bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pseudomonas aeruginosa maintains an inducible array of novel and diverse prophages over lengthy persistence in cystic fibrosis lungs
Authors: Kyrkou Ifigeneia , Bartell Jennifer , Lechuga Ana , Lood Cédric , Marvig Rasmus L , Lavigne Rob , Molin Søren , Krogh Johansen Helle 
Published: February 2025

Abstract
Pseudomonas aeruginosa has increasing clinical relevance and commonly occupies the cystic fibrosis (CF) airways. Its ability to colonize and persist in diverse niches is attributed to its large accessory genome, where prophages represent a common feature and may contribute to its fitness and persistence. We focused on the CF airways niche and used 197 longitudinal isolates from 12 patients persistently infected by P. aeruginosa. We computationally predicted intact prophages for each longitudinal group and scored their long-term persistence. We then confirmed prophage inducibility and mapped their location in the host chromosome with lysate sequencing. Using comparative genomics, we evaluated prophage genomic diversity, long-term persistence, and level of genomic maintenance. Our findings support previous findings that most P. aeruginosa genomes harbour prophages some of which can self-induce, and that a common CF-treating antibiotic, ciprofloxacin, can induce prophages. Induced prophage genomes displayed high diversity and even genomic novelty. Finally, all induced prophages persisted long-term with their genomes avoiding gene loss and degradation over 4 years of host replication in the stressful CF airways niche. This and our detection of phage genes, which contribute to host competitiveness and adaptation, lends support to our hypothesis that the vast majority of prophages detected as intact and inducible in this study facilitated their host fitness and persistence.
“French Phage Network” annual conference—eighth meeting report
Authors: Armal Carole , Arnaud Charles-Adrien , Cenraud Emilie , Le Cras Youn , Pastouriaux Pierre-Alexandre , Pellegri Callypso , Debarbieux Laurent 
Published: February 2025

Abstract
The French Phage Network organizes a scientific meeting every year in which the community of researchers from academia and industry, as well as clinicians participate due to the growing interest in phage therapy. Although centered on giving exposure to future generations of scientists from the French community with senior investigators invited as main speakers, the meeting has also welcomed participants from other countries. Covering almost every aspect of bacteriophage biology, the meeting is an opportunity not only to expose the youngest to a broad range of topics, but also to share their most recent “work in progress” without undergoing a stringent selection process to obtain an oral presentation slot. This report reflects the dynamism of the research field on bacteriophages across multiple disciplines, including molecular and structural biology, ecology, evolution, therapy, and biotechnology.
A Bayesian approach to correcting the attenuation bias of regression using polygenic risk score
Authors: Zhou Geyu , Qie Xinyue , Zhao Hongyu 
Published: February 2025

Abstract
Polygenic risk score has become increasingly popular for predicting the value of complex traits. In many settings, polygenic risk score is used as a covariate in regression analysis to study the association between different phenotypes. However, measurement error in polygenic risk score causes attenuation bias in the estimation of regression coefficients. In this paper, we employ a Bayesian approach to accounting for the measurement error of polygenic risk score and correcting the attenuation bias in linear and logistic regression. Through simulation, we show that our approach is able to obtain approximately unbiased estimation of coefficients and credible intervals with correct coverage probability. We also empirically compare our Bayesian measurement error model with the conventional regression model by analyzing real traits in the UK Biobank. The results demonstrate the effectiveness of our approach as it significantly reduces the error in coefficient estimates.
The Rac1 homolog CED-10 is a component of the MES-1/SRC-1 pathway for asymmetric division of the C. elegans EMS blastomere
Authors: Lamb Helen , Fernholz McKenzi , Liro Małgorzata J , Myles Krista M , Anderson Holly , Rose Lesilee S 
Published: February 2025

