVNS applied), measured by both cortical oscillatory power and synchronization, particularly at beta and gamma frequencies. Importantly, we found tVNS-induced changes in synchrony, correlating strongly with tinnitus handicap inventory scores, at whole-head beta-band (r = -0.857, p = 0.007), whole-head gamma-band (r = -0.952, p = 0.0003), and frontal gamma-band (r = -0.952, p = 0.0003).»\n\nQuestion: Does vagus nerve contribute to the development of steatohepatitis and obesity in phosphatidylethanolamine N-methyltransferase deficient mice?\n\nReasoning: Let's think step by step in order to Answer: Yes, the hepatic branch of the vagus nerve plays a role in the development of diet-induced obesity and steatohepatitis in Pemt(-/-) mice. Disruption of the hepatic vagus nerve abolished protection against high-fat diet-induced obesity and glucose intolerance in these mice, while also normalizing phospholipid content and preventing steatohepatitis.\n\nAnswer: Yes, the hepatic branch of the vagus nerve plays a role in the development of diet-induced obesity and steatohepatitis in Pemt(-/-) mice.\n\n---\n\nContext:\n[1] «Psammaplin A (PsA) is a natural product isolated from marine sponges, which has been demonstrated to have anticancer activity against several human cancer cell lines via the induction of cell cycle arrest and apoptosis. New drugs that are less toxic and more effective against multidrug-resistant cancers are urgently needed. We tested cell proliferation, cell cycle progression and autophagic cell death pathway in doxorubicin-resistant MCF-7 (MCF-7/adr) human breast cancer cells. The potency of PsA was further determined using an in vivo xenograft model.»\n[2] «The purpose of this study was to investigate the relationship between huntingtin-associated protein1 (HAP1) gene and radiation therapy of breast cancer cells. HAP1 gene was transfected into breast cancer MCF-7 cells, which was confirmed by quantitative reverse transcription-polymerase chain reaction analysis (qRT-PCR) and Western blot in vitro. The changes of cell radiosensitivity were assessed by colony formation assay. Apoptosis were examined by flow cytometry. The expressions of two radiation-induced genes were evaluated by Western blot. Tumor growth was investigated in nude mice xenograft models in vivo. Our data showed that HAP1 gene expression was significantly increased in HAP1-transfected MCF-7 cells in comparison with the parental cells or negative control cells. The survival rate in MCF-7/HAP1 cells was significantly decreased after irradiation (0, 2, 4, 6, 8Gy), compared to cells in MCF-7 and MCF-7/Pb groups in vitro. HAP1 gene increased apoptosis in MCF-7 cells after irradiation. Additionally, the tumor volume and weight in MCF-7/HAP1+RT group were observably lower than in MCF-7/HAP1 group and MCF-7/Pb+RT group.»\n[3] «Due to the chemo resistant nature of cancer cells and adverse effects of current therapies, researchers are looking for the most efficient therapeutic approach which has the lowest side effects and the highest toxicity on cancer cells. The aim of the present study was to investigate the synergic effect of Urtica dioica extract in combination with paclitaxel on cell death and invasion of human breast cancer MDA-MB-468 cell line. To determine the cytotoxic effects of Urtica dioica extract with paclitaxel, MTT assay was performed. The scratch test was exploited to assess the effects of Urtica dioica, Paclitaxel alone and combination on migration of cancer cells. The expression levels of snail-1, ZEB1, ZEB2, twist, Cdc2, cyclin B1 and Wee1 genes were quantified using qRT-PCR and western blot performed for snail-1expression. The effects of plant extract, Paclitaxel alone and combination on different phases of cell cycle was analyzed using flow cytometry. Results of MTT assay showed that Urtica dioica significantly destroyed cancer cells. Interestingly, Concurrent use of Urtica dioica extract with paclitaxel resulted in decreased IC50 dose of paclitaxel. Moreover, findings of scratch assay exhibited the inhibitory effects of Urtica dioica, Paclitaxel alone and combination on migration of MDA-MB-468 cell line. Our findings also demonstrated that the extract substantially decreased the Snail-1 and related gene expression. Ultimately, Cell cycle arrest occurred at G2/M phase post-treatment by deregulating Cdc2 and wee1.»\n\nQuestion: Does psammaplin A induce Sirtuin 1-dependent autophagic cell death in doxorubicin-resistant MCF-7/adr human breast cancer cells and xenografts?\n\nReasoning: Let's think step by step in order to produce the answer. We know that psammaplin A has been shown to induce cell cycle arrest and apoptosis in cancer cells. Additionally, the study tested cell proliferation, cell cycle progression, and autophagic cell death pathway in doxorubicin-resistant MCF-7/adr human breast cancer cells.\n\nAnswer: Psammaplin A induces Sirtuin 1-dependent autophagic cell death in doxorubicin-resistant MCF-7/adr human breast cancer cells and xenografts.