bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel insights in cryptic diversity of snow and glacier ice algae communities combining 18S rRNA gene and ITS2 amplicon sequencing
Authors: Remias Daniel , Procházková Lenka , Nedbalová Linda , Benning Liane G , Lutz Stefanie 
Published: October 2023

Abstract
Melting snow and glacier surfaces host microalgal blooms in polar and mountainous regions. The aim of this study was to determine the dominant taxa at the species level in the European Arctic and the Alps. A standardized protocol for amplicon metabarcoding using the 18S rRNA gene and ITS2 markers was developed. This is important because previous biodiversity studies have been hampered by the dominance of closely related algal taxa in snow and ice. Due to the limited resolution of partial 18S rRNA Illumina sequences, the hypervariable ITS2 region was used to further discriminate between the genotypes. Our results show that red snow was caused by the cosmopolitan Sanguina nivaloides (Chlamydomonadales, Chlorophyta) and two as of yet undescribed Sanguina species. Arctic orange snow was dominated by S. aurantia, which was not found in the Alps. On glaciers, at least three Ancylonema species (Zygnematales, Streptophyta) dominated. Golden-brown blooms consisted of Hydrurus spp. (Hydrurales, Stramenophiles) and these were mainly an Arctic phenomenon. For chrysophytes, only the 18S rRNA gene but not ITS2 sequences were amplified, showcasing how delicate the selection of eukaryotic ‘universal’ primers for community studies is and that primer specificity will affect diversity results dramatically. We propose our approach as a ‘best practice’.
Gray Divorce During the COVID-19 Pandemic
Authors: Brown Susan L , Lin I-Fen , Julian Christopher A 
Published: October 2023

Abstract

Objectives
Drawing on emerging evidence that the pandemic appears to have impeded both the divorce process and actual divorces, we examined whether the gray divorce rate (i.e., divorce among adults aged 50+) declined following the onset of the COVID-19 pandemic.

Methods
Data from the 2019 and 2021 American Community Survey (ACS) were used to track changes in gray divorce. With the 2021 ACS, we estimated pandemic-era gray divorce rates across sociodemographic subgroups for middle-aged and older adults. We then pooled the 2019 (N = 892,700) and 2021 (N = 898,828) data to examine whether the risk of divorce changed with the onset of the pandemic net of sociodemographic characteristics, distinguishing trends for middle-aged versus older adults.

Results
The gray divorce rate dropped following the onset of the pandemic. This drop was more pronounced among middle-aged than older adults. For older adults, the divorce rate essentially stalled.

Discussion
The gray divorce rate now mirrors the overall trend of modest decline in U.S. divorce patterns. Whether the gray divorce rate continues to shrink as society transitions to a postpandemic environment awaits future research.
Memory Trajectories and Disability Among Older Couples: The Mediating Role of Depressive Symptoms
Authors: Kong Dexia , Lu Peiyi , Jiang Da , Chan Helen Yue Lai 
Published: October 2023

Abstract

Objectives
Using a dyadic approach, this study examined the mediating effect of depressive symptoms on the longitudinal relationships between husbands’ and wives’ memory trajectories and their prospective disability status.

Methods
Longitudinal data from the Health and Retirement Study 2004–2018 were used. Older (aged 50+) heterosexual couples who had no limitations in the activity of daily living at the baseline (2004) were included (N = 1,310). Latent class growth analysis grouped wives and husbands into distinct memory trajectories in 2004–2014. A structural equation model examined the actor and partner effects of memory trajectories on depressive symptoms in 2016 and disability status in 2018. The mediating effect of depressive symptoms was tested.

Results
A total of 4 distinct memory trajectories were found: persistently high, high and slow decline, moderate and slow decline, and low and rapid decline. Only the wife’s low and rapid decline memory trajectory predicted her own more depressive symptoms (β = 0.588, 95% CI: 0.209, 0.967) and her husband’s more depressive symptoms (β = 0.326, 95% CI: 0.004, 0.648). Meanwhile, depressive symptoms had strong and significant actor effects on disability (β = 0.046, 95% CI: = 0.036, 0.057 for wives; β = 0.060, 95% CI: = 0.046, 0.074 for husbands).

