bluuebunny/crossref_metadata_2025 huggingface dataset:
A neural basis for prosocial behavior toward unresponsive individuals
Authors: Sun Fangmiao , Wu Ye Emily , Hong Weizhe
Published: February 2025

Humans often take actions to assist others experiencing unresponsiveness, such as transient loss of consciousness. How other animals react to unresponsive conspecifics—and the neural mechanisms driving such behaviors—remain largely unexplored. In this study, we demonstrated that mice exhibit rescue-like social behaviors toward unresponsive conspecifics, characterized by intense physical contact and grooming directed at the recipient’s facial and mouth areas, which expedite their recovery from unresponsiveness. We identified the medial amygdala (MeA) as a key region that encodes the unresponsive state of others and drives this head-directed physical contact. Notably, the behavioral responses toward unresponsive conspecifics differed from those directed at awake, stressed individuals, and these responses were differentially represented in the MeA. These findings shed light on the neural mechanisms underlying prosocial responses toward unresponsive individuals.
Quantum computing requires high-performance software
Authors: Chow Jerry M.
Published: February 2025

Quantum computing is maturing at a rapid pace, and it is quite plausible that quantum computers capable of solving problems of value to businesses will be available this decade. At the same time, quantum computing likely will not supplant classical computing in the foreseeable future—after all, quantum computing architectures are best equipped to solve certain problems, but not every problem. Quantum computers almost certainly will work in concert with classical processing, where each computing architecture will handle those parts of a calculation that it is best suited to tackle. For that to happen, the quantum computing hardware will require software that combines quantum with classical computing. It also must be devised in a user-friendly way so that nonquantum scientists and software developers working on problems such as modeling molecules with unprecedented accuracy and calculating interesting properties of structured datasets can run quantum computational tasks without having in-depth knowledge of quantum computing.
Connecting the dots for cooling
Authors: Perren Lara , Yarema Maksym
Published: February 2025

Semiconductor particles are fused to make a thermoelectric cooler
Deciphering meropenem persistence in
Acinetobacter baumannii
facilitates discovery of anti-persister activity of thymol
Authors: Hussain Arsalan , Bhando Timsy , Casius Ananth , Gupta Rinki , Pathania Ranjana
Published: February 2025

Decades of antibiotic misuse have accelerated the emergence of multi- and extensively drug-resistant bacteria. Bacterial pathogens employ several strategies such as antibiotic resistance, tolerance, and biofilm formation in response to extreme environments and antibiotic stress. Another crucial survival mechanism involves the stochastic generation of bacterial subpopulations known as persisters, which can endure high concentrations of antibiotics. Upon removal of antibiotic stress, these subpopulations revert back to their original phenotype which links them to the relapse and recalcitrance of chronic infections, a significant problem in clinical settings. Persistent infections are particularly notable in
Acinetobacter baumannii
, a top-priority ESKAPE pathogen, where carbapenems serve as last-resort antibiotics. Several reports indicate the rising therapeutic failure of carbapenems due to persistence, underscoring the importance of developing anti-persister therapeutics. In this study, we explored the mechanisms of transient persister formation in
A. baumannii
against meropenem. Our investigation revealed significant changes in membrane properties and energetics in meropenem persisters of
A. baumannii
, including a noteworthy increase in tolerance to other antibiotics. This understanding guided the evaluation of an in-house collection of GRAS status compounds for their potential anti-persister activity. The compound thymol demonstrated remarkable inhibitory activity against meropenem persisters of
A. baumannii
and other ESKAPE pathogens. Further investigation revealed its impact on persister cell physiology, including efflux pump inhibition and disruption of cellular respiration. Given our results, we propose a compelling strategy where thymol could be employed either as a monotherapy or in combination with meropenem in anti-persister therapeutics.
A CURE lab in an introductory biology course has minimal impact on student outcomes, self-confidence, and preferences compared to a traditional lab
Authors: Mashintonio Andrew F. , Heineman Richard H.
Published: February 2025

Course-based undergraduate research experiences (CUREs) have grown in popularity, particularly within introductory biology courses, to provide more students with authentic research experiences. CUREs have been shown to have many of the same positive effects as conventional research experiences; however, most assessments of CUREs lack an appropriate comparison group to evaluate their effectiveness. Here, we introduced a CURE into an introductory biology lab at a regional public university but maintained a traditional, “cookie-cutter” lab in half the lab sections over a 3-year period. We compared changes in test scores and survey responses, final lab and lecture scores, and D, F, withdrawal, and incomplete (DFWI) and retention rates between non-honors biology students in each group. While both groups showed significant improvement in test scores, only transfer students had significantly greater improvement in the CURE vs traditional lab. Students in both groups showed significant increases in self-confidence in some lab-related tasks, but differences in these changes were generally not significant between groups. There were no significant differences in final lecture score, lab score, DFWI rate, or retention rate. Factors affecting the lack of measured CURE success may include the type of CURE chosen, student career interests, and COVID-19; other positive impacts of the CURE may not have been captured by our measurements. This study demonstrates the importance of carefully choosing a CURE to match the student population, as well as assessing the CURE’s impact against a comparison group.
Large-scale genomic analysis reveals significant role of insertion sequences in antimicrobial resistance of
Acinetobacter baumannii
Authors: Xie Fei , Wang Lifeng , Li Song , Hu Long , Wen Yanhua , Li Xuming , Ye Kun , Duan Zhimei , Wang Qi , Guan Yuanlin , Zhang Ye , Shi Qiqi , Yang Jiyong , Xia Han , Xie Lixin
Published: February 2025

