cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28561912
title: Association of <i>XRCC</i> gene family and <i>CDH1</i> gene polymorphisms with gastric cancer risk in a Chinese population

description: Gastric carcinogenesis is associated with defects in DNA damage repair pathways, in which the <i>XRCC</i> gene family (<i>XRCC1</i>, <i>XRCC5</i>, and <i>XRCC6</i>) play an important role in DNA repair. It is also well known that the <i>CDH1</i> gene, as a tumor suppressor, influences the development of gastric cancer. We recruited 484 gastric cancer patients and 471 controls. DNA genotyping and <i>Helicobacter pylori</i> infection were determined by commercial kits. Association between polymorphisms and gastric cancer risk and survival was evaluated through SPSS 26.0. Stratified analysis revealed that <i>XRCC1</i> rs25487 TC/TT was associated with increased gastric cancer risk in the following four subgroups of males (adjusted OR = 1.40, 95% CI: 1.03–1.90, <i>p</i> = 0.031), positive <i>Helicobacter pylori</i> (adjusted OR = 1.58, 95% CI: 1.09–2.28, <i>p</i> = 0.015), tumor stage III-IV (adjusted OR = 1.42, 95% CI: 1.06–1.89, <i>p</i> = 0.017), and non-gastric cardiac adenocarcinoma (adjusted OR = 1.36, 95% CI: 1.02–1.82, <i>p</i> = 0.034). Additionally, survival analysis indicated that <i>XRCC1</i> rs25487 TC/TT genotype (HR = 1.35, 95% CI: 1.08–1.69, <i>p</i> = 0.010) was associated with unfavorable survival in gastric cancer patients. <i>XRCC1</i> rs25487 CC genotype decreased the risk of gastric cancer, and predicted a favorable survival prognosis.
DOI: 10.6084/m9.figshare.28561912.v1
title: Association of <i>XRCC</i> gene family and <i>CDH1</i> gene polymorphisms with gastric cancer risk in a Chinese population

description: Gastric carcinogenesis is associated with defects in DNA damage repair pathways, in which the <i>XRCC</i> gene family (<i>XRCC1</i>, <i>XRCC5</i>, and <i>XRCC6</i>) play an important role in DNA repair. It is also well known that the <i>CDH1</i> gene, as a tumor suppressor, influences the development of gastric cancer. We recruited 484 gastric cancer patients and 471 controls. DNA genotyping and <i>Helicobacter pylori</i> infection were determined by commercial kits. Association between polymorphisms and gastric cancer risk and survival was evaluated through SPSS 26.0. Stratified analysis revealed that <i>XRCC1</i> rs25487 TC/TT was associated with increased gastric cancer risk in the following four subgroups of males (adjusted OR = 1.40, 95% CI: 1.03–1.90, <i>p</i> = 0.031), positive <i>Helicobacter pylori</i> (adjusted OR = 1.58, 95% CI: 1.09–2.28, <i>p</i> = 0.015), tumor stage III-IV (adjusted OR = 1.42, 95% CI: 1.06–1.89, <i>p</i> = 0.017), and non-gastric cardiac adenocarcinoma (adjusted OR = 1.36, 95% CI: 1.02–1.82, <i>p</i> = 0.034). Additionally, survival analysis indicated that <i>XRCC1</i> rs25487 TC/TT genotype (HR = 1.35, 95% CI: 1.08–1.69, <i>p</i> = 0.010) was associated with unfavorable survival in gastric cancer patients. <i>XRCC1</i> rs25487 CC genotype decreased the risk of gastric cancer, and predicted a favorable survival prognosis.
DOI: 10.6084/m9.figshare.28581327
title: Developing the Workplace Learning Social System: considerations for genomics implementation and workforce preparedness

description: Innovations, such as genomics, are expected to transform the practice of the healthcare workforce. Workplace learning is an established and fundamental component of healthcare workforce training. We propose that it can be leveraged to facilitate workforce preparedness to adopt innovations relevant to practice. To explore this, this study aimed to develop a workplace learning framework premised on primary literature. Four databases were systematically searched to identify and synthesize contemporary research articles investigating doctors’ workplace learning, with an additional focus on genetics/genomics. From the articles included, factors influencing workplace learning were extracted. Informed by structuration and workplace learning theories, thematic analysis was conducted on these factors to generate the framework. Despite the lack of articles on doctors’ genetics/genomics workplace learning, 50 articles on doctors’ workplace learning were included. Extracted influencing factors were synthesized into five major domains, across three social system levels and the agentic learner, to generate the Workplace Learning Social System framework. Innovations in healthcare require its workforce to change work practices. The Workplace Learning Social System framework holistically conceptualizes workplace learning based on contemporary literature. It provides pragmatic insights to inform workforce development when implementing innovations as part of system-wide change.
DOI: 10.6084/m9.figshare.28581327.v1
title: Developing the Workplace Learning Social System: considerations for genomics implementation and workforce preparedness

