bluuebunny/crossref_metadata_2025 huggingface dataset:
Review of Marine Invasive Species Distribution Pattern in Indonesia
Authors: Zalzabil A R , Lestari D F , Fadillah S N , Maharani R S , Zulfikri M A , Farahdillah R E , Zabrina W S , Azzachra S , Lamtiur S L M , Amigunani Z W , Cahyati N A D , Nabihah N , Christy P A , Djemadjid S P , Nuzulia S R , Alfarabi F M , Zahrani S R , Hasyim M W , Sidhiq M F , Mulkiyah M D , Maysaroh S , Febridelita A , Cakasana Nadya , Madduppa H M
Published: October 2023

Marine invasive species may replace native species, change habitats, and affect community structures and ecological processes. The impact of introduced species can seriously damage areas and high-value biodiversity in Indonesian waters. This study aims to determine Indonesia’s distribution pattern of marine invasive species based on literature review. The data were collected through literature studies from various publications. Mollusca is the highest invasive phylum found which is 27%, followed by Echinoderms 16% and Chlorophyta 13% from all of the total data collected. The distribution of marine invasive species is influenced by ships, canals, and aquaculture activities, and introduced species to a new habitat. The publication of articles on invasive species are dominated by western part of Indonesia data as much 46 from 85 tabulated data. The habitat of invasive species is dominated by coral reefs used by various biota as a self-defence area, spawning ground, and shelter from predatory threats. As many as 64% of invasive species have Not Evaluated (NE) status at the IUCN site.
Synthesis of heparin-and-poloxamer P407-based nanogel carrying PTX for orientating in treatment of breast cancer
Authors: Nguyen Ngoc The
Published: October 2023

In this study, nanogels based on the conjugation of heparin and poloxamer P407 (HR-P407) with different grafting ratios were successfully synthesised. The structural properties of products were evaluated by Fourier-transform infrared spectroscopy (FT-IR) and proton nuclear magnetic resonance (1H-NMR). The morphology and size of nanoparticles were assessed by dynamic light scattering (DLS) method, which showed that particle size distribution was from 144 nm to 214 nm. The HR-P407 nanogel systems were biocompatible and non-toxic to healthy cells. While free PTX displayed rapid and potent cytotoxic effects, PTX released from HR-P407 (1:10)/PTX demonstrated a gradual and sustained cytotoxicity. This controlled release mechanism allowed prolonged drug exposure, reducing acute toxicity and enhancing cytotoxicity over time. The results suggest that the synthesised nanogels can be used as an effective hydrophobic anticancer drug carrier system.
Characterization of pulsed-tungsten inert gas (PTIG) welding on AA5754-H111 alloy: mechanical properties and microstructural analysis
Authors: Tamil Kumaran G , Jayakumar K S , Amala Mithin Minther Singh A
Published: October 2023

Aluminium and its alloys were widely used in engineering because they are lightweight, strong, and resistant to corrosion. However, using standard arc welding techniques can be difficult when dealing with such materials. Pulsed-Tungsten Inert Gas (PTIG) welding is being researched as a potential solution to this problem. This study is the first to investigate the use of the straightforward and intuitive PTIG technique on the ubiquitous AA5754 wrought aluminium alloy. Welded samples were supplied for examination of mechanical parameters such as surface hardness and strength under impact and tensile loading. The results of a statistical analysis of the mechanical characterization of a PTIG-welded permanent joint fabricated from AA5754 aluminium alloy were presented and discussed. The heat-affected zone (HAZ) on the AA5754 retracting side of the weld had a hardness of 50–70 Hv0.5, while the HAZ on the AA5756 side had a hardness of 90–100 Hv0.5, as measured by testing on the perfect weld specimen. Samples taken from different parts of the weldment all showed that the HAZ is the softest and weakest. The shattered surface of the welded sample consisted of flat facets and quasi-cleavage patterns, as revealed by scanning electron microscopy. Analysis of the HAZ microstructure revealed widespread dissolution of Mg2Si precipitates in the AA5754-H111.
Enhancing photo voltaic solar panel efficiency by using a combination of silica based and phase change material coating
Authors: Sankaran Durairaj , Pappan Balakrishnan , Balakrishnan Kirubakaran
Published: October 2023