Acinetobacter baumannii
, a prominent nosocomial pathogen renowned for its extensive resistance to antimicrobial agents, poses a significant challenge in the accurate prediction of antimicrobial resistance (AMR) from genomic data. Despite thorough researches on the molecular mechanisms of AMR, gaps remain in our understanding of key contributors. This study utilized rule-based and three machine learning models to predict AMR phenotypes, aiming to decipher key genomic factors associated with AMR. Genomes and antibiotic resistance phenotypes from 1,012 public isolates were employed for model construction and training. To validate the models, a data set comprising 164 self-collected strains underwent next-generation sequencing, nanopore long-read sequencing, and antimicrobial susceptibility testing using the broth dilution method. It was found that the presence of antibiotic resistance genes (ARGs) alone was insufficient to accurately predict AMR phenotype for the majority of antibiotics (90%, 18 out of 20) in the public data set. Conversely, it was observed that combining ARGs with insertion sequence (IS) elements significantly enhanced predictive performance. The Random Forest model was found to outperform the support vector machine (SVM), logistic regression model, and rule-based method across all 20 antibiotics, with accuracies ranging from 83.80% to 97.70%. In the validation data set, even higher accuracies were achieved, ranging from 85.63% to 99.31%. Furthermore, conserved sequence patterns between IS elements and ARGs were validated using self-collected long-read sequencing data, substantially enhancing the accuracy of AMR prediction in
A. baumannii
. This study underscores the pivotal role of IS elements in AMR.

IMPORTANCE

The interplay between insertion sequences (ISs) and antibiotic resistance genes (ARGs) in
Acinetobacter baumannii
contributes to resistance against specific antibiotics. Conventionally, genetic variations and ARGs have been utilized for predicting resistance phenotypes, with the potential pivotal role of IS elements largely overlooked. Our study advances this approach by integrating both rule-based and machine learning models to predict AMR in
A. baumannii
. This significantly enhances the accuracy of AMR prediction, emphasizing the pivotal function of IS elements in antibiotic resistance. Notably, we uncover a series of conserved sequence patterns linking IS elements and ARGs, which outperform ARGs alone in phenotypic prediction. Our findings are crucial for bioinformatics strategies aimed at studying and tracking AMR, offering novel insights into combating the escalating AMR challenge.
Cross-laboratory replication of pseudomyxoma peritonei tumor microbiome reveals reproducible microbial signatures
Authors: Nieciecki Victoria F. , Blum Faith C. , Johnson Ryan C. , Testerman Traci L. , McAvoy Tom J. , King Mary Caitlin , Gushchin Vadim , Whitmire Jeannette M. , Frey Kenneth G. , Glang Lindsay , Peña-Gomez Dessiree , Bishop-Lilly Kimberly A. , Sardi Armando , Merrell D. Scott , Metcalf Jessica L.
Published: February 2025

Recent work has demonstrated that cancer-specific microbial communities often colonize tumor tissues. However, untangling low-biomass signals from environmental contamination makes this research technically challenging. We utilize pseudomyxoma peritonei (PMP), a cancer characterized by the spread of mucus-secreting cells throughout the peritoneal cavity, to develop a robust workflow for identifying reproducible tumor microbiomes. Typically originating from the rupture of an appendiceal tumor into the peritoneal cavity, metastasized tumors have been previously shown to harbor a core set of microbes. However, that work did not control for the potential contamination of these low microbial biomass samples. We expand upon these prior findings by characterizing the microbiome of 70 additional PMP tumors and six normal peritoneal control tissues along with appropriate laboratory controls. Additionally, DNA from a subset of 25 tissues was extracted and sequenced at an independent laboratory. We found evidence of reproducible microbial signatures between the replicates of six different PMP tumors that include a set of core taxa that may be introduced from surgical contamination, as well as patient-specific taxa that are also commonly implicated in colorectal cancer. In addition, preoperative chemotherapy treatment was found to reduce tumor microbiome diversity. Our findings demonstrate how independent sample replication can be a powerful approach to investigate low-biomass microbial communities associated with tumor tissues that will improve low microbial biomass research.