description: Innovations, such as genomics, are expected to transform the practice of the healthcare workforce. Workplace learning is an established and fundamental component of healthcare workforce training. We propose that it can be leveraged to facilitate workforce preparedness to adopt innovations relevant to practice. To explore this, this study aimed to develop a workplace learning framework premised on primary literature. Four databases were systematically searched to identify and synthesize contemporary research articles investigating doctors’ workplace learning, with an additional focus on genetics/genomics. From the articles included, factors influencing workplace learning were extracted. Informed by structuration and workplace learning theories, thematic analysis was conducted on these factors to generate the framework. Despite the lack of articles on doctors’ genetics/genomics workplace learning, 50 articles on doctors’ workplace learning were included. Extracted influencing factors were synthesized into five major domains, across three social system levels and the agentic learner, to generate the Workplace Learning Social System framework. Innovations in healthcare require its workforce to change work practices. The Workplace Learning Social System framework holistically conceptualizes workplace learning based on contemporary literature. It provides pragmatic insights to inform workforce development when implementing innovations as part of system-wide change.
DOI: 10.6084/m9.figshare.28616326
title: How people undergoing genomic sequencing interpret and react to varied secondary findings with limited actionability

description: To investigate patient reactions to and understanding of secondary genomic findings with limited to no medical actionability (LMA-SFs) from diagnostic genome sequencing. We analyzed LMA-SFs returned to 47 adults who elected to receive a broad set of these results from 6 categories. Findings indicated elevated risk (reportable/positive) or not (negative/normal). Most participants (<i>N</i> = 43) also completed surveys to report their distress, decision regret, expected health anxiety, and whether and how they perceived results as reassuring or troubling. Most participants received some reportable LMA-SFs for common risk, pharmacogenetic, and carrier status variants. Fewer received reportable <i>APOE</i> haplotype or monogenetic condition variants. None received results indicating high risk for severe neurological disease. Overall, participants (76.7% female, 97.7% White) had low distress, decision regret, and expected health anxiety. None described negative/normal findings as troubling. However, their interpretations of reportable/positive results varied. Even within the same result type, some participants found them troubling, while others found them reassuring based on their perception of the results’ utility. Participants’ short-term well-being was not reduced by receiving LMA-SFs. Their interpretations suggested varied personal utilities and the need for post-test resources to aid understanding of these types of results and their health significance. Genomic sequencing can find a diagnosis for people who have symptoms that suggest they may have a hereditary disease. It can also find results that do not change medical treatment for most people. This study looks at whether people feel distressed when they get secondary findings that will give them little to no medically useful information. Because these findings can be hard to understand, we also asked people to explain what their findings meant to them. We found that learning these findings did not make people feel distressed. Also, people who received the same or similar results felt differently about the results they received. Some felt their results were good news, while others were worried. Even when they learned about higher health risk, some people felt it was useful because it helps them plan. In sum, we found NO/LITTLE evidence that secondary findings caused distress in patients. We should learn more about how personal understanding influences future health decisions.
DOI: 10.6084/m9.figshare.28616326.v1
title: How people undergoing genomic sequencing interpret and react to varied secondary findings with limited actionability

description: To investigate patient reactions to and understanding of secondary genomic findings with limited to no medical actionability (LMA-SFs) from diagnostic genome sequencing. We analyzed LMA-SFs returned to 47 adults who elected to receive a broad set of these results from 6 categories. Findings indicated elevated risk (reportable/positive) or not (negative/normal). Most participants (<i>N</i> = 43) also completed surveys to report their distress, decision regret, expected health anxiety, and whether and how they perceived results as reassuring or troubling. Most participants received some reportable LMA-SFs for common risk, pharmacogenetic, and carrier status variants. Fewer received reportable <i>APOE</i> haplotype or monogenetic condition variants. None received results indicating high risk for severe neurological disease. Overall, participants (76.7% female, 97.7% White) had low distress, decision regret, and expected health anxiety. None described negative/normal findings as troubling. However, their interpretations of reportable/positive results varied. Even within the same result type, some participants found them troubling, while others found them reassuring based on their perception of the results’ utility. Participants’ short-term well-being was not reduced by receiving LMA-SFs. Their interpretations suggested varied personal utilities and the need for post-test resources to aid understanding of these types of results and their health significance. Genomic sequencing can find a diagnosis for people who have symptoms that suggest they may have a hereditary disease. It can also find results that do not change medical treatment for most people. This study looks at whether people feel distressed when they get secondary findings that will give them little to no medically useful information. Because these findings can be hard to understand, we also asked people to explain what their findings meant to them. We found that learning these findings did not make people feel distressed. Also, people who received the same or similar results felt differently about the results they received. Some felt their results were good news, while others were worried. Even when they learned about higher health risk, some people felt it was useful because it helps them plan. In sum, we found NO/LITTLE evidence that secondary findings caused distress in patients. We should learn more about how personal understanding influences future health decisions.
DOI: 10.15468/dl.ah9y9z
title: Occurrence Download

description: A dataset containing 50104 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "TaxonKey is Crocus vernus (L.) Hill"
 ]
}

