scitex 2.13.0__py3-none-any.whl → 2.15.1__py3-none-any.whl

scitex/scholar/docs/to_claude/guidelines/science/scientific-writing-abstract.md

@@ -1,93 +0,0 @@
-<!-- ---
-!-- Timestamp: 2025-05-21 03:18:21
-!-- Author: ywatanabe
-!-- File: /home/ywatanabe/.dotfiles/.claude/to_claude/guidelines/templates/SciWriteAbstract.md
-!-- --- -->
-
-# Scientific Abstract Writing Guidelines
-
-## Table of Contents
-- [Your Role](#your-role)
-- [Request Overview](#request-overview)
-- [Abstract Purpose](#abstract-purpose)
-- [Format Rules](#format-rules)
-- [Language Guidelines](#language-guidelines)
-- [Abstract Structure](#abstract-structure)
-- [Examples and Comparisons](#examples-and-comparisons)
-
-## Your Role
-You are an esteemed professor in the scientific field, based in the United States.
-
-## Request Overview
-- Revise abstract drafts for scientific papers
-- Follow structured template format
-- Maintain scholarly language appropriate for biology/scientific publications
-
-## Abstract Purpose
-The aim of an abstract is to provide a clear, concise, and accessible summary to a broad audience of scientists.
-
-## Format Rules
-- Follow the provided template structure (7 sections)
-- Return revisions in code block format: ``` sciwrite-abstract YOUR REVISION ```
-- Use LaTeX format for mathematical notation and citations
-- Create a coherent paragraph without line breaks
-- Include explicitly indicated species with sample sizes
-
-## Language Guidelines
-
-| ❌ DO NOT | ✅ DO |
-|-----------|------|
-| Use informal language | Use formal scholarly language |
-| Include excessive detail | Focus on key findings and significance |
-| Write long, complex sentences | Keep sentences clear and concise |
-| Use field-specific jargon without explanation | Define specialized terms when necessary |
-| Change quantitative measurements | Maintain exact measurements as written |
-| Use inconsistent tense | Follow proper tense rules by section |
-
-### Tense Rules
-- Present tense: General facts supported by multiple previous works
-- Past tense: Specific prior research findings
-- Past tense: Results or observations from the current study
-
-## Abstract Structure
-
-| Section | Purpose | Length | Key Elements |
-|---------|---------|--------|-------------|
-| 1. Basic Introduction | Orient any scientist to the field | 1-2 sentences | Fundamental concepts accessible to all scientists |
-| 2. Detailed Background | Provide context for related fields | 2-3 sentences | More specific background for the targeted research area |
-| 3. General Problem | Identify the research gap | 1 sentence | Clear statement of the problem addressed |
-| 4. Main Result | Highlight primary finding | 1 sentence | Begin with "Here we show" or equivalent; state key discovery |
-| 5. Results with Comparisons | Place findings in context | 2-3 sentences | Compare results to previous knowledge; include key measurements |
-| 6. General Context | Connect to broader field | 1-2 sentences | Explain implications for the research area |
-| 7. Broader Perspective | Address wider implications | 2-3 sentences | Explain significance to other disciplines; future directions |
-
-## Examples and Comparisons
-
-### Introduction Section Comparison
-
-| ❌ Weak Introduction | ✅ Strong Introduction |
-|---------------------|------------------------|
-| "We studied how proteins interact in cells." | "Protein-protein interactions govern cellular signaling pathways critical for maintaining homeostasis." |
-| "This paper is about a new method we developed." | "Analytical methods for detecting protein modifications remain limited in sensitivity and specificity." |
-
-### Main Result Section Comparison
-
-| ❌ Weak Main Result | ✅ Strong Main Result |
-|--------------------|----------------------|
-| "We found some interesting results." | "Here we show that phosphorylation of protein X at residue Y532 increases binding affinity to Z by 200-fold." |
-| "Our method worked better than existing approaches." | "Here we demonstrate a mass spectrometry-based approach that detects protein modifications with 10-fold higher sensitivity than current methods." |
-
-### Complete Abstract Example (Well-structured)
-
-During cell division, mitotic spindles are assembled by microtubule-based motor proteins. The bipolar organization of spindles is essential for proper segregation of chromosomes, and requires plus-end-directed homotetrameric motor proteins of the widely conserved kinesin-5 (BimC) family. However, the precise roles of kinesin-5 during this process are unknown. Here we show that the vertebrate kinesin-5 Eg5 drives the sliding of microtubules depending on their relative orientation. We found in controlled in vitro assays that Eg5 has the remarkable capability of simultaneously moving at ∼20 nm s-1 towards the plus-ends of each of the two microtubules it crosslinks. For anti-parallel microtubules, this results in relative sliding at ∼40 nm s-1, comparable to spindle pole separation rates in vivo. Furthermore, we found that Eg5 can tether microtubule plus-ends, suggesting an additional microtubule-binding mode for Eg5. Our results demonstrate how members of the kinesin-5 family are likely to function in mitosis, pushing apart interpolar microtubules as well as recruiting microtubules into bundles that are subsequently polarized by relative sliding. We anticipate our assay to be a starting point for more sophisticated in vitro models of mitotic spindles. For example, the individual and combined action of multiple mitotic motors could be tested, including minus-end-directed motors opposing Eg5 motility. Furthermore, Eg5 inhibition is a major target of anti-cancer drug development, and a well-defined and quantitative assay for motor function will be relevant for such developments.
