bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract SY23-03: Rhabdomyosarcoma: New research tools for precision medicine
Authors: Linardic Corinne Mary 
Published: April 2023

Abstract
Rhabdomyosarcoma (RMS) is a cancer of skeletal muscle histogenesis and the most common soft tissue sarcoma of childhood. Despite decades of basic and clinical research, survival for patients with high-risk disease has not improved since the 1970s, remaining &lt;30% at five years. Genomic landscape studies have identified the most frequently occurring alterations, parsing out fusion-negative RMS driven by RAS pathway mutations, and fusion-positive RMS driven by signature fusion genes including PAX3-FOXO1. However, this information has not yet translated into improved outcomes. Here, we highlight multi-institutional efforts to generate new tools for RMS precision medicine, including the NCI FusOnC2 Cancer Moonshot program to target PAX3-FOXO1, the NCI CCDI Molecular Characterization Initiative to analyze every child’s RMS tumor nucleic acids, and the application of machine learning to RMS tumor images to predict molecular subtype and improve risk stratification.
Citation Format: Corinne Mary Linardic. Rhabdomyosarcoma: New research tools for precision medicine. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr SY23-03.
Abstract SY30-02: Oncosomes in the early stages of breast cancer
Authors: Kuhn Peter 
Published: April 2023

Abstract
Comprehensive analysis of cellular, acellular and plasma components of the Liquid Biopsy provides the opportunity to investigate cancer evolution and the interactions with the immune system at the systemic level in the individual patient. This presentation will discuss early findings supporting the relevance of oncosomes, large extracellular vesicles, in early-stage breast cancer and its potential utility in early detection and cell-level staging of the disease when combined with the cellular profiles.
Breast cancer (BC) affects 1 in every 8 women in the United States and is currently the most prevalent cancer worldwide. Precise staging at diagnosis and prognosis are essential components for the clinical management of BC patients. We set out to evaluate the feasibility of a next generation liquid biopsy platform to stratify late-stage BC, early-stage BC, and age- and gender matched controls using peripheral blood samples. Utilizing 5 biomarkers, we can identify rare circulating events with epithelial, mesenchymal, endothelial and hematological origin. We detected a higher level of CTCs in late-stage patients, compared to the early-stage and normal donors. We observed more tumor-associated oncosomes in the early-stage, compared to late-stage and the normal donor groups. Overall, we were able to detect reproducible patterns in the enumeration of rare cells and oncosomes of cancer vs. normal donors with an AUC of 99%. An initial concept for cell-level staging with the liquid biopsy was applied to early-stage vs. late-stage BC samples and reached an AUC of 91% allowing for robust stratification.
Citation Format: Peter Kuhn. Oncosomes in the early stages of breast cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr SY30-02.
Pintotable1.xlsx from Clinical and Functional Significance of TP53 Exon 4–Intron 4 Splice Junction Variants
Authors: Pinto Emilia M. , Maxwell Kara N. , Halalsheh Hadeel , Phillips Aaron , Powers Jacquelyn , MacFarland Suzanne , Walsh Michael F. , Breen Kelsey , Formiga Maria N. , Kriwacki Richard , Nichols Kim E. , Mostafavi Roya , Wang Jinling , Clay Michael R. , Rodriguez-Galindo Carlos , Ribeiro Raul C. , Zambetti Gerard P. 
Published: April 2023

Pintotable1.xlsx<p>Table S1a. Cohort characteristicsTable S1b. Frequencies and features of TP53 variants at codon 125 in public databasesTable S1c. Annotation and interpretation of TP53 variants at codon 125 and surrounding basesTable S1d. Splice site predictionTable S1e. Primers sequences for mutagenesis constructs and cDNA sequencing Table S1f. STR profiling of Saos-2 and H1299 cell lines</p>
PSReliP: an integrated pipeline for analysis and visualization of population structure and relatedness based on genome-wide genetic variant data
Authors: Solovieva Elena , Sakai Hiroaki 
Published: April 2023