IMPORTANCE

Recent work has demonstrated that microbial communities colonize over 30 different types of tumor tissues. The origin of these communities and their possible involvement in carcinogenesis or cancer treatment outcomes remains an unclear, yet important area of research. A current major challenge in characterizing low-biomass, tumor-associated microbiomes is the introduction of environmental contamination during collection, handling, DNA extraction, PCR, and sequencing. Here, we provide a framework for replicating low-biomass tumor microbiome samples to help identify tumors with robust microbial signals and low background contamination. Using this replication approach, we show that pseudomyxoma peritonei (PMP) tumors host reproducible microbial communities, including organisms that have previously been associated with colorectal cancer. Incorporating sample replication into future tumor microbiome studies is a promising approach that will help identify robust signals and increase reproducibility in the field.
Adenovirus: a possible trigger for IgA vasculitis in children
Authors: Mannu Anand , Vasudevan Biju , Kashif Ahmed Waheed , Kumari Lalita
Published: February 2025

IgA vasculitis (IgAV), also called Henoch–Schönlein purpura (HSP), is an immune complex vasculitis characterised by IgA1‐dominant immune deposits affecting small vessels (predominantly capillaries, venules or arterioles). It often involves the skin and gastrointestinal tract, frequently causes arthritis and rarely causes vasculitis in the kidney indistinguishable from IgA nephropathy. It usually presents as a purpuric non-blanching rash mostly on the lower limbs, although it may extend to the upper limbs and the trunk, and more rarely to the face. Respiratory tract infection or a history of exposure to antigens from certain foods, insects, drugs or vaccines may trigger the pathogenesis of IgAV. Adenovirus mostly causes acute respiratory diseases and occasionally causes gastroenteritis. Literature on the adenovirus as a trigger or direct involvement in the onset of IgAV is scarce. We report a few cases where IgAV is associated with adenovirus infection, and more research is required to establish this association.
Concurrent diphtheria and COVID-19 infection in an unvaccinated child
Authors: Gundalli Shivanand , Poojari Srihari , Balasubramanian Aakash , Das Sayandeep
Published: February 2025

We report the case of a girl in her middle childhood who presented with progressive neck swelling, sore throat, dysphagia, low-grade fever and malaise, and with no prior vaccinations. Examination revealed a ‘bull neck’ appearance with pseudomembranous pharyngitis, which showed bleeding on membrane removal. The patient did not have any respiratory distress, but RT-PCR confirmed the concurrent coinfection of DPT with SARS-CoV-2. The laboratory investigations exhibited a leucocyte count of 17.2 × 10⁹/L and ALT raised at 113 U/L, indicative of systemic involvement. Imaging showed mild tonsillar calcifications with ground-glass opacities on the chest CT, which placed a CT severity score for cough severity of 13/25, indicating moderate COVID-19 pneumonia. Treatment was intravenous DPT antitoxin (100 000 units) and cefotaxime (1 g two times per day for 14 days). Symptomatic resolution occurred within 10 days, including clearing inflammatory markers and membranes. Recovery was complete and uncomplicated, with no sequelae after 3 months.
Exploring the value Australian community leaders see in a system dynamics model calibrated with local data: social norms and childhood obesity
Authors: Crielaard Loes , Brown Andrew D , Nicolaou Mary , Hayward Joshua , Stronks Karien , Allender Steven
Published: February 2025

Objectives

Systems approaches (SAs) seek to understand the dynamics behind system behaviour and formulate effective actions given these dynamics. In public health, SAs often rely on qualitative systems maps visualising factors and their interconnections, frequently developed through group model building. Quantitative system dynamics models (SDMs) can offer additional insights: SDMs can simulate how system behaviour would change if we were to make an adjustment to the system, in what-if scenarios. We explored what (added) value Australian community leaders involved in SAs see in an SDM for understanding a system and its behaviour.

Setting

The Whole of Systems Trial of Prevention Strategies for Childhood Obesity (WHOSTOPS), a community-level collaboration between researchers and community leaders in South-Western Victoria, Australia.

Design

We calibrated an existing small and high-level SDM with local data from the WHOSTOPS communities, so that the simulations pertained to their local context. The SDM was developed to simulate potential interventions addressing either social norms regarding body weight or individual weight-related behaviour. We presented the SDM to the community leaders via an interactive interface in an online workshop.

Participants

We calibrated the SDM using WHOSTOPS’ baseline measurement (2015), with an 80% participation rate among eligible children (1792/2516). 11 community leaders participated in the workshop.

Results

The community leaders’ first impression of the SDM was that it could be a valuable additional tool, particularly because of its ability to compare what-if scenarios resembling individual vs systems perspectives, intuitive presentation of simulation results, and use of local data.

Conclusions

Our preliminary exploration showed that the small and high-level SDM, using what-if scenarios reflecting interventions on different system levels, could contribute to the understanding and communication of (community-based) SAs.
Efficacy of psychotherapy versus pharmacotherapy, or their combination, in chronic depression: study protocol for a systematic review and network meta-analysis using aggregated and individual patient data
Authors: Schramm Elisabeth , Elsaesser Moritz , Müller Julia , Kwarteng Nana-Adjoa , Evrenoglou Theodoros , Cuijpers Pim , Orestis Efthimiou , Klein Daniel N , Keller Martin B , Furukawa Toshi A , Nikolakopoulou Adriani
Published: February 2025

Introduction

Chronic depression represents a common and highly disabling disorder. Several randomised controlled trials (RCTs) investigated the effectiveness of psychological, pharmacological and combined treatments for chronic depression. This is the first overarching systematic review and network meta-analysis (NMA) based on aggregated and individual patient data comparing the efficacy and acceptability of various treatment options for all subtypes of chronic depression. Furthermore, individual demographic and clinical characteristics that predict or moderate therapy outcomes will be investigated.

