bluuebunny/crossref_metadata_2025 huggingface dataset:
Reinforcement in Laparoscopic Sleeve Gastrectomy: Is It Effective?
Authors: Coşkun Mümin , Uprak Tevfik Kivilcim , Günal Ömer , Aliyeva Aygün , Cingi Asim
Published: May 2024

Background:

Despite the success of bariatric surgery in treating obesity, it can still lead to complications. The most serious and feared technical complications are bleeding and leakage from the gastric staple line. In this study, stapler line reinforcement was investigated to determine whether it affects postoperative leakage and bleeding rates and their management.

Materials and Methods:

Overall, 510 patients who underwent sleeve gastrectomy were evaluated retrospectively. They were divided into 2 groups according to whether reinforcement of the staple line with running imbricating sutures was performed.

Results:

In the reinforcement group, there were two leaks (0.7%), which were diagnosed seven and eight days after surgery. In the non-reinforcement group, there were nine leaks (4%). There was no difference between the two groups in staple line bleeding.

Conclusions:

This study shows that reinforcement with continuous imbricating sutures is associated with less stapler line leakage and a lower reoperation rate at the cost of increased operative time.
Emergency department pediatric readiness of United States trauma centers in 2021: Trauma center facility characteristics and opportunities for improvement
Authors: Melhado Caroline G. , Remick Katherine , Miskovic Amy , Patel Bhavin , Hewes Hilary A. , Newgard Craig D. , Nathens Avery B. , Macias Charles , Gray Lisa , Yorkgitis Brian K. , Dingeldein Michael W. , Jensen Aaron R.
Published: May 2024

BACKGROUND

Emergency department (ED) pediatric readiness has been associated with lower mortality for injured children but has historically been suboptimal in nonpediatric trauma centers. Over the past decade, the National Pediatric Readiness Project (NPRP) has invested resources in improving ED pediatric readiness. This study aimed to quantify current trauma center pediatric readiness and identify associations with center-level characteristics to target further efforts to guide improvement.

METHODS

The study cohort included all centers that responded to the 2021 NPRP national assessment and contributed data to the National Trauma Data Bank (NTDB) the same calendar year. Center characteristics and pediatric (0–15 years) volume from the NTDB were linked to weighted pediatric readiness scores (wPRSs) obtained from the NPRP assessment. Univariate and multivariable analyses were used to determine associations between wPRS and trauma center type as well as center-level facility characteristics.

RESULTS

The wPRS was reported for 77% (749 of 973) of centers that contributed to the NTDB. Emergency department pediatric readiness was highest in American College of Surgeons level 1 pediatric trauma centers, but wPRS in the highest quartile was seen among all adult and pediatric trauma center types. Independent predictors of high wPRS included American College of Surgeons level 1 pediatric trauma center verification, pediatric trauma volume, and the presence of a pediatric intensive care unit. Higher-level adult trauma centers and pediatric trauma centers were more likely to have pediatric-specific physician requirements, pediatric emergency care coordinators, and pediatric quality improvement initiatives.

CONCLUSION

Emergency department pediatric readiness in trauma centers remains variable and is predictably lower in centers that lack inpatient resources. There is, however, no aspect of ED pediatric readiness that is constrained to high-level pediatric facilities, and a highest quartile wPRS was achieved in all types of adult centers in our study. Ongoing efforts to improve pediatric readiness for initial stabilization at nonpediatric centers are needed, particularly in centers that routinely transfer children out.

LEVEL OF EVIDENCE

Prognostic and Epidemiological; Level III.
Cosmic dust impacts on the Hubble Space Telescope
Authors: Kearsley A. T. , Webb R. P. , Grime G. W. , Wozniakiewicz P. J. , Price M. C. , Burchell M. J. , Salge T. , Spratt J.
Published: May 2024

