bluuebunny/crossref_metadata_2025 huggingface dataset:
Minimally Invasive Pilonidal Sinus Treatment: EPSIT Versus PEBAI Method
Authors: Gulcu Baris , Ozturk Ersin
Published: November 2023

Purpose:

We aimed to compare endoscopic pilonidal sinus treatment (EPSIT) and pit/sinus punch needle excision, brushing, ablation and irrigation (PEBAI) method that was performed with principles similar to EPSIT but without fistuloscope and vision in the treatment of pilonidal sinus disease (PSD).

Methods:

Patients who underwent EPSIT and PEBAI methods for PSD in a single center between January 2020 and October 2021 were retrospectively analyzed. The primary endpoint was healing, the secondary endpoints were operative time, pain, wound closure, quality of life, cosmetic results, and cost.

Results:

One hundred 4 patients who underwent EPSIT and 184 patients who underwent PEBAI were included in the study. Age (P=0.871), sex (P=0.669), BMI (P=0.176), number of pits (P=0.99) were similar in both groups. The operative time for PEBAI [20 min (18 to 32)] was shorter than EPSIT [32 min (24 to 44)] (P<0.0000, u value=3096, z-score=-9.459). Postoperative first (P=0.147) and 14th day(P=0.382) pain scores, postoperative analgesic requirements (P=0.609), time to return to daily activities (P=0.747), time to return to work (P=0.345), and wound complications (P=0.816) were similar, whereas the wound closure time was earlier after EPSIT [32 d (24 to 41)] than after PEBAI [37 d (26 to 58)] (P<0.00001, u value=5344, z-score=6.22141). The median follow-up was 24 (12 to 34) months. Complete wound healing (P=0.382), recurrence rate (P=0.533), quality of life at first month and (Wound evaluation scale score at first year (P=0.252) were similar in both groups. However, the cost of PEBAI [54.8 € (50.13 to 64.96)] was significantly lower than cost of EPSIT [147.36 € (132.53 to 169.60)] (P<0.00001, u value=0, z-score=7.210).

Conclusions:

PEBAI method is a cheaper alternative to EPSIT with similar surgical principles and clinical outcomes.
Clamp-crushing Pancreatic Transection in Minimally Invasive Distal Pancreatectomy
Authors: Sakamoto Katsunori , Ogawa Kohei , Tamura Kei , Honjo Masahiko , Hikida Takahiro , Iwata Miku , Ito Chihiro , Sakamoto Akimasa , Shine Mikiya , Nishi Yusuke , Uraoka Mio , Nagaoka Tomoyuki , Funamizu Naotake , Takada Yasutsugu
Published: November 2023

Background:

Minimally invasive distal pancreatectomy has become a widely accepted procedure for tumors located in the pancreatic body or tail. However, pancreatic transection by linear stapler is generally avoided for pancreatic body tumors located above the portal vein because the surgical margin width is narrowed after taking into account the cutting allowance for insertion of the stapling device. Herein, we report a parenchymal clamp-crushing procedure that provides a sufficient surgical margin in pancreatic transection.

Methods:

Two patients with suspected early pancreatic cancer underwent pancreatic transection using the clamp-crushing procedure. The planned pancreatic transection line was set just to the left of the gastroduodenal artery in both cases. Robotic and laparoscopic distal pancreatectomy were performed in 1 patient each. Patients were positioned supine with split legs. Parenchymal transection was performed with crushing by VIO 3 (ERBE Elektromedizin) operated in softCOAG Bipolar mode with Effect 2/modulation 50. After crushing, remnant tissue was cut in autoCUT Bipolar mode operated by VIO 3 with Effect 2/modulation 50, or cut after secured by clipping.

Results:

The surgical duration was 253 and 212 minutes, and estimated blood loss was 0 and 50 mL in the 2 patients, and both were discharged with uneventful courses. Pathologic examination confirmed a negative surgical margin in both patients.

Conclusion:

Clamp-crushing pancreatic transection for distal pancreatectomy might be a suitable treatment option for achieving sufficient surgical margin in pancreatic body tumors located close to the portal vein.
Exploring the Therapeutic Potential of Cannabis Constituents in Parkinson’s Disease: Insights from Molecular Docking Studies
Authors: Aziz Moawaz , Rehman Hafsa , Iqbal Azhar , Nawaz Allah , Hussain Momina , Siddique Tehmina , Sehgal Sheikh Arslan Ashraf , Sajid Muhammad
Published: November 2023

Cannabis, often known as marihuana, marijuana, hashish, and hash, belongs to the genus Cannabis sativa L. This plant has excellent potential for the treatment of several brain disorders. Phytochemical compounds in this plant act as antioxidants, preserving synaptic plasticity and preventing neuronal degeneration. The neurodegenerative condition Parkinson’s has emerged as one of the most significant health concerns of the twenty-first century. A detailed in silico molecular docking study was carried out to assess the neuroprotective effects of cannabis compounds against four potential targets of PD, including monoamine oxidase B (MAO-B), catechol-O-methyltransferase (COMT), alpha-synuclein (ASN), and Adenosine A2A receptor (A2A). Physicochemical properties, drug-likeness, toxicity, and ADMET profiles were also investigated. In this docking study, the cannabis compound cannabicyclol showed a superior docking score of −10.8 kcal/mol with the MAO-B protein. Based on these results, cannabicyclol and the target protein MAO-B were used to perform MD simulations to analyze their stability at 100 ns. Furthermore, it is crucial to carry out in vitro and in vivo investigations to enhance the potency of cannabis components and understand the processes underlying the suppression of Parkinson’s disease-related enzymes.