This study attempts to enhance the overall efficiency of a photo voltaic solar panel by employing a dual-coating approach. The initial coating consists of a Silica-based anti-reflective material synthesized through an acid-catalyzed sol–gel process, utilizing cetyltrimethylammonium bromide as a template. Subsequently, the second coating was formulated using a phase change material, such as expanded graphite infused with paraffin jelly. The coating materials were characterized using Ultraviolet-Visual ray spectroscopy, Fourier Transform-Infrared Ray spectroscopy, Field Emission-Scanning Electron Microscopy, x-ray Diffraction sepctroscopy, and Thermogravimetry analysis. The panels’ performance had been investigated under three conditions: uncoated, single-coated, and double-coated. These panels were subjected to both indoor and outdoor experiments. Indoor tests were conducted in a laboratory with induced irradiance levels of 350, 600, and 850 W/m2. The corresponding variations in maximum power output, maximum surface temperature and peak current were recorded. For the outdoor experiments, two sets of panels were installed on a rooftop. One set underwent daily surface cleaning, while the other was left untouched, allowing dust accumulation. Over a 45-day period, outdoor experiments were carried out (daily cleaned and unclean panels) to examine the impact of dust accumulation on power loss, current, voltage, surface temperature, energy generation and panel efficiency. Upon comparing the performance of uncoated, single-coated, and double-coated solar panels, it was observed that photovoltaic solar panels coated with both silica-based anti-reflective coating and paraffin jelly-infused expanded graphite coating exhibited superior performance when compared to other coating options.
A disruptive clickable antibody design for the generation of antibody-drug conjugates
Authors: Rakotoarinoro Nathanaël , Dyck Yan F K , Krebs Simon K , Assi Miriam-Kousso , Parr Maria K , Stech Marlitt
Published: October 2023

Background

Antibody-drug conjugates are cancer therapeutics that combine specificity and toxicity. A highly cytotoxic drug is covalently attached to an antibody that directs it to cancer cells. The conjugation of the drug-linker to the antibody is a key point in research and development as well as in industrial production. The consensus is to conjugate the drug to a surface-exposed part of the antibody to ensure maximum conjugation efficiency. However, the hydrophobic nature of the majority of drugs used in antibody-drug conjugates leads to an increased hydrophobicity of the generated antibody-drug conjugates, resulting in higher liver clearance and decreased stability.

Methods

In contrast, we describe a non-conventional approach in which the drug is conjugated in a buried part of the antibody. To achieve this, a ready-to-click antibody design was created in which an azido-based non-canonical amino acid is introduced within the Fab cavity during antibody synthesis using nonsense suppression technology. The Fab cavity was preferred over the Fc cavity to circumvent issues related to cleavage of the IgG1 lower hinge region in the tumor microenvironment.

Results

This antibody design significantly increased the hydrophilicity of the generated antibody-drug conjugates compared to the current best-in-class designs based on non-canonical amino acids, while conjugation efficiency and functionality were maintained. The robustness of this native shielding effect and the versatility of this approach were also investigated.

Conclusions

This pioneer design may become a starting point for the improvement of antibody-drug conjugates and an option to consider for protecting drugs and linkers from unspecific interactions.
Normative Data for the 12-Item Sniffin’ Sticks Odor Identification Test in Older Adults
Authors: Kamath Vidyulata , Chen Honglei , Shrestha Srishti , Mechanic-Hamilton Dawn , Deal Jennifer A , Mosley Thomas H , Schneider Andrea L C
Published: October 2023

Objective

Quantitative olfactory assessment has demonstrated clinical utility for the evaluation of a range of neurologic, psychiatric, and sinonasal conditions. Here, we provide age, sex, race, and education-specific normative data for the 12-item Sniffin Sticks Odor Identification Test (SSOIT-12) in older Black and White U.S. adults without preclinical or clinical dementia or sinonasal disease.