Abstract
Background
Population structure and cryptic relatedness between individuals (samples) are two major factors affecting false positives in genome-wide association studies (GWAS). In addition, population stratification and genetic relatedness in genomic selection in animal and plant breeding can affect prediction accuracy. The methods commonly used for solving these problems are principal component analysis (to adjust for population stratification) and marker-based kinship estimates (to correct for the confounding effects of genetic relatedness). Currently, many tools and software are available that analyze genetic variation among individuals to determine population structure and genetic relationships. However, none of these tools or pipelines perform such analyses in a single workflow and visualize all the various results in a single interactive web application.

Results
We developed PSReliP, a standalone, freely available pipeline for the analysis and visualization of population structure and relatedness between individuals in a user-specified genetic variant dataset. The analysis stage of PSReliP is responsible for executing all steps of data filtering and analysis and contains an ordered sequence of commands from PLINK, a whole-genome association analysis toolset, along with in-house shell scripts and Perl programs that support data pipelining. The visualization stage is provided by Shiny apps, an R-based interactive web application. In this study, we describe the characteristics and features of PSReliP and demonstrate how it can be applied to real genome-wide genetic variant data.

Conclusions
The PSReliP pipeline allows users to quickly analyze genetic variants such as single nucleotide polymorphisms and small insertions or deletions at the genome level to estimate population structure and cryptic relatedness using PLINK software and to visualize the analysis results in interactive tables, plots, and charts using Shiny technology. The analysis and assessment of population stratification and genetic relatedness can aid in choosing an appropriate approach for the statistical analysis of GWAS data and predictions in genomic selection. The various outputs from PLINK can be used for further downstream analysis. The code and manual for PSReliP are available at https://github.com/solelena/PSReliP.
Are medical students happy despite unhappy conditions: a qualitative exploration of medical student cohorts during disruptive conditions
Authors: Esguerra Stephen , Chiu Fiona Thuy , Espinoza Alyssa , Williams Dan , Clithero-Eridon Amy 
Published: April 2023

AbstractBackgroundShortly after the World Health Organization declared the SARS-CoV-2 outbreak a worldwide pandemic, medical school governing bodies issued guidance recommending pausing clinical rotations. Prior to the availability of COVD-19 vaccines, many schools implemented exclusively online curriculums in the didactic and clinical years. These unprecedented events and paradigm changes in medical education could contribute to trainee burnout, wellness, and mental health.MethodsThis single-institution study interviewed first, second, and third-year medical students from a medical school in the southwestern United States. A semi-structured interview was conducted with paper-based Likert scale questions rating perceived happiness were administered both at the time of the interview and one year later in order to understand how their student experience and happiness were impacted. In addition, we asked participants to describe any major life events they experienced since the first interview.ResultsTwenty-seven volunteers participated in the original interview. Twenty-four from the original cohort participated in the one-year follow-up. Happiness as a sense of self and who you “should be” was challenged during the pandemic and changes in happiness over time were not systematic across classes. Stress was caused not only by the pandemic which was experienced by all, but by a tripartite state of individual circumstances, academic workload requirements, and the world at large. Primary themes from the interviews were clustered around the individual, learner, and future professional levels and focused on the primacy of relationships, emotional wellness, stress management, professional identity, and impacts of educational disruptions. These themes created risk factors for developing imposter syndrome. Students demonstrated resiliency across cohorts and were able to utilize a variety of strategies to achieve and maintain both physical and mental health, but the primacy of relationships both personally and professionally was noted.ConclusionMedical students’ identities as individual persons, a learner, and future medical professionals were all impacted by the pandemic. The results from this study suggest that the COVID-19 pandemic and changes in the learning format and environment may create a new risk factor in the development of imposter syndrome. There is also an opportunity to re-consider resources to achieve and maintain wellness during a disrupted academic environment.
Application of computed tomography-guided hook-wire localization technique in thoracoscopic surgery for small pulmonary nodules (≤ 10 mm)
Authors: Yang Yuan , Qin Chenhui , Ma Yue , Lu Zhongting , Zhang Yun , Li Tao 
Published: April 2023

Abstract
Objective
This study aimed to investigate the safety and efficacy of the computed tomography (CT)-guided hook-wire localization technique in thoracoscopic surgery for small pulmonary nodules (≤ 10 mm) and to identify the risk factors for localization-related complications.