Abstract Figure
Breastfeeding enhances intestinal gluconeogenesis in infants
Authors: Ni Duan , Tan Jian , Macia Laurence , Nanan Ralph
Published: November 2023

Objectives

Breastfeeding confers metabolic benefits to the infants, including reducing risks for metabolic syndromes such as obesity and diabetes later in life, but the underlying mechanisms is not yet fully understood. Hence, we aim to investigate the impacts of breastfeeding on the metabolic organs of infants.

Methods

Previous literatures directly studying the influences of breastfeeding on offspring’s metabolic organs were comprehensively reviewed. A microarray dataset of intestinal gene expression comparing infants fed on breastmilk versus formula milk was reanalyzed.

Results

Reanalysis of microarray data showed that breastfeeding significantly enhanced gluconeogenesis in infants’ intestine. This resembled observations in other mammalian species where breastfeeding also promoted gluconeogenesis.

Conclusions

Breastfeeding enhances intestinal gluconeogenesis in infants, which may underlie its metabolic advantages through finetuning the metabolic homeostasis. Such effect seems to be conserved across species, hinting its biological significance.
Similar metabolic pathways are affected in both Congenital Myasthenic Syndrome-22 and Prader-Willi Syndrome
Authors: Bhalla Kritika , Rosier Karen , Monnens Yenthe , Meulemans Sandra , Vervoort Ellen , Thorrez Lieven , Agostinis Patrizia , Meier Daniel T. , Rochtus Anne , Resnick James L , Creemers John W.M.
Published: November 2023

Loss of prolyl endopeptidase-like (PREPL) encoding a serine hydrolase with (thio)esterase activity leads to the recessive metabolic disorder Congenital Myasthenic Syndrome-22 (CMS22). It is characterized by severe neonatal hypotonia, feeding problems, growth retardation, and hyperphagia leading to rapid weight gain later in childhood. The phenotypic similarities with Prader-Willi syndrome (PWS) are striking, suggesting that similar pathways are affected. The aim of this study was to identify changes in the hypothalamic-pituitary axis in mouse models for both disorders and to examine mitochondrial function in skin fibroblasts of patients and knockout cell lines. We have demonstrated thatPreplis downregulated in the brains of neonatal PWS-IC-p/+mmice. In addition, the hypothalamic-pituitary axis is similarly affected in bothPrepl-/-and PWS-IC-p/+mmice resulting in defective orexigenic signaling and growth retardation. Furthermore, we demonstrated that mitochondrial function is altered inPREPLknockout HEK293T cells and can be rescued with the supplementation of coenzyme Q10. Finally, PREPL-deficient and PWS patient skin fibroblasts display defective mitochondrial bioenergetics. The mitochondrial dysfunction in PWS fibroblasts can be rescued by overexpression of PREPL. In conclusion, we provide the first molecular links between CMS22 and PWS, raising the possibility that PREPL substrates might become therapeutic targets for treating both disorders.

Graphical Abstract
Genetic Diversity and Structural Complexity of the Killer-Cell Immunoglobulin-Like Receptor Gene Complex: A Comprehensive Analysis Using Human Pangenome Assemblies
Authors: Hung Tsung-Kai , Liu Wan-Chi , Lai Sheng-Kai , Chuang Hui-Wen , Lee Yi-Che , Lin Hong-Ye , Hsu Chia-Lang , Chen Chien-Yu , Yang Ya-Chien , Hsu Jacob Shujui , Chen Pei-Lung
Published: November 2023

The killer-cell immunoglobulin-like receptor (KIR) gene complex, a highly polymorphic region of the human genome that encodes proteins involved in immune responses, poses strong challenges in genotyping due to its remarkable genetic diversity and structural intricacy. Accurate analysis of KIR alleles, including their structural variations, is crucial for understanding their roles in various immune responses. Leveraging the high-quality genome assemblies from the Human Pangenome Reference Consortium (HPRC), we present a novel bioinformatic tool, the Structural KIR annoTator (SKIRT), to investigate gene diversity and facilitate precise KIR allele analysis. We applied SKIRT on 47 HPRC-phased assemblies and identified a recurrent novelKIR2DS4/3DL1fusion gene in the paternal haplotype of HG02630 and maternal haplotype of NA19240. Additionally, SKIRT accurately identifies eight structural variants and 17 novel nonsynonymous alleles, all of which were independently validated using short-read data or quantitative polymerase chain reaction. Our study has discovered a total of 570 novel alleles, among which eight haplotypes harbor at least one KIR gene duplication, six haplotypes have lost at least one framework gene, and 75 out of 94 haplotypes (79.8%) carry at least five novel alleles, thus confirming KIR genetic diversity. These findings are pivotal in providing insights into KIR gene diversity and serve as a solid foundation for understanding the functional consequences of KIR structural variations. High-resolution genome assemblies offer unprecedented opportunities to explore polymorphic regions that are challenging to investigate using short-read sequencing methods. The SKIRT pipeline emerges as a highly efficient tool, enabling the comprehensive detection of the complete spectrum of KIR alleles within human genome assemblies.
TranSiGen: Deep representation learning of chemical-induced transcriptional profile
Authors: Tong Xiaochu , Qu Ning , Kong Xiangtai , Ni Shengkun , Wang Kun , Zhang Lehan , Wen Yiming , Zhang Sulin , Li Xutong , Zheng Mingyue
Published: November 2023

