bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dissecting AlphaFold2’s capabilities with limited sequence information
Authors: Gut Jannik Adrian , Lemmin Thomas 
Published: November 2024

Abstract

Summary
Protein structure prediction aims to infer a protein’s three-dimensional (3D) structure from its amino acid sequence. Protein structure is pivotal for elucidating protein functions, interactions, and driving biotechnological innovation. The deep learning model AlphaFold2, has revolutionized this field by leveraging phylogenetic information from multiple sequence alignments (MSAs) to achieve remarkable accuracy in protein structure prediction. However, a key question remains: how well does AlphaFold2 understand protein structures? This study investigates AlphaFold2’s capabilities when relying primarily on high-quality template structures, without the additional information provided by MSAs. By designing experiments that probe local and global structural understanding, we aimed to dissect its dependence on specific features and its ability to handle missing information. Our findings revealed AlphaFold2’s reliance on sterically valid Cβ for correctly interpreting structural templates. Additionally, we observed its remarkable ability to recover 3D structures from certain perturbations and the negligible impact of the previous structure in recycling. Collectively, these results support the hypothesis that AlphaFold2 has learned an accurate biophysical energy function. However, this function seems most effective for local interactions. Our work advances understanding of how deep learning models predict protein structures and provides guidance for researchers aiming to overcome limitations in these models.

Availability and implementation
Data and implementation are available at https://github.com/ibmm-unibe-ch/template-analysis.
Zoonotic and other veterinary chlamydiae – an update, the role of the plasmid and plasmid-mediated transformation
Authors: Marti Hanna , Shima Kensuke , Boutin Sebastien , Rupp Jan , Clarke Ian N , Laroucau Karine , Borel Nicole 
Published: November 2024

Abstract
The obligate intracellular bacterial genus Chlamydia harbours species with zoonotic potential, particularly C. psittaci, causative agent of psittacosis, and C. abortus, which may lead to miscarriage in pregnant women. The impact of other bird chlamydiae such as C. avium, C. gallinaceae, and C. buteonis, or reptilian species such as C. crocodili, amongst others, on human health is unclear. The chlamydial native plasmid, a suspected virulence factor, is present in all currently described 14 Chlamydia species except for some plasmid-free strains. The plasmid is also the primary tool to study chlamydial genetics, a still developing field that has mostly focused on C. trachomatis. Only recently, genetic transformation of C. felis, C. pecorum, C. pneumoniae, C. psittaci, and C. suis has succeeded, but existing methods have yet to be refined. In this review article, we will provide an update on the recent developments concerning the zoonotic potential of chlamydiae. Furthermore, we present an overview about the current state of knowledge regarding the chlamydial plasmid in terms of prevalence and significance as a virulence factor. Finally, we give insights into the progress of developing genetic tools for chlamydial species other than C. trachomatis with a special focus on zoonotic and veterinary chlamydiae.
Long-term effects of group selection, single-tree selection, and clearcutting on individual-tree and stand volume growth in northern hardwoods of the Great Lakes region
Authors: Halpin Corey R , Lorimer Craig G , Burton Julia I , Webster Christopher R , Palik Brian J 
Published: November 2024

Abstract
Group selection and small patch cutting are widely viewed as more aesthetically acceptable alternatives to clearcutting for regenerating tree species of low shade tolerance, and they may enhance resilience in the face of climate change. However, little evidence is available on how production rates compare with those of other silvicultural systems. We used CANOPY, a spatially explicit, individual-tree model, to investigate the link between individual-tree growth and net volume growth at the stand level under alternative silvicultural systems in northern hardwood forests. The model predicted peak growing space efficiency (volume increment per unit of crown projection area) in the pole or mature stage under all silvicultural systems and a decline for larger and older trees. Trees in uneven-aged stands were generally less efficient, slower growing at a given size, and harvested at more advanced ages compared to even-aged stands. Nevertheless, there was little predicted difference in net growth between single-tree selection, group selection, and thinned even-aged stands. However, stands managed by small patch cutting (800–2000-m2 openings) without thinning, as well as unthinned even-aged stands, had substantially lower net growth and higher mortality rates. The paradox that lower efficiency of trees in uneven-aged stands did not result in lower net growth at the stand level was not explainable by improved efficiency of mature trees due to adjacent canopy gaps or by low harvest volumes of smaller, less efficient trees. Rather, production in even-aged stands was lower than expected due to the slow recovery of merchantable growing stock following clearcutting, which negated the higher productivity of even-aged stands during the mature phase. A secondary factor was the asymptotic trend of production rates beyond an opening size of 200 m2, so that larger openings under group selection or clearcutting did not stimulate higher production levels.
TIdeS: A Comprehensive Framework for Accurate Open Reading Frame Identification and Classification in Eukaryotic Transcriptomes
Authors: Maurer-Alcalá Xyrus X , Kim Eunsoo 
Published: November 2024

