bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimating amino acid substitution models from genome datasets: a simulation study on the performance of estimated models
Authors: Tinh Nguyen Huy , Dang Cuong Cao , Vinh Le Sy 
Published: December 2023

Abstract
Estimating parameters of amino acid substitution models is a crucial task in bioinformatics. The maximum likelihood (ML) approach has been proposed to estimate amino acid substitution models from large datasets. The quality of newly estimated models is normally assessed by comparing with the existing models in building ML trees. Two important questions remained are the correlation of the estimated models with the true models and the required size of the training datasets to estimate reliable models. In this article, we performed a simulation study to answer these two questions based on simulated data. We simulated genome datasets with different numbers of genes/alignments based on predefined models (called true models) and predefined trees (called true trees). The simulated datasets were used to estimate amino acid substitution model using the ML estimation methods. Our experiments showed that models estimated by the ML methods from simulated datasets with more than 100 genes have high correlations with the true models. The estimated models performed well in building ML trees in comparison with the true models. The results suggest that amino acid substitution models estimated by the ML methods from large genome datasets are a reliable tool for analyzing amino acid sequences.
Effects of different Ficus feeding experiences on host preference of Perina nuda larvae (Lepidoptera: Lymantriidae)
Authors: Liao Songkai , Lin Haoyu , Wang Jiajin , Wang Qi , Wei Hongjian , Chen Hui 
Published: December 2023

Abstract
Perina nuda (Lepidoptera: Lymantriidae) is a serious pest of banyan trees (Ficus spp.), which is distributed in South China, but little is known about the host preference on the different banyan tree species. To address this gap, we conducted experiments to investigate larval feeding preferences, assessing the impact of feeding experience in both choice and no-choice conditions. Fifth and sixth instars were exposed to 4 banyan species, and food intake, feeding area, and relative ingestion index were measured. Our findings reveal that Ficus concinna was the preferred host of fifth instars in choice tests, while sixth instars exhibited a preference for this host in no-choice tests. In contrast, fifth instars did not display a significant preference for any of the 4 species in no-choice tests. However, sixth instars fed on F. microcarpa, F. altissima, and F. concinna continued to exhibit a preference for the original host. These observations indicate that larval feeding preference changes with instar, and feeding experience contributes to a preference for the original host. Consequently, the feeding preference of P. nuda larvae is influenced by multiple factors, including instar and previous feeding experience. These findings enhance our understanding of P. nuda’s ecological interactions and its potential impact on various banyan tree species.
Should We Call for Criminal Accountability During Ongoing Conflicts?
Authors: Bdiwi Ghuna 
Published: December 2023

Abstract
This article suggests an account in the language of criminal law that merits the language for criminal accountability over the language of human rights, as a form of accountability, when prosecution is not possible. Calling for the prosecution of those most responsible for international crimes seems to be feasible after the war has ended, or at least when there is a vision for a political transition, but the war in Syria is ongoing and a vision for political transition remains elusive. The Syrian conflict has produced almost all kinds of heinous crimes, yet there is no clear political will to hold the alleged perpetrators of atrocity crimes accountable. At the same time, calls for criminal accountability in Syria, and discourse to achieve international criminal justice are taking place before the civil war ends. This article relies on the expressive theory of punishment to assess the rationales of calls for criminal accountability during the ongoing conflict in Syria. Out of many rationales, the article notes that calls for criminal accountability open the possibility of punishment and send a message of condemnation to perpetrators as well as a message of acknowledgment to victims. Furthermore, using the language of criminal accountability as a basis for the calls is stronger than using the language of human rights. The article discusses the problem of standing to call those responsible for international crimes to account and proposes that our shared humanity provides the authority for such calls while also pointing out limitations of this approach.
Preventing unfair competition in Australia, New Zealand and South Pacific countries: the intertwined roles of passing off and consumer protection statutes
Authors: Handler Michael 
Published: December 2023