Methods and analysis

A systematic literature search of the Cochrane Library, MEDLINE via Ovid, PsycINFO, Web of Science and metapsy databases will be conducted from database inception without language restrictions to include all available samples from RCTs that investigated the efficacy of psychotherapy versus pharmacotherapy, or their combination in adult inpatients or outpatients with a primary diagnosis of chronic depression. Exclusively internet-based treatment studies will be excluded. The main outcome is depression severity measured on a continuous observer-rated scale for depression at 6 months post-treatment (range 3–12 months). Two reviewers will independently screen and select eligible studies based on the predefined inclusion and exclusion criteria. Risk of bias will be assessed using version 2 of the Cochrane risk-of-bias tool for randomised trials (RoB 2). Individual patient data (IPD) will be requested and incorporated in the network when provided, as it is the gold standard of evidence. For studies which do not provide IPD, aggregate data (AD) will be extracted and incorporated in lieu of IPD for the NMA, strengthening the evidence base and leveraging all existing evidence regardless of data availability restrictions. An NMA comparing psychotherapies and a network meta-regression estimating individualised treatment effects of psychotherapy will be implemented assuming a Bayesian framework. All models will be fitted in R with calls to JAGS. Empirical informative prior distributions will be used for model parameters where available, and non-informative priors will be used in cases where empirical priors are not available.

Ethics and dissemination

This IPD-NMA requires no ethical approval. All results will be disseminated as peer-reviewed publication in a leading journal in this field and presented at (inter)national scientific conferences.

PROSPERO registration number

CRD42024526755.
Contemporary European practice in left atrial appendage closure: results from a survey focusing on planning, techniques and post-implantation management
Authors: Garot Philippe , Nielsen-Kudsk Jens-Erik , Freixa Xavier , Berti Sergio , Wunderlich Nina , Cruz-Gonzalez Ignacio , Räber Lorenz , Aminian Adel , De Backer Ole
Published: February 2025

Objectives

The purpose of this European survey was to describe current preprocedural planning, procedure techniques and post-implantation management of left atrial appendage closure (LAAC).

Design

Prospective survey regarding current practice for LAAC between March and August 2023.

Setting

357 participating European LAAC centres in 14 countries.

Results

In 2022, the participating centres performed a total number of 9447 LAAC procedures, with a mean of 26 LAAC cases per centre (median 20; IQR 10–35). Preprocedure planning was performed with transoesophageal echocardiography (TOE) in 63% of centres, cardiac CT in 16%, or both in 21%. LAAC procedures were performed under general anaesthesia (59%), conscious sedation (36%) or with local anaesthesia only (5%). Device implantation was guided by conventional TOE (94%), intracardiac echocardiography (6%), miniaturised TOE probes (4%) or CT/fluoroscopy fusion (2%). The standard post-procedural antithrombotic regimen was dual antiplatelet therapy (73%), followed by single antiplatelet therapy (18%), conventional dose direct oral anticoagulant (DOAC) (7%) or half dose DOAC (1%), and no antithrombotic treatment (1%). There was a large heterogeneity between regions in terms of procedure volumes, hospital organisation, preprocedural planning, as well as procedural techniques and post-procedure management.

Conclusions

The present survey indicates that LAAC has become a widespread procedure in Europe. The findings highlight considerable heterogeneity among European countries in terms of preprocedural planning, procedural techniques including guidance and the post-procedural antithrombotic regimen. There is a need to evaluate the outcomes of different practices.
Telephonic verbal autopsies among adults in South Africa: a feasibility and acceptability pilot study
Authors: Sant Fruchtman Carmen , Neethling Ian , Bradshaw Debbie , Cobos Muñoz Daniel , Morof Diane , Ngobeni Sizzy , Ngwenya Xolani , Edwards Anita , Glass Tracy , Kahn Kathleen , Herbst Kobus , Morden Erna , Zinyakatira Nesbert , Groenewald Pamela
Published: February 2025

Objective

This pilot study explores the feasibility and acceptability of using telephonic verbal autopsies (teleVAs) in South Africa to collect information on causes of death.

Design

Quantitative and qualitative data collection methods were used to evaluate the feasibility and acceptability of these telephonic interviews.

Setting

The teleVA pilot was conducted in South Africa’s Western Cape province. The qualitative component also included two rural South African Population Research Infrastructure Network nodes (Africa Health Research Institute in KwaZulu-Natal and Agincourt in Mpumalanga), which had transitioned to teleVAs during COVID-19, allowing exploration of teleVA’s feasibility in both urban and rural settings.

Participants

We recruited 229 respondents to participate in a pilot teleVA. After each VA, VA interviewers filled in a survey to assess their perceptions and discern if they experienced any technical challenges. We also conducted 18 in-depth interviews with both interviewers (n=6) and respondents (n=12) to explore their views on the acceptability of the teleVA. We conducted a thematic analysis of these interviews.

