bluuebunny/crossref_metadata_2025_split huggingface dataset:
Examining the Influence of Imbalanced Social Contact Matrices in Epidemic Models
Authors: Hamilton Mackenzie A , Knight Jesse , Mishra Sharmistha 
Published: September 2023

Abstract
Transmissible infections such as those caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spread according to who contacts whom. Therefore, many epidemic models incorporate contact patterns through contact matrices. Contact matrices can be generated from social contact survey data. However, the resulting matrices are often imbalanced, such that the total number of contacts reported by group A with group B do not match those reported by group B with group A. We examined the theoretical influence of imbalanced contact matrices on the estimated basic reproduction number (R0). We then explored how imbalanced matrices may bias model-based epidemic projections using an illustrative simulation model of SARS-CoV-2 with 2 age groups (&lt;15 and ≥15 years). Models with imbalanced matrices underestimated the initial spread of SARS-CoV-2, had later time to peak incidence, and had smaller peak incidence. Imbalanced matrices also influenced cumulative infections observed per age group, as well as the estimated impact of an age-specific vaccination strategy. Stratified transmission models that do not consider contact balancing may generate biased projections of epidemic trajectory and the impact of targeted public health interventions. Therefore, modeling studies should implement and report methods used to balance contact matrices for stratified transmission models.
White-tailed deer responses to acoustic predator cues are contingent upon past land use and contemporary fire regime
Authors: Bartel Savannah L , Kilgo John C , Orrock John L 
Published: September 2023

Abstract
Prey can assess the immediate risk of predation by detecting cues of predator presence, and it is expected that prey should invest in costly antipredator behaviors when a cue of predator presence is detected. Features of the habitat in which the cue is detected, such as vegetative concealment, serve as indirect cues of risk and can mediate how prey respond to direct cues of predator presence. Past agricultural land use and contemporary fire regimes are common disturbances that may modify prey perceptions of risk and could, therefore, alter prey responses to direct cues of predator presence. We examined whether the overlap of these two disturbances affected white-tailed deer (Odocoileus virginianus) responses to cues of predator presence by measuring deer vigilance and foraging bout duration in response to coyote (Canis latrans) vocalizations across 20 woodlands that varied in past land use and contemporary fire regime. Frequent fire regimes consistently increased deer visibility to predators across both land-use history contexts. Deer exhibited no behavioral response to the predator cue in habitats containing infrequent fire regimes or agricultural legacies. Deer responded to the cue in frequently burned woodlands without agricultural legacies through increased vigilance and time spent at a foraging location. These findings reveal that land-use legacies and contemporary fire regimes can mediate how prey respond to direct cues of risk. They also suggest that prey may balance the uncertainty associated with cues of predation risk with the urgency of responding to a potential attack by being vigilant and remaining in place.
INTEGRATE-Circ and INTEGRATE-Vis: unbiased detection and visualization of fusion-derived circular RNA
Authors: Webster Jace , Mai Hung , Ly Amy , Maher Christopher 
Published: September 2023

AbstractMotivationBacksplicing of RNA results in circularized rather than linear transcripts, known as circular RNA (circRNA). A recently discovered and poorly understood subset of circRNAs that are composed of multiple genes, termed fusion-derived circular RNAs (fcircRNAs), represent a class of potential biomarkers shown to have oncogenic potential. Detection of fcircRNAs eludes existing analytical tools, making it difficult to more comprehensively assess their prevalence and function. Improved detection methods may lead to additional biological and clinical insights related to fcircRNAs.ResultsWe developed the first unbiased tool for detecting fcircRNAs (INTEGRATE-Circ) and visualizing fcircRNAs (INTEGRATE-Vis) from RNA-Seq data. We found that INTEGRATE-Circ was more sensitive, precise and accurate than other tools based on our analysis of simulated RNA-Seq data and our tool was able to outperform other tools in an analysis of public lymphoblast cell line data. Finally, we were able to validate in vitro three novel fcircRNAs detected by INTEGRATE-Circ in a well-characterized breast cancer cell line.Availability and implementationOpen source code for INTEGRATE-Circ and INTEGRATE-Vis is available at https://www.github.com/ChrisMaherLab/INTEGRATE-CIRC and https://www.github.com/ChrisMaherLab/INTEGRATE-Vis.
AFsample: improving multimer prediction with AlphaFold using massive sampling
Authors: Wallner Björn 
Published: September 2023