Methods
The medical records of 150 patients with small pulmonary nodules treated from January 2018 to June 2021 were retrospectively analyzed. According to preoperative hook-wire positioning status, they were divided into the localization group (50 cases) or the control group (100 cases). The operation time, intraoperative blood loss, hospital stay, and conversion rate to thoracotomy were recorded and compared between groups. Uni- and multivariate binary logistic regression analysis was used to identify the risk factors for localization-related complications.

Results
A total of 58 nodules were localized in 50 patients in the localization group, and the localization success rate was 98.3% (57/58). In one case, the positioning pin fell off before wedge resection was performed. The mean nodule diameter was 7.05 mm (range, 2.8–10.0 mm), while the mean depth from the pleura was 22.40 mm (range, 5.47–79.47 mm). There were 8 cases (16%) of asymptomatic pneumothorax, 2 (4%) of intrapulmonary hemorrhage, and 1 (2%) of pleural reaction.The mean operation time of the localization group (103.88 ± 41.74 min) was significantly shorter than that of the control group (133.30 ± 45.42 min) (P < 0.05). The mean intraoperative blood loss of the localization group (44.20 ± 34.17 mL) was significantly lower than that of the control group (112.30 ± 219.90 mL) (P < 0.05). The mean hospital stay of the localization group (7.96 ± 2.34 days) was significantly shorter than that of the control group (9.21 ± 3.25 days).Multivariate binary logistic analysis showed that localization times of small pulmonary nodules in the localization group was an independent risk factor for localization-related pneumothorax.

Conclusions
Our results suggest that the CT-guided hook-wire localization technique is beneficial for localizing small pulmonary nodules. Specifically, it is helpful for the diagnosis and treatment of early lung cancer because it can accurately remove lesions, decrease intraoperative blood loss, shorten operation time and hospitalization stay, and reduce thoracotomy conversion rate. Simultaneous positioning of multiple nodules can easily lead to positioning-related pneumothorax.
Dihydroartemisinin-piperaquine or sulphadoxine-pyrimethamine for the chemoprevention of malaria in children with sickle cell anaemia in eastern and southern Africa (CHEMCHA): a protocol for a multi-centre, two-arm, double-blind, randomised, placebo-controlled superiority trial
Authors: Nkosi-Gondwe Thandile , Robberstad Bjarne , Opoka Robert , Kalibbala Dennis , Rujumba Joseph , Galileya Lufina Tsirizani , Akun Pamela , Nambatya Winnie , Ssenkusu John , TerKuile Feiko , Phiri Kamija , Idro Richard 
Published: April 2023

Abstract
Background
An estimated 300,000 babies are born with sickle cell anaemia (SCA) annually. Affected children have chronic ill health and suffer premature death. Febrile illnesses such as malaria commonly precipitate acute crises in children with SCA. Thus, chemoprophylaxis for malaria is an important preventive strategy, but current regimes are either sub-optimally effective (e.g. monthly sulphadoxine-pyrimethamine, SP) or difficult to adhere to (e.g. daily proguanil). We propose dihydroartemisinin-piperaquine (DP) as the agent with the most potential to be used across Africa.