Interventions

VA was piloted over the phone, instead of face-to-face.

Primary and secondary outcome measures

Primary outcomes focused on the feasibility and acceptability of phone VAs among both interviewers and respondents. Secondary outcomes evaluated the quality of teleVAs.

Results

Participants expressed willingness to participate in teleVAs, considering them valuable for public health planning and decision-making. The feasibility of collecting next-of-kin information proved challenging, with incomplete or incorrect contact details posing future logistic issues. Only one question out of 76, showed a statistically significant difference in the proportions of non-informative teleVA compared with face-to-face VA.

Conclusions

The study offers valuable insights into using teleVAs to gather cause of death information in resource-limited settings. It highlights the feasibility and acceptability of teleVAs while emphasising the need for comprehensive planning, integration with the civil registration and vital statistics system and community participation enhancement.
Implementation of decarbonisation actions in general practice: a systematic review and narrative synthesis
Authors: Nunes Ana Raquel , Karaba Florence , Geddes Olivia , Bickerton Abi , Atherton Helen , Dahlmann Frederik , Eccles Abi , Gregg Michael , Spencer Rachel , Twohig Helen , Dale Jeremy
Published: February 2025

Objectives

To summarise and synthesise existing literature on the implementation of decarbonisation actions in general practice, to outline the actions being implemented, factors influencing decarbonisation, identify evidence gaps and questions for future research.

Design

A systematic review and narrative synthesis.

Data sources

MEDLINE, Embase, CINAHL, Web of Science and ProQuest (grey literature) were searched for literature published up to 29 March 2024.

Eligibility criteria for selecting studies

Studies of any design investigating the implementation of decarbonisation actions in general practice.

Data extraction and synthesis

Two reviewers extracted data and conducted quality assessments using a mixed methods appraisal tool. Narrative synthesis was used to analyse findings.

Results

Fifteen studies were included. Studies were primarily from the UK (n=5), followed by Australia (n=3), USA (n=2), Germany (n=2) and one each from France, Switzerland and Israel. Study designs were qualitative (n=7), quantitative (n=7) and one mixed methods. Participants included healthcare staff (n=7), patients (n=5), health stakeholders (n=2) and the general public (n=1). There was evidence of general practices adopting decarbonisation actions such as resource reuse, improved waste management, energy-efficient systems and preventive care to reduce overmedication, with strong leadership and institutional support being crucial for their success. However, barriers such as high costs, resource constraints and limited awareness among clinicians and patients highlighted the need for enhanced communication, education and the structured promotion of initiatives to improve patient and community engagement.

Conclusions

There is limited evidence on the implementation of decarbonisation actions in general practice. A range of factors may impact on the extent to which implementation occurs. Addressing these will be crucial for effectively promoting and scaling decarbonisation actions in general practice. Future research should focus on understanding the role of institutional context, evaluating the real-world impact of interventions on greenhouse gas emissions and exploring patient and community involvement.

PROSPERO registration number

CRD42023470889.
School participation, supports and barriers of children with and without attention deficit hyperactivity disorder
Authors: Kara Koray , Kaya Kara Ozgun , Kose Barkin , Doğan Mert , Cetin Sebahat Yaprak , Sahin Sedef , Anaby Dana
Published: February 2025

Objectives

To investigate the differences in participation patterns, environmental barriers and supports across specific activities typically done at school between children with attention deficit hyperactivity disorder (ADHD) and without ADHD.

Design

Prospective cross-sectional study.

Setting

The children and adolescents with ADHD were selected from those routinely referred to the Health Sciences University Research and Training Hospital’s child and adolescent psychiatry department, which is a reference centre for the region.

Participants

A total of 365 children (nchildren with ADHD=175, nchildren without ADHD=190, mean age 11.66 years, SD 2.96 years) and their primary caregivers were included in the study.

Primary outcome measures

Participation and Environment Measure for Children and Youth was used to evaluate children.

Results

The mean frequency of participation in five different school activities was significantly lower in children with ADHD than in children without ADHD, with moderate to large effect sizes. Children with ADHD were less likely to be involved in any activity type than children without ADHD, with moderate to large effect sizes. The characteristics of the school environment typically made it more challenging for children with ADHD to participate than for children without ADHD, with moderate effect sizes.

Conclusions

Children with ADHD have challenges in classroom activities and with socialising with peers outside class, cognitive demands, sensorial qualities and safety. Relationships with friends, cultural acceptance and support could improve the school participation of children with ADHD.
Investigating the timing of catheter removal after traumatic bladder injury: a single-institution 12-year experience
Authors: Wilson Danielle J , Melin Isaac , Shah Nayan , O’Connor R Corey , Carver Thomas
Published: February 2025

Introduction

Traumatic bladder injuries, although rare, may result in significant patient morbidity. Operative management is recommended for intraperitoneal (IP), mixed, and select extraperitoneal (EP) injuries. Current guidelines lack recommendations on catheter duration following operative repair and suggest follow-up cystography may be unnecessary for simple, repaired injuries. This has led to practice variation in postoperative management at our institution. We hypothesized that the trauma surgery service would have a shorter catheter duration and obtain fewer follow-up cystograms compared with the urology service, without increased complications.