With the advancement of high-throughput RNA sequencing technologies, the use of chemical-induced transcriptional profiling has greatly increased in biomedical research. However, the usefulness of transcriptomics data is limited by inherent random noise and technical artefacts that may cause systematical biases. These limitations make it challenging to identify the true signal of perturbation and extract knowledge from the data. In this study, we propose a deep generative model called Transcriptional Signatures Generator (TranSiGen), which aims to denoise and reconstruct transcriptional profiles through self-supervised representation learning.TranSiGen uses cell basal gene expression and compound molecular structure representation to infer the chemical-induced transcriptional profile. Results demonstrate the effectiveness of TranSiGen in learning and predicting differential expression genes. The representation derived from TranSiGen can also serve as an alternative phenotype information, with applications in ligand-based virtual screening, drug response prediction, and phenotype-based drug repurposing. We envisage that integrating TranSiGen into the drug discovery and mechanism research pipeline will promote the development of biomedicine.
The genetic architecture of the load linked to dominant and recessive self-incompatibility alleles inArabidopsis halleriandA. lyrata
Authors: Le Veve Audrey , Genete Mathieu , Lepers-Blassiau Christelle , Ponitzki Chloé , Poux Céline , Vekemans Xavier , Durand Eleonore , Castric Vincent
Published: November 2023

The long-term balancing selection acting on mating-types or sex determining genes is expected to lead to the accumulation of deleterious mutations in the tightly linked chromosomal segments that are locally “sheltered” from purifying selection. However, the factors determining the extent of this accumulation are poorly understood. Here, we took advantage of variations in the intensity of balancing selection along a dominance hierarchy formed by alleles at the sporophytic self-incompatibility system of the Brassicaceae to compare the pace at which linked deleterious mutations accumulate among them. We first experimentally measured the phenotypic manifestation of the linked load at three different levels of the dominance hierarchy. We then sequenced and phased polymorphisms in the chromosomal regions linked to 126 distinct copies ofS-alleles in two populations ofArabidopsis halleriand three populations ofA. lyrata. We find that linkage to theS-locus locally distorts phylogenies over about 10-30kb along the chromosome. The more intense balancing selection on dominantS-alleles results in greater fixation of linked deleterious mutations, while recessiveS-alleles accumulate more linked deleterious mutations that are segregating. Hence, the structure rather than the overall magnitude of the linked genetic load differs between dominant and recessiveS-alleles. Our results have consequences for the long-term evolution of newS-alleles, the evolution of dominance modifiers between them, and raise the question of why the non-recombining regions of some sex and mating type chromosomes expand over evolutionary times while others, such as that theS-locus of the Brassicaceae, remain restricted to small chromosomal regions.
AptamerRunner: An accessible aptamer structure prediction and clustering algorithm for visualization of selected aptamers
Authors: Ruiz-Ciancio Dario , Veeramani Suresh , Embree Eric , Ortman Chris , Thiel Kristina W. , Thiel William H
Published: November 2023

Aptamers are short single-stranded DNA or RNA molecules with high affinity and specificity for targets and are generated using the iterative Systematic Evolution of Ligands by EXponential enrichment (SELEX) process. Next-generation sequencing (NGS) revolutionized aptamer selections by allowing a more comprehensive analysis of SELEX-enriched aptamers as compared to Sanger sequencing. The current challenge with aptamer NGS datasets is identifying a diverse cohort of candidate aptamers with the highest likelihood of successful experimental validation. Herein we present AptamerRunner, an aptamer clustering algorithm that generates visual networks of aptamers that are related by sequence and/or structure. These networks can then be overlayed with ranking data, such as fold enrichment or data from scoring algorithms. The ability to visually integrate data using AptamerRunner represents a significant advancement over existing clustering tools by providing a natural context to depict groups of aptamers from which ranked or scored candidates can be chosen for experimental validation. The inherent flexibility, user-friendly design, and prospects for future enhancements with AptamerRunner has broad-reaching implications for aptamer researchers across a wide range of disciplines.

GRAPHICAL ABSTRACT
No evidence for the presence and control of tumor growth by cytoplasmic stress granules in pancreatic cancer
Authors: Libert Maxime , Fain Jean , Bouchart Christelle , Arsenijevic Tatjana , Van Laethem Jean-Luc , Jacquemin Patrick
Published: November 2023

Cytoplasmic stress granules (SG) are attracting growing attention in cancer research1. As such, a study published in Cell2has certainly served as a trigger for this trend which currently asserts that SG are a relevant therapeutic target. Here, we would like to express a warning about the conclusions of this article, as well as of the subsequent study3, and more generally on a methodological approach frequently used in research studying SG in cancer and which we believe to be misleading.
Copepodamides in marine and freshwater copepods-similar but different
Authors: Arnoldt Sina , Pourdanandeh Milad , Spikkeland Ingvar , Andersson Mats X. , Selander Erik
Published: November 2023