Abstract

Summary
The AlphaFold2 neural network model has revolutionized structural biology with unprecedented performance. We demonstrate that by stochastically perturbing the neural network by enabling dropout at inference combined with massive sampling, it is possible to improve the quality of the generated models. We generated ∼6000 models per target compared with 25 default for AlphaFold-Multimer, with v1 and v2 multimer network models, with and without templates, and increased the number of recycles within the network. The method was benchmarked in CASP15, and compared with AlphaFold-Multimer v2 it improved the average DockQ from 0.41 to 0.55 using identical input and was ranked at the very top in the protein assembly category when compared with all other groups participating in CASP15. The simplicity of the method should facilitate the adaptation by the field, and the method should be useful for anyone interested in modeling multimeric structures, alternate conformations, or flexible structures.

Availability and implementation
AFsample is available online at http://wallnerlab.org/AFsample.
Demographic processes, refugia and dispersal routes during the Pleistocene in a sigmodontine rodent assemblage from the South American Pampas
Authors: Ortiz N , Pinotti J D , Trimarchi L I , Gardenal C N , González-Ittig R E , Rivera P C 
Published: September 2023

Abstract
The Pampas of South America represents one of the most extended subtropical–temperate grasslands in the world. This ecoregion was influenced by Pleistocene climate oscillations. The sigmodontine rodent assemblage inhabiting this region is a good model system to analyse the impact of these climate changes on evolutionary histories. We performed a comparative phylogeographical study on seven species to evaluate the concordance of phylogeographical patterns among them, to assess if they experienced congruent and synchronous demographic changes, and posit putative centres of origin and dispersal routes. Four species (Calomys musculinus, Oligoryzomys flavescens, Oxymycterus nasutus and Oligoryzomys nigripes) showed evidence of demographic expansion. In the first three, population increases started during Marine Isotope Stage 5 (MIS 5) while in Ol. nigripes, the rise started during MIS 7; this rise would have continued to the present in all cases. Necromys lasiurus, Scapteromys tumidus and Scapteromys aquaticus did not show a pattern of expansion. Four centres of origin were identified; in general, populations sharing the same putative refugium followed common dispersal routes. Our results indicate that the Pampas offered relatively stable habitats over time, mainly in areas associated with watercourses or coastlines, suggesting that recent Pleistocene climate oscillations have had a moderate impact on this ecoregion compared to other regions of South America.
The Sphagnum cuspidatum complex: phylogeny, species delimitation, and morphology
Authors: Robinson Sean C , Nieto-Lugilde Marta , Duffy Aaron M , Martinez Muñoz Katherine , Aguero Blanka , Merced Amelia , Hassel Kristian , Flatberg Kjell Ivar , Shaw A Jonathan 
Published: September 2023

Abstract
The use of species as a concept is an important metric for assessing biological diversity and ecosystem function. However, delimiting species based on morphological characters can be difficult, especially in aquatic plants that exhibit high levels of variation and overlap. The Sphagnum cuspidatum complex, which includes plants that dominate peatland hollows, provides an example of challenges in species delimitation. Microscopic characters that have been used to define taxa and the possibility that these characters may simply be phenoplastic responses to variation in water availability make species delimitation in this group especially difficult. In particular, the use of leaf shape and serration, which have been used to separate species in the complex, have resulted in divergent taxonomic treatments. Using a combination of high-resolution population genomic data (RADseq) and a robust morphological assessment of plants representing the focal species, we provide evidence to evaluate putative species in this complex. Our data support the recognition of S. cuspidatum, S. fitzgeraldii, S. mississippiense, and S. trinitense as genetically distinct species that can be separated morphologically. These results indicate that S. viride does not differ genetically from S. cuspidatum. Our results are broadly relevant to other aquatic groups where leaf shape and marginal teeth are used to distinguish species.
Rapid cryptic divergence of the Anastrepha fraterculus complex in the Late Pleistocene: a phylogeographical–ecological approach
Authors: Freilij Damián , Vilardi Juan César , Gómez-Cendra Paula 
Published: September 2023

