bluuebunny/crossref_metadata_2025_split huggingface dataset:
Progress and opportunities of foundation models in bioinformatics
Authors: Li Qing , Hu Zhihang , Wang Yixuan , Li Lei , Fan Yimin , King Irwin , Jia Gengjie , Wang Sheng , Song Le , Li Yu 
Published: October 2024

Abstract
Bioinformatics has undergone a paradigm shift in artificial intelligence (AI), particularly through foundation models (FMs), which address longstanding challenges in bioinformatics such as limited annotated data and data noise. These AI techniques have demonstrated remarkable efficacy across various downstream validation tasks, effectively representing diverse biological entities and heralding a new era in computational biology. The primary goal of this survey is to conduct a general investigation and summary of FMs in bioinformatics, tracing their evolutionary trajectory, current research landscape, and methodological frameworks. Our primary focus is on elucidating the application of FMs to specific biological problems, offering insights to guide the research community in choosing appropriate FMs for tasks like sequence analysis, structure prediction, and function annotation. Each section delves into the intricacies of the targeted challenges, contrasting the architectures and advancements of FMs with conventional methods and showcasing their utility across different biological domains. Further, this review scrutinizes the hurdles and constraints encountered by FMs in biology, including issues of data noise, model interpretability, and potential biases. This analysis provides a theoretical groundwork for understanding the circumstances under which certain FMs may exhibit suboptimal performance. Lastly, we outline prospective pathways and methodologies for the future development of FMs in biological research, facilitating ongoing innovation in the field. This comprehensive examination not only serves as an academic reference but also as a roadmap for forthcoming explorations and applications of FMs in biology.
Working in precarity: examining mainstream discourses about street hawking in Ghana
Authors: Karikari Eric , Wood Sandra 
Published: October 2024

Abstract
This study sought to analyze how the media and the general public position street hawking in an economic environment typically constrained by neoliberal orthodoxy. We conducted a critical textual analysis of news articles, op-eds, and video clips from some of the most popular news media sources in Ghana and found that while informal work is often done in turbulent material conditions, marginality and precarity of street hawking are exacerbated by media and popular discourses that are anchored by neoliberalism. We also found that such discourses are resisted by counter-discourses. The study challenges neoliberal analyses of work and labor by explicating the tensions between the attraction to neoliberalism and the reality of its failures for informal work.
Kidney transplantation in patients with polycystic kidney disease: increased risk of infection does not compromise graft and patient survival
Authors: Waiser Johannes , Klotsche Jens , Glander Petra , Schmidt Danilo , Naik Marcel , Liefeldt Lutz , Budde Klemens , Halbritter Jan , Halleck Fabian , Zukunft Bianca , Peters Robert , Friedersdorff Frank , Lachmann Nils , Eckardt Kai-Uwe , d'Anjou Leonie , Bachmann Friederike 
Published: October 2024

ABSTRACT

Background
Patients with autosomal dominant polycystic kidney disease (ADPKD) represent &gt;10% of patients awaiting kidney transplantation. These patients are prone to potentially severe urinary tract (UTI) and liver cyst infections after transplantation. Whether such infections compromise outcome is unclear.

Methods
Between 2000 and 2017 we performed 193 kidney transplantations in patients with ADPKD. In 189 patients, we assessed the occurrence, frequency, and severity of infection episodes requiring inpatient treatment and their impact on graft and patient outcomes compared with 189 matched controls. Risk factors were analyzed by uni- and multivariable analyses.

Results
During a mean observation period of 77 months UTIs occurred more frequently in ADPKD patients (39.1% vs. 26.7%, P = .022; 0.8 ± 1.4 vs. 0.5 ± 1.1 episodes, P &lt; .001). Eight ADPKD patients suffered from 19 episodes of liver cyst infection. Steroid medication (RR 3.04; P &lt; .001) and recipient age (RR 1.05; P = .003) increased the risk for UTI/urosepsis, while nephrectomy reduced it (unilateral, RR 0.60; P = .088; bilateral, RR 0.45; P = .020). Patient survival was similar in both groups. The risk of graft failure was lower in ADPKD patients [hazard ratio (HR) 0.67; P = .047] due to a lower risk of death-censored graft loss (HR 0.47; P = .014). Donor age (HR 1.34; P = .002) and rejection (HR 8.47; P &lt; .001) were risk factors for death-censored graft loss.

