bluuebunny/crossref_metadata_2025_split huggingface dataset:
Latent characterization of the complete BATSE gamma-ray bursts catalogue using Gaussian mixture of factor analysers and model-estimated overlap-based syncytial clustering
Authors: Dai Fan , Maitra Ranjan 
Published: November 2024

ABSTRACT
Characterizing and distinguishing gamma-ray bursts (GRBs) has interested astronomers for many decades. While some authors have found two or three groups of GRBs by analysing only a few parameters, recent work identified five ellipsoidally shaped groups upon considering nine parameters $T_{50}, T_{90}, F_1, F_2, F_3, F_4, P_{64}, P_{256}, P_{1024}$. Yet others suggest subclasses within the two or three groups found earlier. Using a mixture model of Gaussian factor analysers, we analysed 1150 GRBs, that had nine parameters observed, from the current Burst and Transient Source Experiment (BATSE) catalogue, and again established five ellipsoidal-shaped groups to describe the GRBs. These five groups are characterized in terms of their average duration, fluence, and spectrum as shorter-faint-hard, long-intermediate-soft, long-intermediate-intermediate, long-bright-intermediate, and short-faint-hard. The use of factor analysers in describing individual group densities allows for a more thorough group-wise characterization of the parameters in terms of a few latent features. However, given the discrepancy with many other existing studies that advocated for two or three groups, we also performed model-estimated overlap-based syncytial clustering that successively merges poorer separated groups. The five ellipsoidal groups merge into three and then into two groups, one with GRBs of low durations and the other having longer duration GRBs. These groups are also characterized in terms of a few latent factors made up of the nine parameters. Our analysis provides context for all three sets of results, and in doing so, details a multilayered characterization of the BATSE GRBs, while also explaining the structure in their variability.
The impact of astrophysical priors on parameter inference for GW230529
Authors: Chattopadhyay Debatri , Al-Shammari Sama , Antonini Fabio , Fairhurst Stephen , Miles Benjamin , Raymond Vivien 
Published: November 2024

ABSTRACT
We investigate the effects of prior selection on the inferred mass and spin parameters of the neutron star–black hole merger GW230529_181500. Specifically, we explore models motivated by astrophysical considerations, including massive binary and pulsar evolution. We examine mass and spin distributions of neutron stars constrained by radio pulsar observations, alongside black hole spin observations from previous gravitational-wave detections. We show that the inferred mass distribution highly depends upon the spin prior. Specifically, under the most restrictive, binary stellar evolution models, we obtain narrower distributions of masses with a black hole mass of $4.3^{+0.1}_{-0.1}\ {\rm M}_{\odot }$ and neutron star mass of $1.3^{+0.03}_{-0.03}\ {\rm M}_{\odot }$ where, somewhat surprisingly, it is the prior on component spins that has the greatest impact on the inferred mass distributions. Re-weighting using neutron star mass and spin priors from observations of radio pulsars, with black hole spins from observations of gravitational waves, yields the black hole and the neutron star masses to be $3.8^{+0.5}_{-0.6}$ and $1.4^{+0.2}_{-0.1} \ \mathrm{ M}_\odot$, respectively. The sequence of compact object formation – whether the neutron star or the black hole formed first – cannot be determined at the observed signal-to-noise ratio. However, there is no evidence that the black hole was tidally spun up.
Testing ecological function in the carving of anomalodesmatan morphospace (Mollusca: Bivalvia: Anomalodesmata)
Authors: Deng Yue 
Published: November 2024

ABSTRACT
Today, the most taxonomically rich bivalve clade is Imparidentia. However, 300 million years ago, Imparidentia's sister clade, Anomalodesmata, was dominant among marine bivalves, while Imparidentia was much less diverse. Both clades are ecologically diverse but infaunal suspension-feeding is the dominant mode of life in each. When taxonomic diversity and morphological disparity are plotted through time for each clade, Imparidentia diversified faster in the Mesozoic than Anomalodesmata until the K/Pg boundary, when the extinction event interrupts the pattern, and both clades then diversified in parallel through the Cenozoic. In this paper, I test the hypothesis that life mode has an effect on morphological disparification and taxonomic diversification, that by ecologically separating themselves from the dominant infaunal suspension-feeding mode, some ‘divergent’ anomalodesmatan lineages may have been able to free themselves from direct competition with imparidents and once more start to rise in morphological and taxonomic diversity. During the Cenozoic, morphological disparity of divergent Anomalodesmata does increase compared to their infaunal suspension-feeding relatives. However, taxonomic diversity does not differ between divergent and infaunal suspension-feeding anomalodesmatan lineages. This suggests that functional partitioning drives morphological disparification, but not taxonomic diversification.
BitterDB: 2024 update on bitter ligands and taste receptors
Authors: Ziaikin Evgenii , David Moran , Uspenskaya Sofya , Niv Masha Y 
Published: November 2024

