bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adapting beyond borders: Insights from the 19th Student Council Symposium (SCS2023), the first hybrid ISCB Student Council global event
Authors: Al Sium Syed Muktadir , Torrejón Estefania , Chowdhury Sanjana Fatema , Ahmed Rubaiat , Jain Aakriti , Treccani Mirko , Veschetti Laura , Riaz Arsalan , Eranti Pradeep , Olguín-Orellana Gabriel J 
Published: April 2024

Abstract

Summary
The 19th ISCB Student Council Symposium (SCS2023) organized by ISCB-SC adopted a hybrid format for the first time, allowing participants to engage in-person in Lyon, France, and virtually via an interactive online platform. The symposium prioritized inclusivity, featuring on-site sessions, poster presentations, and social activities for in-person attendees, while virtual participants accessed live sessions, interactive Q&A, and a virtual exhibit hall. Attendee statistics revealed a global reach, with Europe as the major contributor. SCS2023’s success in bridging in-person and virtual experiences sets a precedent for future events in Computational Biology and Bioinformatics.

Availability and Implementation
The details of the symposium, speaker information, schedules, and accepted abstracts, are available in the program booklet (https://doi.org/10.5281/zenodo.8173977). For organizers interested in adopting a similar hybrid model, it would be beneficial to have access to details regarding the online platform used, the types of sessions offered, and the challenges faced. Future iterations of SCS can address these aspects to further enhance accessibility and inclusivity.
Extending BioMASS to construct mathematical models from external knowledge
Authors: Arakane Kiwamu , Imoto Hiroaki , Ormersbach Fabian , Okada Mariko 
Published: April 2024

Abstract

Motivation
Mechanistic modeling based on ordinary differential equations has led to numerous findings in systems biology by integrating prior knowledge and experimental data. However, the manual curation of knowledge necessary when constructing models poses a bottleneck. As the speed of knowledge accumulation continues to grow, there is a demand for a scalable means of constructing executable models.

Results
We previously introduced BioMASS—an open-source, Python-based framework–to construct, simulate, and analyze mechanistic models of signaling networks. With one of its features, Text2Model, BioMASS allows users to define models in a natural language-like format, thereby facilitating the construction of large-scale models. We demonstrate that Text2Model can serve as a tool for integrating external knowledge for mathematical modeling by generating Text2Model files from a pathway database or through the use of a large language model, and simulating its dynamics through BioMASS. Our findings reveal the tool's capabilities to encourage exploration from prior knowledge and pave the way for a fully data-driven approach to constructing mathematical models.

Availability and implementation
The code and documentation for BioMASS are available at https://github.com/biomass-dev/biomass and https://biomass-core.readthedocs.io, respectively. The code used in this article are available at https://github.com/okadalabipr/text2model-from-knowledge.
Adjusting for covariates and assessing modeling fitness in machine learning using MUVR2
Authors: Yan Yingxiao , Schillemans Tessa , Skantze Viktor , Brunius Carl 
Published: April 2024

Abstract

Motivation
Machine learning (ML) methods are frequently used in Omics research to examine associations between molecular data and for example exposures and health conditions. ML is also used for feature selection to facilitate biological interpretation. Our previous MUVR algorithm was shown to generate predictions and variable selections at state-of-the-art performance. However, a general framework for assessing modeling fitness is still lacking. In addition, enabling to adjust for covariates is a highly desired, but largely lacking trait in ML. We aimed to address these issues in the new MUVR2 framework.

Results
The MUVR2 algorithm was developed to include the regularized regression framework elastic net in addition to partial least squares and random forest modeling. Compared with other cross-validation strategies, MUVR2 consistently showed state-of-the-art performance, including variable selection, while minimizing overfitting. Testing on simulated and real-world data, we also showed that MUVR2 allows for the adjustment for covariates using elastic net modeling, but not using partial least squares or random forest.