Conclusions
ADPKD patients are at increased risk of UTI and liver cyst infection after transplantation. Steroid medication and recipient age seem to increase the risk of UTI/urosepsis, while nephrectomy seems to reduce it. Nevertheless, patient survival was similar compared to non-ADPKD patients and death-censored graft survival even better.
Comparative efficacy of non-pharmacological interventions on xerostomia and salivary flow rate among haemodialysis patients: A systematic review and network meta-analysis
Authors: Sharifnia Amir Masoud , Chu Ginger , Zhang Xiaoming , Green Heidi , Fernandez Ritin 
Published: October 2024

ABSTRACT

Background
Xerostomia is a distressing symptom experienced by patients undergoing dialysis. We sought to compare and rank the efficacy of different non-pharmacological interventions on xerostomia and salivary flow rate among dialysis patients.

Methods
A systematic search was conducted in six English-language databases: PubMed, CINAHL, Scopus, Web of Science, Embase and Cochrane Central Register of Controlled Trials, in April 2023. Screening, quality appraisal and data extraction were undertaken by two independent reviewers. A network meta-analysis was performed to assess the relative efficacy of different non-pharmacological interventions.

Results
The analysis included 11 randomized controlled trials involving 739 patients and eight non-pharmacological interventions. The pairwise analysis indicated that compared with the control group, sugarless candy, chewing sugarless gum, acupressure auricular and licorice mouthwash had a significant positive effect on reducing the severity of xerostomia; also, transcutaneous electrical nerve stimulation (TENS), licorice mouthwash, sugarless chewing gum, photobiomodulation and pure water mouthwash significantly improved the saliva flow rate. The network analysis indicated that sugarless chewing gum significantly reduced the symptoms of xerostomia, while TENS and sugarless chewing gum were effective in improving the unstimulated whole salivary rate. Among dialysis patients, chewing sugarless gum and using TENS were the top-ranked interventions for relieving xerostomia and enhancing saliva flow rate, respectively.

Conclusions
Several non-pharmacological interventions have demonstrated effectiveness in relieving xerostomia and enhancing saliva flow rate. While further research may be needed to confirm and refine these findings, the interventions used in this review offer promising results and should be incorporated into the standard care of dialysis patients experiencing these symptoms to enhance their quality of life and oral health.
Spontaneous coronary artery dissection ‘storm’ in post-partum: a case report
Authors: Combaret Nicolas , Souteyrand Géraud , Motreff Pascal 
Published: October 2024

Abstract

Background
Spontaneous coronary artery dissection (SCAD) remains a rare form of acute coronary syndrome (ACS) in young women. It is not always easy to diagnose and its management can be complex, particularly in the case of severe forms.

Case summary
A 29-year-old Mahorese woman presented with non-ST-elevation acute coronary syndrome 72 h after vaginal delivery of an uncomplicated twin pregnancy. Coronary angiography revealed a SCAD of the left anterior descending artery (LAD) treated medically. At Day 4, urgent coronary angiography was performed due to recurrent ACS with unfavourable evolution on LAD SCAD with worsening flow and appearance of right coronary artery (RCA) dissection. Percutaneous coronary intervention (PCI) was performed with drug-eluting stent (DES) implantation in LAD under optical coherence tomography (OCT) guidance. At Day 6, the patient suffered from inferior ST segment elevation myocardial infarction due to extension of the RCA SCAD with occlusion of the posterior descending artery. Once again, under OCT guidance, PCI was performed in RCA with implantation of four DES. At Day 8, the patient presented with an intra-hospital cardiac arrest by electromechanical dissociation. Urgent coronary angiography revealed a diffuse extension of the SCAD to the circumflex artery and the left main trunk (LM). Rescue PCI of the LM was performed under OCT guidance, and a femoro-femoral extracorporeal life support was implanted because of haemodynamic instability. With no hope of left ventricular ejection fraction recovery, the patient eventually benefited from a heart transplant 12 days after the first ACS with excellent evolution.