Discussion
The wife’s low and rapid decline trajectory was associated with her own and her husband’s more depressive symptoms, which in turn increased the disability risk for both partners. Timely identification and treatment of memory decline among wives have the potential to mitigate couples’ depressive symptoms and, ultimately, disability risks.
Smart Speaker and ICT Use in Relationship With Social Connectedness During the Pandemic: Loneliness and Social Isolation Found in Older Adults in Low-Income Housing
Authors: Chung Jane , Gendron Tracey , Winship Jodi , Wood Rachel E , Mansion Natalie , Parsons Pamela , Demiris George 
Published: October 2023

Abstract

Background and Objectives
Social well-being of older adults living in low-income housing was disproportionately affected by the coronavirus disease 2019 pandemic. We explored low-income residents’ experiences of social isolation and loneliness and strategies to remain socially connected during the pandemic.

Research Design and Methods
As part of a larger, 3-phase user-centered design study, we conducted a qualitative study using focus groups to gain insights into social isolation experiences and the role of information and communication technologies (ICTs), including smart speakers, in social connectedness (N = 25, 76% African American). We also collected survey data to describe social isolation, loneliness, and current ICT use in the sample. Participants included both smart speaker users and nonusers.

Results
Experiences of social isolation and loneliness varied by participants’ sociodemographic characteristics and previous experiences with smart speakers. Qualitative analysis showed participants demonstrated coping strategies developed during the pandemic to adapt to new norms of connecting with others, including technology-enabled social interactions. Participants expressed a strong desire to build community together in their facilities and highlighted the potential role of smart speakers in making meaningful social connections, encompassing safety checks to have a means for emergencies, and providing a virtual companion. Access, digital literacy, training, security, and privacy issues were discussed as factors affecting their adoption of new ICT for enhanced social connectedness.

Discussion and Implications
This study highlights the importance of understanding the unique social isolation experience, demographics, and social determinants of health of low-income residents to develop ICT-based interventions for social connectedness.
Cellsnake: a user-friendly tool for single-cell RNA sequencing analysis
Authors: Umu Sinan U , Rapp Vander-Elst Karoline , Karlsen Victoria T , Chouliara Manto , Bækkevold Espen Sønderaal , Jahnsen Frode Lars , Domanska Diana 
Published: October 2023

Abstract

Background
Single-cell RNA sequencing (scRNA-seq) provides high-resolution transcriptome data to understand the heterogeneity of cell populations at the single-cell level. The analysis of scRNA-seq data requires the utilization of numerous computational tools. However, nonexpert users usually experience installation issues, a lack of critical functionality or batch analysis modes, and the steep learning curves of existing pipelines.

Results
We have developed cellsnake, a comprehensive, reproducible, and accessible single-cell data analysis workflow, to overcome these problems. Cellsnake offers advanced features for standard users and facilitates downstream analyses in both R and Python environments. It is also designed for easy integration into existing workflows, allowing for rapid analyses of multiple samples.

Conclusion
As an open-source tool, cellsnake is accessible through Bioconda, PyPi, Docker, and GitHub, making it a cost-effective and user-friendly option for researchers. By using cellsnake, researchers can streamline the analysis of scRNA-seq data and gain insights into the complex biology of single cells.
Developing best practices for genotyping-by-sequencing analysis in the construction of linkage maps
Authors: Taniguti Cristiane Hayumi , Taniguti Lucas Mitsuo , Amadeu Rodrigo Rampazo , Lau Jeekin , Gesteira Gabriel de Siqueira , Oliveira Thiago de Paula , Ferreira Getulio Caixeta , Pereira Guilherme da Silva , Byrne David , Mollinari Marcelo , Riera-Lizarazu Oscar , Garcia Antonio Augusto Franco 
Published: October 2023

Abstract

Background
Genotyping-by-sequencing (GBS) provides affordable methods for genotyping hundreds of individuals using millions of markers. However, this challenges bioinformatic procedures that must overcome possible artifacts such as the bias generated by polymerase chain reaction duplicates and sequencing errors. Genotyping errors lead to data that deviate from what is expected from regular meiosis. This, in turn, leads to difficulties in grouping and ordering markers, resulting in inflated and incorrect linkage maps. Therefore, genotyping errors can be easily detected by linkage map quality evaluations.