Methods

A retrospective review was conducted at a single level 1 trauma center between January 2010 and December 2022. All patients with traumatic bladder injuries during this period were included from the trauma registry. Those who were <18 years of age, lacked a full-thickness injury, died within 7 days of presentation, had a concomitant urethral injury or complex injury, did not undergo surgical repair, were lost to follow-up, underwent surgical management elsewhere, or had an iatrogenic injury were excluded. Data on patient demographics, management, and complications were recorded. Injuries were classified as complex when involving the trigone, ureters, or bladder neck, or were described as complex in the operative report.

Results

Of the 178 patients identified, 86 met the inclusion criteria. IP injuries were most common (43%), followed by EP (31%), and mixed (26%). Patient outcomes following the repair of simple injuries were similar regardless of the team performing the repair, although differences in catheter duration (11 days vs 17 days, p=0.006) and use of postoperative cystography (77% vs 100%, p<0.001) were observed (trauma vs urology, respectively).

Conclusion

Variations in postoperative management regarding catheter drainage and follow-up imaging for simple bladder repairs resulted in similar leak and complication rates. Our findings present an opportunity to reduce the duration of postoperative catheter drainage and cystography use in simple repairs.

Level of evidence

IV.
Small science and big science entanglement: the advent of a new era of synchrotron light sources for chemical research-chemistry at the edge
Authors: Sham Tsun-Kong
Published: February 2025

Large facilities (big science) that provide advanced capabilities not available in researchers’ laboratories in universities and institutions have become increasingly indipensible to advance research and innovation. A synchrotron light source is one of such facilities crucial to chemical research. Herein, the entanglement of small science and big science in general is described with emphasis placed on the interplay of research in individuals’ laboratory (small science), and advanced tools at the synchrotron light source (big science) from the perspective of matching scientific problems with techniques at the synchrotron for solution, and the interaction of users with the staff and management of the facility (human activity). The discussion is focused on one phenomenon, X-ray absorption and related techniques which are element specific and ideally suited for probing structure and bonding of materials and their functionality. I will describe why X-ray Absorption Spectroscopy (XAS) is literally “Chemistry at the Edge.” The sociology of synchrotron research and its impact on science will also be presented. The evolution of synchrotron science and technology globally will be noted, especially the history of R&D of synchrotron research in Canada and the bright prospect for chemical research using future synchrotron light sources.
Bayesian Species Recognition and Abundance Estimation: Unravelling the Mysteries of Salmonid Migration in the Teno River
Authors: Räty Antti , Pulkkinen Henni , Erkinaro Jaakko , Orell Panu , Falkegård Morten , Mäntyniemi Samu
Published: February 2025

In Teno River, annual sonar monitoring is used to estimate the abundance of three salmonid species: Atlantic salmon, pink salmon and sea trout. However, the size distribution of these species is partially overlapping making species recognition impossible from plain sonar data. A Bayesian model was developed to tackle this problem and to estimate abundance and migration timing for these three species. The model integrates multiple sources of data including catch, video count, daily average school sizes and expert knowledge. Given the limited catch and video statistics for 2021, the use of school size data and expert knowledge on migration intensity enhanced the estimation when other data sources were unavailable. The model estimated a median of 11.8 thousand Atlantic salmon, 6.6 thousand sea trout and 52.0 thousand pink salmon migrating into the river during 2021. These findings offer a more accurate representation of species distribution, support future conservation and management efforts, and provide a modelling-based solution for distinguishing similarly sized species from sonar counting data.
Urban Climate Resilient Development: Analysis of the Potential to Build Low-Carbon-Resilient City in China
Authors: ZHENG Yan , YUAN Yuan , TIAN Jianguo , ZHUANG Guiyang
Published: February 2025

The Sixth Assessment Report (AR6) of the United Nations Intergovernmental Panel on Climate Change (IPCC) highlights that Climate Resilient Development (CRD) can support sustainable development for all by reducing greenhouse gas emissions and offering adaptation options, while also contributing to innovation and transformation in urban areas. Based on China’s national pilot projects for low-carbon cities, sponge cities, and climate-resilient cities, this paper analyzes the potential and feasibility of Chinese cities in exploring the construction of “low-carbon-resilient cities”. First, referring to the relevant studies, the “Climate-Resilient Index” and “Low-Carbon Development Index” are constructed for 178 cities at or above the prefecture level in China. Second, by comparing the climate resilience index and the level of low-carbon development, this paper categorizes 178 Chinese cities into four groups with the potential to the co-benefits of synergy actions in mitigation and adaptation. Third, this paper showcases the potential and progress from some pilot model cities of the “climate-adaptive cities” in achieving the goal of “climate resilient development”. This paper will help advance China’s synergistic implementation of climate adaptation and mitigation policies, and provide examples and insights for cities in other developing countries to promote climate resilient development.
Is concrete gunning in volcanic tunnelling effective in reducing the presence of radon gas? Experience in road tunnels, the Canary Islands (Spain)
Authors: Santamarta Juan C. , Cruz-Pérez Noelia , Lario-Bascones Rafael J. , Anzulovć Ana , Rodríguez-Martín Jesica , Rodríguez-Alcántara Joselin S. , Hernández-Gutiérrez Luis E.
Published: February 2025

