bluuebunny/crossref_metadata_2025_split huggingface dataset:
Data integration strategies for whole-cell modeling
Authors: Tummler Katja , Klipp Edda 
Published: March 2024

Abstract
Data makes the world go round—and high quality data is a prerequisite for precise models, especially for whole-cell models (WCM). Data for WCM must be reusable, contain information about the exact experimental background, and should—in its entirety—cover all relevant processes in the cell. Here, we review basic requirements to data for WCM and strategies how to combine them. As a species-specific resource, we introduce the Yeast Cell Model Data Base (YCMDB) to illustrate requirements and solutions. We discuss recent standards for data as well as for computational models including the modeling process as data to be reported. We outline strategies for constructions of WCM despite their inherent complexity.
Identification of Parthenogenesis-Inducing Effector Proteins in Wolbachia
Authors: Fricke Laura C , Lindsey Amelia R I 
Published: March 2024

Abstract
Bacteria in the genus Wolbachia have evolved numerous strategies to manipulate arthropod sex, including the conversion of would-be male offspring to asexually reproducing females. This so-called “parthenogenesis induction” phenotype can be found in a number of Wolbachia strains that infect arthropods with haplodiploid sex determination systems, including parasitoid wasps. Despite the discovery of microbe-mediated parthenogenesis more than 30 yr ago, the underlying genetic mechanisms have remained elusive. We used a suite of genomic, computational, and molecular tools to identify and characterize two proteins that are uniquely found in parthenogenesis-inducing Wolbachia and have strong signatures of host-associated bacterial effector proteins. These putative parthenogenesis-inducing proteins have structural homology to eukaryotic protein domains including nucleoporins, the key insect sex determining factor Transformer, and a eukaryotic-like serine–threonine kinase with leucine-rich repeats. Furthermore, these proteins significantly impact eukaryotic cell biology in the model Saccharomyces cerevisiae. We suggest that these proteins are parthenogenesis-inducing factors and our results indicate that this would be made possible by a novel mechanism of bacterial-host interaction.
Fixation times of de novo and standing beneficial variants in subdivided populations
Authors: Sudbrack Vitor , Mullon Charles 
Published: March 2024

Abstract
The rate at which beneficial alleles fix in a population depends on the probability of and time to fixation of such alleles. Both of these quantities can be significantly impacted by population subdivision and limited gene flow. Here, we investigate how limited dispersal influences the rate of fixation of beneficial de novo mutations, as well as fixation time from standing genetic variation. We investigate this for a population structured according to the island model of dispersal allowing us to use the diffusion approximation, which we complement with simulations. We find that fixation may take on average fewer generations under limited dispersal than under panmixia when selection is moderate. This is especially the case if adaptation occurs from de novo recessive mutations, and dispersal is not too limited (such that approximately FST&lt;0.2). The reason is that mildly limited dispersal leads to only a moderate increase in effective population size (which slows down fixation), but is sufficient to cause a relative excess of homozygosity due to inbreeding, thereby exposing rare recessive alleles to selection (which accelerates fixation). We also explore the effect of metapopulation dynamics through local extinction followed by recolonization, finding that such dynamics always accelerate fixation from standing genetic variation, while de novo mutations show faster fixation interspersed with longer waiting times. Finally, we discuss the implications of our results for the detection of sweeps, suggesting that limited dispersal mitigates the expected differences between the genetic signatures of sweeps involving recessive and dominant alleles.
Exploring salt tolerance mechanisms using machine learning for transcriptomic insights: case study in Spartina alterniflora
Authors: Huang Zhangping , Chen Shoukun , He Kunhui , Yu Tingxi , Fu Junjie , Gao Shang , Li Huihui 
Published: March 2024