Availability and implementation
Algorithms, data, scripts, and a tutorial are open source under GPL-3 license and available in the MUVR2 R package at https://github.com/MetaboComp/MUVR2.
phylaGAN: data augmentation through conditional GANs and autoencoders for improving disease prediction accuracy using microbiome data
Authors: Sharma Divya , Lou Wendy , Xu Wei 
Published: April 2024

Abstract

Motivation
Research is improving our understanding of how the microbiome interacts with the human body and its impact on human health. Existing machine learning methods have shown great potential in discriminating healthy from diseased microbiome states. However, Machine Learning based prediction using microbiome data has challenges such as, small sample size, imbalance between cases and controls and high cost of collecting large number of samples. To address these challenges, we propose a deep learning framework phylaGAN to augment the existing datasets with generated microbiome data using a combination of conditional generative adversarial network (C-GAN) and autoencoder. Conditional generative adversarial networks train two models against each other to compute larger simulated datasets that are representative of the original dataset. Autoencoder maps the original and the generated samples onto a common subspace to make the prediction more accurate.

Results
Extensive evaluation and predictive analysis was conducted on two datasets, T2D study and Cirrhosis study showing an improvement in mean AUC using data augmentation by 11% and 5% respectively. External validation on a cohort classifying between obese and lean subjects, with a smaller sample size provided an improvement in mean AUC close to 32% when augmented through phylaGAN as compared to using the original cohort. Our findings not only indicate that the generative adversarial networks can create samples that mimic the original data across various diversity metrics, but also highlight the potential of enhancing disease prediction through machine learning models trained on synthetic data.

Availability and implementation
https://github.com/divya031090/phylaGAN.
Pacybara: accurate long-read sequencing for barcoded mutagenized allelic libraries
Authors: Weile Jochen , Ferra Gabrielle , Boyle Gabriel , Pendyala Sriram , Amorosi Clara , Yeh Chiann-Ling , Cote Atina G , Kishore Nishka , Tabet Daniel , van Loggerenberg Warren , Rayhan Ashyad , Fowler Douglas M , Dunham Maitreya J , Roth Frederick P 
Published: April 2024

Abstract

Motivation
Long-read sequencing technologies, an attractive solution for many applications, often suffer from higher error rates. Alignment of multiple reads can improve base-calling accuracy, but some applications, e.g. sequencing mutagenized libraries where multiple distinct clones differ by one or few variants, require the use of barcodes or unique molecular identifiers. Unfortunately, sequencing errors can interfere with correct barcode identification, and a given barcode sequence may be linked to multiple independent clones within a given library.

Results
Here we focus on the target application of sequencing mutagenized libraries in the context of multiplexed assays of variant effects (MAVEs). MAVEs are increasingly used to create comprehensive genotype-phenotype maps that can aid clinical variant interpretation. Many MAVE methods use long-read sequencing of barcoded mutant libraries for accurate association of barcode with genotype. Existing long-read sequencing pipelines do not account for inaccurate sequencing or nonunique barcodes. Here, we describe Pacybara, which handles these issues by clustering long reads based on the similarities of (error-prone) barcodes while also detecting barcodes that have been associated with multiple genotypes. Pacybara also detects recombinant (chimeric) clones and reduces false positive indel calls. In three example applications, we show that Pacybara identifies and correctly resolves these issues.

Availability and implementation
Pacybara, freely available at https://github.com/rothlab/pacybara, is implemented using R, Python, and bash for Linux. It runs on GNU/Linux HPC clusters via Slurm, PBS, or GridEngine schedulers. A single-machine simplex version is also available.
How to explore a new environment: exploratory tactics of the black rat (Rattus rattus)
Authors: Štolhoferová Iveta , Rudolfová Veronika , Skalíková Hana , Vobrubová Barbora , Frynta Daniel 
Published: April 2024

AbstractThe black rat (Rattus rattus) is a unique model for studying exploratory tactics due to its enormous colonizing potential. Considerable behavioral variability and consistent interindividual differences might help populations inhabit new environments and persist there even under intense pressure. Additionally, the affinity of the black rat for climbing might be another advantage, widening their potential niche. In this study, we describe the exploratory tactics of the black rats when introduced to a novel environment. In the first experiment, we tested 12 rats and calculated repeatability of their behaviors across 12 sessions of an enriched open-field test. We concluded that climbing is a highly repeatable behavior that serves as an important source of interindividual variability. In the second experiment, we tested 24 black rats in a unique L-shaped arena. Each rat was tested twice. We found that the majority of rats distributed their activity evenly, exploring each part of the apparatus for a similar amount of time, thus maximizing their chances of finding resources. Nevertheless, these “even” explorers still greatly differed in their level of activity, orderliness and affinity for climbing, generating large variability. In contrast, the minority of rats concentrated their activity only on a section of the new environment and were therefore characterized as selective explorers. Overall, we concluded that a combination of such exploratory tactics as well as a bias for even explorers enables black rats to quickly colonize new environments and persist there even under unfavorable conditions.
Distinct communities under the snow: describing characteristics of subnivium arthropod communities
Authors: Ziadeh Christopher P , Ziadeh Shayleigh B , Aflague Breanne H , Townley Mark A , Ayres Matthew P , Contosta Alexandra R , Garnas Jeff R 
Published: April 2024