Results
We developed and used the Reads2Map workflow to build linkage maps with simulated and empirical GBS data of diploid outcrossing populations. The workflows run GATK, Stacks, TASSEL, and Freebayes for single-nucleotide polymorphism calling and updog, polyRAD, and SuperMASSA for genotype calling, as well as OneMap and GUSMap to build linkage maps. Using simulated data, we observed which genotype call software fails in identifying common errors in GBS sequencing data and proposed specific filters to better handle them. We tested whether it is possible to overcome errors in a linkage map using genotype probabilities from each software or global error rates to estimate genetic distances with an updated version of OneMap. We also evaluated the impact of segregation distortion, contaminant samples, and haplotype-based multiallelic markers in the final linkage maps. Through our evaluations, we observed that some of the approaches produce different results depending on the dataset (dataset dependent) and others produce consistent advantageous results among them (dataset independent).

Conclusions
We set as default in the Reads2Map workflows the approaches that showed to be dataset independent for GBS datasets according to our results. This reduces the number of required tests to identify optimal pipelines and parameters for other empirical datasets. Using Reads2Map, users can select the pipeline and parameters that best fit their data context. The Reads2MapApp shiny app provides a graphical representation of the results to facilitate their interpretation.
Characterizing and predicting ccRCC-causing missense mutations in Von Hippel-Lindau disease
Authors: Serghini Adam , Portelli Stephanie , Troadec Guillaume , Song Catherine , Pan Qisheng , Pires Douglas E V , Ascher David B 
Published: October 2023

Abstract
Background: Mutations within the Von Hippel-Lindau (VHL) tumor suppressor gene are known to cause VHL disease, which is characterized by the formation of cysts and tumors in multiple organs of the body, particularly clear cell renal cell carcinoma (ccRCC). A major challenge in clinical practice is determining tumor risk from a given mutation in the VHL gene. Previous efforts have been hindered by limited available clinical data and technological constraints. Methods: To overcome this, we initially manually curated the largest set of clinically validated VHL mutations to date, enabling a robust assessment of existing predictive tools on an independent test set. Additionally, we comprehensively characterized the effects of mutations within VHL using in silico biophysical tools describing changes in protein stability, dynamics and affinity to binding partners to provide insights into the structure-phenotype relationship. These descriptive properties were used as molecular features for the construction of a machine learning model, designed to predict the risk of ccRCC development as a result of a VHL missense mutation. Results: Analysis of our model showed an accuracy of 0.81 in the identification of ccRCC-causing missense mutations, and a Matthew’s Correlation Coefficient of 0.44 on a non-redundant blind test, a significant improvement in comparison to the previous available approaches. Conclusion: This work highlights the power of using protein 3D structure to fully explore the range of molecular and functional consequences of genomic variants. We believe this optimized model will better enable its clinical implementation and assist guiding patient risk stratification and management.
Modeling the habitat suitability of two exotic freshwater crayfishes in Mesoamerica and the Caribbean:Cherax quadricarinatus(von Martens, 1868) andProcambarus clarkiiGirard, 1852 (Decapoda: Astacidea: Parastacidae, Cambaridae)
Authors: Azofeifa-Solano Juan Carlos , Villalobos-Rojas Fresia , Romero-Chaves Raquel , Wehrtmann Ingo S 
Published: October 2023

AbstractBiological invasions are among the main threats to the diversity of freshwater ecosystems, particularly invasions of freshwater crayfishes, which have negatively impacted native populations and ecosystem functions. Various invasions of freshwater crayfishes have been relatively well documented, allowing the use of Ecological Niche Modeling (ENM) techniques to forecast their potential invasive distribution. Modeling the most environmentally suitable areas for exotic species can provide guidelines to allocate resources, thus contributing to the control and management of invasions. We modelled the potential distribution of Cherax quadricarinatus (von Martens, 1868) and Procambarus clarkiiGirard, 1852 in Mesoamerica and the Caribbean using global occurrence data and ten environmental variables to ensemble a model using nine different algorithms. Our models showed that C. quadricarinatus has a high probability of invasion in tropical lowland areas, with the presence of exotic populations of this species already reported. Our results support that P. clarkii has a higher probability of invasion in some of the mountain ranges and plateaus of the study region, where this species has already established non-native populations. These models visualize the high-risk areas of invasion of these two non-native crayfish species in Mesoamerica and the Caribbean. A regional approach for monitoring and control of the invasive populations is encouraged as well as regulations for trade and aquaculture of freshwater crayfishes.
Improved snow ablation optimizer with heat transfer and condensation strategy for global optimization problem
Authors: Jia Heming , You Fangkai , Wu Di , Rao Honghua , Wu Hangqu , Abualigah Laith 
Published: October 2023