Abstract
Australia, New Zealand and other South Pacific countries whose laws are based on English law tend to rely on a patchwork of intellectual property statutes, equitable doctrines and common law actions to prevent acts of unfair competition. The most distinctive feature of the laws of these countries is their reliance on consumer protection statutes that contain broadly worded prohibitions on parties engaging in misleading or deceptive conduct in trade or commerce, in addition to the tort of passing off, to safeguard against unfair competition. This article traces the complex relationship between passing off and consumer protection statutes in Australia, New Zealand and throughout the South Pacific. It shows how the actions have come to have a largely mixed or merged operation that seeks to balance interests in protecting trading reputation, in ensuring that consumers are not deceived, and in leaving space for competitors, especially given the limits of intellectual property statutes and other doctrines. It does so in the course of providing a detailed explanation of how Australia, New Zealand and other countries in the region give effect to their obligations under Article 10bis of the Paris Convention.
Towards patient welfare-centred pharmaceutical patents—a sustainable perspective
Authors: Lorenzo-Rego Irene 
Published: December 2023

Abstract
Encouraging innovation by rewarding pharmaceutical patent holders is a key to societal progress, given mandatory disclosure and adequate reimbursement. Following debate on fair prices from a competition law perspective, the recent Health Trade Assessment Regulation provides Member States with a harmonized tool to help them set prices in a more sustainable way. This article discusses the extent to which the Regulation will provide comprehensive access to healthcare as an expression of patient welfare, framing the debate in terms of sustainability.
Large cystic lymphangioma of the pancreas: unusual finding with differential diagnosis and therapeutic considerations
Authors: Tasis Nikolaos , Mpalampou Eleni , Sarafi Aikaterini , Skafida Evangelia , Tsouknidas Ioannis , Fradelos Evangelos , Manatakis Dimitrios K , Korkolis Dimitrios P 
Published: December 2023

Abstract
Lymphangiomas are rare benign tumours of lymphatic vascular origin. They are more common in the paediatric population and manifest mainly in the neck and axillary region. Retroperitoneal lymphangiomas are &lt;1% and pancreatic origin is even rarer. We present a case of a pancreatic cystic lymphangioma in a 60-year-old woman with chronic diffuse symptoms, diagnosed because of newly onset of diabetes mellitus. She was successfully managed with distal pancreatectomy and spleenectomy en-bloc with the cystic mass without any complications. Cystic lymphangioma of the pancreas is a rare entity presenting with a challenging preoperative diagnosis as imaging modalities may provide ambiguous information. The clinician should be aware of its complicated differential diagnosis and its persistent and subtle symptomatology.
Yellow fever vaccine-associated neurologic and viscerotropic disease: a 10-year case series of the French National Reference Center for Arboviruses with clinical and immunological insights
Authors: Le Hir Anne , Durand Guillaume A , Boucraut José , Garnier Annabelle , Mura Marie , Diamantis Sylvain , Carles Michel , Durand Claire , Schweitzer Cyril , Audouard Claire , Decroix Véronique , Boyez Romain , Van Dendriessche Anne , Leclancher Alexandre , Kaphan Elsa , Barbat du Closel Luce , Verdon Renaud , du Cheyron Damien , Vabret Astrid , Vergnon Delphine , Grard Gilda , Charrel Rémi , de Lamballerie Xavier , Eldin Carole 
Published: December 2023

Abstract

Background
Immunization against the Yellow fever virus (YFV) with the 17D live-attenuated vaccine is the most effective way to prevent the disease. However, unexpected severe adverse events can occur. They consist in a neurological impairment - neurological disease (YEL-AND), a YF-like illness - viscerotropic disease (YEL-AVD) or anaphylaxis. In this article, we describe the epidemiology, clinical and biological features of YEL-AND and YEL-AVD cases reported to the French National Reference Center for Arboviruses (NRCA) in the past 10 years.

Methods
We conducted a national, retrospective study using the database of the NRCA from June 2012 to June 2022. All patients whose biological samples were sent to the NRCA for detection of YFV by serology and/or RT-qPCR for a suspected vaccine-associated adverse event were included. We collected data by reading medical records and conducted complementary neuro-immunological analysis, followed by a search for autoimmunity against type-1-interferon when samples were available at the NRCA.