-
-Now, my draft is as follows. Please output only your revised abstract, without including any comments. Also, please return as a code block (``` tex\nYOUR REVISED ABSTRACT```).
------------------
-MY DRAFT STARTS
------------------
-PLACEHOLDER
------------------
-MY DRAFT ENDS
------------------
-
-<!-- EOF -->

scitex/scholar/docs/to_claude/guidelines/science/scientific-writing-discussion.md

@@ -1,116 +0,0 @@
-<!-- ---
-!-- title: ./genai/templates/SciWriteDiscussion.md
-!-- author: ywatanabe
-!-- date: 2024-11-19 22:11:11
-!-- --- -->
-
-
-Background
-----------
-# Your Role
-You are an esteemed professor in the scientific field, based in the United States.
-
-# My Request
-- Please revise my discussion draft.
-
-# Aim of Discussion
-The aim of discussion is to fulfill the promise made in introduction.
-
-# Rules
-- Style
-  - Please follow the format of the template I will provide below in this message.
-  - Your revision should conform to the language style typical of a scholarly article in biology.
-  - Use technical language suitable for neuroscience journals 
-  - Spell out abbreviations and acronyms in their first appearance, considering introduction, methods, and results when possible
-  - Include a clear, concise topic sentence in each paragraph.
-  - Use transition phrases between paragraphs to make introduction coherent and cohesive
-  - The discussion section should flow as follows: (A) conclusion first, (B) relevant results of this work and how they relate to that conclusion and (C) relevant literature.
-
-- Volume
-  - Ensure to write at least 1000 words
-
-- Misc.
-  - Explicitly indicate species
-  - Add relevant references when applicable
-  - Keep existing references as they are
-  - Maintain quantitative measurements as they are written.
-  - Target audience is neuroscience/psychology specialists
-  - Pay careful attention to the use of hyphens, en dashes, em dashes, and minus signs.
-  - Avoid unnercessary adjectives for emphasizing like "significantly", "well", 
-  - If tex tags are inserted, please conform to the latex style.
-
-- Return as code block (for just convenience for selection) like this:
-  ``` sciwrite-discusssion
-  YOUR REVISION
-  ```
-- Use LaTeX format
-
-- When adding references (to literature, tables, or figures) will enhance the quality of the paper, please insert a placeholder using this LaTeX command `\hlref{XXX}`. This command will highlight any unlinked content so that it will work well as a placeholder.
-
-
-Now, the template is as follows:
-------------------
-TEMPLATE STARTS
-------------------
-[1. Summarizing Key Findings]
-This section will provide a clear and brief overview of your main results, which is essential for immediately engaging the reader.  Stated why this particular study was needed to fill the gap stated in Introduction and why that gap needed filling in the first place.
-
-[2. Comparison with Previous Evidence]
-Here, you'll place your findings in the context of existing research, reinforcing the validity and relevance of your work.
-
-[3. Supporting Your Findings]
-In this part, you address potential counterarguments or contradictory findings, enhancing the robustness of your research by explaining why your results are preferable or more accurate.
-
-[4. Limitations]
- Acknowledging limitations in methodology or approach helps strengthen your credibility as a researcher. Study limitations are not simply a list of mistakes made in the study. Rather, limitations help provide a more detailed picture of what can or cannot be concluded from your findings.
-
-[5. Implications]
-This final section is crucial for illustrating the broader impact of your work, discussing its biological significance, practical usefulness, and potential applications, which can be particularly persuasive for funding bodies or stakeholders. End with a concise summary explaining the big-picture impact of the current study on our understanding of the subject matter. Now, it is time to end with “how your research filled that gap.”
-----------------
-TEMPLATE ENDS
-----------------
-
-For example, the discussion below is well-written, following the provided template. You may realize that the order of paragraphs may be exchangeable, and it's not always easy to allocate tags.