Discussion
Although the majority of SCAD have a favourable outcome with spontaneous healing, it is important to keep in mind that certain severe forms exist and could require specific management as PCI under OCT guidance and potential transfer to surgical centres where heart transplants and mechanical circulatory support are available.
Machine learning based prediction models for cardiovascular disease risk using electronic health records data: systematic review and meta-analysis
Authors: Liu Tianyi , Krentz Andrew , Lu Lei , Curcin Vasa 
Published: October 2024

Abstract
Cardiovascular disease (CVD) remains a major cause of mortality in the UK, prompting the need for improved risk predictive models for primary prevention. Machine learning (ML) models utilizing electronic health records (EHRs) offer potential enhancements over traditional risk scores like QRISK3 and ASCVD. To systematically evaluate and compare the efficacy of ML models against conventional CVD risk prediction algorithms using EHR data for medium to long-term (5–10 years) CVD risk prediction. A systematic review and random-effect meta-analysis were conducted according to preferred reporting items for systematic reviews and meta-analyses guidelines, assessing studies from 2010 to 2024. We retrieved 32 ML models and 26 conventional statistical models from 20 selected studies, focusing on performance metrics such as area under the curve (AUC) and heterogeneity across models. ML models, particularly random forest and deep learning, demonstrated superior performance, with the highest recorded pooled AUCs of 0.865 (95% CI: 0.812–0.917) and 0.847 (95% CI: 0.766–0.927), respectively. These significantly outperformed the conventional risk score of 0.765 (95% CI: 0.734–0.796). However, significant heterogeneity (I² &gt; 99%) and potential publication bias were noted across the studies. While ML models show enhanced calibration for CVD risk, substantial variability and methodological concerns limit their current clinical applicability. Future research should address these issues by enhancing methodological transparency and standardization to improve the reliability and utility of these models in clinical settings. This study highlights the advanced capabilities of ML models in CVD risk prediction and emphasizes the need for rigorous validation to facilitate their integration into clinical practice.
Distinguishing Gram-positive and Gram-negative bloodstream infections through leukocytes, C-reactive protein, procalcitonin, and D-Dimer: an empirical antibiotic guidance
Authors: Li Jiru , Xia Hao 
Published: October 2024

Abstract
This retrospective study aimed to compare the difference of the levels of white blood cells (WBC), C-reactive protein (CRP), procalcitonin, and D-Dimer in the bloodstream infection (BSI) patients, and their values in distinguishing bacterial categories. A total of 847 BSI patients were analysed and divided into Gram-positive BSI (GP-BSI) and Gram-negative BSI (GN-BSI) groups. Most frequently isolated pathogens in GP-BSI were Staphylococcus epidermidis (35.75%), followed by Staphylococcus hominis (18.33%), and Streptococcus haemolyticus (10.16%), while in GN-BSI, Escherichia coli (30.07%), Klebsiella pneumoniae (23.98%), and Acinetobacter baumannii (13.18%) were the most common. The predictive value was evaluated based on 3 years of patient data, which showed an area under the curve (AUC) of 0.828. It was further validated using 2 years of data, which yielded an AUC of 0.925. Significant differences existed in the procalcitonin, D-Dimer, and CRP levels between GN-BSI and GP-BSI. The current results provide a more effective strategy for early differential diagnosis in bacterial categorization of BSI when combining WBC, CRP, procalcitonin, and D-Dimer measurements.
Expansion of MHC-IIB Has Constrained the Evolution of MHC-IIA in Passerines
Authors: Ruesink-Bueno Iris Liesbeth , Drews Anna , O’Connor Emily Amelia , Westerdahl Helena 
Published: October 2024