Abstract
Asymmetric cell division is essential for the creation of cell types with different identities and functions. The EMS blastomere of the four-cell Caenorhabditis elegans embryo undergoes an asymmetric division in response to partially redundant signaling pathways. One pathway involves a Wnt signal from the neighboring P2 cell, while the other pathway is defined by the receptor-like MES-1 transmembrane protein localized at the EMS-P2 cell contact, and the cytoplasmic kinase SRC-1. In response to these signals, the EMS nuclear-centrosome complex rotates so that the spindle forms on the anterior-posterior axis; after division, the daughter cell contacting P2 becomes the endodermal precursor cell. Here we identify the Rac1 homolog CED-10 as a new component of the MES-1/SRC-1 pathway. Loss of CED-10 affects both spindle positioning and endoderm specification in the EMS cell. SRC-1 dependent phosphorylation at the EMS-P2 contact is reduced. However, the asymmetric division of the P2 cell, which is also MES-1 and SRC-1 dependent, appears normal in ced-10 mutants. These and other results suggest that CED-10 acts upstream of, or at the level of, SRC-1 activity in the EMS cell. In addition, we find that the branched actin regulator ARX-2 is enriched at the EMS-P2 cell contact site, in a CED-10 dependent manner. Loss of ARX-2 results in EMS spindle orientation defects, suggesting that CED-10 acts through branched actin to promote spindle orientation in the EMS cell.
A multifaceted citizen-science approach for characterizing shark depredation in Florida’s recreational fisheries
Authors: McCallister Michael P , Brewster Lauran , Dean Cheryl , Drymon J Marcus , Hutt Cliff , Ostendorf Thomas J , Ajemian Matthew J 
Published: February 2025

Abstract
Depredation (i.e. partial removal of target catch prior to retrieval) caused by sharks is a prevalent issue affecting several fisheries in the southeastern USA. While US fisheries managers have begun monitoring shark depredation in commercial fisheries, there have been few attempts to quantify these interactions in the recreational fishing sector. To address this knowledge gap, we initiated a citizen-science-based project to provide an in-depth characterization of shark depredation in Florida’s recreational fisheries. This was done via multiple approaches, including social media content analysis, online angler surveys, and cooperative fishery-dependent charters. Across methodologies, snapper-grouper species were the most frequently depredated target species group, and bull and sandbar sharks were the most commonly identified depredating species. Forty-three percent of anglers experienced depredation, and the probability of experiencing depredation ranged from 10% to 60% and varied both regionally and seasonally. In addition, average depredation rates ranged from 31% to 47% and were within the range of reported rates from other recreational fisheries. These results will help build a comprehensive understanding of this human-wildlife conflict and could aid fishery managers in developing management measures to address this fisheries conflict. Furthermore, this study highlights the benefit of incorporating citizen science when addressing complex fisheries issues involving stakeholder conflict.
Pulmonary expanded polytetrafluoroethylene conduits with a hand-sewn tricuspid valve
Authors: Matsushima Shunsuke , Takahashi Ryota , Kubo Sara , Higashida Akihiko , Oshima Yoshihiro , Matsuhisa Hironori 
Published: February 2025

Abstract

OBJECTIVES
The biocompatibility of expanded polytetrafluoroethylene in the pulmonary position seems better than allogenic or xenogeneic reactivity. This study reviewed the application of pulmonary expanded polytetrafluoroethylene conduits having a hand-sewn tricuspid valve with diameters of 18–24 mm.

METHODS
All patients receiving this conduit between 2010 and 2022 were evaluated. A 0.1-mm-thick membrane and a standard-wall tube of expanded polytetrafluoroethylene were used for cusp and conduit material, respectively.