Abstract
Salt stress poses a significant threat to global cereal crop production, emphasizing the need for a comprehensive understanding of salt tolerance mechanisms. Accurate functional annotations of differentially expressed genes are crucial for gaining insights into the salt tolerance mechanism. The challenge of predicting gene functions in under-studied species, especially when excluding infrequent GO terms, persists. Therefore, we proposed the use of NetGO 3.0, a machine learning-based annotation method that does not rely on homology information between species, to predict the functions of differentially expressed genes under salt stress. Spartina alterniflora, a halophyte with salt glands, exhibits remarkable salt tolerance, making it an excellent candidate for in-depth transcriptomic analysis. However, current research on the S. alterniflora transcriptome under salt stress is limited. In this study we used S. alterniflora as an example to investigate its transcriptional responses to various salt concentrations, with a focus on understanding its salt tolerance mechanisms. Transcriptomic analysis revealed substantial changes impacting key pathways, such as gene transcription, ion transport, and ROS metabolism. Notably, we identified a member of the SWEET gene family in S. alterniflora, SA_12G129900.m1, showing convergent selection with the rice ortholog SWEET15. Additionally, our genome-wide analyses explored alternative splicing responses to salt stress, providing insights into the parallel functions of alternative splicing and transcriptional regulation in enhancing salt tolerance in S. alterniflora. Surprisingly, there was minimal overlap between differentially expressed and differentially spliced genes following salt exposure. This innovative approach, combining transcriptomic analysis with machine learning-based annotation, avoids the reliance on homology information and facilitates the discovery of unknown gene functions, and is applicable across all sequenced species.
In patients supported with peripheral veno-arterial extracorporeal membrane oxygenation, what factors are associated with the development of spinal cord ischaemia?
Authors: Zhu Alison , Tan Charis , Chard Richard , Orr Yishay 
Published: March 2024

Summary
A best evidence topic in cardiac surgery was written according to a structured protocol. The question addressed was ‘in patients supported with peripheral veno-arterial extracorporeal membrane oxygenation, what factors are associated with the development of spinal cord ischaemia’? Altogether, more than 22 papers were found using the reported search, of which 10 represented the best evidence to answer the clinical question. The authors, journal, date and country of publication, patient group studied, study type, relevant outcomes and results of these papers are tabulated. Of the 28 patients reported by included studies, the thoracic spinal cord was most commonly affected. Twenty patients (71%) survived to hospital discharge and 7 (25%) were reported to have neurological recovery. Potential confounders included coronary angiography, cardiac arrest requiring chest compressions and concomitant intra-aortic balloon pump. Consequently, all papers highlighted the likely multifactorial aetiology of spinal cord infarction in these patients. We propose that close neurological observation, particularly in patients who have received chest compressions, and management of potential aetiological factors is crucial to aid in timely diagnosis and potential prevention of this rare complication. Limiting sedation and neuromuscular blockade to enable neurologic assessment of the lower limbs may allow more timely diagnosis.
Evaluation of 5 Polymerase Chain Reaction Assays for the Detection of Mpox Virus
Authors: Fattouh Ramzi , Boissinot Karel , Jeong Esther , Mendlowitz Andrew B , Sjaarda Calvin P , Wong Henry , Kozak Robert , Sheth Prameet M , Matukas Larissa M 
Published: March 2024

Abstract

Background
In 2022, the global dissemination of mpox virus (MPXV) outside endemic regions prompted the expansion of diagnostic testing worldwide. This study assesses the performance characteristics of 5 real-time polymerase chain reaction (PCR) assays in detecting MPXV during the 2022 outbreak.

Methods
Clinical specimens collected from patients across Ontario, Canada, were tested on the following assays: RealStar Orthopoxyvirus PCR and FlexStar Monkeypox virus PCR (Altona Diagnostics), Novaplex MPXV (Seegene), VIASURE Monkeypox virus Real Time PCR Reagents (CerTest Biotec), and a laboratory-developed test. Positive percent agreement (PPA), negative percent agreement (NPA), relative limit of detection (LOD), and precision were evaluated and MPXV lineages were determined using an amplicon-based whole-genome sequencing (WGS) assay.

Results
Swabs were collected from various anatomic sites (65 positive and 30 negative). All assays demonstrated 100% NPA (95% confidence interval, 88.4%/88.1%–100.0%), with PPA ranging from 92.2% (82.7%–97.4%) to 96.9% (89.3%–99.6%). LOD and precision were comparable across assays, with coefficient of variations &lt;3%. WGS analysis identified 6 lineages, all belonging to subclade IIb.