\n\n---\n\nContext:\n[1] «This study examined links between DNA methylation and birth weight centile (BWC), and explored the impact of genetic variation. Using HumanMethylation450 arrays, we examined candidate gene-associated CpGs in cord blood from newborns with low (<15th centile), medium (40-60th centile) and high (>85th centile) BWC (n = 12). Candidates were examined in an investigation cohort (n = 110) using pyrosequencing and genotyping for putative methylation-associated polymorphisms performed using standard PCR. Array analysis identified 314 candidate genes associated with BWC extremes, four of which showed ≥ 4 BWC-linked CpGs. Of these, PM20D1 and MI886 suggested genetically determined methylation levels. However, methylation at three CpGs in FGFR2 remained significantly associated with high BWC (p = 0.004-0.027).»\n[2] «Studies performed in Andean populations living in high altitude, indicate that the reduced availability of oxygen could be associated to both a fetal growth retardation and a lower birth weight. These variables are predictive of morbidity and mortality during the first year of life. To study perinatal variables of newborns of mothers living at contrasting altitudinal levels, harboring different degrees of Aymara ancestry. Review of medical records of 5,295 women whose deliveries occurred between February 2004 and August 2010. Information was obtained on place of residence, grouped into two categories: coast (150 to 3,000 m) and high plateau (3,000 to 4,300 m), ancestry was estimated using number of Aymara surnames that were homologated to percentages of Amerindian admixture, gestational age, birth weight, height, head circumference and obstetric variables. Gestational age showed a tendency to increase and birth weight, height and head circumference to decrease with altitude of residence. Only weight reached statistical significance. Women with Aymara ancestry gave birth to children with a significantly higher gestational age, weight and cranial circumference.»\n[3] «Preterm delivery and sub-optimal fetal growth are associated with each other and affect both mother and infant. Our aim was to determine (i) whether there are detectable differences in DNA methylation between early and late gestation and (ii) whether changes in DNA methylation from entry are associated with spontaneous preterm delivery with and without reduced fetal growth. We conducted a case-control study nested within a large prospective cohort. Gene specific methylation was measured by Methyl-Profiler PCR Array in a Human Breast Cancer Signature Panel of 24 genes from maternal peripheral leukocytes genomic DNA at entry and 3 There was significantly decrease in DNA methylation in 15 of 24 genes during the 3»\n\nQuestion: Is methylation of the FGFR2 gene associated with high birth weight centile in humans?\n\nReasoning: Let's think step by step in order to produce the answer. We know that the study identified methylation at three CpGs in the FGFR2 gene that remained significantly associated with high birth weight centile.\n\nAnswer: Yes, methylation of the FGFR2 gene is associated with high birth weight centile in humans.\n\n---\n\nContext:\n[1] «Minimally invasive retroperitoneoscopic surgery (MIS) for psoas abscess (PA) in patients with thoracolumbar tuberculosis is not well-illustrated and has not reached the status of being fully clinically assessed when we review the English literatures. The aim of this study is to introduce and investigate on efficacy and feasibility of MIS (retroperitoneoscopic technique) for PA in patients with thoracolumbar tuberculosis. From January 2008 to 2013, 39 consecutive patients of the diagnosis of PA with thoracolumbar tuberculosis received the debridement of abscesses and cavity walls of abscesses by the retroperitoneoscopic technique (MIS) in combination with anti-tuberculosis chemotherapy. Medical records and follow-up data were retrospectively studied. CRP and ESR of every patient preoperatively and postoperatively were analyzed Immediate relief in clinical symptoms and signs, and amelioration in imaging and laboratory examinations were obviously observed in all the patients. The follow-up had proceeded for 12-48 (mean 23) months. No complication was observed during the follow-up postoperatively.»\n[2] «Current diagnostic tests for gastroesophageal reflux disease (GERD) do not consistently measure chronicity of reflux. Mucosal impedance (MI) is a minimally invasive measurement to assess esophageal conductivity changes due to GERD. We aimed to investigate MI pattern in patients with symptoms of extraesophageal reflux (EER) in a prospective longitudinal cohort study. Patients with potential symptoms of EER undergoing esophagogastroduodenoscopy (EGD) with wireless pH monitoring were studied. Participants included those with erosive esophagitis (E+), normal EGD/abnormal pH (E-/pH+), and normal EGD/normal pH (E-/pH-). MI was measured from the site of injury in patients with E+, as well as at 2, 5, and 10 cm above the squamocolumnar junction (SCJ) in all participants. Forty-one patients with symptoms of EER were studied. MI measurements at 2\u2009cm above the SCJ were significantly (P\u2009=\u20090.04) different among the three groups, with MI lowest for E+ and greatest for E-/pH- patients. Although not statistically significant, there is a graded increase in median (interquartile range) MI axially along the esophagus at 5\u2009cm (P\u2009=\u20090.20) and at 10\u2009cm (P\u2009=\u20090.27) above the SCJ, with those with reflux (E+ and E-/pH+) having a lower MI than those without.»