RESULTS
Eighty-four consecutive patients were included. The median operative age and weight were 12 (range, 1.2–40) years and 34 (range, 9.1–82) kg, respectively. Eighteen-, 20-, 22- and 24-mm conduits were used in 19, 5, 3 and 57 patients, respectively. The overall survival was 94% at 5 and 10 years with four non-valve-related deaths. There were five conduit replacements, all for 18-mm conduit stenosis. Freedom from conduit replacement was 98% and 83% at 5 and 10 years, respectively. Freedom from conduit stenosis ≥ moderate was 83% and 54% at 5 and 10 years, respectively. Freedom from pulmonary regurgitation ≥ moderate was 98% at 5 and 10 years. Linear mixed-effects models with echocardiographic data implied that 24-mm conduits functioned with a peak velocity &lt;3.0 m/s and without moderate/severe regurgitation in patients with a body weight of up to 75 kg and a body surface area of up to 2.0 m2 for &gt;12 years postoperatively.

CONCLUSIONS
This conduit has shown favourable clinical outcomes and is a valid alternative, especially in young patients with increased risk for early failure of the existing products.
Durability of doravirine/dolutegravir dual combination in a multicentre cohort of elderly people with HIV
Authors: Mazzitelli Maria , Cozzolino Claudia , Gervasoni Cristina , Pagano Simone , Reato Serena , Ripamonti Diego , Comi Laura , Scaglione Vincenzo , Mengato Daniele , Formica Giuseppe , Lagi Filippo , Cascio Antonio , Trizzino Marcello , Iannone Valentina , Farinacci Damiano , Cattelan Annamaria 
Published: February 2025

Abstract

Background
Even though the doravirine/dolutegravir combination is not mentioned by guidelines, real-life data has begun to emerge on its use. We aimed to describe the durability of doravirine/dolutegravir in a multicentre Italian cohort of elderly people with HIV (EPWH).

Methods
We included all EPWH who ever started the doravirine/dolutegravir combination in six Italian centres and were followed up until treatment discontinuation (TD) for any reason (virological failure, death, treatment interruption for other reasons) on 31 March 2024. Descriptive statistics were used to describe the study population; Kaplan–Meier curves and Cox regression analyses were used to estimate incidence and associated predictors of time to TD.

Results
We included 157 people; 61.1% were male, the median age was 59 years (IQR: 55–64), 75.2% had multimorbidity, 38.9% were on polypharmacy, and 91.1% had HIV-RNA of &lt;50 copies/mL. No genotype resistance test was available for 19.4% of people who started doravirine/dolutegravir. The main reasons for starting doravirine/dolutegravir were high cardiovascular risk (51.6%), simplification (52.9%) and drug–drug interactions (25.5%). During a median follow-up of 27.85 (IQR: 22.92–31.79) months, 8 (5.1%) participants experienced TD (2 toxicities, 2 virological failures, 2 switches to long-acting drugs, 1 death and 1 transferred). The incidence of TD was 2.27 per 100 person-years of follow-up. Multivariable Cox regression analyses did not show any factors as predictors of TD.

Conclusions
In this multicentre cohort of EPWH with clinical complexity, the doravirine/dolutegravir combination showed good durability over time. TD probability was very low, and no significant factors seem to predict it, likely due to the limited number and heterogeneity of cases of TD.
Using bacterial and mitochondrial DNA markers to assess fecal pollution sources in stream water and sediments of a mixed land-use watershed
Authors: Ren Wenjing , Brantley Eve F , Wang Xu , Rose Joan B , Feng Yucheng 
Published: February 2025

Abstract

Aims
Although stream bed sediment can be an important reservoir of fecal bacteria and pathogens, it is rarely analyzed when assessing microbial water quality. This study aims to identify fecal contamination sources in stream water and sediment and evaluates the impact of rainfall events on microbial water quality in a mixed land-use watershed.

Methods and Results
Quantitative polymerase chain reaction was employed to quantify human-, cattle-, and chicken-associated genetic markers during dry and wet periods in the Middle Tallapoosa watershed in Alabama, USA. Human- and cattle-associated markers were consistently detected in water samples, irrespective of precipitation, whereas chicken-associated markers were predominantly found following significant rainfall events. In the sediment, all markers were detected at higher concentrations but with a lower frequency than in the water. Escherichia coli concentrations in water samples correlated significantly with 2-day antecedent rainfall and streamflow and were substantially lower than in the sediment.