Abstract
Arthropods are active during the winter in temperate regions. Many use the seasonal snowpack as a buffer against harsh ambient conditions and are active in a refugium known as the subnivium. While the use of the subnivium by arthropods is well established, far less is known about subnivium community composition, abundance, biomass, and diversity and how these characteristics compare with the community in the summer. Understanding subnivium communities is especially important given the observed and anticipated changes in snowpack depth and duration due to the changing climate. We compared subnivium arthropod communities with those active during the summer using pitfall trapping in northern New Hampshire. We found that compositions of ground-active arthropod communities in the subnivium differed from those in the summer. The subnivium arthropod community featured moderate levels of richness and other measures of diversity that tended to be lower than the summer community. More strikingly, the subnivium community was much lower in overall abundance and biomass. Interestingly, some arthropods were dominant in the subnivium but either rare or absent in summer collections. These putative “subnivium specialists” included the spider Cicurina brevis (Emerton 1890) (Araneae: Hahniidae) and 3 rove beetles (Coleoptera: Staphylinidae): Arpedium cribratum Fauvel, 1878, Lesteva pallipes LeConte, 1863, and Porrhodites inflatus (Hatch, 1957). This study provides a detailed account of the subnivium arthropod community, establishes baseline information on arthropod communities in temperate forests of northeastern North America, and explores the idea of subnivium specialist taxa that are highly active in winter and might be especially vulnerable to climate change.
Ceramides: a potential cardiovascular biomarker in young adult childhood cancer survivors?
Authors: Broberg Olof , Weismann Constance G , Øra Ingrid , Wiebe Thomas , Laaksonen Reijo , Liuba Petru 
Published: April 2024

Abstract

Aims
The aim of this study was to investigate circulating ceramides involved in cardiovascular disease (CVD) in young adult childhood cancer survivors (CCS) and their correlations to previously reported adverse cardiovascular changes in this cohort.

Methods and results
Fifty-seven CCS and 53 healthy controls (age 20–30 years) were studied. Plasma long-chain ceramides, known to be cardiotoxic (C16:0, C18:0, C24:0, and C24:1), were analysed by mass spectrometry. The coronary event risk test 2 (CERT2) score was calculated from the ceramide data. Cardiac and carotid artery ultrasound data and lipid data available from previous studies of this cohort were used to study partial correlations with ceramide and CERT2 score data. All four analysed ceramides were elevated in CCS compared with controls (P ≤ 0.012). The greatest difference was noted for C18:0, which was 33% higher in CCS compared with controls adjusted for sex, age, and body mass index (BMI) (P &lt; 0.001). The CERT2 score was higher in CCS compared with controls (P &lt; 0.001). In the CCS group, 35% had a high to very high CERT2 score (7–12) when compared with 9% in the control group (P &lt; 0.001). The CCS subgroup with a CERT2 score ≥ 7 had higher heart rate, systolic blood pressure, and higher levels of apolipoprotein B compared with CCS with a CERT2 score &lt; 6 (P ≤ 0.011). When adjusted for age, sex, and BMI, CERT2 score was significantly correlated with arterial stiffness, growth hormone, and cranial radiotherapy (P &lt; 0.044).