-
-----------------
-EXAMPLE STARTS
-----------------
-[START of 1. Summarizing Key Findings] We have generated a knockout mouse strain lacking the NMDAR1 subunit in the CA1 region of the hippocampus. These mice seem to grow normally and do not present obvious behavioral abnormalities. We have shown that the mutant mice lack NMDAR-mediated EPSCs and LTP in the CA1 region and are impaired in the hidden-platform version of the Morris water maze (a measure of spatial memory) but not in nonspatial learning tasks. Previously, it has been suggested that NMDA receptor-dependent LTP underlies the acquisition of new memories in the hippocampus (reviewed by4, 40). Our results provide a strong support for this view and makes it more specific: the NMDA receptor-dependent LTP in the CA1 region is crucially involved in the formation of certain types of memory. [END of 1. Summarizing Key Findings] [START of 4. Limitations] We cannot exclude the possibility that the NMDA receptor-dependent synaptic plasticity crucial for memory formation is LTD, given that the CA1-KO mice seem to lack NMDAR-dependent LTD. [ENDS of 4. Limitations] [START of 3. Supporting Your Findings] However, we think that this is unlikely because spatial learning is apparently intact in knockout mice deficient in protein kinase A that lack CA1 LTD (Brandon et al. 1995). [END of Supporting Your Findings]
-[START of 2. Comparison with Previous Evidence] Previous work has used pharmacological and genetic tools to examine whether synaptic plasticity is the mechanism for memory formation. Although the evidence is consistent with this notion many issues have remained unresolved. For example, the most sophisticated pharmacological studies that have been done thus far are based on the infusion of NMDAR antagonists directly into the brain (39, 9). Since the infusion cannot be localized to a particular region (such as the CA1 region) with the exclusion of the rest of brain, it is not possible to determine the contribution of specific areas to memory formation. Moreover, it has been reported that NMDARs contribute substantially to the basal synaptic transmission in some areas of the neocortex (Hestrin 1996). Thus, the memory impairment could be explained at least in part by a defect in the computational ability of the neocortex rather than by an impairment in the synaptic plasticity within the hippocampus.  
-Several drawbacks also accompany the conventional gene knockout studies. In particular, the ubiquitous deletion of the gene may cause undesirable developmental and behavioral consequences. Our work circumvents these concerns because the deletion of the NMDAR1 subunit occurs in a restricted manner, only in the CA1 region. [END of 2. Comparison with Previous Evidence] [START of 3. Supporting Your Findings] We have not yet shown directly the precise developmental timing of the Cre/loxP recombination that deletes the NMDAR1 gene. However, an accompanying article (Tsien et al. 1996) in which we use the expression of β-galactosidase as a reporter for the recombination shows that it occurs during the third postnatal week, about 2 weeks after the CA1 region of the hippocampus has completed its cellular organization and connections (44, 45, 52). Thus, it is likely that the NMDAR1 gene is also deleted at this time, providing a postnatal knockout of the gene and thus avoiding the developmental concerns. [END of 3. Supporting Your Findings]
-[START of 4. Limitations] Consideration into the Mixed Genetic Background Another caveat associated with the behavioral studies done in gene knockout mice stems from the fact that ES cells from the mouse strain 129/Sv are commonly used to generate the mutant mice (reviewed byGerlai 1996). The 129/Sv mice demonstrate behavioral defects such as the inability to perform the Morris water maze task (Gerlai 1996). Consequently, most behavioral studies with knockout mice have been carried out after crossing them to a behaviorally “normal” strain, such as C57BL/6. This of course causes animal-to-animal variations in the ability to perform a certain behavioral task, variation that is attributed to the difference in the genetic background. The problem is best resolved by using ES cells derived from a behaviorally normal strain, such as C57BL/6. Recently, ES cells from this strain that have an acceptable frequency of germline transmission have become available (Kawase et al. 1994; Köntgen et al. 1993; Ledermann and Bürki 1991). In the current study, the genetic background issue has not been resolved completely. However, we avoided a major source of variation for the Morris water maze task by eliminating “floating” individuals from both the mutant and control groups (see Experimental Procedures). [END of 4. Limitations]
-[START of 3. Supporting Your Findings] Gene Knockout Studies Point to a Pivotal Role of CA1 Synaptic Plasticity Previous studies examined the correlation between spatial memory and the site of hippocampal LTP (i.e., CA1, CA3, and dentate gyrus) by using a variety of conventional knockout mice (reviewed byChen and Tonegawa 1997). These studies found a correlated impairment in Scc-CA1 LTP and spatial memory (but seeConquet et al. 1994). It is important to point out that the only exceptional case, namely that of the mGluR1 mutant mice, is complicated by the fact that two groups have generated and analyzed these mutants independently and have obtained opposing results (1, 13, 11). By contrast, it has been shown that impairments of mossy fiber–CA3 LTP (Huang et al. 1995) and perforant path–dentate LTP (Nosten-Bertrand et al. 1996) are not correlated with spatial memory deficit.