Abstract
BitterDB (http://bitterdb.agri.huji.ac.il) was introduced in 2012 as a central resource for information on bitter-tasting molecules and their receptors, and was updated in 2019. The information in BitterDB is used for tasks such as exploring the bitter chemical space, choosing suitable ligands for experimental studies, analyzing receptors’ selectivity and promiscuity, and developing machine learning predictors for taste. Here, we describe a major upgrade of the database, including significant increase in content as well as new features. BitterDB now holds over 2200 bitter molecules. For ∼700 molecules, at least one associated bitter taste receptor (TAS2R) is reported. The overall number of ligand-TAS2R associations is now close to 1800. BitterDB is extended to a total of 66 species (including dog, birds, fishes and primates). Following advances in computational structure prediction by AlphaFold and related methods, and the experimental determination of TAS2R structures by cryo-electron microscopy, BitterDB provides links to available structures of TAS2Rs.
MarkerDB 2.0: a comprehensive molecular biomarker database for 2025
Authors: Jackson Hayley , Oler Eponine , Torres-Calzada Claudia , Kruger Ray , Hira Amandeep Singh , López-Hernández Yamilé , Pandit Devanshi , Wang Jiaxuan , Yang Kellie , Fatokun Omolola , Berjanskii Mark , MacKay Scott , Sajed Tanvir , Han Scott , Woudstra Robyn , Sykes Gina , Poelzer Jenna , Sivakumaran Aadhavya , Gautam Vasuk , Wong Gane , Wishart David S 
Published: November 2024

Abstract
MarkerDB (https://markerdb.ca) has become a leading resource for comprehensive information on molecular biomarkers. Over the past 3 years, the database has evolved significantly, reflecting the dynamic landscape of biomarker research and increasing demands from its user community. This year’s update, which is called MarkerDB 2.0, introduces key improvements to enhance the database’s usability, consistency and the range of biomarkers covered. These improvements include (i) the addition of thousands of new biomarkers and associated health conditions, (ii) the inclusion of many new biomarker types and categories, (iii) upgraded searches and data filtering functionalities, (iv) new features for exploring and understanding biomarker panels and (v) significantly expanded and improved descriptions. These upgrades, along with numerous minor improvements in content, interface, layout and overall website performance, have greatly enhanced MarkerDB’s usability and capacity to facilitate biomarker interpretation across various research domains. MarkerDB remains committed to providing a free, publicly accessible platform for consolidated information on a wide range of molecular (protein, genetic, chromosomal and chemical/small molecule) biomarkers, covering diagnostic, prognostic, risk, monitoring, safety and response-related biomarkers. We are confident that these upgrades and updates will improve MarkerDB’s user friendliness, increase its utility and greatly expand its potential applications to many other areas of clinical medicine and biomedical research.
OrthoDB and BUSCO update: annotation of orthologs with wider sampling of genomes
Authors: Tegenfeldt Fredrik , Kuznetsov Dmitry , Manni Mosè , Berkeley Matthew , Zdobnov Evgeny M , Kriventseva Evgenia V 
Published: November 2024