Conclusion
Ceramides could be important biomarkers in understanding the pathophysiology of CVD and in predicting CVD disease risk in young adult CCS.
Borrowing Constraints and Demand for Remedial Education: Evidence from Tanzania
Authors: Burchardi Konrad , de Quidt Jonathan , Gulesci Selim , Sulaiman Munshi 
Published: April 2024

Abstract
We use a cash transfer to relax households’ borrowing constraints, then elicit their willingness to pay for a remedial education programme offering tutoring and life skills training. Lottery losers were willing to pay 3,300 Tanzanian Shillings for the programme, which is 7% of per capita monthly expenditures. For those identified at baseline as able to borrow, willingness to pay increases by 3% upon winning a lottery prize of 3,200 Tanzanian Shillings. For those unable to borrow, willingness to pay increases by 27% upon winning the lottery. We conclude that borrowing constraints limit access to educational programmes, and may increase inequality of educational attainment.
Extended septal myectomy versus alcohol septal ablation: clinical results at a national referral centre
Authors: de Villarreal-Soto Juan Esteban , Oteo-Domínguez Juan Francisco , Martínez-López Daniel , Ríos-Rosado Elsa Carolina , Vera-Puente Beatriz , Olivo-Soto Jean Carlo , Arízaga-Arce Fernando , García-Pavía Pablo , Ospina Mosquera Víctor Manuel , Villar García Susana , García Suárez Jessica , Cavero Miguel Ángel , Martín-López Carlos Esteban , Forteza-Gil Alberto 
Published: April 2024

Abstract

OBJECTIVES
Extended septal myectomy and alcohol septal ablation are 2 invasive treatments for hypertrophic obstructive cardiomyopathy. Our goal was to compare which of these techniques achieved a higher reduction in gradients, improvement in New York Heart Association (NYHA) functional class and reduction in medical treatment.

METHODS
It is a single-centre observational and retrospective analysis. We used multivariable regression analyses to assess the association of ablation/myectomy with different outcomes. The odds ratio or coefficient along with the 95% confidence interval was estimated according to the group and adjusted for the corresponding preprocedural variables and EuroSCORE II.

RESULTS
A total of 78 patients underwent septal myectomy, and 25 patients underwent alcohol septal ablation. Basal and Valsalva gradients after myectomy were reduced to a higher degree in comparison to ablation: 21.0 mmHg [P &lt; 0.001, 95% confidence interval -30.7; -11.3], and 34.3 mmHg (P &lt; 0.001, -49.1; -19.5) respectively. Those patients who received a myectomy had a lower probability of having moderate mitral regurgitation (odds ratio = 0.18, P = 0.054). Patients after septal myectomy were more likely to be NYHA functional class I (80.4%), whereas patients after ablation were more likely to be NYHA functional class III (48%). Both groups continued with beta-blocker therapy, but disopyramide could be discontinued after the myectomy in more cases (20%–36% vs 59%–1.3%; P &lt; 0.001), and there was a tendency to discontinue calcium channel blockers (48%–16% vs 15.4–3.8%; P = 0.054).

CONCLUSIONS
After adjustment using preprocedural gradients and EuroSCORE II, myectomy achieves greater reduction in left ventricular outflow tract gradients compared to septal ablation.
Derived Equivalence for Elliptic K3 Surfaces and Jacobians
Authors: Meinsma Reinder , Shinder Evgeny 
Published: April 2024

Abstract
We present a detailed study of elliptic fibrations on Fourier-Mukai partners of K3 surfaces, which we call derived elliptic structures. We fully classify derived elliptic structures in terms of Hodge-theoretic data, similar to the Derived Torelli Theorem that describes Fourier-Mukai partners. In Picard rank two, derived elliptic structures are fully determined by the Lagrangian subgroups of the discriminant group. As a consequence, we prove that for a large class of Picard rank 2 elliptic K3 surfaces all Fourier-Mukai partners are Jacobians, and we partially extend this result to non-closed fields. We also show that there exist elliptic K3 surfaces with Fourier-Mukai partners, which are not Jacobians of the original K3 surface. This gives a negative answer to a question raised by Hassett and Tschinkel.
Individual and institutional predisposing factors of MRSA surgical site infection and outcomes—a retrospective case-control-study in 14 European high-volume surgical centres
Authors: Rutz Jule , Naendrup Jan-Hendrik , Bruns Caroline , Classen Annika Y , Salmanton-García Jon , Seifert Harald , Sprute Rosanne , Stemler Jannik , Walker Sarah V , Cornely Oliver A , Liss Blasius J , Mellinghoff Sibylle C ,   SALT study group, Ankert Juliane , Bernard Louis , Bataille Camille , Couvé-Deacon Elodie , Ferrer María Fernández , Fortún Jesus , Galar Alicia , Guimard Thomas , Horcajada Juan P , Mollar Joan , Muñoz Patricia , Pletz Mathias W , Serracino-Inglott Ferdinand , Soriano Alex , Vilz Tim O 
Published: April 2024

Abstract

Objectives
To assess incidence rates of surgical site infections (SSI) by MRSA and to determine related factors and clinical outcome compared to MSSA, including country-specific, institutional and patient determinants.