Marine copepods, the most abundant group of zooplankton in the worlds oceans, imprint their surrounding waters with chemical cues, called copepodamides. Copepodamides induce defensive traits such as toxin production, bioluminescence, and colony size plasticity in a variety of marine phytoplankton. The role of copepodamides in freshwater ecosystems is, however, unknown. Here we report the consistent presence of copepodamides in copepods from six Swedish lakes. Copepodamide concentrations in freshwater copepods are similar to those of marine copepods, around 0.1 ppt of dry mass in millimetre sized individuals. The composition substantially overlaps with marine copepodamides but is also distinctly different. Freshwater copepods are largely dominated by one of the two subgroups of copepodamides, the dihydro-copepodamides, whereas marine copepods more commonly contain representatives from both subgroups. We describe 10 new copepodamide structures, four of which only found in freshwater copepods. Taxonomic groups had consistent copepodamide profiles across sampling sites and timepoints, supporting the presence of species specific copepodamide signatures. The presence of copepodamides in freshwater environments warrants study into their potential function as predator alarm cues also in freshwater systems.
Only cortical prediction error signals are involved in visual learning, despite availability of subcortical prediction error signals
Authors: Kim Dongho , Wang Zhiyan , Sakagami Masamichi , Sasaki Yuka , Watanabe Takeo
Published: November 2023

Both the midbrain systems, encompassing the ventral striatum (VS), and the cortical systems, including the dorsal anterior cingulate cortex (dACC), play roles in reinforcing and enhancing learning. However, the specific contributions of signals from these regions in learning remains unclear. To investigate this, we examined how VS and dACC are involved in visual perceptual learning (VPL) through an orientation discrimination task. In the primary experiment, subjects fasted for 5 hours before each of 14 days of training sessions and 3 days of test sessions. Subjects were rewarded with water for accurate trial responses. During the test sessions, BOLD signals were recorded from regions including VS and dACC. Although BOLD signals in both areas were associated with positive and negative RPEs, only those in dACC associated with negative RPE showed a significant correlation with performance improvement. Additionally, no significant correlation was observed between BOLD signals associated with RPEs in VS and dACC. These results suggest that although signals associated with positive and negative RPEs from both midbrain and cortical systems are readily accessible, only RPE signals in the prefrontal system, generated without linking to RPE signals in VS, are utilized for the enhancement of VPL.
Azole resistance: Insights from Y132 substitutions inCandidasterol 14α-demethylase
Authors: Rao R. Shyama Prasad , Pinto Larina , Suravajhala Renuka , Shenoy Belle Damodara , Ghate Sudeep D.
Published: November 2023

Background

Azole-resistantCandidainfections are on the rise. Resistant substitutions at Y132 in sterol 14α-demethylase, the key target of azole drugs, are frequent. However, it is unclear why only some Y132 substitutions are favoured or how they exert differential effects on different azoles.

Materials and Methods

Reported instances of Y132 substitutions were collected from the literature. Extensive molecular dynamics simulations of sterol 14α-demethylase bound to fluconazole or VT1161 (VT1) were performed, and the ligand-binding free energies were computed to quantify the effects of various Y132 substitutions on azole binding/interactions.

Results

Three azole-resistant substitutions, Y to C/F/H, were reported at residue position 132 in sterol 14α-demethylase. The Y132H was the most common substitution inC. albicans, while it was Y132F in other species. Ligand-binding free energies were -13.81 kcal/mol and -35.04 kcal/mol for fluconazole and VT1, respectively. There were differences in the ligand-binding free energies after substitutions compared to the wild type protein.

Conclusion

Y132F and Y132H were the most frequent substitutions inCandidasterol 14α-demethylase. Far higher binding free energy of fluconazole in comparison with VT1 might partly explain its susceptibility to azole-resistant substitutions. The results give key insights into azole resistance, and antifungal drug discovery and optimization.
ScRNAbox: Empowering Single-Cell RNA Sequencing on High Performance Computing Systems
Authors: Thomas R.A. , Fiorini M.R. , Amiri S. , Fon E.A. , Farhan S.M.K.
Published: November 2023

Motivation

Single-cell RNA sequencing (scRNAseq) offers powerful insights, but the surge in sample sizes demands more computational power than local workstations can provide. Consequently, high-performance computing (HPC) systems have become imperative. Existing web apps designed to analyze scRNAseq data lack scalability and integration capabilities, while analysis packages demand coding expertise, hindering accessibility.

Results

In response, we introduce scRNAbox, an innovative scRNAseq analysis pipeline meticulously crafted for HPC systems. This end-to-end solution, executed via the SLURM workload manager, efficiently processes raw data from standard and Hashtag samples. It incorporates quality control filtering, sample integration, clustering, cluster annotation tools, and facilitates cell type-specific differential gene expression analysis between two groups.

Implementation

Open-source code and comprehensive usage instructions with examples are available athttps://neurobioinfo.github.io/scrnabox/site/.

Supplementary Information

Supplementary data are available at Bioinformatics online.
Development and Analysis of Multiscale Models for Tuberculosis: From Molecules to Populations
Authors: Nanda Pariksheet , Budak Maral , Michael Christian T. , Krupinsky Kathryn , Kirschner Denise E.
Published: November 2023

Abstract

Although infectious disease dynamics are often analyzed at the macro-scale, increasing numbers of drug-resistant infections highlight the importance of within-host modeling that simultaneously solves across multiple scales to effectively respond to epidemics. We review multiscale modeling approaches for complex, interconnected biological systems and discuss critical steps involved in building, analyzing, and applying such models within the discipline of model credibility. We also present our two tools: CaliPro, for calibrating multiscale models (MSMs) to datasets, and tunable resolution, for fine- and coarse-graining sub-models while retaining insights. We include as an example our work simulating infection withMycobacterium tuberculosisto demonstrate modeling choices and how predictions are made to generate new insights and test interventions. We discuss some of the current challenges of incorporating novel datasets, rigorously training computational biologists, and increasing the reach of MSMs. We also offer several promising future research directions of incorporating within-host dynamics into applications ranging from combinatorial treatment to epidemic response.
Gut protectiveKlebsiellaspecies promotes microbiota recovery and pathobiont clearance while preventing inflammation
Authors: Cabral Vitor , Oliveira Rita A. , Correia Margarida B. , Pedro Miguel F. , Ubeda Carles , Xavier Karina B.
Published: November 2023