Exposure of the Hubble Space Telescope to space in low Earth orbit resulted in numerous hypervelocity impacts by cosmic dust (micrometeoroids) and anthropogenic particles (orbital debris) on the solar arrays and the radiator shield of the Wide Field and Planetary Camera 2, both subsequently returned to Earth. Solar cells preserve residues from smaller cosmic dust (and orbital debris) but give less reliable information from larger particles. Here, we present images and analyses from electron, ion and X-ray fluorescence microscopes for larger impact features (millimetre- to centimetre-scale) on the radiator shield. Validated by laboratory experiments, these allow interpretation of composition, probable origin and likely dimensions of the larger impactors. The majority (~90%) of impacts by grains greater than 50 μm in size were made by micrometeoroids, dominated by magnesium- and iron-rich silicates and iron sulfides, metallic iron-nickel and chromium-rich spinel similar to that in ordinary chondrite meteorites of asteroid origin. Our re-evaluation of the largest impact features shows substantially fewer large orbital debris impacts than reported by earlier authors. Mismatch to the NASA ORDEM and ESA MASTER models of particle populations in orbit may be partly due to model overestimation of orbital debris flux and underestimation of larger micrometeoroid numbers.

This article is part of the theme issue ‘Dust in the Solar System and beyond’.
The DESTINY
+
Dust Analyser — a dust telescope for analysing cosmic dust dynamics and composition
Authors: Simolka Jonas , Blanco Roberto , Ingerl Stephan , Krüger Harald , Sommer Maximilian , Srama Ralf , Strack Heiko , Wagner Carsten , Arai Tomoko , Bauer Marcel , Fröhlich Patrick , Gläser Jan , Gräßlin Michael , Henselowsky Carsten , Hillier Jon , Hirai Takayuki , Ito Motoo , Kempf Sascha , Khawaja Nozair , Kimura Hiroshi , Klinkner Sabine , Kobayashi Masanori , Lengowski Michael , Li Yanwei , Mocker Anna , Moragas-Klostermeyer Georg , Postberg Frank , Rieth Florian , Sasaki Sho , Schmidt Jürgen , Sterken Veerle , Sternovsky Zoltan , Strub Peter , Szalay Jamey , Trieloff Mario , Yabuta Hikaru
Published: May 2024

The DESTINY
+
(Demonstration and Experiment of Space Technology for INterplanetary voYage with Phaethon fLyby and dUst Science) Dust Analyser (DDA) is a state-of-the-art dust telescope for the
in situ
analysis of cosmic dust particles. As the primary scientific payload of the DESTINY
+
mission, it serves the purpose of characterizing the dust environment within the Earth–Moon system, investigating interplanetary and interstellar dust populations at 1 AU from the Sun and studying the dust cloud enveloping the asteroid (3200) Phaethon. DDA features a two-axis pointing platform for increasing the accessible fraction of the sky. The instrument combines a trajectory sensor with an impact ionization time-of-flight mass spectrometer, enabling the correlation of dynamical, physical and compositional properties for individual dust grains. For each dust measurement, a set of nine signals provides the surface charge, particle size, velocity vector, as well as the atomic, molecular and isotopic composition of the dust grain. With its capabilities, DDA is a key asset in advancing our understanding of the cosmic dust populations present along the orbit of DESTINY
+
. In addition to providing the scientific context, we are presenting an overview of the instrument’s design and functionality, showing first laboratory measurements and giving insights into the observation planning.

This article is part of a theme issue ‘Dust in the Solar System and beyond’.
Selected ice nanoparticle accelerator hypervelocity impact mass spectrometer (SELINA-HIMS): features and impacts of charged particles
Authors: Spesyvyi Anatolii , Žabka Ján , Polášek Miroslav , Malečková Michaela , Khawaja Nozair , Schmidt Jürgen , Kempf Sascha , Postberg Frank , Charvat Ales , Abel Bernd
Published: May 2024