Results
There were 10 cases of YEL-AND and 2 cases of YEL-AVD reported to the NRCA in the past 10 years, which represented an overall incidence of 0.6 for 100 000 doses. A total of 6/12 cases were previously healthy patients (50%, mean age 31 years), and 4/12 cases had cardiovascular co-morbidities (42%, mean age 56 years). The majority of YEL-AND had a favourable outcome at 6 months of follow up. One YEL-AVD patient passed. In secondary analyses, we evidenced a significant blood cerebrospinal fluid (CSF) barrier dysfunction, without intrathecal synthesis of immunoglobulin and without argument for a neuron damage. We further detected a significant rate of anti-type-1alpha interferon antibodies in 3/10 tested patients (2 YEL-AND and 1 YEL-AVD).

Conclusion
YEL-AND and YEL-AVD are rare events that can underlie defect in the innate immunity of apparently healthy or mild co-morbid subjects. Outcome was generally favourable in the YEL-AND cases of our series, but still life-threatening or even fatal in the YEL-AVD cases.
Method validation for the recovery of the porcine respiratory and reproductive syndrome virus, a potential SARS-CoV-2 surrogate, from stainless steel
Authors: Dhakal Janak , Vu Hiep , Chaudhari Jayeshbhai , Nguyen Khang , Chaves Byron D 
Published: December 2023

Abstract
Virus survival on fomites may represent a vehicle for transmission to humans. This study was conducted to optimize and validate a recovery method for the porcine respiratory and reproductive syndrome virus (PRRSV), a potential SARS-CoV-2 surrogate, from stainless steel. Coupons (1.5 × 1.5 cm) inoculated with ca. 7 logs TCID50 of PRRSV were dried for 15 min at room temperature, followed by incubation at 4°C and 35% relative humidity. After 1 h and 24 h, the coupons were processed by four different methods: vortex in DMEM media, vortex in DMEM media with beads, vortex in elution buffer, and shake in elution buffer. The rinsates were processed for titration using the TCID50 method in the MARC-145 cell line. All four methods were equally effective to recover the virus from the soiled SS surfaces (&gt; 79% recovery). The amount of infectious virus recovered after 24 h was similar (P &gt; 0.05) to that recovered after 1 h, indicating that the virus was stable at 4°C for up to 24 h. Using an elution buffer followed by shaking was the least labor-intensive and most economical method. Therefore, this method will be used for future experiments on PRRSV survival and transfer from food-contact surfaces.
Military Health Care Team Cohesion and Performance During Simulation Training
Authors: Melo Estefania , Cole Rebekah 
Published: December 2023

ABSTRACT

Introduction
Military health care team cohesion has been linked to improved performance during simulation training. However, there is a gap in current research regarding the processes by which teams become cohesive within simulation training. The purpose of this study was to explore how health care teams evolve during high-fidelity simulation training and the ways in which team cohesion impacts their performance.

Materials and Methods
The participants in our study were fourth-year military medical students participating in a 5-day high-fidelity military medical simulation during Fall 2022.Twenty-three students volunteered to participate in our study. We interviewed each participant twice during the simulation and then transcribed each interview using an automated transcription service. Guided by the grounded theory tradition of qualitative data analysis, we used open, axial, and selective coding to analyze the interview data.

Results
Our data analysis revealed that teams went through a process of (1) struggle, (2) adaptation, (3) perceived improvement, (4) gained confidence, and (5) perceived team cohesion. Teams struggled through the various barriers to group cohesion (i.e., power dynamics, role designation and competency, and task failures and low team confidence) in order to understand their weaknesses. As teams adjusted and noticed improvement, they adapted new patterns, protocols, and standards of practice based on previous failures, improving their overall confidence. The participants perceived their teams as successful once they had progressed through these phases and ended the simulation as a cohesive unit.