Methods
This will be a randomised, double-blind, parallel-group superiority trial of weekly single-day courses of DP compared to monthly single-day courses of SP in children with SCA. The study will be conducted in eastern (Uganda) and southern (Malawi) Africa using randomisation stratified by body weight and study centre. Participants will be randomised using an allocation of 1:1 to DP or SP. We will investigate the efficacy, safety, acceptability and uptake and cost-effectiveness of malaria chemoprevention with weekly courses of DP vs monthly SP in 548 to 824 children with SCA followed up for 12–18 months. We will also assess toxicity from cumulative DP dosing and the development of resistance. Participant recruitment commenced on 30 April 2021; follow-up is ongoing.

Discussion
At the end of this study, findings will be used to inform regional health policy. This manuscript is prepared from protocol version 2.1 dated 1 January 2022.

Trial registration
The trial was registered at ClinicalTrials.gov, NCT04844099. Registered on 08 April 2021.
A qualitative insight into researchers’ perceptions of gender inequality in medical and dental research institutions in Nigeria
Authors: Folayan Morenike Oluwatoyin , Olowokeere Adekemi , Lusher Joanne , Aina Olabisi , Gascon Ana , Martínez-Pérez Guillermo Z. 
Published: April 2023

ObjectiveThe aim of the study was to gain a qualitative insight into scientific researchers’ perceptions of gender inequality inside Nigerian research institutions through an investigation of how gender equality is enacted in medical and dental research institutions in Nigeria.MethodsThis descriptive and cross-sectional qualitative study probed decision-making around navigating gender inequity and explored opinions about how a supportive environment for female medical and dental researchers could be established. Data were collected through semi-structured telephone interviews with 54 scientific researchers across 17 medical and dental academic institutions in Nigeria between March and July 2022. Data were transcribed verbatim and analyzed using thematic analysis.ResultsThree core themes emerged: institutionalized male dominance in research institutions; changing narratives on gender equalities in research and academic enterprise; and women driving the conscience for change in research institutions. Female medical and dental researchers’ perceived gender equality was challenging mainstream androcentric values in knowledge production within the medical and dental field; and queries the entrenchment of patriarchal values that promote a low number of female medical and dental trainees, fewer female research outputs, and few women in senior/managerial positions in the medical fields.ConclusionDespite the general view that change is occurring, a great deal remains to be done to facilitate the creation of a supportive environment for female medical and dental researchers in Nigeria.
The Effect of Physical Activity on State of Mind: The Mediating Role of Mental Resilience during the COVID-19 Pandemic
Authors: Mi Xuan , Zhang Meng , Zhang Guoli 
Published: April 2023

Abstract
To investigate the current state of home-based physical activity during the COVID-19 pandemic and to explore the effects of physical activity on state of mind and the mediating role of mental resilience, we selected five hundred people from across China to fill out the relevant scales by a convenience sampling method. The data were statistically analyzed using SPSS 22.0 and Amos 22.0. This study found that residents living at home during the COVID-19 pandemic reported reduced physical activity. Home-based physical activity can improve the state of mind directly and improve it indirectly by influencing mental resilience. Residents are advised to participate in physical activity when they stay at home, as doing so benefits their physical and mental health.
Evaluation of associations between TP53 codon 72 polymorphism and onset and progression of oral potentially malignant disorders based on case-control studies
Authors: Zhou Shanxin , Liu Yu , Yang Xi , Zhou Qin 
Published: April 2023