The microbiota inhabiting the mammalian gut serves as a protective barrier against pathogen invasion through a mechanism known as colonization resistance. Antibiotic treatments can inadvertently disturb the gut microbiota, compromising colonization resistance and increasing host’s susceptible to infections. Non-pneumoniae Klebsiellaspp. members of the gut microbiota play a crucial role in colonization resistance and clearance from the gut of pathogenicEnterobacteriaceaefollowing antibiotic-induced perturbations. Specifically,Klebsiellastrain ARO112 a gut microbiota isolate, can effectively resist and clearEscherichia colicolonization after antibiotic-induced dysbiosis.

We assessed the potential ofKlebsiellasp ARO112 to promote clearance ofEnterobacteriaceaepathobiont Adherent-InvasiveE. coli(AIEC) in an Inflammatory Bowel Disease (IBD) mouse model susceptible to inflammatory episodes. In antibiotic-treated IBD-predisposed mice infected with the AIEC,Klebsiellasp. ARO112 promoted a faster recovery of gut microbiota members potentially involved in butyrate production and accelerated pathobiont clearance. Functionally, ARO112-driven microbiota recovery promoted higher butyrate levels and prevented intestinal inflammation compared to untreated animals. Conversely, treatment with the well-known probioticE. coliNissle 1917 enhanced AIEC colonization and inflammation. Furthermore, we assessed the safety of ARO112 as a potential next-generation probiotic; phenotypic comparison of ARO112 against closely relatedEnterobacteriaceaerevealed its lower pathogenic potential, including being more recalcitrant to antibiotic resistance acquisition.

Overall, our results showing thatKlebsiellasp. ARO112 can resolve infections while contributing to the promotion of intestinal health, underscore its potential as a biotherapy agent that can disrupt inflammation-treatment-infection cycles. This potential extends beyond IBD patients, encompassing individuals with other inflammatory-based conditions related to microbiota imbalances.
COVID-19-related research data availability and quality according to the FAIR principles: A meta-research study
Authors: Sofi-Mahmudi Ahmad , Raittio Eero , Khazaei Yeganeh , Ashraf Javed , Schwendicke Falk , Uribe Sergio E. , Moher David
Published: November 2023

Background

As per the FAIR principles (Findable, Accessible, Interoperable, and Reusable), scientific research data should be findable, accessible, interoperable, and reusable. The COVID-19 pandemic has led to massive research activities and an unprecedented number of topical publications in a short time. There has not been any evaluation to assess if this COVID-19-related research data complied with FAIR principles (or FAIRness) so far.

Objective

Our objective was to investigate the availability of open data in COVID-19-related research and to assess compliance with FAIRness.

Methods

We conducted a comprehensive search and retrieved all open-access articles related to COVID-19 from journals indexed in PubMed, available in the Europe PubMed Central database, published from January 2020 through June 2023, using themetareadrpackage. Usingrtransparent, a validated automated tool, we identified articles that included a link to their raw data hosted in a public repository. We then screened the link and included those repositories which included data specifically for their pertaining paper. Subsequently, we automatically assessed the adherence of the repositories to the FAIR principles using FAIRsFAIR Research Data Object Assessment Service (F-UJI) andrfujipackage. The FAIR scores ranged from 1–22 and had four components. We reported descriptive analysis for each article type, journal category and repository. We used linear regression models to find the most influential factors on the FAIRness of data.

Results

5,700 URLs were included in the final analysis, sharing their data in a general-purpose repository. The mean (standard deviation, SD) level of compliance with FAIR metrics was 9.4 (4.88). The percentages of moderate or advanced compliance were as follows: Findability: 100.0%, Accessibility: 21.5%, Interoperability: 46.7%, and Reusability: 61.3%. The overall and component-wise monthly trends were consistent over the follow-up. Reviews (9.80, SD=5.06, n=160), and articles in dental journals (13.67, SD=3.51, n=3) and Harvard Dataverse (15.79, SD=3.65, n=244) had the highest mean FAIRness scores, whereas letters (7.83, SD=4.30, n=55), articles in neuroscience journals (8.16, SD=3.73, n=63), and those deposited in GitHub (4.50, SD=0.13, n=2,152) showed the lowest scores. Regression models showed that the most influential factor on FAIRness scores was the repository (R2=0.809).