Conclusions
The assays exhibited excellent PPA, NPA, LOD, and precision. Ongoing performance monitoring is essential to detect assay escape mutants and ensure universal detection of evolving MPXV strains.
Comparative Diagnostic Utility of SARS-CoV-2 Rapid Antigen and Molecular Testing in a Community Setting
Authors: Kim Ashley E , Bennett Julia C , Luiten Kyle , O’Hanlon Jessica A , Wolf Caitlin R , Magedson Ariana , Han Peter D , Acker Zack , Regelbrugge Lani , McCaffrey Kathryn M , Stone Jeremey , Reinhart David , Capodanno Benjamin J , Morse Stephen S , Bedford Trevor , Englund Janet A , Boeckh Michael , Starita Lea M , Uyeki Timothy M , Carone Marco , Weil Ana , Chu Helen Y 
Published: March 2024

Abstract

Background
SARS-CoV-2 antigen-detection rapid diagnostic tests (Ag-RDTs) have become widely utilized but longitudinal characterization of their community-based performance remains incompletely understood.

Methods
This prospective longitudinal study at a large public university in Seattle, WA utilized remote enrollment, online surveys, and self-collected nasal swab specimens to evaluate Ag-RDT performance against real-time reverse transcription polymerase chain reaction (rRT-PCR) in the context of SARS-CoV-2 Omicron. Ag-RDT sensitivity and specificity within 1 day of rRT-PCR were evaluated by symptom status throughout the illness episode and Orf1b cycle threshold (Ct).

Results
From February to December 2022, 5757 participants reported 17 572 Ag-RDT results and completed 12 674 rRT-PCR tests, of which 995 (7.9%) were rRT-PCR positive. Overall sensitivity and specificity were 53.0% (95% confidence interval [CI], 49.6%–56.4%) and 98.8% (95% CI, 98.5%–99.0%), respectively. Sensitivity was comparatively higher for Ag-RDTs used 1 day after rRT-PCR (69.0%), 4–7 days after symptom onset (70.1%), and Orf1b Ct ≤20 (82.7%). Serial Ag-RDT sensitivity increased with repeat testing ≥2 (68.5%) and ≥4 (75.8%) days after an initial Ag-RDT-negative result.

Conclusions
Ag-RDT performance varied by clinical characteristics and temporal testing patterns. Our findings support recommendations for serial testing following an initial Ag-RDT-negative result, especially among recently symptomatic persons or those at high risk for SARS-CoV-2 infection.
Sect, Sectarian, Sectarianism: The Birth, Death, and Resurrection of an Analytical Category in the Study of Western Religions
Authors: Moss Yonatan 
Published: March 2024

Abstract
This article charts the changing uses of the interconnected terms sect, sectarian, sectarianist, and sectarianism in the academic study of Judaism, Christianity, and Islam. Following a review of the term sect’s early roots in Greco-Roman antiquity and its distinctly Christian transformation, three main steps are analyzed in the genealogy of the category in modern scholarship: (1) deployments by Weber and his early followers; (2) an influential sociological turn in the latter half of the twentieth century; and (3) a sharp decline in the years around the turn of the century in the popularity of sect as a category, followed by a redefinition of its derivative terms (sectarian, etc.) in recent years. Toward the end of the article, lessons are drawn from this genealogy for the future use of the category within scholarship.
Maternal diabetes and fracture risk in offspring: a population-based analysis
Authors: Shah Viral N , Leslie William D , Lautatzis Maria-Elena , Liu Kun , Prior Heather J , Wicklow Brandy 
Published: March 2024