The Canary Islands are a radon-prone volcanic territory in Spain. The radon gas concentrations in the enclosed areas must be considered in terms of human health. Measurements of radon in the selected tunnel structures of Gran Canaria and Tenerife are taken to evaluate radon gas activity and possible harmful effects on workers if the advised radon concentrations are exceeded. Although there is a tendency toward high radon values on objects that are in contact with the ground, the obtained results show radon concentrations under the European regulatory limit concentrations (300 Bq/m
3
). Average radon values measured with both passive and active detectors are less than 55 Bq/m
3
. Properties of the intermediate media that separates the ground from the tunnel, which in this case is concrete, seems to be a deciding factor for the observed low radon concentrations.
Artificial Intelligence as Catalyst for Biodiversity Understanding
Authors: Santos Charles Morphy D. , Gois João Paulo
Published: February 2025

Blending traditional methods and technological advancements.
Deep Reinforcement Learning for Demand Driven Services in Logistics and Transportation Systems: A Survey
Authors: Zong Zefang , Wang Jingwei , Feng Tao , Xia Tong , Li Yong
Published: February 2025

Recent technology development brings the boom of numerous new Demand-Driven Services (DDS) into urban lives, including ridesharing, on-demand delivery, express systems and warehousing. In DDS, a service loop is an elemental structure, including its service worker, the service providers and corresponding service targets. The service workers should transport either people or parcels from the providers to the target locations. Various planning tasks within DDS can thus be classified into two individual stages: 1) Dispatching, which is to form service loops from demand/supply distributions, and 2) Routing, which is to decide specific serving orders within the constructed loops. Generating high-quality strategies in both stages is important to develop DDS but faces several challenges. Meanwhile, deep reinforcement learning (DRL) has been developed rapidly in recent years. It is a powerful tool to solve these problems since DRL can learn a parametric model without relying on too many problem-based assumptions and optimize long-term effects by learning sequential decisions. In this survey, we first define DDS, then highlight common applications and important decision/control problems within. For each problem, we comprehensively introduce the existing DRL solutions. We also introduce open simulation environments for development and evaluation of DDS applications. Finally, we analyze remaining challenges and discuss further research opportunities in DRL solutions for DDS.
Toward Understanding FPGA Synthesis Tool Bugs
Authors: Zhang Yi , Jiang He , Guo Shikai , Li Xiaochen , Liu Hui , Shi Chongyang
Published: February 2025

FPGA (Field Programmable Gate Array) synthesis tools are crucial for hardware development and AI acceleration, and their bugs could compromise hardware reliability and risk downstream applications. However, it remains unknown in understanding the characteristics of these bugs.
What are the root causes that trigger bugs in FPGA synthesis tools?
What are the characteristics of these bugs? What are the challenges in detecting and addressing them?
This paper takes the first step towards answering these questions by conducting a comprehensive study of FPGA synthesis tool bugs. We analyze 551 confirmed bugs in both commercial and open source FPGA synthesis tools, i.e., Vivado, Quartus Prime, and Yosys, covering root causes, symptoms, bug-prone components, fix characteristics, and achieve 17 valuable findings. We find that, on average, around 46.2% of bugs result from HDL (Hardware Description Language) standard noncompliance across the three tools. However, it is hard for current formal validations to fully test HDL standards compliance. Additionally, on average over 25.8% bugs show domain-specific optimization traits due to inappropriate optimization and mapping. Meanwhile, beyond 28% of bugs trigger unexpected behavior without clear signs, making the formulation of effective test oracles challenging. These findings help addressing FPGA synthesis tool bugs and guide further research.
TransCL: An Automatic CUDA-to-OpenCL Programs Transformation Framework
Authors: Shi Changqing , Sun Yufei , Chen Rui , Wang Jiahao , Guo Qiang , Gong Chunye , Sui Yicheng , Jin Yutong , Zhang Yuzhi
Published: February 2025

With the rising demand for computational power and the increasing variety of computational scenarios, considerable interest has emerged in transforming existing CUDA programs into more general-purpose OpenCL programs, enabling them to run across diverse hardware platforms. However, manual methods, typically designed for specific applications, lack flexibility. Current automated conversion techniques also face considerable challenges, particularly in handling diverse programming interfaces, memory management, etc., and are insufficient for converting large-scale, complex CUDA projects. In this paper, we propose a novel source-to-source program transformation framework, TransCL, which automates the conversion of CUDA programs in four key aspects: source code, execution model, programming model and memory model. To achieve this, we abstract a set of conversion rules aligned with the latest CUDA standards, develop a transcoder, implement an OpenCL-compatible programming interface library, and establish a memory mapping mechanism between CUDA and OpenCL. Experiments demonstrate that TransCL provides a high level of automation in converting CUDA-based applications and is effective in handling large, complex projects such as TensorFlow. Moreover, the converted AI framework successfully conducted model training for the first time. The experiment also validates that the converted program can execute correctly across multiple platforms and demonstrate good performance.
The Evolution of Systems Biology and Systems Medicine: From Mechanistic Models to Uncertainty Quantification
Authors: Qiao Lingxia , Khalilimeybodi Ali , Linden-Santangeli Nathaniel J. , Rangamani Padmini
Published: February 2025