Method

A sample of 2,224 Atherosclerosis Risk in Communities study participants aged 66–89 years were included. A normative regression equation was developed using a linear model for the association of age, sex, race, and education with odor identification score. Regression-based normative mean scores and percentiles were generated by age, sex, race, and education groups.

Results

Participants (mean age = 74 years, 59% women, 20% Black, 48% > high school education) had a mean SSOIT-12 score of 9.8. Age, sex, race, and education were all associated with odor identification performance (all ps < .05). A linear regression model for the predicted SSOIT-12 score was developed for use with an individual’s actual SSOIT-12 score in order to calculate the Z-score and corresponding percentile for a specific age, sex, race, and education group. Data are also reported in tabular format.

Conclusions

Our study provides SSOIT-12 normative data obtained from a large population of White and Black older adults without preclinical or clinical dementia or sinonasal disease living in the USA. These findings can aid clinicians in assessing the degree of olfactory loss, establishing concordance with a person’s perception of olfactory difficulties and quantitatively monitoring changes in olfactory performance over time.
JSONWP: a static website generator for protein bioinformatics research
Authors: Kilinc Mesih , Jia Kejue , Jernigan Robert L
Published: October 2023

Motivation

Presenting the integrated results of bioinformatics research can be challenging and requires sophisticated visualization components, which can be time-consuming to develop. This article presents a new way to effectively communicate research findings.

Results

We have developed a static web page generator, JSONWP, which is specifically designed for protein bioinformatics research. Utilizing React (a JavaScript library used to build interactive and dynamic user interfaces for web applications), we have integrated publicly available bioinformatics visualization components to provide standardized access to these components. JSON (or JavaScript Object Notation, is a lightweight textual data format often used to structure and exchange information between different software tools.) is used as the input source due to its ability to represent nearly all types of data using key and value pairs. This allows researchers to use their preferred programming language to create a JSON representation, which can then be converted into a website by JSONWP. No server or domain is required to host the website, as only the publicly accessible JSON file is required.

Conclusions

Overall, JSONWP provides a useful new tool for bioinformatics researchers to effectively communicate their findings. The open-source implementation is located at https://github.com/MesihK/react-json-wpbuilder, and the tool can be used at jsonwp.onrender.com.
An evolution strategy approach for the balanced minimum evolution problem
Authors: Gasparin Andrea , Camerota Verdù Federico Julian , Catanzaro Daniele , Castelli Lorenzo
Published: October 2023

Motivation

The Balanced Minimum Evolution (BME) is a powerful distance based phylogenetic estimation model introduced by Desper and Gascuel and nowadays implemented in popular tools for phylogenetic analyses. It was proven to be computationally less demanding than more sophisticated estimation methods, e.g. maximum likelihood or Bayesian inference while preserving the statistical consistency and the ability to run with almost any kind of data for which a dissimilarity measure is available. BME can be stated in terms of a nonlinear non-convex combinatorial optimization problem, usually referred to as the Balanced Minimum Evolution Problem (BMEP). Currently, the state-of-the-art among approximate methods for the BMEP is represented by FastME (version 2.0), a software which implements several deterministic phylogenetic construction heuristics combined with a local search on specific neighbourhoods derived by classical topological tree rearrangements. These combinations, however, may not guarantee convergence to close-to-optimal solutions to the problem due to the lack of solution space exploration, a phenomenon which is exacerbated when tackling molecular datasets characterized by a large number of taxa.

Results

To overcome such convergence issues, in this article, we propose a novel metaheuristic, named PhyloES, which exploits the combination of an exploration phase based on Evolution Strategies, a special type of evolutionary algorithm, with a refinement phase based on two local search algorithms. Extensive computational experiments show that PhyloES consistently outperforms FastME, especially when tackling larger datasets, providing solutions characterized by a shorter tree length but also significantly different from the topological perspective.