The selected ice nanoparticle accelerator, SELINA, was used to prepare beams of single ice particles with positive or negative charge. Positively charged particles were prepared from deionized water and 0.05–0.2 molar solutions of sodium chloride in water, and negatively charged ice particles were generated from water without salt. Depending on the electrospray source configuration, the measured particles vary from 50 to 1000 nm in diameter. The kinetic energy per charge for all particles was set to 200 eV by the collisional equilibration in quadrupoles, which resulted in primary velocities up to 600 m/s for the lowest
m/z
particles. The electrospray ionization and thus particle formation from SELINA become less efficient with increasing salt concentration, resulting in a lower detected particle frequency and size. Good instrument operation is achievable for concentrations below 0.2 M. After we have verified and characterized positively and negatively charged ice particles, we have combined SELINA with a target and time-of-flight spectrometer for a ‘proof-of-principle’ post acceleration of 120 nm particles towards hypervelocity (
v
~ 3000 m/s) and detection of fragments from the particle impact (SELINA-HIMS). General conditions are discussed for the acceleration of particles between 50 and 1000 nm to velocities well above 3000 m/s with SELINA-HIMS instrument.

This article is part of the theme issue ‘Dust in the Solar System and beyond’.
Inferring diet, disease and antibiotic resistance from ancient human oral microbiomes
Authors: Dahlquist-Axe Gwyn , Standeven Francesca J. , Speller Camilla F. , Tedder Andrew , Meehan Conor J.
Published: May 2024

The interaction between a host and its microbiome is an area of intense study. For the human host, it is known that the various body-site-associated microbiomes impact heavily on health and disease states. For instance, the oral microbiome is a source of various pathogens and potential antibiotic resistance gene pools. The effect of historical changes to the human host and environment to the associated microbiome, however, has been less well explored. In this review, we characterize several historical and prehistoric events which are considered to have impacted the oral environment and therefore the bacterial communities residing within it. The link between evolutionary changes to the oral microbiota and the significant societal and behavioural changes occurring during the pre-Neolithic, Agricultural Revolution, Industrial Revolution and Antibiotic Era is outlined. While previous studies suggest the functional profile of these communities may have shifted over the centuries, there is currently a gap in knowledge that needs to be filled. Biomolecular archaeological evidence of innate antimicrobial resistance within the oral microbiome shows an increase in the abundance of antimicrobial resistance genes since the advent and widespread use of antibiotics in the modern era. Nevertheless, a lack of research into the prevalence and evolution of antimicrobial resistance within the oral microbiome throughout history hinders our ability to combat antimicrobial resistance in the modern era.
A Multi-state Non-Markov Framework to Estimate Progression of Chronic Disease
Authors: Ding Ming , Chen Haiyi , Lin Feng-Chang
Published: May 2024

In chronic disease epidemiology, investigation of disease etiology has largely focused on one single endpoint, and progression of chronic disease as a multi-state process is understudied, representing a knowledge gap. Most of existing multi-state regression models require Markov assumption and are unsuitable to estimate progression of chronic diseases that is largely non-memoryless. We propose a new non-Markov framework that allows past states to affect transition rates of current states. The key innovation is that we convert a non-Markov to Markov process by dividing disease states into substates through conditioning on past disease history. Specifically, we apply cause-specific Cox models (CSC) including past states as covariates to obtain transition rates (TR) of substates, which were used to obtain transition probabilities (TP) and state occupational probabilities (SOP) of substates. We applied our model to describe progression of coronary heart disease (CHD) in the ARIC study, where CHD was modeled in healthy, in risk, CHD, heart failure, and mortality states. We presented transition rates, transition probabilities, and state occupational probabilities between states from age 45 to 95 years. In summary, the significance of our framework lies in that transition parameters between disease substates may shed light on new mechanistic insight of chronic disease and may provide more accurate description of non-Markov process than Markov regression models. Our method has potential of wide application in chronic disease epidemiology.
Rapid, Reliable, and Interpretable CNV Curation Visualizations for Diagnostic Settings with SeeNV
Authors: Bradshaw Michael S. , Raychaudhuri Jishnu , Murphy Lachlan , Barnard Rebecca , Firman Taylor , Gaskell Alisa , Layer Ryan M.
Published: May 2024