Conclusions
Humans and cattle were the primary contamination sources in the study area, and runoff from storms and sediment contributed to fecal contamination in the streams.
OpenAI’s patent pledge: a post-Moderna analysis
Authors: Lenarczyk Gabriela , Aboy Mateo 
Published: February 2025

Abstract
Patent pledges have increasingly been used as private ordering mechanisms to facilitate innovation and collaboration while balancing the proprietary interests of patent holders. The Moderna v Pfizer/BioNTech decision by the UK High Court marked the first judicial analysis of the enforceability and interpretation of such pledges. OpenAI’s patent pledge, committing to defensive patent use subject to specific behavioural conditions, raises novel interpretative issues. Their pledge diverges from traditional pledges by focusing on defensive use, conditioned upon specific behavioural triggers such as avoiding harm or legal actions against OpenAI. This article examines the pledge through the lens of the Moderna framework, analysing its scope, revocability and operational limits. The pledge’s reliance on broad behavioural conditions and lack of explicit temporal markers introduce noteworthy legal and practical complexities. These elements affect its enforceability and create challenges for third-party reliance. Our analysis highlights the balance between strategic flexibility for patent holders and the need for clarity to foster trust among implementers. The findings underscore the balance between fostering innovation and protecting proprietary interests.
The conserved IR75 subfamily mediates carboxylic acid detection in insects of public health and agricultural importance
Authors: Cooke Matthew , Chembars Michael S , Pitts Ronald Jason 
Published: February 2025

Abstract
Insects perceive and respond to carboxylic acids (CAs), amines, and aldehydes primarily via conserved ionotropic receptors (IRs). These receptors form the basis for a second olfactory system distinct from the well-characterized odorant receptors. Neurons expressing IRs are housed in dedicated sensilla and innervate glomeruli, separate from those innervated by odorant receptor neurons. The IR8a co-receptor is highly conserved across insect orders and, together with ionotropic receptor tuning receptors, primarily detects CAs. The conservation of genes and the anatomical separation of neural pathways underscore the importance of these compound classes and CAs, specifically in insect chemical ecology. We provide a summary of carboxylic acid detection in insects, focusing on dipteran and lepidopteran species of significance to public health and agriculture. An overview of insect behavior toward CAs is provided, as well as a comprehensive update on carboxylic acid receptor function in insects. Phylogenetic analysis of publicly available genome databases reveals several species that encode and express homologs of previously deorphanized carboxylic acid receptors, highlighting avenues for future research.
Structural Volatility Impulse Response Analysis
Authors: Fengler Matthias R , Polivka Jeannine 
Published: February 2025

Abstract
We make three contributions to the volatility impulse response function (VIRF) developed by Hafner and Herwartz (2006). First, we derive its law for multivariate GARCH models of the BEKK type. Second, we present a structural embedding of the VIRF, leveraging recent advancements in the identification of multivariate generalized autoregressive conditional heteroskedasticity models. Third, we show how to endow the VIRF with a causal interpretation. We illustrate the merits of a structural VIRF analysis by investigating the impacts of historical and out-of-sample shock scenarios on the U.S. equity, government bond, and foreign exchange markets.
Changing the Paradigm: Practical Wisdom as True North in Medical Education
Authors: Plews-Ogan Margaret L 
Published: February 2025

Abstract
The practice of medicine is a complex endeavor requiring high levels of knowledge and technical capability, and the capacity to apply the skills and knowledge to do the right thing in the right way, for the right reason, in a particular context. The orchestration of the virtues, managing uncertainty, applying knowledge and technical skills to a particular individual in a particular circumstance, and exercising the virtues in challenging circumstances, are the tasks of practical wisdom. Centuries ago, Aristotle suggested that capacities for wise action are developed through practice, experience, and reflection. Neuroscience and cognitive psychology are now beginning to contribute to our understanding of the complex interplay between emotion, cognition, and behavior that is necessary for wise action, and how this capacity for wise action can be developed. In this paper, I propose that wisdom offers an appropriate true north for medical education. Wisdom shifts the focus beyond the simple acquisition of knowledge and technical skills and integrates essential virtues like compassion, trustworthiness, humility, and the balancing of the virtues, into the professional formation for medical students. Informed by the humanities, the neurosciences, and the social sciences, we must now integrate the skills and practices necessary to the development of practical wisdom into medical education at all levels.
Response to Oleribe
Authors: Riviere Paul , Murphy James D , Vitzthum Lucas K 
Published: February 2025