Abstract
Studying fundamental aspects of eukaryotic biology through genetic information can face numerous challenges, including contamination and intricate biotic interactions, which are particularly pronounced when working with uncultured eukaryotes. However, existing tools for predicting open reading frames (ORFs) from transcriptomes are limited in these scenarios. Here we introduce Transcript Identification and Selection (TIdeS), a framework designed to address these nontrivial challenges associated with current ‘omics approaches. Using transcriptomes from 32 taxa, representing the breadth of eukaryotic diversity, TIdeS outperforms most conventional ORF-prediction methods (i.e. TransDecoder), identifying a greater proportion of complete and in-frame ORFs. Additionally, TIdeS accurately classifies ORFs using minimal input data, even in the presence of “heavy contamination”. This built-in flexibility extends to previously unexplored biological interactions, offering a robust single-stop solution for precise ORF predictions and subsequent decontamination. Beyond applications in phylogenomic-based studies, TIdeS provides a robust means to explore biotic interactions in eukaryotes (e.g. host–symbiont, prey–predator) and for reproducible dataset curation from transcriptomes and genomes.
Comparative evaluation of eravacycline susceptibility testing methods in 587 clinical carbapenem-resistant Acinetobacter baumannii isolates: broth microdilution, MIC test strip and disc diffusion
Authors: Liu Qihui , Li Shirong , Wang Xuan , Lin Yijing , Jiang Haoqin , Li Ning 
Published: November 2024

Abstract

Objectives
The study aimed to evaluate the accuracy of different methods for determining carbapenem-resistant Acinetobacter baumannii (CRAB) susceptibility to eravacycline.

Methods
We collected 587 CRAB strains from Huashan Hospital affiliated to Fudan University between 2019 and 2023. The broth microdilution (BMD) method served as the reference standard. The susceptibility results were evaluated using the clinical breakpoints established by the Chinese Committee on Antimicrobial Susceptibility Testing (ChinaCAST) (susceptible MIC,  ≤ 1 mg/L; inhibition zone diameter,  ≥ 15 mm). The study compared the reliability of the MIC test strip (MTS) and disc diffusion (DD) methods in detecting CRAB susceptibility to eravacycline.

Results
The MICs required to inhibit 50% and 90% of CRAB growth were as follows: BMD, 0.5/1 mg/L; MTS, 0.38/0.75 mg/L. According to the ChinaCAST breakpoints, the BMD method demonstrated a 98.13% (576/587) susceptibility rate, whereas the MTS and DD methods showed susceptibility rates of 97.96% (575/587) and 97.61% (573/587), respectively. The essential agreement rate between the MTS and BMD methods was 94.55%. Categorical agreement (CA) rates for the MTS and DD methods were 99.83% and 99.49%, respectively. The major error (ME) rate for MTS was 0.17%, with no very major errors (VMEs) observed. For the DD method, the ME rate was 0.51%, also with no VMEs.