Conclusions
Our qualitative data analysis provided insight into team cohesion as it was forged by participants in real time as the simulation progressed. The results of our study can be used to promote team cohesion not only during simulation training but also within military health care professional teams in order to enhance their performance in the field.
Accurate fundamental invariant-neural network representation of ab initio potential energy surfaces
Authors: Fu Bina , Zhang Dong H 
Published: December 2023

ABSTRACT
Highly accurate potential energy surfaces are critically important for chemical reaction dynamics. The large number of degrees of freedom and the intricate symmetry adaption pose a big challenge to accurately representing potential energy surfaces (PESs) for polyatomic reactions. Recently, our group has made substantial progress in this direction by developing the fundamental invariant-neural network (FI-NN) approach. Here, we review these advances, demonstrating that the FI-NN approach can represent highly accurate, global, full-dimensional PESs for reactive systems with even more than 10 atoms. These multi-channel reactions typically involve many intermediates, transition states, and products. The complexity and ruggedness of this potential energy landscape present even greater challenges for full-dimensional PES representation. These PESs exhibit a high level of complexity, molecular size, and accuracy of fit. Dynamics simulations based on these PESs have unveiled intriguing and novel reaction mechanisms, providing deep insights into the intricate dynamics involved in combustion, atmospheric, and organic chemistry.
Cigarette Prices and Disparities in Smoking Cessation in the United States
Authors: Kalousova Lucie , Xie Yanmei , Levy David , Meza Rafael , Thrasher James F , Elliott Michael R , Titus Andrea R , Fleischer Nancy L 
Published: December 2023

Abstract

Introduction
Achieving cessation in people with established smoking patterns remains a challenge. Increasing cigarette prices has been one of the most successful strategies for lowering smoking rates. The extent to which it has remained effective in encouraging cessation among adults in recent years and how the effectiveness has varied by sociodemographic characteristics is unclear.

Aims and Methods
Using repeated cross-sectional data collected by the Tobacco Use Supplement of the Current Population Survey, we investigate the relationship between cigarette prices and cessation from 2003 to 2019 in adults at least 25 years old. We examine the associations between price and cessation in the population overall and by sex, race and ethnicity, and socioeconomic status.

Results
We found mixed support for associations between greater local prices and cessation. Unadjusted models showed that greater local prices were associated with greater odds of cessation, but the associations did not persist after controlling for sociodemographic characteristics. The associations did not significantly differ by respondent characteristics. Sensitivity analysis using alternative specifications and retail state price as the main predictor showed similar results. Sensitivity analysis with controls for e-cigarette use in the 2014–2019 period showed that greater local price was associated with cessation among adults with less than a high school degree. When stratified by year of data collection, results show that greater local prices were associated with cessation after 2009.

Conclusions
Overall, the study adds to the conflicting evidence on the effectiveness of increasing prices on smoking cessation among adults with established smoking patterns.

Implications
Higher cigarette prices have been one of the most successful tools for lowering smoking prevalence. It remains unclear how effective they have been in recent years in encouraging adults with established smoking patterns to quit. The study’s results show that greater local prices were associated with higher odds of cessation, but the association did not persist after sociodemographic adjustment. In a sensitivity analysis, greater local price was associated with cessation among people with less than a high school degree in models controlling for e-cigarette use. We also found evidence that greater local price was associated with cessation after 2009. More comprehensive smoke-free coverage was also associated with greater odds of cessation. The study’s results highlight that encouraging cessation among adults with an established smoking pattern remains a challenging policy problem even when cigarette prices rise.
Incidence of Lyme Carditis and Lyme Carditis as a Cause of Pacemaker Implantation: A Nationwide Registry-Based Case-Control Study
Authors: Avellan Sanna , Mehlig Kirsten , Robertson Josefina , Bremell Daniel 
Published: December 2023

Abstract

Background
Lyme borreliosis (LB) of the heart is called Lyme carditis (LC), which often manifests with high-grade atrioventricular block (AVB) requiring pacemaker implantation. LC is treated with antibiotics, and most patients recover fully after treatment. The overall incidence of LC, and of LC as a cause of pacemaker implantation, has not previously been systematically studied.

Methods
This was a case-control study based on data from Swedish national registers. The study was divided into two parts; part 1 including all patients diagnosed with AVB between 2001 and 2018, and part 2 including all patients who had received a pacemaker due to AVB between 2010 and 2018. Patients diagnosed with LB 90 days before and 180 days after the AVB diagnosis were identified among the patients and compared to matched control groups generated from the general population.