Availability and implementation

The software and the data are available at https://github.com/andygaspar/PHYLOES.
TT3D: Leveraging precomputed protein 3D sequence models to predict protein–protein interactions
Authors: Sledzieski Samuel , Devkota Kapil , Singh Rohit , Cowen Lenore , Berger Bonnie
Published: October 2023

Motivation

High-quality computational structural models are now precomputed and available for nearly every protein in UniProt. However, the best way to leverage these models to predict which pairs of proteins interact in a high-throughput manner is not immediately clear. The recent Foldseek method of van Kempen et al. encodes the structural information of distances and angles along the protein backbone into a linear string of the same length as the protein string, using tokens from a 21-letter discretized structural alphabet (3Di).

Results

We show that using both the amino acid sequence and the 3Di sequence generated by Foldseek as inputs to our recent deep-learning method, Topsy-Turvy, substantially improves the performance of predicting protein–protein interactions cross-species. Thus TT3D (Topsy-Turvy 3D) presents a way to reuse all the computational effort going into producing high-quality structural models from sequence, while being sufficiently lightweight so that high-quality binary protein–protein interaction predictions across all protein pairs can be made genome-wide.

Availability and Implementation

TT3D is available at https://github.com/samsledje/D-SCRIPT. An archived version of the code at time of submission can be found at https://zenodo.org/records/10037674.
Training Pearl: Welcome to the CC360 Fellow’s Corner
Authors: Michel Hilary K , Malter Lisa
Published: October 2023

The Crohn’s & Colitis Foundation has grown to appreciate the needs of gastroenterology trainees with numerous initiatives designed to provide education, academic opportunities, and mentoring in inflammatory bowel disease (IBD) in recent years. The editors and staff at Crohn’s and Colitis 360 (CC360) have launched 2 new initiatives, the Fellow’s Corner and the CC360 Editorial Fellowship, to support trainees in gaining knowledge and skills regarding peer review and publication as well as offering guidance on training in IBD and an opportunity for publication in this peer-reviewed, open access, quarterly online journal. These opportunities are described in this manuscript.
Diagnostic and prognostic value of the sex-specific 99th percentile of four high-sensitivity cardiac troponin assays in patients with suspected myocardial infarction
Authors: Lehmacher Jonas , Sörensen Nils Arne , Twerenbold Raphael , Goßling Alina , Haller Paul Michael , Hartikainen Tau Sarra , Schock Alina , Toprak Betül , Zeller Tanja , Westermann Dirk , Neumann Johannes Tobias
Published: October 2023

Aims

High-sensitivity cardiac troponin (hs-cTn) assays are used for detection of myocardial infarction (MI). Ninety-ninth percentiles show wide inter-assay variation. The use of sex-specific cut-offs is recommended as definitory cut-off for MI. We compared diagnostic performance and prognostic value of sex-specific 99th percentiles of four hs-cTn assays in patients with suspected MI.

Methods and results

Concentrations of four hs-cTn assays were measured at presentation and after 3 h in patients with suspected MI. Final diagnoses were adjudicated according to the 4th Universal Definition of MI. Unisex and sex-specific 99th percentiles were evaluated as diagnostic cut-offs following the ESC 0/3 h algorithm. These cut-offs were used in Cox-regression analyses to investigate the association with a composite endpoint of MI, revascularization, cardiac rehospitalization, and death. Non-ST-elevation MI was diagnosed in 368 of 2718 patients. Applying the unisex 99th percentile, Elecsys hs-cTnT provided highest negative predictive value (NPV) of 99.7 and a positive predictive value (PPV) of 75.9. The analysed hs-cTnI assays showed slightly lower NPVs and comparable PPVs [Architect (NPV 98.0, PPV of 71.4); Atellica (NPV 97.7, PPV of 76.1); Pathfast (NPV 97.7, PPV of 66.6)]. Application of sex-specific 99th percentiles did not significantly affect diagnostic performance. Concentrations above 99th percentile were independent predictors for impaired long-term outcome (hazard ratios 1.2–1.5, P < 0.001).