Abstract
Background
Recently, a systematic review and meta-analysis demonstrated that overexpression of p53 immunoprotein was significantly associated with progression risk of oral potentially malignant disorders (OPMD). However, the results of investigations on TP53 genetic typing in OPMD were inconsistent and inconclusive.
Methods
A systematic evaluation was conducted to identify all eligible case-control studies on the associations between TP53 codon 72 polymorphism and both onset and progression of OPMD.
Results
A total of 768 OPMD patients and 1173 healthy individuals were identified from 12 eligible case-control studies on TP53 codon 72 polymorphism OPMD onset. In overall and subgroup analyses, no significantly risk of OPMD onset was observed in the cases for genetic models including allele C vs. G, homozygote CC vs. GG, heterozygote GC vs. GG, dominant GC + CC vs. GG, and recessive CC vs. GG + GC (all P-value of association test > 0.05). Further, a total of 465 OPMD patients and 775 oral squamous cell carcinoma (OSCC) ones were identified from 8 eligible case-control studies on this polymorphism in OPMD progression to OSCC. The analyses revealed that there was also no significantly risk of OPMD progression in the cases for the genetic models (all P-value of association test > 0.05).
Conclusion
Our data of a pooled-analysis indicates that TP53 codon 72 polymorphism may not act as genetic factor for the risk of OPMD onset and progression. Combined with the conclusion by a systematic review and meta-analysis, we put forward a new opinion that TP53 genetic typing cloud not influence p53 protein expression in OPMD.
P53 upregulation by USP7-engaging molecular glues
Authors: Lu Boxun , Li Zhaoyang , Wang Ziying , An Ping , Zhang Hang , Zhong Chao , Liu Rui , Ma Zhiqiang , Lu Junmei , Pan Chengfang , Xing Dong , Fei Yiyan , Ding Yu 
Published: April 2023

Abstract
Molecular glues are typically small chemical molecules that act on the interface between the target protein and the degradation machinery to trigger ternary complex formation. Identification of molecular glues is challenging, and there has been a lack of target-upregulating molecular glues, which are desired for many targets such as tumor suppressor proteins (TSPs). TSPs are usually degraded by the proteasome through polyubiquitination (poly-ub) by specific E3 ligases, whereas deubiquitinases (DUBs) are capable of removing poly-ub conjugates to counteract these E3 ligases. Thus, small molecular glues that enhance the anchoring of TSPs to DUBs may stabilize them through deubiquitination. Here, through small-molecule microarray-based technology and unbiased screening, we identified three potential molecular glues that may tether P53 to the DUB USP7 and elevate the P53 level. Among them, bromocriptine (BC) is an FDA-approved drug showing the most robust effects. We further demonstrated that BC increased P53 stability via the predicted molecular glue mechanism engaging USP7. To confirm the generality of the screening platform, we identified another USP7-engaging molecular glue that upregulates PTEN, which is another well-known TSP. Taken together, we established a potential screening platform that may facilitate the discovery of novel molecular glues stabilizing TSPs via engaging the DUB USP7. Similar strategies could be applied to the identification of other types of molecular glues that may benefit drug discovery and chemical biology studies.
Earthquake Source Parameters in Zagros Region (Iran) From the Time -Evolutive P-wave Displacement
Authors: Nazeri Sahar , Abdi Fatemeh , Ismail Amir , Rahimi Habib , Zollo Aldo 
Published: April 2023

AbstractThe rupture process of the recent moderate-to-large earthquakes in the Zagros area along the Iran plateau is investigated by analysing the strong motion data provided by the Iranian Building and Housing Research Centre (BHRC). The selected dataset includes the largest and deadliest 2017 Mw 7.3, Iran-Iraq (Ezgeleh) earthquake. The earthquake source parameters (moment magnitude, rupture duration and length, average slip, and static stress drop) are determined using a time-domain, parametric modelling technique based on the time evolution of the P-wave displacement signals. The earthquake source parameters are calculated from simulated triangular moment-rate functions assuming the circular source models for a constant rupture velocity. The anelastic attenuation effect is modelled through the independent frequency-Q parameter ranging from 50 to 200 and accounted for by a post-processing procedure that retrieves the attenuation-corrected, moment-rate triangular shape. Results show that the average static stress-drop with different \({Q}_{P}\), varies between < Δ𝜎>=0.9 (0.7 − 1.2) MPa and < Δ𝜎>=1.6 (1.2 − 2.0) MPa. Assuming a circular rupture model for Ezgeleh earthquake, we estimate a moment magnitude of 6.9, rupture duration of 7 seconds, source radius of 16 km, average slip of about 2 m and static stress drop of 3.4 MPa.