Abstract
OrthoDB (https://www.orthodb.org) offers evolutionary and functional annotations of orthologous genes in the widest sampling of eukaryotes, prokaryotes, and viruses, extending experimental gene function knowledge to newly sequenced genomes. We collect gene annotations, delineate hierarchical gene orthology and annotate the orthologous groups (OGs) with functional and evolutionary traits. OrthoDB is the leading resource for species diversity, striving to sample the most diverse and well-researched organisms with the highest quality genomic data. This update expands to include 5827 eukaryotic genomes. We have also added coding DNA sequences (CDSs) and gene loci coordinates. OrthoDB can be browsed, downloaded, or accessed using REST API, SPARQL/RDF and now also via API packages for Python and R Bioconductor. OrthoLoger (https://orthologer.ezlab.org), the tool used for inferring orthologs in OrthoDB, is now available as a Conda package and through BioContainers. ODB-mapper, a component of OrthoLoger, streamlines annotation of genes from newly sequenced genomes with OrthoDB evolutionary and functional descriptors. The benchmarking sets of universal single-copy orthologs (BUSCO), derived from OrthoDB, had correspondingly a major update. The BUSCO tool (https://busco.ezlab.org) has become a standard in genomics, uniquely capable of assessing both eukaryotic and prokaryotic species. It is applicable to gene sets, transcriptomes, genome assemblies and metagenomic bins.
The potential for improving cardio-renal outcomes in chronic kidney disease with the aldosterone synthase inhibitor vicadrostat (BI 690517): a rationale for the EASi-KIDNEY trial
Authors: Judge Parminder K , Tuttle Katherine R , Staplin Natalie , Hauske Sibylle J , Zhu Doreen , Sardell Rebecca , Cronin Lisa , Green Jennifer B , Agrawal Nikita , Arimoto Ryoki , Mayne Kaitlin J , Sammons Emily , Brueckmann Martina , Shah Shimoli V , Rossing Peter , Nangaku Masaomi , Landray Martin J , Wanner Christoph , Baigent Colin , Haynes Richard , Herrington William G 
Published: November 2024

ABSTRACT
Patients with chronic kidney disease (CKD) are at risk of progressive loss of kidney function, heart failure, and cardiovascular death despite current proven therapies, including renin-angiotensin system inhibitors (RASi), sodium glucose co-transporter-2 inhibitors (SGLT2i), and statin-based regimens. RASi and SGLT2i reduce risk of CKD progression irrespective of primary cause of kidney disease, suggesting they target final common pathways. Targeting aldosterone overactivity with a nonsteroidal mineralocorticoid receptor antagonist (MRA) also reduces cardiorenal risk in patients with albuminuric diabetic kidney disease already treated with RASi. Together, these observations provide the rationale for trials to assess effects of inhibiting the aldosterone pathway in a broader range of patients with CKD, including those with non-diabetic causes of CKD or low albuminuria. Aldosterone synthase inhibitors (ASi) have emerged as an alternative to MRAs for aldosterone pathway inhibition. Phase II data from 586 patients with albuminuric CKD have shown that 10 mg of an ASi, vicadrostat (BI 690517), reduced urine albumin-to-creatinine ratio by ∼40% compared with placebo, with or without concurrent empagliflozin treatment. MRA and ASi increase risk of hyperkalaemia. Combining their use with an SGLT2i may mitigate some of this risk, improving tolerability, and allowing a wider range of patients to be treated (including those with higher levels of blood potassium than in previous trials). The EASi-KIDNEY (NCT06531824) double-blind placebo-controlled trial will test this approach by assessing the safety and cardiorenal efficacy of vicadrostat in combination with empagliflozin in ∼11 000 patients with CKD. It will be sufficiently large to assess effects in patients with and without diabetes separately.
Meningiomas: Sex-Specific Differences and Prognostic Implications of a Chromosome X Loss
Authors: Berghaus Natalie , Hielscher Thomas , Savran Dilan , Schrimpf Daniel , Maas Sybren L N , Preusser Matthias , Weller Michael , Acker Till , Herold-Mende Christel , Wick Wolfgang , von Deimling Andreas , Sahm Felix 
Published: November 2024

Abstract

Background
Meningiomas are the most common primary intracranial tumours in adults. Several studies proposed new stratification systems with a more accurate risk prediction than the WHO grading, e.g. based on methylation and copy number variations (CNVs). Yet, common shortcomings in these analyses are either a lack of stratification by sex of patients or excluding the gonososmes from CNV assessment.

Methods
Within this study, DNA methylation array data from 7,424 meningioma samples as well as targeted sequencing, clinical annotations and morphology subtyping of 796 samples were examined for differences between females and males regarding mutations, methylation classes, copy number variations and histology.

Results
Meningiomas from females accounted for about 53 % of the malignant tumours and present a loss of one X chromosome in 57 % of these malignant cases. In the group of benign tumours, females comprised about 75 % of the patients. Therein, a loss of one X chromosome was detected in only about 10 % of the cases but was associated with a significantly worse progression free survival.