Conclusion

We describe a good diagnostic accuracy of four hs-cTn assays using the assay-specific 99th percentile for detection of MI. Application of sex-specific 99th percentiles did neither affect diagnostic performance nor prognostic value significantly. Finally, values above the 99th percentile were associated with poor long-term outcome.
Triglyceride-glucose index, low-density lipoprotein levels, and cardiovascular outcomes in chronic stable cardiovascular disease: results from the ONTARGET and TRANSCEND trials
Authors: Haring Bernhard , Schumacher Helmut , Mancia Giuseppe , Teo Koon K , Lonn Eva M , Mahfoud Felix , Schmieder Roland , Mann Johannes F E , Sliwa Karen , Yusuf Salim , Böhm Michael
Published: October 2023

Aims

The triglyceride-glucose index (TyG) has been proposed as an alternative to insulin resistance and as a predictor of cardiovascular outcomes. Little is known on its role in chronic stable cardiovascular disease and its predictive power at controlled low density lipoprotein (LDL) levels.

Methods and results

Our study population consisted of 29 960 participants in the ONTARGET and TRANSCEND trials that enrolled patients with known atherosclerotic disease. Triglycerides and glucose were measured at baseline. TyG was calculated as the logarithmized product of fasting triglycerides and glucose divided by 2. The primary endpoint of both trials was a composite of cardiovascular death, myocardial infarction, stroke, or hospitalization for heart failure. The secondary endpoint was all-cause death and the components of the primary endpoint. Cox proportional hazards models were used to estimate hazard ratios (HRs) and 95% confidence intervals (CI) with extensive covariate adjustment for demographic, medical history, and lifestyle factors. During a mean follow-up of 4.3 years, 4895 primary endpoints and 3571 all-cause deaths occurred. In fully adjusted models, individuals in the highest compared to the lowest quartile of the TyG index were at higher risk for the primary endpoint (HR 1.14; 95% CI 1.05–1.25) and for myocardial infarction (HR 1.30; 95% CI 1.11–1.53). A higher TyG index did not associate with the primary endpoint in individuals with LDL levels < 100 mg/dL.

Conclusion

A higher TyG index is associated with a modestly increased cardiovascular risk in chronic stable cardiovascular disease. This association is largely attenuated when LDL levels are controlled.

Registration

www.clinicaltrials.gov: NCT00153101
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

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

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

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

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

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

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

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

Biological 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

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

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

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.
Refugees and migrants at the heart of the synergies between universal health coverage, health security and health promotion
Authors: Bellizzi Saverio , Severoni Santino
Published: October 2023

Responding to the health need of refugees and migrants is key to accommodate universal health coverage, health security and health promotion to guarantee the well-being and protection of populations. This is in line with the human rights agenda as well as with the adoption of a coherent efficient comprehensive health system.
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

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

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

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.
Flares confirmed for the first time to be from the primary component of an eclipsing binary
Authors: Li Ling-Zhi , Li Kai , Gao Xiang , Chen Xiao-Dian , Gao Xing , Sun Guo-You
Published: October 2023

Only a handful of precise observations of flare detected from a contact binary so far. This paper presents the photometric and spectroscopic analysis of a contact binary (ASAS J082243+1927.0). Two flare events detected from this object were observed in the data of TESS. The two flare events both occurred at the secondary minimum. Considering the totally eclipsing secondary minimum, it is pretty sure that the two flares are both from the primary component. This is the first time to definitely identify a flare that comes from which component in an eclipsing binary system. This system is a low-mass ratio (q ∼ 0.094) and deep contact binary ($f\sim 69.4~{{\ \rm per\ cent}}$). LAMOST spectra of this object exhibit excess emissions in the H α line, indicating its chromospheric activity. The continuous variation of the TESS light curves is explained by using the variation of a dark spot added to the secondary component. Through analysing the relationship between the variation of the longitude of the spot and the O–C variation of the primary minima, we discover the spot rotation is prograde as viewed in the frame rotating with the orbital motion.