Abstract
We would like to thank Dr Oleribe for their interest in the study, “Predicting Persistent Opioid Use, Abuse, and Toxicity Among Cancer Survivors”. In the critical appraisal, the author concludes that there is an increased rate of persistent opioid use among Black veterans because the proportion of veterans with persistent opioid use who were Black was higher than the proportion of African American veterans on a census bureau report of veterans. While we appreciate the author’s investigation into potential racial disparities in adverse opioid outcomes, we do not agree with their methodology and do not believe the data supports their conclusion.
Free metatarsophalangeal joint to metacarpophalangeal joint transfer – a unique surgical technique
Authors: Asghar Zoha , Sheikh Zubaid Moazzam , Asif Muhammad 
Published: February 2025

Abstract
Giant cell tumors of metacarpal bones is a rare occurrence. The tumor particularly exhibits an aggressive behavior in small bones of the extremities. Different techniques such as curettage with or without bone grafting, en bloc resection (more commonly preferred) and reconstruction have been discussed but a unique way of reconstruction is using the metatarsal for substitution. Other options include the fibular graft or using a portion of the iliac crest. We report the case of a young female with a giant cell tumor of the fourth metacarpal bone where we reconstructed the diseased joint with the metatarsal bone while achieving good local control, preserving lower limb and hand function along with cosmesis. The transfer of osteoarticular ligamentous complexes of the metatarsal bone for reconstruction of metacarpal bone defects is a technique that provides good cosmetic outcomes, excellent function with minimum effects to the donor site function.
A rare case of nephroblastoma arising in a multicystic dysplastic kidney: a case report and review of the literature
Authors: Youssef Sabrine Ben , Dghaies Rim , Toumi Afef , Njima Manel , Salem Randa , Fredj Myriam Ben , Ammar Nouha , Chabchoub Imene , Ksia Amine , Sahnoun Lassaad 
Published: February 2025

Abstract
The simultaneous occurrence of Wilms tumor (WT) and multicystic kidney disease (MCKD) is extremely uncommon. Diagnosing WT in pediatric patients with multicystic dysplastic kidney (MCDK) substantially impacts management strategies, especially in surgical interventions and long-term outcomes. In summary, while the exact prevalence of WT in children with MCKD is not well-defined, children with MCDK are followed up throughout childhood by ultrasound because of the perceived risk of developing WT, although this risk is poorly defined and somewhat controversial. Herein, we present the case of an 8-year-old child diagnosed with WT arising in a clearly defined MCDK, discovered incidentally through histological analysis. This case contributes to the ongoing discussion by adding to the existing reports in the literature.
Mitral autograft for partial tricuspid valve replacement: a case report
Authors: El Mourabit Yassin , Tribak Mohammed , El Bakkali Abderahmane , Mermade Lahcen , Moughil Said 
Published: February 2025

Abstract
Surgical management of tricuspid valve infective endocarditis is controversial. We report a case of infective endocarditis of the mitral and tricuspid valves which was treated by partial replacement of the tricuspid valve with a mitral autograft and replacement of the mitral valve with a mechanical prosthesis. Indication for surgical treatment was persistent tricuspid valve vegetations &gt;20 mm after recurrent pulmonary emboli. After an 18-month postoperative follow-up, the patient was in good clinical condition with no residual tricuspid regurgitation. Mitral autograft replacement of the tricuspid valve expands the possibilities for tricuspid valve repair in the context of infective endocarditis.