Understanding interaction mechanisms within cells, tissues, and organisms is crucial for driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating such biological systems. Building on experiments, mechanistic models are widely used to describe small-scale intracellular networks. The development of sequencing techniques and computational tools has recently enabled multiscale models. Combining such larger scale network modeling with mechanistic modeling provides us with an opportunity to reveal previously unknown disease mechanisms and pharmacological interventions. Here, we review systems biology models from mechanistic models to multiscale models that integrate multiple layers of cellular networks and discuss how they can be used to shed light on disease states and even wellness-related states. Additionally, we introduce several methods that increase the certainty and accuracy of model predictions. Thus, combining mechanistic models with emerging mathematical and computational techniques can provide us with increasingly powerful tools to understand disease states and inspire drug discoveries.
Soft Modes as a Predictive Framework for Low-Dimensional Biological Systems Across Scales
Authors: Russo Christopher Joel , Husain Kabir , Murugan Arvind
Published: February 2025

All biological systems are subject to perturbations arising from thermal fluctuations, external environments, or mutations. Yet, while biological systems consist of thousands of interacting components, recent high-throughput experiments have shown that their response to perturbations is surprisingly low dimensional: confined to only a few stereotyped changes out of the many possible. In this review, we explore a unifying dynamical systems framework—soft modes—to explain and analyze low dimensionality in biology, from molecules to ecosystems. We argue that this soft mode framework makes nontrivial predictions that generalize classic ideas from developmental biology to disparate systems, namely phenocopying, dual buffering, and global epistasis. While some of these predictions have been borne out in experiments, we discuss how soft modes allow for a surprisingly far-reaching and unifying framework in which to analyze data from protein biophysics to microbial ecology.
The Rising Incidence of Food Allergies and Infant Food Allergies
Authors: Jaiswal Yogini S. , Williams Leonard L.
Published: February 2025

Infant food allergies have become a continually rising global health issue. There is a lack of global standardized recommendations on measures for prevention and treatment of infant food allergies because of the variations in ethnic, social, educational, and healthcare practices that affect the outcomes of research studies. Food allergies can cause mild to severe reactions and can affect social and emotional aspects of life up to the adolescent stage and are sometimes never outgrown. Maternal factors such as in utero supply of antibodies, dietary diversity, genetics, food allergen consumption during pregnancy, gut microbiota, and breastfeeding characteristics are the cornerstones of the development of an infant's immune system. In this review, we discuss how prenatal and postnatal factors affect the gut microbiota and development of an infant's immune system, and the current therapies available. The importance of food processing and education of stakeholders in the care of infants with food allergies is also discussed.
Anesthetics as Treatments for Depression: Clinical Insights and Underlying Mechanisms
Authors: Breault Macauley Smith , Orguc Sirma , Kwon Ohyoon , Kang Gloria H. , Tseng Bryan , Schreier David R. , Brown Emery N.
Published: February 2025

Major depressive disorder and treatment-resistant depression are significant worldwide health problems that need new therapies. The success of the anesthetic ketamine as an antidepressant is well known. It is less widely known that several other anesthetic agents have also shown antidepressant effects. These include nitrous oxide, propofol, isoflurane, sevoflurane, dexmedetomidine, and xenon. We review clinical and basic science investigations that have studied the therapeutic value of these anesthetics for treating depression. We propose potential neurophysiological mechanisms underlying the antidepressant effects of anesthetics by combining our understanding of how anesthetics modulate brain dynamics to alter arousal states, current theories of depression pathophysiology, and findings from other depression treatment modalities.
Organization and Dynamics of Chromosomes
Authors: Thirumalai D. , Shi Guang , Shin Sucheol , Hyeon Changbong
Published: February 2025

How long thread-like eukaryotic chromosomes fit tidily in the small volume of the nucleus without significant entanglement is just beginning to be understood, thanks to major advances in experimental techniques. Several polymer models, which reproduce contact maps that measure the probabilities that two loci are in spatial contact, have predicted the 3D structures of interphase chromosomes. Data-driven approaches, using contact maps as input, predict that mitotic helical chromosomes are characterized by a switch in handedness, referred to as perversion. By using experimentally derived effective interactions between chromatin loci in simulations, structures of conventional and inverted nuclei have been accurately predicted. Polymer theory and simulations show that the dynamics of individual loci in chromatin exhibit subdiffusive behavior but the diffusion exponents are broadly distributed, which accords well with experiments. Although coarse-grained models are successful, many challenging problems remain, which require the creation of new experimental and computational tools to understand genome biology.