Conclusion
Although genomic instability is a common feature of malignant meningiomas, particularly loss of the X chromosome in tumours of female patients in otherwise histologically and molecularly low-risk tumours confers higher risk. Hence, the gonosomal copy number status can be leveraged for increased diagnostic accuracy.
Using a Pre-Radiation Window to Identify Potentially Active Cytotoxic Agents in Adults with Newly Diagnosed Glioblastoma
Authors: Bazer Danielle A , Wolff Antonio C , Grossman Stuart A 
Published: November 2024

Abstract

Background
Therapies shown to improve outcomes in patients with recurrent cancers are commonly used in the neoadjuvant setting to optimize surgery, reduce radiation fields, and treat micro-metastatic disease. While pre-radiation chemotherapy (PRC) use has flourished in systemic cancers, it has not in glioblastomas. This review documents these trajectories and highlights the potential of PRC to rapidly and safely screen cytotoxic drugs for efficacy in patients with newly diagnosed glioblastoma.

Methods
Prospective trials of adults with newly diagnosed systemic and brain cancers treated with PRC published between 1980 and 2023 were identified in PubMed. NCCN guidelines were used to document the standard use of PRC in patients with systemic and brain cancers.

Results
Over 5,000 prospective PRC trials in solid tumors were identified. These accrued &gt;1 million patients and resulted in neoadjuvant therapies being standard-of-care in ~28 systemic cancers. Only 50 similar trials (2,206 patients) were identified in high grade gliomas. In 13 trials containing PRC temozolomide (n=846), radiographic responses ranged from 6-53% with a median survival of ~13 months. Glioblastoma PRC trials were not associated with unexpected toxicities or major negative impacts on survival.

Conclusions
PRC in patients with glioblastoma appears safe and feasible. The pre-radiation window is ideally suited to rapidly screen cytotoxic agents for efficacy. It permits radiographic response as a primary outcome, small sample sizes, and initiation of standard therapies a few months after diagnosis. PRC may be most appropriate in patients with glioblastoma who are unlikely to benefit from temozolomide.
TRIM21-mediated ubiquitination and phosphorylation of ERK1/2 promotes cell proliferation and drug resistance in pituitary adenomas
Authors: Liu Yanting , Liu Fang , Li Chuanbao , Zhang Tao , Han Tianyi , Dai Yuting , Huang Ning , Tang Hao , Wang Xiaobin , Lin Shaojian , Xue Li , Wu Zhe Bao 
Published: November 2024

Abstract

Background
Pituitary adenomas (PAs) are common intracranial tumors and the TRIM family plays a crucial role in cell proliferation and therapeutic resistance of tumors. However, the role of the TRIM family in PAs is not well recognized.

Methods
CRISPR screening explored the role of the TRIM family in cell proliferation and drug resistance in PAs. In vitro and in vivo experiments were performed to evaluate the effects of Tripartite Motif Containing 21 (TRIM21). RNA-sequencing, mass spectrometry, immunoprecipitation, and ubiquitination experiments were performed to explore the molecular mechanism. NanoBiT assays were used to screen the drugs reducing TRIM21 expression.

Results
CRISPR-Cas9 screens identified that TRIM21 facilitated cell proliferation and drug resistance in PAs. Mechanistically, TRIM21 interacted with ERK1/2 through PRY-SPRY domain, leading to ERK1/2 K27-linked ubiquitination. The ERK1/2 ubiquitination promotes the interaction between ERK1/2 and MEK1/2, thereby facilitating the phosphorylation of ERK1/2. However, an excess presence of TRIM21 suppressed the phosphorylation of ERK1/2 and cell proliferation via activating ERK1/2 negative feedback pathways. Importantly, TRIM21 was upregulated in dopamine-resistant prolactinomas and cabergoline-resistant MMQ cells. Furthermore, drug screening identified that Fimepinostat and Quisinostat, can reduce the protein levels of TRIM21, inhibit tumor progression, and increase drug sensitivity.

Conclusions
TRIM21 may represent a therapeutic target for tumors, and inhibiting TRIM21 could be a potential strategy for tumor treatment.
Bioengineered therapeutic systems for improving antitumor immunity
Authors: Cao Ying , Yan Wenlu , Yi Wenzhe , Yin Qi , Li Yaping 
Published: November 2024