Copy number variants (CNVs), structural alterations in the genome involving duplication or deletion of DNA segments, are implicated in various health conditions. Despite their clinical significance, accurate identification and interpretation of CNVs remain challenging, especially in the context of whole exome sequencing (WES), which is commonly used in clinical diagnostic laboratories. While WES offers economic advantages over whole genome sequencing (WGS), it struggles with CNV detection due to technical noise introduced by laboratory and analytic processes. Manual curation of CNV calls generated by these tools is labor-intensive and error-prone. To address this, we introduce SeeNV, a command-line tool designed to aid manual curation of CNVs at scale. SeeNV is one solution to these issues developed in collaboration with and used by the Precision Diagnostics Laboratory at Children’s Hospital Colorado. SeeNV generates static infographics for each CNV, incorporating sample and cohort sequencing coverage statistics, CNV population frequency, and more, facilitating rapid and precise assessment. Using CNVs calls identified in publicly available WES and WGS samples, we show users can rapidly and reliably curate CNV calls, needing only 4.3 seconds to curate a call, achieving 0.93 precision and 0.72 recall. SeeNV is freely available for download on GitHub:https://github.com/MSBradshaw/SeeNV.
stDyer enables spatial domain clustering with dynamic graph embedding
Authors: Xu Ke , Xu Yu , Wang Zirui , Zhou Xin , Zhang Lu
Published: May 2024

Spatially resolved transcriptomics (SRT) data provide critical insights into gene expression patterns within tissue contexts, necessitating effective methods for identifying spatial domains. Traditional clustering techniques often over-look spatial information, leading to disjointed domains. Current computational approaches integrate spatial information but still face challenges in recognizing domain boundaries, scalability, and the need of independent clustering steps. We introduce stDyer, an end-to-end deep learning framework designed for spatial domain clustering in SRT data. stDyer combines a Gaussian Mixture Variational AutoEncoder (GMVAE) with graph attention networks (GATs) to simultaneously learn deep representations and perform clustering for units. A unique feature of stDyer is the dynamic graphs it adopts, which adaptively links units based on Gaussian Mixture assignments in the latent space, thereby improving spatial domain clustering and producing smoother domain boundaries. Additionally, stDyer’s mini-batch neighbor sampling strategy facilitates scalability to large datasets and enables multi-GPU training. Benchmarking against state-of-the-art tools across various SRT technologies, stDyer demonstrates superior performance in spatial domain clustering, multi-slice analysis, and large-scale dataset handling.
Predicting transcriptional activation domain function using Graph Neural Networks
Authors: Farheen Farhanaz , Broyles Bradley K. , Zhang Yuanyuan , Ibtehaz Nabil , Erkine Alexandre M. , Kihara Daisuke
Published: May 2024

Analysis of factors that lead to the functionality of transcriptional activation domains remains a crucial and yet challenging task owing to the significant diversity in their sequences and their intrinsically disordered nature. Almost all existing methods that have aimed to predict activation domains have involved traditional machine learning approaches, such as logistic regression, that are unable to capture complex patterns in data or plain convolutional neural networks and have been limited in exploration of structural features. However, there is a tremendous potential in the inspection of the structural properties of activation domains, and an opportunity to investigate complex relationships between features of residues in the sequence. To address these, we have utilized the power of graph neural networks which can represent structural data in the form of nodes and edges, allowing nodes to exchange information among themselves. We have experimented with two kinds of graph formulations, one involving residues as nodes and the other assigning atoms to be the nodes. A logistic regression model was also developed to analyze feature importance. For all the models, several feature combinations were experimented with. The residue-level GNN model with amino acid type, residue position, acidic/basic/aromatic property and secondary structure feature combination gave the best performing model with accuracy, F1 score and AUROC of 97.9%, 71% and 97.1% respectively which outperformed other existing methods in the literature when applied on the dataset we used. Among the other structure-based features that were analyzed, the amphipathic property of helices also proved to be an important feature for classification. Logistic regression results showed that the most dominant feature that makes a sequence functional is the frequency of different types of amino acids in the sequence. Our results consistent have shown that functional sequences have more acidic and aromatic residues whereas basic residues are seen more in non-functional sequences.
A qualitative investigation of crisis cafés in England: their role, implementation, and accessibility
Authors: Staples Heather , Cadorna Gianna , Nyikavaranda Patrick , Maconick Lucy , Lloyd-Evans Brynmor , Johnson Sonia
Published: May 2024

Background

Crisis cafés (also known as crisis sanctuaries or havens) are community-based services which support people in mental health crises, aiming to provide an informal, non-clinical and accessible setting. This model is increasingly popular in the UK; however, we are aware of no peer-reviewed literature focused on this model. We aimed to use qualitative methods to investigate managers’ views of the aims of crisis cafés, how they operate in practice and the factors that affect access to these services and implementation of the intended model.