Conclusion
The MTS and DD methods demonstrated strong consistency with the BMD reference method, with CA, ME and VME rates meeting methodological evaluation criteria. Both MTS and DD methods are reliable alternatives for assessing the antibacterial activity of eravacycline in clinical microbiology laboratories.
Expanding the ICC’s Jurisdiction Over the Crime of Aggression
Authors: McDougall Carrie 
Published: November 2024

Abstract
The Global Institute for the Prevention of Aggression (GIPA) recently prepared model amendments to the International Criminal Court (ICC) Statute, aimed at aligning the ICC’s jurisdiction over the crime of aggression with its jurisdiction over genocide, crimes against humanity and war crimes. GIPA also prepared a draft resolution under which the recommended amendments could be adopted, and a brief explanatory memorandum to assist States Parties in their consideration of these texts. In consultation with other members of GIPA’s Council of Advisers, I was the primary author of these documents. This article details the reasons for the shape of the recommended amendments and key resolution provisions. Through an explanation of the interpretive debate surrounding the provision governing the exercise of the ICC’s jurisdiction over crimes of aggression involving States Parties, the article demonstrates that the simple deletion of offending limitations on the ICC’s jurisdiction, or parts thereof, would be unwise, because such an approach could inadvertently result in a further narrowing of the Court’s jurisdiction. The article also explains the technical issues and policy imperatives that lie behind the choice of the provision to govern the amendments’ entry into force, and why it is prudent to set out the effect of the proposed amendment for both states that have already ratified the 2010 aggression amendments, and states yet to ratify those amendments, or the ICC Statute.
Assessment of antibiotic utilization and prescribing quality in a teaching hospital in Iraq
Authors: Abdullah Marwan I , Essa Narmin S , Aladul Mohammed I , Taki Abdulrahman M , Taki Ismael M 
Published: November 2024

Abstract

Objectives
This study aimed to assess the prevalence of antibiotic use, quantify antibiotic consumption, and evaluate the quality of prescribing.

Methods
This was a point prevalence study conducted at a teaching hospital in Mosul, Iraq. The antibiotics prescribing data were retrieved from the medical records of admitted patients between January and February 2023. The trends of utilization of prescribed antibiotics were expressed in defined daily doses per 100 bed days (DDD/100 BD).

Key findings
The records of 546 patients were checked. Antibiotics were prescribed for 88.46% of admitted patients. The main mode of antibiotic therapy in gynecology and obstetrics (97.59%) and surgical (86.84%) wards was surgical prophylaxis and 54% of these patients received antibiotics for more than 24 hours. The overall antibiotic consumption in the hospital was 135.09 DDD/100 BD. The highest consumption was in the gynecology and obstetrics ward (242.17 DDD/100 BD). Ceftriaxone (73.65 DDD/100 BD) and metronidazole (41.76 DDD/100 BD) were the most frequently prescribed antibiotics for the admitted patients. The internal medicine ward had the highest percentage (94.22%) of Watch-class antibiotic use, while the gynecology and obstetrics ward had the highest percentage (64.53%) of Access-class antibiotic use.

Conclusions
This study highlighted the high prevalence of antibiotic use, particularly ceftriaxone. Furthermore, the study highlighted the lack of adherence to both national and international guidelines. Urgent action should be undertaken to implement antimicrobial stewardship programs.
Evidence-based approach for the generation of a multivariate logistic regression model that predicts instrument failure
Authors: Cleveland Stephan L , Carman Carol A , Vyas Niti , Salazar Jose H , Rojo Juan U 
Published: November 2024

Abstract

Objective
Identification of instrument failure (IF) represents a point to improve the quality of services provided by medical laboratories. Here, a logistic regression model was created to define the relationship between instrument downtime and laboratory quality management systems.

Methods
Interval-level quality control (QC) and categorical quality assurance data from 3 identical chemistry analyzers was utilized to generate a logistic regression model able to predict IF. A case-control approach and the forward stepwise likelihood-ratio method was used to develop the logistic regression model. The model was tested using a case-control dataset and again using the complete sample.

Results
A total of 650 downtime events were identified. A total of 22,880 QC data points, 187 calibrations, 24 proficiency testing events, and 107 maintenance records were analyzed. The regression model was able to correctly predict 59.2% of no instrument downtime events and 69.2% of instrument downtime events using the case-control data. Using the entire data set, the sensitivity of the model was 69.2% and the specificity was 58.2%.