Abstract
Factors affecting intrauterine environment exerts influence on skeletal health and fracture risk in later life. Diabetes during pregnancy is known to influence birth weight and is associated with fetal overgrowth. However, the effects of maternal diabetes on fracture risk in offspring is unknown. This study was aimed to evaluate the association between maternal diabetes and fracture risk in offspring. Using population-based administrative health data for Manitoba, Canada, we identified deliveries complicated by gestational diabetes and type 2 diabetes between April 1, 1980, and March 31, 2020. The cohort was followed for a median of 15.8 yr. The primary outcome was any incident fracture in offspring. Secondary outcomes were long bone upper extremity fracture, long bone lower extremity fracture, vertebral fracture, and any non-trauma fractures. Cox proportional hazard regression models were used to estimate fracture risk in offspring by maternal diabetes status adjusted for relevant covariates. Of the 585 176 deliveries, 26 397 offspring were born to women with diabetes (3.0% gestational diabetes and 1.5% type 2 diabetes), and 558 779 were born to women without diabetes. The adjusted risk for any fracture was 7% (hazard ratio, 1.07; 95% CI, 2.7–11.5%) higher in the offspring of mothers with diabetes than offspring of mothers without diabetes. Types of fractures were similar between the 2 groups with a predominance of long bone upper extremity fractures. In conclusion, maternal diabetes was associated with a modest increase in fracture risk in offspring. Longitudinal prospective studies are needed to understand intrauterine and postnatal factors that may influence fracture risk in the offspring of mothers with diabetes.
Observation of key phenological stages of hemlock woolly adelgid (Hemiptera: Adelgidae): using citizen science as a tool to inform research and management
Authors: Dietschler Nicholas J , Bittner Tonya D , Lefebvre Marshall Bigler , Schmidt Jasmine , Jubb Carrie S , James Aryanna , Salom Scott M , Whitmore Mark C 
Published: March 2024

Abstract
Increasing efficiency of data gathering at the landscape scale on the growing number of pests and pathogens threatening forests worldwide has potential to improve management outcomes. Citizen science is expanding, with growing support and utility in environmental and conservation fields. We present a case study showing how citizen science observations can be used to inform research and management of a devastating forest pest. Hemlock woolly adelgid, Adelges tsugae Annand (Hemiptera: Adelgidae), was introduced to eastern North America, leading to decline and mortality of eastern [Tsuga canadensis (L.) Carrière] (Pinales: Pinaceae) and Carolina hemlock (Tsuga caroliniana Engelmann) trees. Management activities, most notably biological control, rely on observations of A. tsugae phenology to inform the timing of releases and monitoring surveys of their highly synchronized specialist predators. In this article, we outline a citizen science program and report phenological observations on A. tsugae. Additionally, we report data comparing A. tsugae estivation break in Virginia (VA) and New York (NY) State, revealing that estivation break is synchronized between NY and VA. This observation is supported by 6 years of citizen scientist observations, showing similar patterns throughout NY, with egg laying shown to be much more variable than estivation break.
Food and time: dietary plasticity of different sources of a generalist insect herbivore
Authors: Hernandez Katherine , Bowers M Deane 
Published: March 2024

Abstract
Painted lady butterflies (Vanessa cardui L., Nymphalidae) are generalist herbivores and serve as a model system across several fields of biology. While it has been demonstrated that V. cardui caterpillars can develop on different host plants, much of this work has been done on commercially sourced caterpillars, which could limit our understanding of wild V. cardui populations. In this study, we sought to explore possible differences in how commercial and wild V. cardui caterpillars may respond to feeding on different host plants, and subsequently, how their diet impacts immune response and survival. Here, we analyzed performance, survival, and immune response of wild and commercially sourced V. cardui caterpillars over several generations on diets that consisted of either 1 of 4 different host plant species or a mixed diet including all 4 species. Qualitatively, we observed that wild larvae had a better larval performance and hemocyte counts compared to the commercial larvae. The results demonstrate that both wild and commercially sourced caterpillars grew and survived best on the same diet treatments (mallow, narrowleaf plantain, and a mixed diet) during development across generations. Immune responses showed similar patterns across host plants between wild and commercial populations, with individuals showing lowered immune responses on dandelion and lupine and higher ones on mallow, plantain and the mixed diet; although the relative rankings on those 3 diets varied. Survival also demonstrated similar patterns, in that individuals reared on dandelion and lupine had the lowest survival.
The role of leukocytes in myeloproliferative neoplasm thromboinflammation
Authors: Liu Yu , Wang Yingying , Huang Gang , Wu Sanyun , Liu Xiaoyan , Chen Shuo , Luo Ping , Liu Chang , Zuo Xuelan 
Published: March 2024