Abstract
The snow ablation optimizer (SAO) is a new metaheuristic algorithm proposed in April 2023. It simulates the phenomenon of snow sublimation and melting in nature and has a good optimization effect. The SAO proposes a new two-population mechanism. By introducing Brownian motion to simulate the random motion of gas molecules in space. However, as the temperature factor changes, most water molecules are converted into water vapor, which breaks the balance between exploration and exploitation, and reduces the optimization ability of the algorithm in the later stage. Especially in the face of high-dimensional problems, it is easy to fall into local optimal. In order to improve the efficiency of the algorithm, this paper proposes an improved snow ablation optimizer with heat transfer and condensation strategy (SAOHTC). Firstly, this article proposes a heat transfer strategy, which utilizes gas molecules to transfer heat from high to low temperatures and move their positions from low to high temperatures, causing individuals with lower fitness in the population to move towards individuals with higher fitness, thereby improving the optimization efficiency of the original algorithm. Secondly, a condensation strategy is proposed, which can transform water vapor into water by simulating condensation in nature, improve the deficiency of the original two-population mechanism, and improve the convergence speed. Finally, to verify the performance of SAOHTC, in this paper, two benchmark experiments of IEEE CEC2014 and IEEE CEC2017 and five engineering problems are used to test the superior performance of SAOHTC.
Simultaneous second-stage Fowler–Stephens Orchiopexy and microvascular testicular autotransplantation in a patient with prune belly syndrome with cryptorchidism
Authors: Larson Brandon M , Francis Ashish , McMahon Daniel R , Massanyi Eric Z , Murthy Ananth 
Published: October 2023

Abstract
We present a case of simultaneous second-stage Fowler–Stephens Orchiopexy (FSO) with microvascular testicular autotransplantation for cryptorchidism and in a patient with prune belly syndrome. At 5 months old, the patient underwent laparoscopic bilateral first-stage FSO with the right testicle located 1 cm from the liver and the left slightly more caudal. An ultrasound on postoperative Day 72 following second-stage FSO and microvascular autotransplantation showed patent testicular vasculature. Our experience shows that this combination technique is safe and effective to supercharge the testicle and augment collateral vessels if clinical suspicion for monotherapy failure is high.
Bony mallet toe of the hallux treated with screws: a case report
Authors: Tomizuka Yoshiaki , Nagao Soya , Tanimoto Koji , Okugawa Kana , Shiraishi Hiroko , Iwama Genki , Kinoshita Tomonori , Suruga Makoto , Lee Hyunho , Nakanishi Kazuyoshi 
Published: October 2023

Abstract
Traumatic avulsion fracture of the distal phalanx of the hallux, known as the bony mallet toe of the hallux, is rare, and there is no consensus regarding its treatment. Few reports of treatment methods exist, such as nonsurgical treatment using a splint, Kirschner wires, and suture anchors, but there are no reports of screw fixation. We describe the case of a 54-year-old man with a bony mallet toe of the hallux treated with screws and augmented with strong sutures. The interphalangeal joint of the hallux was fixed with a Kirschner wire for 4 weeks after surgery, and weight bearing was allowed on the hallux 5 weeks postoperatively. A total of 20 months after the surgery, the patient had no symptoms or complications. Because of screw fixation and augmentation with strong sutures, fixation strength increased. We showed the feasibility of this new technique for treating an uncommon bony mallet toe of the hallux.
The Victorian anti-vaccination discourse corpus (VicVaDis): construction and exploration
Authors: Hardaker Claire , Deignan Alice , Semino Elena , Coltman-Patel Tara , Dance William , Demjén Zsófia , Sanderson Chris , Gatherer Derek 
Published: October 2023