Methods

Semi-structured interviews were conducted with 12 managers of crisis cafés across England. Data were analysed using a thematic approach.

Results

We identified five main perceived aims for crisis cafés: providing an alternative to A&E; improving access to crisis care; providing people in acute distress with someone to talk to in a safe and comfortable space; triaging effectively; and improving crisis planning and people’s coping skills. Factors seen as influencing the effectiveness of crisis cafés included accessibility, being able to deliver person-centred care, relationships with other services, and staffing. These factors could both help and hinder access to care and the implementation of the intended model. There were a number of trade-offs that services had to consider when designing and running a crisis café: 1. Balancing an open-door policy with managing demand for the service through referral routes, 2. Balancing risk management procedures with the remit of offering a non-clinical environment and 3. Increasing awareness of the service in the community whilst avoiding stigmatising perceptions of it.

Conclusions

Findings illustrate the aims of the crisis café model of care and factors which are influential in its implementation in current practice. Future research is needed to evaluate the efficacy of these services in relation to their aims. Crisis café service users’ views, and views of stakeholders from the wider crisis care system should also be ascertained.
Mechanical activation of VE-cadherin stimulates AMPK to increase endothelial cell metabolism and vasodilation
Authors: Cronin Nicholas M. , Dawson Logan W. , DeMali Kris A.
Published: May 2024

Endothelia cells respond to mechanical force by stimulating cellular signaling, but how these pathways are linked to elevations in cell metabolism and whether metabolism supports the mechanical response remains poorly understood. Here, we show that application of force to VE-cadherin stimulates liver kinase B1 (LKB1) to activate AMP-activated protein kinase (AMPK), a master regulator of energy homeostasis. VE-cadherin stimulated AMPK increases eNOS activity and localization to the plasma membrane as well as reinforcement of the actin cytoskeleton and cadherin adhesion complex, and glucose uptake. We present evidence for the increase in metabolism being necessary to fortify the adhesion complex, actin cytoskeleton, and cellular alignment. Together these data extend the paradigm for how mechanotransduction and metabolism are linked to include a connection to vasodilation, thereby providing new insight into how diseases involving contractile, metabolic, and vasodilatory disturbances arise.
Improving Drug Sensitivity Prediction and Inference by Multi-Task Learning
Authors: Strauch Jared , Asiaee Amir
Published: May 2024

The development of models to predict sensitivity to anticancer drugs is an area of significant interest, given the diverse responses to treatment among patients and the considerable expense and time involved in anticancer drug development. Leveraging “omic” data and anticancer response information from the Cancer Cell Line Encyclopedia, we propose a novel approach utilizing multitask learning to enhance prediction accuracy and inference. We extended a multitask learning framework called the Data Shared Lasso to develop the Data Shared Elastic Net. This enabled the construction of tissue-specific models with information sharing while maintaining the attractive properties of Elastic Net regression. By employing this approach, we observed improvements in prediction accuracy compared to single-task Elastic Net models, particularly for cell lines displaying high sensitivity to treatment. Furthermore, the Data Shared Elastic Net facilitated the identification of predictors for anticancer drug sensitivity within specific tissue types, shedding light on cellular pathways targeted by these drugs across tissues. We also investigated the impact of data leakage on modeling outcomes from previous studies, which led to underestimating prediction error and erroneous inferences
Fluorescence labeling strategies for the study of ion channel and receptor cell surface expression: A comprehensive toolkit for extracellular labeling of TRPV1
Authors: Mott Taylor M. , Wulffraat Grace C. , Eddins Alex J. , Mehl Ryan A. , Senning Eric N.
Published: May 2024