Conclusion
A logistic regression model can predict instrument downtime nearly 70% of the time. This study acts as a proof of concept using a limited data set collected by the chemistry laboratory.
Isolation of Lactiplantibacillus plantarum for treatment of Salmonella infection in mice
Authors: Zhang Silu , Liu Tian , Zhou Xiaoli , Wang Jun , Zhang Tengxun , Xiao Guoxun , Huang Song , Rao Chitong , Teng Xin 
Published: November 2024

Abstract
Salmonella infections, often acquired through contaminated food or water, pose significant health risks, particularly amid rising antibiotic resistance and the adverse effects of conventional treatments on gut microbiota. This study isolated the probiotic Lactiplantibacillus plantarum GOLDGUT-LP618 from healthy human fecal samples, demonstrating its potential against Salmonella enterica. Lactiplantibacillus plantarum LP618 produced high levels of short-chain fatty acids (SCFAs) and exhibited robust inhibition of Salmonella in vitro. The strain showed resilience in gastric and bile environments, effectively curbing Salmonella growth. Post-infection treatment with L. plantarum LP618 significantly alleviated diarrhea, improved body weight, and moderated inflammatory responses. Histological analysis indicated restoration of intestinal structure, suggesting protection against mucosal damage. These results highlight L. plantarum LP618 as a promising probiotic candidate, offering a safe and effective alternative to antibiotics for managing Salmonella infections and promoting recovery in affected individuals.
Lower Extremity Musculoskeletal Injuries in United States Active Duty Service Members: Prevalence/Incidence, Health Care Utilization, and Cost Analysis Spanning Fiscal Years 2016–2021
Authors: Isaacson Brad , Hando Ben , Pav Veronika , Wagner Linzie , Colahan Courtney , Pasquina Paul , Yuan Xiaoning 
Published: November 2024

ABSTRACT

Introduction
Lower Extremity musculoskeletal injuries (LE MSKIs) represent a significant portion of overuse injuries in active duty service members (ADSMs). However, variations in study methods and research gaps related to LE MSKIs have prevented Department of Defense (DoD) leaders from assessing the burden of these conditions. The purpose of this study was to report the incidence, prevalence, and types of LE MSKIs sustained by ADSMs across four branches of service and describe associated health care utilization and private sector costs.

Materials and Methods
This was a retrospective, longitudinal population study, including ADSMs from the Air Force, Army, Marine Corps, and Navy. Prevalence and incidence rates for LE MSKIs, associated health care utilization, and costs were obtained by querying electronic health records (EHR) from military treatment facilities (MTFs), private sector care (PC) claims, and theater medical data from the Military Health System Data Repository (MDR) from October 1, 2015 to September 30, 2021 (FY16–21). Utilization associated with LE MSKIs in both the direct care (DC) and PC settings was classified into mutually exclusive outpatient encounter categories and acute inpatient stays. PC costs related to LE MSKIs were captured for each year.

Results
In FY21, LE MSKIs occurred in 25.3% of ADSMs (n = 378,615). A higher proportion of females sustained an LE MSKI (33.3%), compared to males (23.7%). From FY16–21, the Army had the highest annual prevalence of LE MSKIs (30.9–35.5%), followed by the Air Force (23.8–31.0%), Marine Corps (23.4–27.0%), and Navy (17.2–19.8%). Incidence rate patterns were similar, with the Army sustaining LE MSKIs at 320 to 377 injuries per 1,000 person-years, followed by the Air Force (241–318), Marines (255–288), and Navy (173–203). Overuse/non-specific MSKIs of the knee were the most common injury type and body region affected, respectively. There were 10,675,543 DC and 1,875,307 PC outpatient encounters from FY16–21 with a primary or secondary diagnosis of LE MSKI. The Air Force was most reliant on PC, with 21.5 to 36.8% of LE MSKI-related encounters occurring outside MTFs during FY16–21. Over $99 million was paid by TRICARE on LE MSKI in FY21 alone with Same Day Surgeries accounting for almost half ($48 million) of this total.