Conclusion

This paper underscored the potential for improvement across all facets of FAIR principles, with a specific emphasis on enhancing Interoperability and Reusability in the data shared within general repositories during the COVID-19 pandemic.
Two Septin Complexes Mediate Actin Dynamics During Cell Wound Repair
Authors: Stjepić Viktor , Nakamura Mitsutoshi , Hui Justin , Parkhurst Susan M.
Published: November 2023

Cells have robust wound repair systems to prevent further damage or infection and to quickly restore cell cortex integrity when exposed to mechanical and chemical stress. Actomyosin ring formation and contraction at the wound edge are major events during closure of the plasma membrane and underlying cytoskeleton during cell wound repair. Here, we show that all fiveDrosophilaSeptins are required for efficient cell wound repair. Based on their different recruitment patterns and knockdown/mutant phenotypes, two distinct Septin complexes, Sep1-Sep2-Pnut and Sep4-Sep5-Pnut, are assembled to regulate actin ring assembly, contraction, and remodeling during the repair process. Intriguingly, we find that these two Septin complexes have different F-actin bending activities. In addition, we find that Anillin regulates the recruitment of only one of two Septin complexes upon wounding. Our results demonstrate that two functionally distinct Septin complexes work side-by-side to discretely regulate actomyosin ring dynamics during cell wound repair.
Transcriptional profile of the rat cardiovascular system at single cell resolution
Authors: Arduini Alessandro , Fleming Stephen J. , Xiao Ling , Hall Amelia W. , Akkad Amer-Denis , Chaffin Mark , Bendinelli Kayla J. , Tucker Nathan R. , Papangeli Irinna , Mantineo Helene , Babadi Mehrtash , Stegmann Christian M. , García-Cardeña Guillermo , Lindsay Mark E. , Klattenhoff Carla , Ellinor Patrick T.
Published: November 2023

Background

Despite the critical role of the cardiovascular system, our understanding of its cellular and transcriptional diversity remains limited. We therefore sought to characterize the cellular composition, phenotypes, molecular pathways, and communication networks between cell types at the tissue and sub-tissue level across the cardiovascular system of the healthy Wistar rat, an important model in preclinical cardiovascular research. We obtained high quality tissue samples under controlled conditions that reveal a level of cellular detail so far inaccessible in human studies.

Methods and Results

We performed single nucleus RNA-sequencing in 78 samples in 10 distinct regions including the four chambers of the heart, ventricular septum, sinoatrial node, atrioventricular node, aorta, pulmonary artery, and pulmonary veins (PV), which produced an aggregate map of 505,835 nuclei. We identified 26 distinct cell types and additional subtypes, including a number of rare cell types such as PV cardiomyocytes and non-myelinating Schwann cells (NMSCs), and unique groups of vascular smooth muscle cells (VSMCs), endothelial cells (ECs) and fibroblasts (FBs), which gave rise to a detailed cell type distribution across tissues. We demonstrated differences in the cellular composition across different cardiac regions and tissue-specific differences in transcription for each cell type, highlighting the molecular diversity and complex tissue architecture of the cardiovascular system. Specifically, we observed great transcriptional heterogeneities among ECs and FBs. Importantly, several cell subtypes had a unique regional localization such as a subtype of VSMCs enriched in the large vasculature. We found the cellular makeup of PV tissue is closer to heart tissue than to the large arteries. We further explored the ligand-receptor repertoire across cell clusters and tissues, and observed tissue-enriched cellular communication networks, including heightenedNppa-Npr1/2/3signaling in the sinoatrial node.

Conclusions

Through a large single nucleus sequencing effort encompassing over 500,000 nuclei, we broadened our understanding of cellular transcription in the healthy cardiovascular system. The existence of tissue-restricted cellular phenotypes suggests regional regulation of cardiovascular physiology. The overall conservation in gene expression and molecular pathways across rat and human cell types, together with our detailed transcriptional characterization of each cell type, offers the potential to identify novel therapeutic targets and improve preclinical models of cardiovascular disease.
Antibiotic resistance alters the ability ofPseudomonas aeruginosato invade the respiratory microbiome
Authors: Lindon Selina , Shah Sarah , Gifford Danna R. , Gomis Font Maria A. , Kaur Divjot , Oliver Antonio , MacLean R. Craig , Wheatley Rachel M.
Published: November 2023

The emergence and spread of antibiotic resistance in bacterial pathogens is a global health threat. One important unanswered question is how antibiotic resistance influences the ability of a pathogen to invade the host-associated microbiome. Here we investigate how antibiotic resistance impacts the ability of the opportunistic bacterial pathogenPseudomonas aeruginosato invade the respiratory microbiome, by measuring the ability ofP. aeruginosaspontaneous antibiotic resistant mutants to invade pre-established cultures of commensal respiratory microbes. We find that commensal respiratory microbes tend to inhibit the growth ofP. aeruginosa, and antibiotic resistance is a double-edged sword that can either help or hinder the ability ofP. aeruginosato overcome this inhibition. The directionality of this help or hinderance depends on bothP. aeruginosagenotype and respiratory microbe identity. Antibiotic resistance facilitates the invasion ofP. aeruginosaintoStaphylococcus lugdunensis,yet impairs invasion intoRothia mucilaginosaandStaphylococcus epidermidis.Streptococcusspecies provide the strongest inhibition toP. aeruginosainvasion, and this is maintained regardless of antibiotic resistance genotype. Our study demonstrates how antibiotic resistance can alter the ability of a bacterial pathogen to invade the respiratory microbiome and suggests that attempts to manipulate the microbiome should focus on promoting the growth of commensals that can provide robust inhibition of both wildtype and antibiotic resistant pathogen strains.
GTExome: Modeling commonly expressed missense mutations in the human genome
Authors: Hoffman Jill , Tan Henry , Sandoval-Cooper Clara , de Villiers Kaelyn , Reed Scott M.
Published: November 2023