-Our new evidence, while still correlational, is much stronger than that in the earlier reports because we have singled out the CA1 synapses as a site of plasticity impairment. What structural and functional features could explain this pivotal role of CA1 synapses as sites of plasticity underlying spatial memory? It is well known that the CA1 region is a crucial component of the “hippocampal formation” system that is involved in the acquisition of certain types of memory. In rodents, this system consists of several structures connected within a loop that encompasses (Figure 9) the entorhinal cortex (EC), with inputs from higher sensory cortices; dentate gyrus (DG), with inputs from EC; CA3, with “external” inputs from EC and DG and “internal” inputs from CA3; CA1, with inputs from CA3 and EC; and subiculum (SUB), with inputs from CA1 and outputs to EC (33, 2). In lieu of the evidence currently available, it would seem that the minimal system required as a locus for memory acquisition would be the EC-CA3-CA1-SUB-EC loop. This is because first, the plasticity in the EC-DG and DG-CA3 synapses seems to be dispensable (25, 42); second, the direct EC-CA1 connection appears to be too weak to sustain the EC-CA1-SUB-EC loop as the locus for memory (Empson and Heinemann 1995); and third, the evidence presented in this article points to the special role of the CA3-CA1 synapses. [END of 3. Supporting Your Findings]
-[START of 5. Implications] The plasticity of the EC-CA3 synapses has not been well studied, but our proposed scenario predicts that they are important in implementing the memory system. Most probably, both the EC-CA3 pathway and the EC-DG-CA3 pathway provide parallel inputs to the CA3 network during learning, and the CA3-CA3 synapses work as autoassociative memory devices, as has long been proposed (Marr 1971). Thus, it is desirable to generate a CA3 region–specific knockout of the NMDA receptor to allow direct examination of the contribution of these synapses to learning. [END of 5. Implications]
-----------------
-EXAMPLE ENDS
-----------------
-
-Also, plesae note that I have used this type of tags in this prompt:
-----------------
-XXXXX STARTS/ENDS
------------------
-However, these tags are just for better communication with you. So, please do not include similar tags in your output.
-
-Please output only your revised introduction, without including any comments. 
-
-Remember to insert the following section START and END tags in the same manner as the above example:
-- [START of 1. Summarizing Key Findings] 
-- [END of 2. Summarizing Key Findings] 
-- [START of 2. Comparison with Previous Evidence] 
-- [END of 2. Comparison with Previous Evidence] 
-- [START of 3. Supporting Your Findings] 
-- [END of 3. Supporting Your Findings] 
-- [START of 4. Limitations] 
-- [END of 4. Limitations] 
-- [START of 5. Implications]
-- [END of 5. Implications]
-
-Now, my draft is as follows.  Also, please return as a code block (``` tex\nYOUR REVISED ABSTRACT```). 
------------------
-MY DRAFT STARTS
------------------
-PLACEHOLDER
------------------
-MY DRAFT ENDS
------------------

scitex/scholar/docs/to_claude/guidelines/science/scientific-writing-general-1.md

@@ -1,157 +0,0 @@
-<!-- ---
-!-- Timestamp: 2025-05-29 02:32:43
-!-- Author: ywatanabe
-!-- File: /ssh:ywatanabe@sp:/home/ywatanabe/.dotfiles/.claude/to_claude/guidelines/science/scientific-writing-general.md
-!-- --- -->
-
-
-# Scientific Guidelines
-
-## Table of Contents
-- [Figure Rules](#figure-rules)
-- [Statistical Reporting](#statistical-reporting)
-- [Document Format](#document-format)
-
-## Figure Rules
-
-| ❌ DO NOT | ✅ DO |
-|-----------|------|
-| ```python
-# Missing axis labels
-plt.plot(x, y)
-plt.show()
-``` | ```python
-# Complete axis information
-plt.plot(x, y)
-plt.xlabel('Time (s)')
-plt.ylabel('Amplitude (mV)')
-plt.title('Signal Measurement')
-plt.show()
-``` |
-| ```python
-# Bar graph not starting from 0
-plt.bar(categories, values)
-plt.ylim(min(values) - 0.1, max(values) + 0.1)
-``` | ```python
-# Bar graph properly starting from 0
-plt.bar(categories, values)
-plt.ylim(0, max(values) * 1.1)
-``` |
-| ```python
-# Misleading probability range
-plt.plot(x, probabilities)