Abstract
The Anastrepha fraterculus complex (AF complex) is a complex of fruit fly species consisting of eight morphotypes distributed across the Americas. In this study, landscape genetics, phylogeographical inferences and coalescence simulations were used to unveil the evolutionary history of the AF complex. Nuclear ribosomal ITS1 sequences from 331 samples distributed in 10 American countries throughout 32 ecoregions and seven biomes were analysed. Results showed high levels of diversity, intraspecific divergence and structuring associated with the different morphotypes of the complex. The analysis of gene flow and genetic diversity showed a clear geographical and environmental pattern. The morphotype–environment association suggested that the cryptic divergence process has involved local adaptation as a mechanism to withstand harsh, novel or variable conditions. The analysis showed a rapid divergence between morphotypes. Haplotypes have been diverging for ~27 000 years before the present, probably enhanced by environmental changes during the Last Glacial Maximum. Diversity estimators and neutrality tests revealed that populations have been experiencing a recent linear growth, starting in the Early Holocene (~11 500 years before the present). The Bayesian phylogeographical and ecological clustering approach detected five spatially separated and ecologically differentiated clusters. Additionally, equatorial Amazonia was indicated to be the most probable ancestral centre of origin for the AF complex.
Olfactory training: effects of multisensory integration, attention towards odors and physical activity
Authors: Li Zetian , Anne Abriat , Hummel Thomas 
Published: September 2023

Abstract
Olfactory training (OT) has been shown to be of value in the treatment of olfactory dysfunction. The present study aimed to investigate whether the efficacy of OT could be modulated with multisensory integration, attention towards odors, odor complexity, or physical activity assessed with a questionnaire. One hundred healthy participants were recruited and divided into 4 groups. Except for controls (n = 26, mean age ± SD = 36 ± 15 years) all participants performed OT 4 times a day. In the “video” group (n = 26, age 39 ± 19 years) OT was performed while watching specific and congruent video sequences. In the “counter” group (n = 24, 38 ± 17 years) participants additionally counted the number of odors 1 day per week, and in the “training only” group no additional measures were taken in addition to OT (n = 24, 38 ± 20 years). “Single-molecule” odorants or “complex mixtures” were distributed randomly for training stimulation. Sniffin’ sticks tests (odor identification, odor discrimination, and odor threshold), cognitive tests, and a series of scales were measured at both baseline and after 3 months of OT. The degree of physical activity was recorded with a questionnaire. Olfactory function improved in the video and counter groups after OT, especially for odor threshold and discrimination. Yet, odor complexity and the degree of physical activity had limited effects on olfactory improvement after OT. Both multisensory interaction and attention towards odors plus OT appeared to facilitate improvement of olfactory function in healthy individuals compared with OT alone and controls, which could provide new promising treatments for clinical applications.
Pattern of cardiovascular admission diagnoses during the month of Ramadan: a single center experience
Authors: Taha Hesham S , Youssef Ghada , Shaker Mirna M , Ghalab Mohamed , Sayed Hadeer G , Abdullah Suzan H , Thabet Mohamed A , Mostafa Amir 
Published: September 2023

Abstract

Background
Fasting Ramadan has been linked to favorable health profile, yet some unhealthy behaviors were shown to affect the progression of cardiovascular diseases during the holy month.

Purpose
To detect the prevalent diagnoses of cardiovascular admissions during the month of Ramadan and to compare them to the admission diagnoses during the rest of the year.