A web application, GTExome, is described that quickly identifies, classifies, and models missense mutations in commonly expressed human proteins. GTExome can be used to categorize genomic mutation data with tissue specific expression data from the Genotype-Tissue Expression (GTEx) project. Commonly expressed missense mutations in proteins from a wide range of tissue types can be selected and assessed for modeling suitability. Information about the consequences of each mutation is provided to the user including if disulfide bonds, hydrogen bonds, or salt bridges are broken, buried prolines introduced, buried charges are created or lost, charge is swapped, a buried glycine is replaced, or if the residue that would be removed is a proline in the cis configuration. Also, if the mutation site is in a binding pocket the number of pockets and their volumes are reported. The user can assess this information and then select from available experimental or computationally predicted structures of native proteins to create, visualize, and download a model of the mutated protein using Fast and Accurate Side-chain Protein Repacking (FASPR). For AlphaFold modeled proteins, confidence scores for native proteins are provided. Using this tool, we explored a set of 9,666 common missense mutations from a variety of tissues from GTEx and show that most mutations can be modeled using this tool to facilitate studies of proteinprotein and protein-drug interactions. The open-source tool is freely available athttps://pharmacogenomics.clas.ucdenver.edu/gtexome/

Author Summary

GTExome greatly simplifies the process of studying the three-dimensional structures of proteins containing missense mutations that are critical to understanding human health. In contrast to current state-of-the-art methods, users with no external software or specialized training can rapidly produce three-dimensional structures of any possible mutation in nearly any protein in the human exome. Accomplishing this requires reliance on AlphaFold based structural models. We therefore compared the protein models created by GTExome where possible to known experimental structures. We find that by avoiding specific mutations, the majority of proteins are amenable to being modeled by GTExome with similar results to the direct use of AlphaFold.
Reliability and Validity of the Japanese Version of the Survey of Perceived Organizational Support
Authors: Odagami Kiminori , Nagata Tomohisa , Eguchi Hisashi , Inoue Akiomi , Mafune Kosuke , Mori Koji
Published: November 2023

Objectives

This study aimed to validate the Japanese version of the Survey of Perceived Organizational Support (SPOS-J) for the Japanese workforce by examining its reliability, factorial, construct, and test-retest validity.

Methods

We conducted an online baseline survey with 6,220 employed Japanese individuals, followed by a follow-up survey two weeks later to examine the test-retest reliability of the SPOS-J. The SPOS-J was translated in accordance with the ISPOR Task Force Guidelines. Both confirmatory and exploratory factor analyses were utilized to examine factorial validity. Construct validity was assessed using Pearson’s correlation analysis, while internal consistency was determined through the calculation of Cronbach’s alpha values. Additionally, test-retest reliability was evaluated with Cohen’s weighted kappa and intraclass correlation coefficients.

Results

The SPOS-J demonstrated a better fit for a two-factor structure, comprising two subscales - SPOS-J (supported) and SPOS-J (unsupported) – compared to the one-factor structure of the original version. It exhibited high internal consistency, with Cronbach’s alpha coefficients of .93 for the overall SPOS-J, .97 for the SPOS-J (supported), and .95 for the SPOS-J (unsupported). Test-retest reliability was found to be good for the overall SPOS-J (.62) and moderate for its subscales, with Cohen’s weighted kappa values of .54 for SPOS-J (supported) and .42 for SPOS-J (unsupported). The construct validity was confirmed with significant correlations between the SPOS-J, its antecedents, and outcomes.

Conclusions

The SPOS-J is a reliable and valid measure for assessing perceived organizational support among Japanese workers.
Creation of de novo cryptic splicing for ALS/FTD precision medicine
Authors: Wilkins Oscar G. , Chien Max Z.Y.J. , Wlaschin Josette J. , Pisliakova Maria , Thompson David , Digby Holly , Simkin Rebecca L. , Diaz Juan Antinao , Mehta Puja R. , Keuss Matthew J. , Zanovello Matteo , Brown Anna-Leigh , Harley Peter , Darbey Annalucia , Karda Rajvinder , Fisher Elizabeth M.C. , Cunningham Tom J. , Le Pichon Claire E. , Ule Jernej , Fratta Pietro
Published: November 2023

A system enabling the expression of therapeutic proteins specifically in diseased cells would be transformative, providing greatly increased safety and the possibility of pre-emptive treatment. Here we describe “TDP-REG”, a precision medicine approach primarily for amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), which exploits the cryptic splicing events that occur in cells with TDP-43 loss-of-function (TDP-LOF) in order to drive expression specifically in diseased cells. In addition to modifying existing cryptic exons for this purpose, we develop a deep-learning-powered algorithm for generating customisable cryptic splicing events, which can be embedded within virtually any coding sequence. By placing part of a coding sequence within a novel cryptic exon, we tightly couple protein expression to TDP-LOF. Protein expression is activated by TDP-LOFin vitroandin vivo, including TDP-LOF induced by cytoplasmic TDP-43 aggregation. In addition to generating a variety of fluorescent and luminescent reporters, we use this system to perform TDP-LOF-dependent genomic prime editing to ablate theUNC13Acryptic donor splice site. Furthermore, we design a panel of tightly gated, autoregulating vectors encoding a TDP-43/Raver1 fusion protein, which rescue key pathological cryptic splicing events. In summary, we combine deep-learning and rational design to create sophisticated splicing sensors, resulting in a platform that provides far safer therapeutics for neurodegeneration, potentially even enabling preemptive treatment of at-risk individuals.