 The dataset includes 50104 records from 356 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016643-250402121839773/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.10578704
title: Nigerian Software Engineer or American Data Scientist? GitHub Profile Recruitment Bias in Large Language Models

description: This repository serves as the online appendix for the paper "Nigerian Software Engineer or American Data Scientist? GitHub Profile Recruitment Bias in Large Language Models".
description: Large Language Models (LLMs), have taken the world by storm, demonstrating their ability not only to automate tedious tasks, but also to show some degree of proficiency in completing software engineering tasks. A key concern with LLMs is their "black-box" nature, which obscures their internal workings and could lead to societal biases in their outputs. In the software engineering context, in this short paper, we empirically explore how well LLMs can automate recruitment tasks for a geographically diverse software team. We utlize OpenAI’s GPT to conduct an initial set of experiments using GitHub Profiles from four regions (i.e., the United States, India, Nigeria, and Poland) to recruit a six-person software development team, analyzing a total of 3,896 profiles over a 5-year period (2019–2023). The results indicate that GPT tends to prefer some regions over others, even when some profiles have been manipulated to contain counterfactuals, such as swapping the location strings of two profiles. Furthermore, GPT was more likely to assign certain developer roles to users from a specific country, revealing an implicit bias. Overall, this study reveals insights into the inner workings of GPT and has implications for mitigating these potential biases.
DOI: 10.5281/zenodo.10578705
title: Nigerian Software Engineer or American Data Scientist? GitHub Profile Recruitment Bias in Large Language Models

description: This repository serves as the online appendix for the paper "Nigerian Software Engineer or American Data Scientist? GitHub Profile Recruitment Bias in Large Language Models".
description: Large Language Models (LLMs), have taken the world by storm, demonstrating their ability not only to automate tedious tasks, but also to show some degree of proficiency in completing software engineering tasks. A key concern with LLMs is their "black-box" nature, which obscures their internal workings and could lead to societal biases in their outputs. In the software engineering context, in this short paper, we empirically explore how well LLMs can automate recruitment tasks for a geographically diverse software team. We utlize OpenAI’s GPT to conduct an initial set of experiments using GitHub Profiles from four regions (i.e., the United States, India, Nigeria, and Poland) to recruit a six-person software development team, analyzing a total of 3,896 profiles over a 5-year period (2019–2023). The results indicate that GPT tends to prefer some regions over others, even when some profiles have been manipulated to contain counterfactuals, such as swapping the location strings of two profiles. Furthermore, GPT was more likely to assign certain developer roles to users from a specific country, revealing an implicit bias. Overall, this study reveals insights into the inner workings of GPT and has implications for mitigating these potential biases.
DOI: 10.6084/m9.figshare.28380299
title: Online Excel sheet for the manuscript c<i>ross-ancestry genome-wide association meta-analyses of liver function-related quantitative biomarkers enhance insights into causal variants, credible genes and therapeutic targets</i>

description: This Online Excel sheet is part of the supplementary tables for the manuscript c<i>ross-ancestry genome-wide association meta-analyses of liver function-related quantitative biomarkers enhance insights into causal variants, credible genes and therapeutic targets</i>, which includes content not suited to presentation in Word format. Please refer to the Online Supplementary Table file for the remaining tables.
DOI: 10.6084/m9.figshare.28380299.v4
title: Online Excel sheet for the manuscript c<i>ross-ancestry genome-wide association meta-analyses of liver function-related quantitative biomarkers enhance insights into causal variants, credible genes and therapeutic targets</i>

description: This Online Excel sheet is part of the supplementary tables for the manuscript c<i>ross-ancestry genome-wide association meta-analyses of liver function-related quantitative biomarkers enhance insights into causal variants, credible genes and therapeutic targets</i>, which includes content not suited to presentation in Word format. Please refer to the Online Supplementary Table file for the remaining tables.
DOI: 10.6084/m9.figshare.28380299.v3
title: Online Excel sheet for the manuscript <i>Cross-ancestry genome-wide association meta-analyses of liver function-related biomarkers enhance insights into causal variants, credible genes and therapeutic targets</i>