-plt.ylim(min(probabilities), max(probabilities))
-``` | ```python
-# Showing full probability range
-plt.plot(x, probabilities)
-plt.ylim(0, 1)
-``` |
-
-### Axis Requirements
-- Axes must have labels with units
-- Include appropriate ticks (3-5 ticks)
-- Include tick labels
-- Use proper ranges that don't mislead
-
-### Range Guidelines
-- Bar graphs must start from 0
-- Variables within range [0, 1] should be displayed in full [0, 1] range
-- Don't manipulate figures to control impressions
-- Ensure visualizations accurately represent the data
-
-### Importance
-- Figures are among the most important elements in scientific communication
-- Ensure all generated figures are scientifically valid
-- Consider aesthetic aspects while maintaining accuracy
-
-## Statistical Reporting
-
-| ❌ DO NOT | ✅ DO |
-|-----------|------|
-| ```python
-# Incomplete statistical reporting
-p = stats.ttest_ind(group1, group2).pvalue
-print(f"p = {p:.3f}")
-``` | ```python
-# Complete statistical reporting
-result = stats.ttest_ind(group1, group2)
-pval = result.pvalue
-dof = len(group1) + len(group2) - 2
-effect_size = (np.mean(group1) - np.mean(group2)) / np.sqrt((np.std(group1)**2 + np.std(group2)**2) / 2)
-
-results = {
-    "p_value": pval,
-    "stars": scitex.stats.p2stars(pval),
-    "n1": len(group1),
-    "n2": len(group2),
-    "dof": dof,
-    "effsize": effect_size,
-    "test_name": "Independent samples t-test",
-    "statistic": result.statistic,
-    "H0": "The means of the two groups are equal"
-}
-``` |
-| ```python
-# Not handling multiple comparisons
-pvals = [stats.ttest_ind(group, control).pvalue 
-         for group in treatment_groups]
-significant = [p < 0.05 for p in pvals]
-``` | ```python
-# FDR correction for multiple comparisons
-pvals = [stats.ttest_ind(group, control).pvalue 
-         for group in treatment_groups]
-results_df = pd.DataFrame({"p_value": pvals})
-corrected_results = scitex.stats.fdr_correction(results_df)
-significant = corrected_results["p_value_fdr"] < 0.05
-``` |
-
-### Statistical Analysis Guidelines
-- Report all relevant statistical information:
-  - p-value (with stars for significance)
-  - Sample sizes
-  - Degrees of freedom (dof)
-  - Effect size
-  - Test name
-  - Test statistic
-  - Null hypothesis
-- Always use FDR correction for multiple comparisons
-- Round statistical values appropriately (typically 3 digits)
-- Report statistical values in italic font in documents
-- Fix random seed as 42 for reproducibility
-
-## Document Format
-
-| ❌ DO NOT | ✅ DO |
-|-----------|------|
-| ```
-**IMPORTANT NOTE: This analysis shows...**
-*Many asterisks to emphasize points*
-``` | ```
-Minimal formatting:
-1. Analysis results
-2. Key findings
-   - Finding A
-   - Finding B
-``` |
-| ```
-// Inline comments in code
-let value = 42; // This is the answer
-``` | ```
-// Separate comment lines in code
-// This is the answer
-let value = 42;
-``` |
-
-### Minimal Output
-- Avoid unnecessary messages and keep output minimal
-- Reduce use of markdown formatting (avoid bold text, minimize asterisks)
-- Use bullet points with numbering (1.) and simple hyphens (-) with indents
-- Be concise and direct in communications
-
-### Code Formatting
-- Use separate lines of comments instead of trailing comments
-- Code must be wrapped with triple backticks and language indicator
-- Specify file names or paths when showing file content suggestions
-- Don't include headers and footers in code blocks
-
-<!-- EOF -->

scitex/scholar/docs/to_claude/guidelines/science/scientific-writing-general-2.md

@@ -1,83 +0,0 @@
-<!-- ---
-!-- Timestamp: 2025-05-29 02:32:54
-!-- Author: ywatanabe
-!-- File: /ssh:ywatanabe@sp:/home/ywatanabe/.dotfiles/.claude/to_claude/guidelines/science/scientific-writing-general-2.md
-!-- --- -->
-
-# Scientific Writing Guidelines
-
-## Table of Contents
-- [Your Role](#your-role)
-- [General Rules](#general-rules)
-- [Formatting Guidelines](#formatting-guidelines)
-- [Language Rules](#language-rules)
-- [Common Scientific Writing Corrections](#common-scientific-writing-corrections)
-- [Section-Specific Guidelines](#section-specific-guidelines)
-
-## Your Role
-You are an esteemed professor in the scientific field, based in the United States.