Patients and methods
We performed a subgroup analysis of the Europe-wide SALT (NCT03353532) study population with MRSA SSI from 14 centres in France, Germany, Italy, Spain and the UK.

Results
An overall MRSA SSI incidence of 0.06% (n = 104) was found in 178 903 patients undergoing invasive surgery in 2016. Frequently observed comorbidities were chronic cardiovascular disease, diabetes and solid tumours. Compared to the overall MRSA SSI incidence, incidence rates were significantly higher in Spain (58 of 67 934 cases) and lower in Germany (16 of 46 443 cases; both P &lt; 0.05). Centres with antibiotic stewardship (ABS) and infectious disease (ID) consultation programmes (n = 3/14) had lower MRSA rates (17 of 43 556 cases versus 61 of 83 048 cases, P &lt; 0.05). In bivariate analyses, MRSA SSI patients were significantly older, had higher BMI and more comorbidities compared to MSSA (P &lt; 0.05 each). Surgery performed between 6:00 and 12:00 pm led to higher MRSA proportions among S. aureus SSI (17 of 104 cases versus 62 of 640 cases, P &lt; 0.05).

Conclusions
This study shows low overall and country-specific incidence rates of MRSA SSI in Europe. We could show significant differences between countries as well as between centres with established ABS and ID consultation programmes were observed. The number of those programmes seems too small against this background.
High prevalence of ceftriaxone-resistant and XDR Neisseria gonorrhoeae in several cities of Cambodia, 2022–23: WHO Enhanced Gonococcal Antimicrobial Surveillance Programme (EGASP)
Authors: Ouk V , Heng L Say , Virak M , Deng S , Lahra M M , Frankson R , Kreisel K , McDonald R , Escher M , Unemo M , Wi T , Maatouk I ,   EGASP Cambodia Working Group, Penh Phnom , Fensham Vivian , Kersh Ellen , Cavailler Philippe , Mundade Yamuna , van Hal Sebastiaan J , Kundu Ratan L , Hogan Tiffany R , Whiley David M , Izumi Kiyohiko , Nishijima Takeshi 
Published: April 2024

Abstract

Objectives
Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a global public health concern. Ceftriaxone is the last effective and recommended option for empirical gonorrhoea therapy worldwide, but several ceftriaxone-resistant cases linked to Asia have been reported internationally. During January 2022–June 2023, the WHO Enhanced Gonococcal Antimicrobial Surveillance Programme (EGASP) investigated N. gonorrhoeae AMR and epidemiological factors in patients from 10 clinical sentinel sites in Cambodia.

Methods
Urethral swabs from males with urethral discharge were cultured. ETEST determined the MIC of five antimicrobials, and EGASP MIC alert values and EUCAST breakpoints were used. EGASP demographic, behavioural and clinical variables were collected using a standardized questionnaire.

Results
From 437 male patients, 306 had positive N. gonorrhoeae cultures, AMR testing and complete epidemiological data. Resistance to ceftriaxone, cefixime, azithromycin and ciprofloxacin was 15.4%, 43.1%, 14.4% and 97.1%, respectively. Nineteen (6.2%) isolates were resistant to all four antimicrobials and, accordingly, categorized as XDR N. gonorrhoeae. These XDR isolates were collected from 7 of the 10 sentinel sites. No EGASP MIC alert values for gentamicin were reported. The nationally recommended cefixime 400 mg plus azithromycin 1 g (65.4%) or ceftriaxone 1 g plus azithromycin 1 g (34.6%) was used for treatment.

Conclusions
A high prevalence of ceftriaxone-resistant, MDR and XDR N. gonorrhoeae in several cities of Cambodia were found during 2022–23 in WHO EGASP. This necessitates expanded N. gonorrhoeae AMR surveillance, revision of the nationally recommended gonorrhoea treatment, mandatory test of cure, enhanced sexual contact notification, and ultimately novel antimicrobials for the treatment of gonorrhoea.