Abstract
The major histocompatibility complex (MHC) is central in adaptive immunity, with the highly polymorphic MHC genes encoding antigen-presenting molecules. Two MHC class II (MHC-II) loci, DA1 and DA2, predate the radiation of extant birds and persist throughout much of the avian phylogeny. Within each locus, the MHC-II molecules are encoded by A-genes (DAA) and B-genes (DAB), which are arranged in A–B dyads. However, in passerines (order Passeriformes), the DA2 locus has been lost, and the ancestral A–B dyad at the DA1 locus has been replaced by a putatively single A-gene (DAA1) and an array of highly polymorphic B-genes (DAB1). In this study, we genotyped the DAA1 gene of 15 passerine species and confirmed that passerines possess just one copy of DAA1. We then compared selection patterns in DAA1 between passerines and nonpasserines and found that exon 2, which encodes the antigen-presenting domain, has been subject to weaker positive selection and stronger negative selection in passerines compared with nonpasserines. Additional comparisons showed that the patterns of selection in the passerine DAA1 gene are unlikely to be related to the loss of the DA2 locus. Instead, our findings suggest that the expansion of DAB1 (MHC-IIB) has imposed an evolutionary constraint on the passerine DAA1 (MHC-IIA) gene. We speculate that this constraint may be the result of each DAA1 chain forming heterodimers with many different DAB1 chains.
Three-dimensional ray tracing in P-wave azimuthal anisotropic media
Authors: Tsunashima Ryo , Zhao Dapeng , Toyokuni Genti 
Published: October 2024

SUMMARY
A new 3-D ray-tracing method is developed for P-wave azimuthal anisotropic (AAN) media. We assume anisotropic media with hexagonal symmetry and take advantage of the property that the AAN symmetry axis, the phase velocity vector and the group velocity vector are located in the same plane. The 3-D ray-tracing method that combines the pseudo-bending technique and Snell's law is improved for the AAN media. We compute isotropic (ISO) and AAN rays in synthetic models and an actual 3-D P-wave AAN model of the East Japan subduction zone. The accuracy of our ray-tracing code is evaluated by comparing the ray-path and travel-time differences between the ISO and AAN rays. Our results show that the AAN rays in each model bend in the right direction and satisfy Fermat's principle, so the theory and approximations adopted in the calculations are reasonable. For long rays (&gt;350 km), the ray-path difference between the ISO and AAN rays is &gt; 20 km, and the travel-time difference is &gt; 0.1 s, suggesting that it is necessary and important to take azimuthal anisotropy into account in the 3-D ray tracing.
Imaging of seismic discontinuities using an adjoint method
Authors: Pollitz F F , Langer L 
Published: October 2024

SUMMARY
For imaging of seismic discontinuities at depth, reverse time migration is a powerful method to apply to recordings of seismic events. It is especially powerful when an extensive receiver array, numerous seismic sources, or both, permit adequate reconstruction of incident and scattered wavefields at depth. Reconstructing either the incident or scattered wavefield at depth becomes less accurate when relatively few recordings of seismic events are available. Here, we explore an inverse scattering approach to imaging discontinuities based on an adjoint method, employing sensitivity kernels (Fréchet derivatives) that represent jumps in material properties across seismic-discontinuity surfaces. When combined with ray-based requirements on scattering geometry, it constitutes a powerful approach to determining the locations and amplitudes of the discontinuities, recovering only those properties that can be resolved by a spatially limited source and/or receiver distribution. This is illustrated by synthetic examples with local sources followed by a field example in a subduction zone setting.
Temporal variation of S-wave attenuation during the 2009 L'Aquila, Central Italy, seismic sequence
Authors: Castro Raúl R , Colavitti Leonardo , Pacor Francesca , Lanzano Giovanni , Sgobba Sara , Spallarossa Daniele 
Published: October 2024