Conclusions
Among U.S. ADSMs, LE MSKIs remain highly prevalent and costly. We observed disparities across the Services in the prevalence and incidence of LE MSKIs, and their respective reliance on the private sector for management of these conditions. Findings from this work may support military leaders and MSKI researchers who seek to reduce the impact of LE MSKIs on the readiness and overall health of the U.S. Military.
The moon-forming impact as a constraint for the inner Solar system’s formation
Authors: Fang Tong , Bi Rongxi , Zhang Hui , Zhou You , Reinhardt Christian , Deng Hongping 
Published: November 2024

ABSTRACT
The Solar system planets are benchmarks for the planet formation theory. Yet two paradigms coexist for the four terrestrial planets: the prolonged collisional growth among planetesimals lasting $\gt 100$ million years (Myr) and the fast formation via planetesimals accreting pebbles within 10 Myr. Despite their dramatic difference, we can hardly tell which theory is more relevant to the true history of the terrestrial planets’ formation. Here, we show that the Moon’s origin puts stringent constraints on the pebble accretion scenario, rendering it less favourable. In the pebble accretion model, the one-off giant impact between proto-Earth and Theia rarely (probability $\lt $ 1‰) occurs at the right timing and configuration for the Moon formation. Even if a potential impact happens by chance, giant impact simulations reveal perfect mixing between proto-Earth and Theia, leaving no room for the observed primordial Earth mantle heterogeneity and the compositional difference, though small, between Earth and the Moon. Thus, the Earth–Moon system along other terrestrial planets should preferably form from chaotic collisional growth in the inner Solar system.
Problem-Solving Courts and the Social Mind-set Model (with Monica K. Miller, Kylie Kulak, and Amber Westbrook)
Authors: Miller Monica K. , Kulak Kylie , Westbrook Amber 
Published: November 2024

Abstract
The Social Mind-set model attempts to explain why societies differ in both what they consider to be a crime and in what they consider to be the proper response (e.g., helping versus imprisoning offenders) to that crime. Societies around the world can vary greatly in their responses to some behaviors, with one society considering the behavior to be a crime and another not. Particularly, the Social Mind-set model describes six factors that influence a society’s social mind-set: (1) high-profile events and social movements, (2) economic and legal situations, (3) cultural beliefs and practices, (4) the use of scientific research and data, (5) a preference for justice principles, and (6) attributions for behavior. This chapter provides examples of these factors and discusses how they might influence the adoption of PSCs.
The Benefits (Pros) and Drawbacks (Cons) of Problem-Solving Courts
Authors: Miller Monica K. , Yelderman Logan A. , Holbrook Mia A. , Kulak Kylie 
Published: November 2024

Abstract
While many scholars and the members of the public view problem-solving courts as beneficial, some scholars suggest that they are more of a drawback than a benefit. This chapter examines the theoretical and evidenced-based arguments for the benefits of problem-solving courts and their drawbacks for society, the courts, and the participants. Various research methodologies have been used to determine the effectiveness of problem-solving courts both at the individual court level and at the broader state or national level, which are included in the discussion of whether or not problem-solving courts are a societal benefit. However, not all PSCs are supported by scientific research. Through rigorous investigations, many potential costs and drawbacks have been identified. This chapter summarizes these pros and cons and also includes a discussion about the legal implications of problem-solving courts and how those relate to the costs and benefits of problem-solving courts.
Society, Science, and Problem-Solving Courts
Authors: Miller Monica K. , Yelderman Logan A. , Holbrook Mia A. , Kulak Kylie 
Published: November 2024

Abstract
Some social scientists believe the world is becoming more “homogenized,” and specifically, more “Americanized,” through globalization. Yet, there is still great variability across countries, particularly in terms of culture, legal procedures, and governmental structures. Societies continue to change over time, and because law is a reflection of culture (and vice versa), the law and court system will also change. Science and technology also provide avenues for changes in law. New legal systems that reflect the legal consciousness of society will require new laws and procedures to guide and regulate these programs to best promote societal and legal goals. Legal systems, have required new approaches to understanding the role of judges, the ethical reach of probation and supervision, and the balance between punishment and community safety. Since their development in the 1980s, problem-solving courts have spread to many countries, and yet others have not adopted this approach for reasons discussed herein. This book reviews the history and development of problem-solving courts in many countries. We posit that science and culture provide a workable foundation to explain these differences within the United States and abroad. This chapter draws conclusions about how science and society have affected the development (or not) of problem-solving courts in the past, resulting in the courts of today. It also makes predictions about how science and society will affect the problem-solving courts of tomorrow. This includes issues of diversity, establishing quality evaluations, ethics, and expansion versus contraction.