-The subsequent passages originate from a student whose first language is not English.
-Please proofread them following the guidelines below.
-
-## General Rules
-- Correct the English without including messages or comments
-- Retain the original syntax as much as possible while conforming to scholarly language
-- Do not modify linguistically correct sections
-- Minimize revisions to avoid endless paraphrasing
-- Exclude comments beyond the revised text
-
-## Formatting Guidelines
-- For figures and tables, use tags like Figure~\ref{fig:01}A or Table~\ref{tab:01}
-- Highlight ambiguous parts requiring manual review using: [fixme ->] This is ambiguous. [<- fixme]
-- When using emdash (---), add spaces on either side
-- Never remove references and LaTeX code
-- Enclose revised text in code block with language "GenAI"
-- Return as code block for easy selection: ``` sciwrite YOUR REVISION ```
-- Use LaTeX format
-- For adding references, insert a placeholder using: `\hlref{XXX}`
-
-## Language Rules
-- Avoid unnecessary adjectives unsuitable for scientific writing ("somewhat," "in-depth," "various")
-- Maintain consistent terminology throughout the manuscript
-- Titles should follow proper capitalization rules (prepositions in lowercase)
-- Prefer singular form without articles (a, an, the) when appropriate
-- Figure/table titles and legends should be in noun form
-
-## Common Scientific Writing Corrections
-
-| ❌ DO NOT | ✅ DO |
-|-----------|------|
-| "We somewhat observed an interesting effect." | "We observed an effect." |
-| "The data shows that..." | "The data show that..." |
-| "Figure 1 shows the results of an in-depth analysis" | "Figure~\ref{fig:01} shows the results of the analysis" |
-| "We did the experiment to see if..." | "We conducted the experiment to determine whether..." |
-| "A lot of samples were tested" | "Multiple samples (n = 42) were tested" |
-| "The results were found to be significant" | "The results were significant (p < 0.05)" |
-| "Various results were obtained" | "Three distinct patterns were observed" |
-
-## Section-Specific Guidelines
-
-| Section | Guidelines |
-|---------|------------|
-| Title | Follow capitalization rules: "Neural Activity in Hippocampus during Modified Tasks" |
-| Abstract | Concise summary with key findings and implications; avoid detailed methods |
-| Introduction | Clear progression from general to specific; end with research questions |
-| Methods | Precise descriptions allowing replication; use past tense passive voice |
-| Results | Present findings without interpretation; refer to figures/tables consistently |
-| Discussion | Interpret results in context of hypothesis and literature; address limitations |
-| References | Maintain consistent format; never modify citation codes |
-
-### Examples of Title Corrections
-
-| ❌ Original Title | ✅ Corrected Title |
-|------------------|-------------------|
-| "A Study about the Effects of Temperature on the Growth Rate of Bacterial Cells" | "Effects of Temperature on Bacterial Cell Growth Rate" |
-| "The investigation into various neural networks which are used in medical imaging" | "Neural Networks in Medical Imaging" |
-| "Analysis of data from immune responses after vaccination in Mice Models" | "Analysis of Immune Responses after Vaccination in Mouse Models" |
-
-----------
-Now, the original manuscript to be revised is as follows:
-----------
-PLACEHOLDER
-
-<!-- EOF -->

scitex/scholar/docs/to_claude/guidelines/science/scientific-writing-introduction.md

@@ -1,123 +0,0 @@
-<!-- ---
-!-- title: ./genai/templates/SciWriteIntroduction.md
-!-- author: ywatanabe
-!-- date: 2024-11-19 22:21:24
-!-- --- -->
-
-
-----------
-Background
-----------
-# Your Role
-You are an esteemed professor in the scientific field, based in the United States.
-
-# My Request
-- Please revise my introduction draft.
-
-# Aim of Introduction
-The aim of introduction is to offer readers with the background necessary to understand your paper: the status of knowledge in your field, the question motivating your work and its significance, how you sought to answer that question (methods), and your main findings. A well-written introduction will broaden your readership by making your findings accessible to a larger audience.
-
-# Rules
-- Style
-  - Please follow the format of the template I will provide below in this message.
-  - Your revision should conform to the language style typical of a scholarly article in biology.
-  - Use technical language suitable for neuroscience journals 
-  - Spell out abbreviations and acronyms in their first appearance
-  - Include a clear, concise topic sentence in each paragraph.
-  - Use transition phrases between paragraphs to make introduction coherent and cohesive
-  - Insert a newline with the tab identation between pargraphs, except for between the first and second paragraphs;both [1. Opening Statement] and [2. Importance of the Field] sections should be in the first paragraph.