One-Sentence Summary

We engineer TDP-43-regulated cryptic exons, enabling exceptionally precise activation of gene therapies in diseased neurons.
Illuminating the complete ß-cell mass of the human pancreas - signifying a new view on the islets of Langerhans
Authors: Lehrstrand Joakim , Davies Wayne I. L. , Hahn Max , Korsgren Olle , Alanentalo Tomas , Ahlgren Ulf
Published: November 2023

Pancreatic islets of Langerhans play a pivotal role in regulating blood glucose homeostasis, but critical information regarding their mass, distribution and composition is lacking within a whole organ context. Here, a new 3D imaging pipeline was applied to generate a first complete account of the insulin-producing islets throughout the human pancreas at a microscopic resolution and within a maintained spatial 3D context. These data show that human islets are far more heterogenous than previously accounted for with regards to their size distribution and cellular make up. By deep tissue 3D imaging, this in-depth study demonstrates that 50% of the human insulin-expressing islets are virtually devoid of glucagon-producing a-cells, an observation with significant implications for both experimental and clinical research.

One Sentence Summary:New islet heterogeneity identified in the human pancreas
Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket
Authors: Huang Chia-Ying , Metz Alexander , Lange Roland , Artico Nadia , Potot Céline , Hazemann Julien , Müller Manon , Santos Marina Dos , Chambovey Alain , Ritz Daniel , Eris Deniz , Meyer Solange , Bourquin Geoffroy , Sharpe May , Sweeney Aengus Mac
Published: November 2023

To identify starting points for therapeutics targeting SARS-CoV-2, the Paul Scherrer Institute and Idorsia decided to collaboratively perform an X-ray crystallographic fragment screen against its main protease. Fragment-based screening was carried out using crystals with a pronounced open conformation of the substrate binding pocket. Of 631 fragments soaked, a total of 29 hits bound either in the active site (24 hits), a remote binding pocket (2 hits) or at crystal packing interfaces (3 hits). Notably, two fragments with a pose sterically incompatible with a more occluded crystal form were identified. Two isatin-based electrophilic fragments bound covalently to the catalytic cysteine residue. Our structures also revealed a surprisingly strong influence of the crystal form on the binding pose of three published fragments used as positive controls, with implications for fragment screening by crystallography.

Synopsis

An X-ray crystallographic screen on SARS-CoV-2 3CL protease resulted in 29 fragment hits, including two isatin-based reversible covalent binders, and revealed a strong influence of the crystal form used for fragment soaking on the bound conformation of three additional reference fragments.
TheHansenula polymorphaMitochondrial Carrier Family proteins Mir1 and Aac2 are dually localized at peroxisomes and mitochondria
Authors: Pedersen Marc Pilegaard , Wolters Justina C. , de Boer Rinse , Krikken Arjen M. , van der Klei Ida J.
Published: November 2023

Peroxisomes are ubiquitous cell organelles involved in various metabolic pathways. In order to properly function, several cofactors, substrates and products of peroxisomal enzymes need to pass the organellar membrane. So far only a few transporter proteins have been identified. We analysed peroxisomal membrane fractions purified from the yeastHansenula polymorphaby untargeted label-free quantitation mass spectrometry. As expected, several known peroxisome-associated proteins were enriched in the peroxisomal membrane fraction. In addition, several other proteins were enriched, including mitochondrial transport proteins. Localization studies revealed that two of them, the mitochondrial carrier family proteins Aac2 and Mir1, have a dual localization on mitochondria and peroxisomes. To better understand the molecular mechanisms of dual sorting, we tested the localization of Mir1 in cells lacking Pex3 or Pex19, two peroxins that play a role in targeting of peroxisomal membrane proteins. In these cells Mir1 only localized to mitochondria, indicating that Pex3 and Pex19 are required to sort Mir1 to peroxisomes. Analysis of the localization of various truncated versions of Mir1 in wild-typeH. polymorphacells revealed that several localized to mitochondria, but only one, consisting of the transmembrane domains 3-6, was peroxisomal. Peroxisomal localization of this construct was lost in aMIR1deletion strain, indicating that full length Mir1 was required for the localization of the truncated protein to peroxisomes. Our data suggest that only full length Mir1 sorts to peroxisomes, while Mir1 contains multiple regions with mitochondrial sorting information.
Structuring effects of archaeal replication origins
Authors: Mottez Clémence , Puech Romain , Flament Didier , Myllykallio Hannu
Published: November 2023

Archaea use eukaryotic-like DNA replication proteins to duplicate circular chromosomes similar to those of bacteria. Although archaeal replication origins have been maintained during the evolution, they are non-essential under laboratory conditions. Here we propose the local deviations from Chargaff’s second parity rule of archaeal chromosomes result from the biased gene orientation and not from mutational biases. Our computational and experimental analyses indicate that the archaeal replication origins prevent head-to-head collisions of replication and transcription complexes as well as participate in coordination of the transfer of genetic information. Our results therefore suggest that the archaeal replication origins have alternative functions not related to their role in initiation of DNA replication.
Pooled screening for biochemically-defined phenotypes using CRISPuRe-Seq
Authors: Harris David T. , Jan Calvin H.
Published: November 2023

Phenotypic genetic screening is a powerful approach for biological discovery. CRISPR technologies have enabled routine genome-scale pooled perturbations in cultured cells, creating an opportunity to develop screening methods capable of accessing molecularly meaningful phenotypes. Here we present a generalized strategy, named CRISPuRe-seq, that enables pooled screening of a broad range of protein-based attributes. This approach utilizes the purification of an RNA-barcoded protein-of-interest to identify causative genetic perturbations. As a proof of concept, we screened for modifiers of Interferon alpha signaling and were able to identify all of the primary components of the type 1 Interferon JAK/STAT signaling pathway.