SUMMARY
We investigate temporal and spatial variations of the spectral decay parameter kappa (κ) before and after the 6 April 2009, L'Aquila earthquake (Mw 6.1), in Central Italy. We analysed foreshocks 10 days before and aftershocks occurring 10 days and 6 months after this main event. We select earthquakes with magnitudes Mw ≥ 3.2 registered by the seismic network of Central Italy within a radius of 20 km from the epicentre of the L'Aquila main shock and having hypocentre distances of less than 170 km. We separate near-source, along-path and near-site contributions of κ for each group of events and we detected temporal variations of this S-wave attenuation parameter. We find that 10 days before the main shock κ along the path has the lowest values, probably due to high tectonic stress accumulated, in agreement with previous investigations performed with other techniques, then κ increases during the main event and remains constant during the first 10 days of aftershocks. The aftershocks that occurred 6 months after show an increase in the regional attenuation probably due to the tectonic stress released during the main shock and the earlier aftershocks. From the spatial point of view, 10 days before the principal event the foreshocks located to the south show an increase in the near-source attenuation towards the northeast, in the direction of the main shock. These spatial variations of κ may be related to the presence of crustal fluids near the rupture area, as evidenced by other previous studies. The first 10 days of aftershocks that concentrate around the main earthquake have high near-source κ, and those located north of the main rupture have lower values. These observations are consistent with previous investigations that show variations of elastic and anisotropic crustal properties during the L'Aquila earthquake sequence due to dilatancy and fluid diffusion processes within the nucleation zone. We conclude that temporal variations of the spectral decay parameter κ provide important clues for the earthquake cycle in Central Italy.
Despite the perception that it is rare, by-catch of marine mammals can lead to population decline
Authors: Authier Matthieu 
Published: October 2024

Abstract
By-catch, the unintentional capture of non-target species in fishing gear, is often described as a rare event when it pertains to marine mammals. Yet, it is the greatest threat to many marine megafauna species, especially small cetaceans. How can both of these statements be true simultaneously? The adjective “rare” is itself rarely defined in a precise and quantitative way. Data collection features are crucial to understand the processes leading to a perception of rarity in samples on by-catch of marine mammals and other protected, endangered and threatened species (PETS). Statistical principles in the design of monitoring schemes must be upheld to ensure sample representativeness when scaling up impact estimates to the level of whole fisheries. Random allocation of observers or monitoring technologies (e.g. Remote Electronic Monitoring) can be strengthened to test the hypothesis that by-catch is a rare event and not only a rarely registered event, especially in monitoring schemes that are not dedicated to PETS by-catch. Even if by-catch is a rare event at the level of a single fishing operation, given the large total number of the latter, and their expansive spatial and temporal extent, by-catch may still impact significantly marine mammal populations.
A posteriori error analysis of a positivity preserving scheme for the power-law diffusion Keller–Segel model
Authors: Giesselmann Jan , Kolbe Niklas 
Published: October 2024

Abstract
We study a finite volume scheme approximating a parabolic-elliptic Keller–Segel system with power-law diffusion with exponent $\gamma \in [1,3]$ and periodic boundary conditions. We derive conditional a posteriori bounds for the error measured in the $L^{\infty }(0,T;H^{1}(\varOmega ))$ norm for the chemoattractant and by a quasi-norm-like quantity for the density. These results are based on stability estimates and suitable conforming reconstructions of the numerical solution. We perform numerical experiments showing that our error bounds are linear in mesh width and elucidating the behavior of the error estimator under changes of $\gamma $.
Carbonic anhydrase-mediated phosphogypsum degradation and enhanced CO2 sequestration: a promising sustainable strategy for biological resource utilization of phosphogypsum
Authors: Sengupta Indraneel , Dhal Paltu Kumar 
Published: October 2024

Abstract

Aims
This study continues our previous investigation of the intrinsic degradation of phosphogypsum (PG) by indigenous microorganisms on amending adequate nutrients. We aim to unravel the intricate mechanisms involved in PG biotransformation by a bacterial consortium.

Methods and results
We isolated and characterized seven multi-metal-resistant bacterial strains from a nutrient-amended PG-contaminated microcosm and identified them through 16S rRNA gene sequencing. Primarily aerobic, Gram-positive chemolithotrophs, these strains demonstrated significant heavy metal uptake and PG degradation potential. Further analysis revealed that all strains produced carbonic anhydrase (CA), while six also produced urease, which may facilitate microbial-induced carbonate precipitation. Microstructural and elemental analysis using scanning electron microscopy-energy-dispersive X-ray and X-Ray Diffraction (XRD) confirmed the PG bio-transformation, indicating substantial increases in carbonate concentrations and reductions in sulfate levels.

Conclusions
The consortium, composed of seven urease- and CA-producing bacterial strains, effectively degraded PG, transforming it from an acidic to an alkaline state and significantly enhancing CO2 sequestration.