Methods
This retrospective observational study included all patients who were admitted to the Cardiology department and the Coronary Care Unit from April 2019 to May 2022, with 4 Ramadan months included. The median number of specific cardiac admission diagnoses during Ramadan months were compared to the median number of similar admission diagnoses during the other months of the year.

Results
The number of patients admitted during the 4 year-study period were 8170 patients, 14.6% of them (n = 1194 patients) were admitted during the 4 Ramadan months. All cardiovascular diagnoses were comparable during Ramadan admissions as compared to the rest of the year, Table. There was a trend towards higher cardiovascular admission rates during Ramadan in almost all diagnoses except for unstable angina, infective endocarditis and pericardial diseases.

Conclusions
The pattern of specific cardiovascular disease admission during Ramadan was not different from the pattern of admission during the rest of the year. Yet, there were numerically higher cardiovascular admissions during the 4 Ramadan months.
Table Comparison of the median number of admission diagnoses in the 4 Ramadan months and the monthly average of the 4 years Ramadan months Median (range) Monthly average of the 4 years Median (range) P value IHD 145.5 (63) 106 (74) 0.486 * CCS 39.5 (35) 17 (11) 0.057 * ACS 107.5 (71) 89 (83) 0.686 - STEMI 49.5 (34) 39 (24) 0.343 - NSTEMI 41 (46) 39.5 (56) 1.0 - UA 8.5 (8) 10 (4) 0.686 ADHF & cardiogenic shock 113.5 (111) 56 (37) 0.486 Arrhythmia 43.5 (39) 34 (10) 0.343 - AF 18.5 (22) 22.5 (5) 0.686 - SVT 9.5 (15) 6 (9) 0.486 - AFL 6 (12) 2.5 (2) 0.2 - CHB 4 (5) 3.5 (3) 0.686 IE 10.5 (7) 14 (6) 0.2 PE 3 (11) 2.5 (1) 0.686 Pericardial disease 2 (6) 6 (11) 0.2 Hypertensive urgency & emergency 12 (23) 9.5 (7) 1.0 IHD, ischemic heart disease; CCS, chronic coronary syndrome; ACS, acute coronary syndrome; STEMI, ST elevation myocardial infarction; NSTEMI, non-ST elevation myocardial infarction; UA, unstable angina; ADHF, acute decompensated heart failure; AF, atrial fibrillation; SVT, supraventricular tachycardia; AFL, atrial flutter; CHD, complete heart block; IE, infective endocarditis; PE, pulmonary embolism.

Additional Content
An author video to accompany this abstract is available on https://academic.oup.com/eurheartjsupp. Please click on the arrow next to ‘More Content’ and then click on ‘Author videos’.
Steps to bridge the gap for better kidney care for cardiac nurses
Authors: El-Khatib Mohamed , Elsayed Hassan , Kandel Mohamed , Mostafa Saber 
Published: September 2023

Abstract

Background
Kidney diseases have been identified as a major threat to patients with cardiac diseases as they can affect 50% of patients with cardiovascular diseases stages 4 and 5. World Kidney Day (WKD) is a global campaign aimed at raising the awareness of the importance of our kidneys.

Aim
Aswan Heart Centre was celebrating WKD by conducting an educational awareness day aiming to enhance and fill the knowledge gap for healthcare workers and patients.

Process
This event was divided as follows:Patients and families: nurses in different departments of the facility ran several educational sessions, and patients group discussions to promote the wellbeing of patients and families regarding the Chronic Kidney Disease (CKD) and the 8 golden rules through the utilization of some interactive materials such as videos and educational posters written in Arabic.Healthcare workers: An online session was conducted for all nurses in Aswan Heart Centre to enhance the knowledge background regarding chronic kidney disease.
Furthermore, an online survey was completed by the nurses to assess the current understanding of the chronic kidney disease prior the online session. Graph1.

Survey result
71 nursing staff took the survey.

Data analysis
Most of the staff were aware about the kidney health as the average of the correctly answered questions is 67.25% as shown in Chart 1.