Abstract
This article introduces and explores the 3.5-million-word Victorian Anti-Vaccination Discourse Corpus (VicVaDis). The corpus is intended to provide a (freely accessible) historical resource for the investigation of the earliest public concerns and arguments against vaccination in England, which revolved around compulsory vaccination against smallpox in the second half of the 19th century. It consists of 133 anti-vaccination pamphlets and publications gathered from 1854 to 1906, a span of 53 years that loosely coincides with the Victorian era (1837–1901). This timeframe was chosen to capture the period between the 1853 Vaccination Act, which made smallpox vaccination for babies compulsory, and the 1907 Act that effectively ended the mandatory nature of vaccination. After an overview of the historical background, this article describes the rationale, design and construction of the corpus, and then demonstrates how it can be exploited to investigate the main arguments against compulsory vaccination by means of widely accessible corpus linguistic tools. Where appropriate, parallels are drawn between Victorian and 21st-century vaccine-hesitant attitudes and arguments. Overall, this article demonstrates the potential of corpus analysis to add to our understanding of historical concerns about vaccination.
Simulating ionization feedback from young massive stars: impact of numerical resolution
Authors: Deng Yunwei , Li Hui , Kannan Rahul , Smith Aaron , Vogelsberger Mark , Bryan Greg L 
Published: October 2023

ABSTRACT
Modelling galaxy formation in hydrodynamic simulations has increasingly adopted various radiative transfer methods to account for photoionization feedback from young massive stars. However, the evolution of H ii regions around stars begins in dense star-forming clouds and spans large dynamical ranges in both space and time, posing severe challenges for numerical simulations in terms of both spatial and temporal resolution that depends strongly on gas density (∝n−1). In this work, we perform a series of idealized H ii region simulations using the moving-mesh radiation-hydrodynamic code arepo-rt to study the effects of numerical resolution. The simulated results match the analytical solutions and the ionization feedback converges only if the Strömgren sphere is resolved by at least 10–100 resolution elements and the size of each time integration step is smaller than 0.1 times the recombination time-scale. Insufficient spatial resolution leads to reduced ionization fraction but enhanced ionized gas mass and momentum feedback from the H ii regions, as well as degrading the multiphase interstellar medium into a diffuse, partially ionized, warm (∼8000 K) gas. On the other hand, insufficient temporal resolution strongly suppresses the effects of ionizing feedback. This is because longer time-steps are not able to resolve the rapid variation of the thermochemistry properties of the gas cells around massive stars, especially when the photon injection and thermochemistry are performed with different cadences. Finally, we provide novel numerical implementations to overcome the above issues when strict resolution requirements are not achievable in practice.
Apparent luminosity and pulsed fraction affected by gravitational lensing of accretion columns in bright X-ray pulsars
Authors: Markozov Ivan D , Mushtukov Alexander A 
Published: October 2023

ABSTRACT
The luminosity of X-ray pulsars is their key parameter determining the geometry and physical conditions of the accretion flow both on the spatial scales of a binary system and on much smaller scales of emitting regions located close to the stellar surface. Traditionally, the luminosity of X-ray pulsars is estimated out of the X-ray energy flux averaged over the pulsed period and the estimated distance to the source. Due to the anisotropy of X-ray emission, the luminosity estimated on the base of the observed pulse profile can differ from the actual one. Super-cw2ritical X-ray pulsars with accretion columns are of particular interest because the X-ray flux from columns is a matter of strong gravitational lensing by a neutron star. Using toy model of an accretion column, we simulate beam patterns in super-critical X-ray pulsars, construct theoretical pulse profiles for different geometries and mutual orientations of pulsars and distant observers and show that despite strong light bending, the typical deviation of the apparent luminosity from the actual one is $\sim 20~{{\ \rm per \, cent}}$ only, and in $\sim 90~{{\ \rm per \, cent}}$ of cases, the apparent luminosity 0.8L ≲ Lapp ≲ 1.25L. However, the shape of the pulse profiles is strongly affected by the geometry of the emitting region. We show that the appearance and growth of accretion columns tend to be accompanied by an increase of observed pulsed fraction, which is in agreement with the recent observations of bright X-ray transients.