-
-- Volume
-  - Ensure to write at least 1000 words
-
-- Misc.
-  - Explicitly indicate species with sample sizes
-  - Add relevant references when applicable
-  - Keep existing references as they are
-  - Maintain quantitative measurements as they are written.
-  - Target audience is neuroscience/psychology specialists
-  - Pay careful attention to the use of hyphens, en dashes, em dashes, and minus signs.
-  - Avoid unnercessary adjectives for emphasizing like "significantly", "well", 
-  - If tex tags are inserted, please conform to the latex style.
-
-- Return as code block (for just convenience for selection) like this:
-  ``` sciwrite-introduction
-  YOUR REVISION
-  ```
-- Use LaTeX format
-
-- When adding references (to literature, tables, or figures) will enhance the quality of the paper, please insert a placeholder using this LaTeX command `\hlref{XXX}`. This command will highlight any unlinked content so that it will work well as a placeholder.
-
-Now, the template is as follows:
-------------------
-TEMPLATE STARTS
-------------------
-[1. Opening Statement]
-The introduction should commence with a broad yet detailed statement about the field of study. It's essential to set the stage for the research, making it engaging and accessible for a general scientific audience while retaining technical accuracy. This part is the first half of the opening paragraph.
-
-[2. Importance of the Field]
-The second half of the opening paragraph should emphasize the importance and relevance of the field. It's crucial to highlight the potential impact of the research area, its significance in advancing scientific knowledge, and its applications in real-world scenarios.
-
-[3. Existing Knowledge and Gaps]
-In the next 1-2 paragraphs, provide a comprehensive summary of the current state of knowledge in the field. This section should identify key gaps or unanswered questions in the existing research, using precise data and measurements where relevant. It sets up the context and necessity for your research, outlining why your study is both timely and important.
-
-[4. Limitations in Previous Works]
-In the next 1-2 paragraphs, this section should critically examine the limitations inherent in previous research within the field. Discuss methodological constraints, such as the use of specific models (e.g., animal models in neuroscience) or tools (like imaging techniques), which may have restricted the scope or applicability of the findings. Additionally, address any logical shortcomings or gaps in previous studies, such as unexplored variables, overlooked correlations, or assumptions that may have influenced the outcomes. Highlighting these limitations not only sets the stage for your research contribution but also contextualizes your work within the broader field, establishing the necessity for your approach and methodology.
-
-[5. Research Question or Hypothesis]
-Dedicate one paragraph to clearly stating the research question or hypothesis of your study. This should be specific, directly related to the gaps identified, and framed in a way that highlights its significance in the broader context of the field.
-
-[6. Approach and Methods]
-Describe the approach and methods used in your research, in one paragraph. This section should give an overview of the methods without delving into excessive detail, but maintain enough technicality to be clear and credible to a scientifically literate audience. Also, highlight the speriority of current study over existing works mensioned in the [3. Limitations in Previous Work].
-
-[7. Overview of Results]
-Optionally, include a paragraph providing a high-level summary of the main findings of your research. This should avoid detailed data but effectively convey the overall outcomes and achievements of the study.
-
-[8. Significance and Implications]
-Conclude with a separate, final paragraph of 1-3 sentences discussing the significance of your findings and their implications for the field. It should articulate how your research contributes to advancing knowledge and what it potentially means for future studies in the field.
-----------------
-TEMPLATE ENDS
-----------------
-
-For example, the introduction below is well-written, following the provided template.