\n[3] «We evaluated the current role of minimally invasive surgery (MIS) in children with small bowel obstruction (SBO) at our institution. A retrospective review of patients undergoing MIS for acute SBO was performed from 2008 to 2013. The study population was compared with a historical control including patients from 2001 to 2008. There were 71 patients who met inclusion criteria; 35 were male, and 36 were female. Sixty-two children underwent laparoscopy for their first episode of SBO, and 12 underwent laparoscopy for recurrent SBO, accounting for 74 episodes of SBO managed with MIS. The most common etiology of SBO was adhesions (n=40). Laparoscopy and laparoscopic-assisted procedures were associated with shorter nasogastric tube decompression (1.4±2 days [P<.001] and 1.5±2.7 days [P=.002], respectively) and time to regular diet (3.9±4 days [P=.002] and 4.6±2.8 days [P=.024], respectively) compared with those converted to laparotomy (5.1±4.9 days of nasogastric tube decompressions and 8±4.7 days to regular diet). There was no difference in postoperative morbidity comparing laparoscopy (11%), laparoscopic-assisted (5%), and laparoscopic converted to open procedures (18%) (P=.48).»\n\nQuestion: Do minimally invasive retroperitoneoscopic surgery for psoas abscess with thoracolumbar tuberculosis?\n\nReasoning: Let's think step by step in order to Answer: Yes, minimally invasive retroperitoneoscopic surgery for psoas abscess in patients with thoracolumbar tuberculosis is effective and feasible. Immediate relief in clinical symptoms and signs, along with improvement in imaging and laboratory examinations, was observed in all patients who underwent this procedure.\n\nAnswer:\x1b[32m Yes, minimally invasive retroperitoneoscopic surgery for psoas abscess in patients with thoracolumbar tuberculosis is effective and feasible.\x1b[0m\n\n\n"
优化后的 Haystack 管道
我们现在可以使用优化后的提示的静态部分(包括示例)来创建一个更好的 Haystack RAG 管道。
我们包含一个 AnswerBuilder,用于捕获生成的相关部分(Answer: 之后的所有文本)。
%%capture
static_prompt = lm.inspect_history(n=1).rpartition("---\n")[0]
from haystack.components.retrievers.in_memory import InMemoryBM25Retriever
from haystack.components.generators import OpenAIGenerator
from haystack.components.builders import PromptBuilder, AnswerBuilder
from haystack import Pipeline
template = static_prompt+"""
---
Context:
{% for document in documents %}
«{{ document.content }}»
{% endfor %}
Question: {{question}}
Reasoning: Let's think step by step in order to
"""
new_prompt_builder = PromptBuilder(template=template)
new_retriever = InMemoryBM25Retriever(document_store, top_k=3)
new_generator = OpenAIGenerator(model="gpt-4o-mini")
answer_builder = AnswerBuilder(pattern="Answer: (.*)")
optimized_rag_pipeline = Pipeline()
optimized_rag_pipeline.add_component("retriever", new_retriever)
optimized_rag_pipeline.add_component("prompt_builder", new_prompt_builder)
optimized_rag_pipeline.add_component("llm", new_generator)
optimized_rag_pipeline.add_component("answer_builder", answer_builder)
optimized_rag_pipeline.connect("retriever", "prompt_builder.documents")
optimized_rag_pipeline.connect("prompt_builder", "llm")
optimized_rag_pipeline.connect("llm.replies", "answer_builder.replies")
<haystack.core.pipeline.pipeline.Pipeline object at 0x7d59ed5f3880>
🚅 Components
- retriever: InMemoryBM25Retriever
- prompt_builder: PromptBuilder
- llm: OpenAIGenerator
- answer_builder: AnswerBuilder
🛤️ Connections
- retriever.documents -> prompt_builder.documents (List[Document])
- prompt_builder.prompt -> llm.prompt (str)
- llm.replies -> answer_builder.replies (List[str])
让我们问和之前一样的问题……
question = "What effects does ketamine have on rat neural stem cells?"
response = optimized_rag_pipeline.run({"retriever": {"query": question}, "prompt_builder": {"question": question}, "answer_builder": {"query": question}})
print(response["answer_builder"]["answers"][0].data)
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Ketamine at higher concentrations inhibits the proliferation of rat neural stem cells, while not affecting
apoptosis. Additionally, it decreases intracellular calcium concentration and suppresses PKCα activation and ERK1/2
phosphorylation in these cells.
question = "Is the anterior cingulate cortex linked to pain-induced depression?"
response = optimized_rag_pipeline.run({"retriever": {"query": question}, "prompt_builder": {"question": question}, "answer_builder": {"query": question}})
print(response["answer_builder"]["answers"][0].data)
Ranking by BM25...: 0%| | 0/1000 [00:00<?, ? docs/s]
Yes, the study found that lesions in the anterior cingulate cortex (ACC) prevented the anxiodepressive consequences of chronic pain, indicating a link between the ACC and pain-induced depression.
答案是正确且比以前更短!
(笔记本由 Stefano Fiorucci 编写)