ABSTRACT
Immunotherapy, a monumental advancement in antitumor therapy, still yields limited clinical benefits owing to its unguaranteed efficacy and safety. Therapeutic systems derived from cellular, bacterial and viral sources possess inherent properties that are conducive to antitumor immunotherapy. However, crude biomimetic systems have restricted functionality and may produce undesired toxicity. With advances in biotechnology, various toolkits are available to add or subtract certain properties of living organisms to create flexible therapeutic platforms. This review elaborates on the creation of bioengineered systems, via gene editing, synthetic biology and surface engineering, to enhance immunotherapy. The modifying strategies of the systems are discussed, including equipment for navigation and recognition systems to improve therapeutic precision, the introduction of controllable components to control the duration and intensity of treatment, the addition of immunomodulatory components to amplify immune activation, and the removal of toxicity factors to ensure biosafety. Finally, we summarize the advantages of bioengineered immunotherapeutic systems and possible directions for their clinical translation.
Remote Practice of Infectious Diseases Through Telemedicine: Improving Access for Patients and Appeal for Physicians
Authors: Nabha Linda , Mehta Steinke Seema 
Published: November 2024

Abstract
The specialty of infectious diseases (ID) is facing headwinds in attracting new physicians into training and clinical practice, leading to workforce shortage and rising burnout among existing ID physicians. The distribution of ID physicians across the country is skewed, and many Americans do not have access to ID expertise. Novel care models are needed to ensure the longevity of the ID specialty and patient access to ID care. ID telemedicine provides a new opportunity for ID physicians with the benefits of residing in one's preferred geographic location, eliminating the need to commute, and structuring the workday to improve work-life balance. This viewpoint, which includes personal experiences in transitioning from in-person to remote ID practice, describes the extent of challenges facing the ID specialty and how telemedicine can reduce burnout among ID physicians, attract more physicians into the specialty, and improve access to ID care.
Shaping the Future of Infectious Diseases: The Journey to Promote Value, Opportunity, and Positive Messaging
Authors: Paras Molly L , Chirch Lisa M , Aziz Mariam , Balba Gayle P , Benson Constance , Butt Saira , James Scott H , McCarty Todd P , Razonable Raymund , Reece Rebecca , Shnekendorf Rachel , Swartz Talia H , Viehman J Alex , Luther Vera P ,   For the Infectious Diseases Society of America Fellowship Training Program Directors Community of Practice and Working Group (complete list of contributing authors in the Working Group listed in acknowledgments), Abdoler Emily , Acharya Kartikey , Angarone Michael , Babik Jennifer , Bartash Rachel , Bhanot Nitin , Blackburn Brian , Blumberg Emily , Blyth Dana M , Bourque Daniel , Bran Andres , Burke Victoria , Carey Adrienne L , Cheney Laura L , Chow Brian D , Clough Lisa A , Cunha Cheston , de Sanctis Jorgelina T , Dobrzynski David M , George Ige A , Goebel Melanie , Goshorn Eli S , Gutierrez Ramiro , Herc Erica S , Hillenbrand Molly J , Kaltsas Anna , Khalil Sarwat , Kiley John , Lebron Dora A , Lee Mikyung , Leuck Anne-Marie , Gil Raul Macias , Mapa Christopher , Marcos Luis A , Matt Brionna , Maziarz Eileen K , Melia Michael , Mitra Subhashis , Monday Lea , Montague Brian , Murphy Holly A , Novick Elizabeth E , Nnedu Obinna N , Nori Priya , Ongunti Sharon , Osorio Georgina , Pepe Rosalie , Perez Federico , Pilkington Edward F , Raybould Jillian E , Reid Gail E , Robinson Sara , Sanchez Martha , Schultz Sara , Sellers Christopher , Simon Matthew , Sisco Lauren , Slosar-Cheah Magdalena , Sobhanie Mohammad Mahdee E , Stapleton Ann , Stead Wendy , Streit Judy , Theodore Deborah A , Wald-Dickler Noah , Weber Devin M , Weisenberg Scott A , Witherspoon Kelsey L , Yabes Joseph M , Zuckerman Richard A 
Published: November 2024

Abstract
The field of infectious diseases (ID) offers a rewarding career path and is widely viewed as an essential subspecialty in medicine. However, in recent years, these positive aspects have been overshadowed by concerns surrounding low fellowship match rates, undercompensation, and burnout. The Infectious Diseases Society of America Fellowship Training Program Directors Committee met in 2023, discussed the future of ID as a specialty, and sought to develop strategies to highlight the value and opportunities of ID for future generations, as well as underscore the importance of and provide tools for positive messaging to trainees about the subspecialty. This paper presents ideas generated at this meeting and is meant to serve as a reference for ID training program directors, as well as the wider ID community, in uplifting and shaping the future of the field.