-
-----------------
-EXAMPLE STARTS
-----------------
-[START of 1. Opening Statement] Dementia, which affects an estimated 50 million people worldwide, is a significant health challenge characterized by the progressive decline of memory, attention, and executive functions, which are pivotal for maintaining daily independence (Prince et al., 2015). [END of 1. Opening Statement] [START of 2. Importance of the Field] Accurate identification of its various subtypes, such as Alzheimer's disease (AD), dementia with Lewy bodies (DLB), and idiopathic normal-pressure hydrocephalus (iNPH), is crucial for appropriate clinical management (Barker et al., 2002; Williams and Malm, 2016; McKeith et al., 2017; Arvanitakis et al., 2019; Leuzy et al., 2022). [END of 2. Importance of the Field]
-
-[START of 4. Limitations in Previous Works] The pursuit of early and precise differentiation of dementia subtypes is hindered by several factors. Traditional diagnostic techniques, such as magnetic resonance imaging (MRI), positron emission tomography (PET), and cerebrospinal fluid (CSF) tests, while effective, are costly, invasive, and not universally accessible, limiting their utility in certain regions (Garn et al., 2017; Hata et al., 2023). Moreover, the mild cognitive impairment (MCI) stage, often a precursor to dementia, presents a diagnostic challenge due to its subtle symptom presentation, complicating its diagnosis in clinical practice (Ieracitano et al., 2020). [END of 4. Limitations in Previous Works]
-
-[START of 5. Research Question or Hypothesis] These issues underscore the necessity for a more accessible, noninvasive, and standardized screening tool capable of discerning the nuanced differences between dementia subtypes. [END of 5. Research Question or Hypothesis]
-
-[START of 3. Existing Knowledge and Gaps] Further highlighting the urgency for early and accurate diagnosis, the recent identification of an antibody targeting amyloid beta protofibrils opens a promising avenue for decelerating the progression of AD in its nascent stages (Swanson et al., 2021). Furthermore, iNPH presents a unique case wherein early detection could lead to significant symptom relief through interventions such as CSF shunting, emphasizing the importance of precise early diagnostic techniques (Williams & Malm, 2016). [END of 3. Existing Knowledge and Gaps]
-
-[Start of 6. Approach and Methods] Responding to the need for noninvasive, cost-effective, and widely available diagnostic methods, our research has pivoted toward the utilization of electroencephalography (EEG). This neurophysiological recording technique, renowned for its noninvasiveness and cost-effectiveness, holds untapped potential for enhancing the early detection and differentiation of dementia. [END of 6. Approach and Methods]
-
-[START of 3. Existing Knowledge and Gaps] The EEG methods proposed by existing studies, however, have often been less successful in practical application due to limited comparative analyses being available in the literature, misapplication of machine learning techniques, e.g., the failure to appropriately segregate datasets from external institutions for independent testing compromises the assessment of a model's true classification accuracy across various clinical settings, and a dearth of generalizable findings (Rossini et al., 2008; Aoki et al., 2015; Bonanni et al., 2016; Ieracitano et al., 2020; Chatzikonstantinou et al., 2021; Sánchez-Reyes et al., 2021; Micchia et al., 2022). [END of 3. Existing Knowledge and Gaps]
-
-[START of 6. Approach and Methods] A particularly promising yet underexplored domain is the use of deep convolutional neural networks (DCNNs) with EEG data for dementia classification; notably, this technique may bypass the intricacies of feature engineering and reveal the nuanced patterns indicative of various dementia subtypes. [END of 6. Approach and Methods]
-
-In this study, we are committed to testing three pivotal hypotheses, each aimed at overcoming the challenges of early diagnosis of dementia and its diverse subtypes. Our first hypothesis contends that the proposed DCNN using EEG data can accurately distinguish between healthy volunteers (HVs) and patients with dementia across multiple institutions; verifying this hypothesis would indicate the robustness and wide applicability of our model. Our second hypothesis posits that this EEG-driven DCNN will be able to adeptly classify dementia subtypes (AD, DLB, or iNPH); evidence in support of this hypothesis would showcase the model's diagnostic precision. Last, our third hypothesis is that identifiable EEG patterns associated with dementia subtypes are anticipated to be present in the preceding MCI stages; if this is the case, it would suggest the existence of potential indicators that may provide insights into the progression from MCI to overt dementia. Our findings could mark a significant advancement in predictive diagnostics and tailor-made therapeutic interventions in the realm of neurodegenerative diseases.
-----------------
-EXAMPLE ENDS
-----------------
-
-Remember to insert the following section tags (START and END ) in the same manner as the above example:
-([START of 1. Opening Statement], [END of 1. Opening Statement], [START of 2. Importance of the Field], [END of 2. Importance of the Field], [START of 3. Existing Knowledge and Gaps], [END of 3. Existing Knowledge and Gaps], [START of 4. Limitations in Previous Works], [END of 4. Limitations in Previous Works], [START of 5. Research Question or Hypothesis], [END of 5. Research Question or Hypothesis], [START of 6. Approach and Methods], [END of 6. Approach and Methods], [START of 7. Overview of Results], [END of 7. Overview of Results], [START of 8. Significance and Implications], and [END of 8. Significance and Implications]).
-
-Also, plesae note that I have used this type of tags in this prompt:
-----------------
-XXXXX STARTS/ENDS
------------------
-However, these tags are just for better communication with you. So, please do not include similar tags in your output.
-
-Now, my draft is as follows. Please output only your revised introduction, without including any comments. Also, please return as a code block (``` tex\nYOUR REVISED ABSTRACT```).
-
------------------
-MY DRAFT STARTS
------------------
-PLACEHOLDER
------------------
-MY DRAFT ENDS
------------------