Recommendation
Such event raises the awareness about our kidneys and encourage patients for systematic screening.

Additional Content
An author video to accompany this abstract is available on https://academic.oup.com/eurheartjsupp. Please click on the arrow next to ‘More Content’ and then click on ‘Author videos’.
Clinical relevance of salivary pepsin detection in diagnosing gastroesophageal reflux disease subtypes
Authors: Zhang Mengyu , Wu Tingting , Tan Niandi , Chen Songfeng , Zhuang Qianjun , Luo Yu , Xiao Yinglian 
Published: September 2023

Abstract

Background
Gastroesophageal reflux disease (GERD) is heterogeneous with a varied symptom spectrum and reflux profiles. Its definite diagnosis often requires invasive tools including endoscopy or reflux monitoring. The aim of this study was to investigate the clinical relevance of salivary pepsin detection as a non-invasive screening tool to diagnose GERD of different subtypes.

Methods
A total of 77 patients with suspected GERD symptoms and 12 asymptomatic controls were analysed. All participants performed symptom evaluation, upper endoscopy, esophageal manometry, and 24-hour multichannel intraluminal impedance-dual pH probe monitoring. Saliva was self-collected across three different time points: at early fasting, postprandially, and at symptom occurrence. Salivary pepsin levels were measured via Peptest. The optimal threshold of salivary pepsin for diagnosing distal or proximal reflux was determined according to a receiver-operating characteristic curve.

Results
The average salivary pepsin concentration of suspected GERD patients was significantly higher than that of controls (100.63 [68.46, 141.38] vs 67.90 [31.60, 115.06] ng/mL, P = 0.044), although no difference was found among patients with different symptom spectrums. The distal reflux group had a higher average pepsin concentration than non-reflux patients (170.54 [106.31, 262.76] vs 91.13 [63.35, 127.63] ng/mL, P = 0.043), while no difference was observed between the distal reflux group and the proximal reflux group. The optimal cut-off value of salivary pepsin concentration for diagnosing pathological distal reflux was 157.10 ng/mL, which was higher than that for diagnosing pathological proximal reflux (122.65 ng/mL). The salivary pepsin concentration was significantly correlated with distal and proximal reflux parameters.

Conclusions
Salivary pepsin measurement can help in identifying true GERD with pathological distal reflux or proximal reflux, regardless of different symptom spectrums. A higher threshold should be applied for diagnosing distal reflux than for proximal reflux.
Genomic Basis of Adaptive Divergence in Leg Length between Ground- and Tree-Dwelling Species within a Bird Family
Authors: Huang Miaomiao , Liu Yanrui , Lu Xin 
Published: September 2023

AbstractHind limbs of tetrapods vary greatly in length and the variability can be associated with locomotor adaptation. Although the phenotypic evolution has been well documented, the underlying genetic basis remains poorly understood. We address this issue by integrating comparative genomics and functional prediction with a study system consisting of ground-dwelling, long-legged and tree-dwelling, short-legged species within the avian family Paridae. Genome-wide divergence and phenotypic correlation analyses jointly identified five highly divergent genomic regions that are significantly related with the difference in leg length between these two groups. Gene annotation for these regions detected three genes involved in skeletal development, that is, PTPA, BRINP1, and MIGA2, with the first one being under the strongest selection. Furthermore, four single nucleotide polymorphisms (SNPs) in the coding region of PTPA can well distinguish the two groups with distinct leg length. Among the four SNPs, one is non-synonymous mutation, and according to the prediction for protein structure and function, it can affect the 3D structure of the encoded protein by altering the corresponding amino acid's position. The alleles of PTPA were found in all sequenced species of the orders Palaeognathae and Psittaciformes, which typically take a ground locomotion style. A whole-genome scanning across bird species uncovered that the four SNPs are more likely to be present in resident passerines with increased leg length/wing length ratios (a proxy of leg-dependent locomotion efficiency). Our findings provide insight into the molecular evolution of locomotion performance based on leg morphology in birds.