Results
Of 81 063 patients with AVB, 102 were diagnosed with LB. In the control group, 27 were diagnosed with LB. The yearly incidence of LC was 0.056 per 100 000 adults and year. Of 25 241 patients who had received a pacemaker for AVB, 31 were diagnosed with LB. In the control group, 8 were diagnosed with LB. The yearly incidence of LC as a cause of pacemaker implantation was 0.033 per 100 000 adults and year. The estimated risk for patients with LC to receive a permanent pacemaker was 59%.

Conclusions
LC is a rare cause of AVB. Nevertheless, more than half of patients with LC receive a permanent pacemaker for a condition that is easily cured with antibiotics.
Feasibility and Acceptability of Human Immunodeficiency Virus Self-Testing for Men of Middle-to-Upper Socioeconomic Status in Botswana: A Pilot Study at 4 Worksites in the Financial Sector
Authors: Kgotlaetsile Keonayang , Bogart Laura M , Phaladze Nthabiseng , Klein David J , Mosepele Mosepele 
Published: December 2023

Abstract

Background
Although Botswana has made great progress in expanding human immunodeficiency virus (HIV) testing, men are less likely to be tested for HIV and test at a later stage compared with women. For Botswana to increase HIV testing coverage among men, HIV self-testing (HIVST) may be a promising supplement to standard, healthcare facility-based HIV testing. We conducted a pilot test of the feasibility and acceptability of HIVST for men of middle-to-upper socioeconomic status in Botswana.

Methods
Thirty-five men were recruited through 4 workplaces (banking sector). Wellness officers emailed all potentially eligible male employees about the opportunity to participate. Men were surveyed at baseline and follow-up on basic sociodemographic characteristics, HIV testing history, HIV stigma, use of the HIVST kit (at follow-up), and confirmatory testing and linkage to care if a preliminary positive result is obtained (at follow-up).

Results
All 35 men used the kit. The proportion who agreed with the statement that getting tested for HIV helps people feel better increased significantly from 80.7% at baseline to 100% at follow-up. In open-ended questions, men described the advantages of HIVST, including improved privacy and convenience, lowered HIV stigma, and enhanced control over testing. Concerns about HIVST included potential negative mental health consequences owing to not receiving pretest and posttest counseling, and not linking to care after a reactive result.

Conclusions
Results suggest that an intervention in which HIVST is discrete, private, and under men’s control can help overcome stigma around HIV testing, resulting in a greater number of men tested.
Structure-based virtual screening identifies small-molecule inhibitors of O-fucosyltransferase SPINDLY in Arabidopsis
Authors: Aizezi Yalikunjiang , Zhao Hongming , Zhang Zhenzhen , Bi Yang , Yang Qiuhua , Guo Guangshuo , Zhang Hongliang , Guo Hongwei , Jiang Kai , Wang Zhi-Yong 
Published: December 2023

Abstract
Protein O-glycosylation is a nutrient signaling mechanism that plays an essential role in maintaining cellular homeostasis across different species. In plants, SPINDLY (SPY) and SECRET AGENT (SEC) posttranslationally modify hundreds of intracellular proteins with O-fucose and O-linked N-acetylglucosamine, respectively. SPY and SEC play overlapping roles in cellular regulation, and loss of both SPY and SEC causes embryo lethality in Arabidopsis (Arabidopsis thaliana). Using structure-based virtual screening of chemical libraries followed by in vitro and in planta assays, we identified a SPY O-fucosyltransferase inhibitor (SOFTI). Computational analyses predicted that SOFTI binds to the GDP-fucose–binding pocket of SPY and competitively inhibits GDP-fucose binding. In vitro assays confirmed that SOFTI interacts with SPY and inhibits its O-fucosyltransferase activity. Docking analysis identified additional SOFTI analogs that showed stronger inhibitory activities. SOFTI treatment of Arabidopsis seedlings decreased protein O-fucosylation and elicited phenotypes similar to the spy mutants, including early seed germination, increased root hair density, and defective sugar-dependent growth. In contrast, SOFTI did not visibly affect the spy mutant. Similarly, SOFTI inhibited the sugar-dependent growth of tomato (Solanum lycopersicum) seedlings. These results demonstrate that SOFTI is a specific SPY O-fucosyltransferase inhibitor that can be used as a chemical tool for functional studies of O-fucosylation and potentially for agricultural management.