description: This Online Excel sheet is part of the supplementary tables for the manuscript <i>Cross-ancestry genome-wide association meta-analyses of liver function-related biomarkers enhance insights into causal variants, credible genes and therapeutic targets</i>, which includes content not suited to presentation in Word format. Please refer to the Online Supplementary Table file for the remaining tables.
DOI: 10.15468/dl.hxxtsf
title: Occurrence Download

description: A dataset containing 41 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Mycosphaerella fijiensis M.Morelet",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 41 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024874-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dghy7p
title: Occurrence Download

description: A dataset containing 442517 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "OccurrenceStatus is Present",
 "TaxonKey is Phoenicopterus roseus Pallas, 1811",
 "Year 1995-2025"
 ]
}

 The dataset includes 442517 records from 298 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024867-250127130748423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14850064
title: Finite element analysis of the osseous spiral lamina's influence on inner ear fluid flow during bone conduction stimulation

description: This repository contains the research data for the article Kersten, S., Taschke, H., & Vorländer, M. (2024). Finite element analysis of the osseous spiral lamina's influence on inner ear fluid flow during bone conduction stimulation. Hearing Research, 109205. https://doi.org/10.1016/j.heares.2025.109205.

It includes a finite element model of the inner ear, simulation results, animations, and a Python script with code used for the analysis.



Abstract





Recent studies have investigated the anatomy and motion of the human cochlear partition, revealing insights into the flexible nature of the osseous spiral lamina (OSL).These investigations have primarily focused on air-conducted stimulation, leaving the impact of the OSL's flexibility during bone-conducted (BC) stimulation largely unexplored. By considering the OSL as either flexible or rigid in a finite element model of the human inner ear, we examined the effect of the OSL's flexibility on the fluid flow in the inner ear during BC stimulation, which was divided into contributors entering via the oval window (OW) and rigid body stimulation.

Our results with rigid body stimulation indicate that the OSL facilitates an increased differential fluid flow at the round window compared to the OW, aligning with experimental observations interpreted as third window effects. Analysis of the OSL motion showed that this contribution results from a compressional motion of the OSL's vestibular and tympanic plates which is significantly lower in magnitude than the plates' translation in the direction of the stimulation. Separately applying OW input and rigid body stimulation provided insights into the interaction of BC sound entering via the OW and the reaction of the stapes to complex interior sound pressure distributions. Combined with the observations from a prior study (https://doi.org/10.1016/j.heares.2024.109127) our results suggest a more important role for the OSL in BC hearing than previously understood. These findings enhance our understanding of the inner ear's response during BC and contribute to ongoing investigations into the interaction of BC mechanisms, while highlighting the need for further research into the deformation of the cochlear boundaries.
DOI: 10.5281/zenodo.14850065
title: Finite element analysis of the osseous spiral lamina's influence on inner ear fluid flow during bone conduction stimulation

description: This repository contains the research data for the article Kersten, S., Taschke, H., & Vorländer, M. (2024). Finite element analysis of the osseous spiral lamina's influence on inner ear fluid flow during bone conduction stimulation. Hearing Research, 109205. https://doi.org/10.1016/j.heares.2025.109205.

It includes a finite element model of the inner ear, simulation results, animations, and a Python script with code used for the analysis.



Abstract





Recent studies have investigated the anatomy and motion of the human cochlear partition, revealing insights into the flexible nature of the osseous spiral lamina (OSL).These investigations have primarily focused on air-conducted stimulation, leaving the impact of the OSL's flexibility during bone-conducted (BC) stimulation largely unexplored. By considering the OSL as either flexible or rigid in a finite element model of the human inner ear, we examined the effect of the OSL's flexibility on the fluid flow in the inner ear during BC stimulation, which was divided into contributors entering via the oval window (OW) and rigid body stimulation.

Our results with rigid body stimulation indicate that the OSL facilitates an increased differential fluid flow at the round window compared to the OW, aligning with experimental observations interpreted as third window effects. Analysis of the OSL motion showed that this contribution results from a compressional motion of the OSL's vestibular and tympanic plates which is significantly lower in magnitude than the plates' translation in the direction of the stimulation. Separately applying OW input and rigid body stimulation provided insights into the interaction of BC sound entering via the OW and the reaction of the stapes to complex interior sound pressure distributions. Combined with the observations from a prior study (https://doi.org/10.1016/j.heares.2024.109127) our results suggest a more important role for the OSL in BC hearing than previously understood. These findings enhance our understanding of the inner ear's response during BC and contribute to ongoing investigations into the interaction of BC mechanisms, while highlighting the need for further research into the deformation of the cochlear boundaries.