Abstract
Classic myeloproliferative neoplasms lacking the Philadelphia chromosome are stem cell disorders characterized by the proliferation of myeloid cells in the bone marrow and increased counts of peripheral blood cells. The occurrence of thrombotic events is a common complication in myeloproliferative neoplasms. The heightened levels of cytokines play a substantial role in the morbidity and mortality of these patients, establishing a persistent proinflammatory condition that culminates in thrombosis. The etiology of thrombosis remains intricate and multifaceted, involving blood cells and endothelial dysfunction, the inflammatory state, and the coagulation cascade, leading to hypercoagulability. Leukocytes play a pivotal role in the thromboinflammatory process of myeloproliferative neoplasms by releasing various proinflammatory and prothrombotic factors as well as interacting with other cells, which contributes to the amplification of the clotting cascade and subsequent thrombosis. The correlation between increased leukocyte counts and thrombotic risk has been established. However, there is a need for an accurate biomarker to assess leukocyte activation. Lastly, tailored treatments to address the thrombotic risk in myeloproliferative neoplasms are needed. Therefore, this review aims to summarize the potential mechanisms of leukocyte involvement in myeloproliferative neoplasm thromboinflammation, propose potential biomarkers for leukocyte activation, and discuss promising treatment options for controlling myeloproliferative neoplasm thromboinflammation.
The EU’s normative justifications of refugee resettlement
Authors: Welfens Natalie 
Published: March 2024

Abstract
The UNHCR promotes resettlement as an important protection tool to express solidarity with vulnerable refugees and countries of refuge. Yet, as resettlement is discretionary, its guiding principles and objectives are not binding and can be reinterpreted by states and supranational organizations. Against the background of UNHCR’s resettlement guidelines, this article examines the EU’s justifications of resettlement. Advancing theories of pragmatic sociology and based on an in-depth qualitative analysis, it teases out justifications of (1) humanitarianism, (2) border security, and (3) assimilability in EU discourses and policies. Revisiting EU policy advancements from the early 2000s until 2023, it shows that these justifications increasingly interlace and present resettlement as an instrument to protect refugees as well as EU borders and access to EU polities. The article argues for the need to understand the EU as a resettlement actor in its own right, with significant power to reshape resettlement as a protection tool.
Dental implant placement with simultaneous localized ridge augmentation using L-shaped titanium mesh in the esthetic zone: a case report
Authors: Albash Ziad , Hnaino Eva , Khalil Ali 
Published: March 2024

Abstract
The aim of this case report is to illustrate a successful technique for dental implant placement in the esthetic zone using simultaneous localized ridge augmentation with L-shaped titanium mesh. A 35-year-old patient presented with a single missing tooth in the esthetic zone requiring dental implant placement. The treatment plan was made to place a dental implant in conjunction with a guided bone regeneration procedure using a prefabricated L-shaped titanium mesh. The procedure achieved successful reconstruction of the deficient ridge, providing ample volume and contour for implant placement. Implant osteointegration was achieved, resulting in a satisfactory functional and esthetically pleasing outcome. The use of L-shaped titanium mesh offers superior stability and biocompatibility, ensuring optimal support and containment of graft material. This case report highlights the feasibility and clinical effectiveness of dental implant placement with simultaneous localized ridge augmentation using L-shaped titanium mesh in the esthetic zone. Further studies are warranted to assess the long-term success and esthetic outcomes of this technique.
Liver impalement with an antique African iron barbed spear. A case report
Authors: Cervantes Barbara Y H , Gavor Samuel E , Jiagge Nuna E , Lopez Duniesky M , Lambert Radisnay G , Almaguer Acevedo Fernando M 
Published: March 2024

Abstract
Impalement injuries happen when an object penetrates a body cavity or organ and remains in situ. We present a case of a 35-year-old fisherman whose act of violence resulted in the lodging of an antique iron spear in segment V of the liver, which was then referred to our institution on the day after the accident. Despite the challenges posed by patient transfer, diagnosis, resuscitation, and, most importantly, handling in the operating room, the object was successfully removed via hepatotomy, and the patient is now in good health. Impalement by an ancient African iron spear, repurposed as a fishing tool in modern times, remains undocumented in the literature, necessitating reporting and a call for further research by the medical community into managing impalement injuries of varying severity.