Regulation of ion channel expression on the plasma membrane is a major determinant of neuronal excitability, and identifying the underlying mechanisms of this expression is critical to our understanding of neurons. A critical aspect of measuring changes in ion channel expression is uniquely identifying ion channels located on the cell surface. To accomplish this goal we demonstrate two orthogonal strategies to label extracellular sites of the ion channel TRPV1 that minimally perturb the function of the channel: 1) We use the amber codon suppression technique to introduce a non-canonical amino acid (ncAA) with tetrazine click chemistry compatible with a trans-cyclooctene coupled fluorescent dye. 2) By inserting the circularly permutated HaloTag (cpHaloTag) in an extracellular loop of TRPV1, we incorporate a click-chemistry site for a chloroalkane-linked fluorescent dye of our choosing. Optimization of ncAA insertion sites was accomplished by screening residue positions between the S1 and S2 transmembrane domains with elevated missense variants in the human population, and we identified T468 as a rapid labeling site (∼5 minutes) based on functional as well as biochemical assays in HEK293T/17 cells. After several rounds of adapting the linker lengths and backbone placement of cpHaloTag on the extracellular side of TRPV1, our efforts led to a channel construct that robustly expressed as a fully functional TRPV1exCellHalo fusion with intact wild-type gating properties. The TRPV1exCellHalo construct was used in a single molecule experiment to track TRPV1 on the cell surface and validate studies that show decreased mobility of the channel upon activation. The success of these extracellular label TRPV1 (exCellTRPV1) constructs as tools to track surface expression of the channel will shed significant light on the mechanisms regulating expression and provide a general scheme to introduce similar modifications to other cell surface receptors.
Chaperonin-mediated Winter Cold Response via Circadian Clock Components inArabidopsis
Authors: Jeong Goowon , Jeon Myeongjune , Kyung Jinseul , Jeong Daesong , Shin Jinwoo , Shin Yourae , Hwang Daehee , Hyun Youbong , Lee Ilha
Published: May 2024

Vernalization and cold acclimation are plant strategies that evolved to enhance their fitness during the winter season. The molecular mechanisms behind these processes in Arabidopsis have been intensively studied. However, how plants measure the duration of long-term cold exposure has not been fully understood. Our research shows that cytosolic chaperonin is crucial for appropriate long-term cold responses by regulating plant circadian clocks. Furthermore, one of the clock components, REVEILLE4 (RVE4) and RVE8 directly activateVERNALIZATION INSENSITIVE 3(VIN3) and theC-REPEAT BINDING FACTOR(CBF)/DEHYDRATION-RESPONSIVE ELEMENT BINDING 1(DREB1) family genes, which are key regulators of vernalization and cold acclimation, respectively. The activation of theVIN3andCBF/DREB1genes was specific to the time of day, indicating that cold exposure during the day is critical for long-term cold responses. Our research delves deeper into understanding the regulatory mechanism governing these two distinct long-term cold responses.
Wolbachiastrengthens the match between pre-mating and early post-mating isolation in spider mites
Authors: Cruz Miguel A. , Magalhães Sara , Bakırdöven Murat , Zélé Flore
Published: May 2024

Endosymbiotic reproductive manipulators are widely studied as sources of post-zygotic isolation in arthropods, but their effect on pre-zygotic isolation between genetically differentiated populations has garnered less attention. We tested this using two partially isolated populations of the red and green colour forms ofTetranychus urticae, either uninfected or infected with differentWolbachiastrains, one inducing cytoplasmic incompatibility and the other not. We first investigated male and female preferences, and found that, in absence of infection, females were not choosy but all males preferred red-form females.Wolbachiaeffects were more subtle, with only the CI-inducing strain slightly strengthening colour-form based preferences. We then performed a double-mating experiment to test how incompatible matings affect subsequent mating behaviour and offspring production, as compared to compatible matings. Females mated with an incompatible male (infected and/or heterotypic) were more attractive and/or receptive to subsequent (compatible) matings, although analyses of offspring production revealed no clear benefit for this re-mating behaviour (i.e., apparently unaltered first male sperm precedence). Finally, by computing the relative contributions of each reproductive barrier to total isolation, we showed that pre-mating isolation matches both host-associated andWolbachia-induced post-mating isolation, suggesting thatWolbachiacould contribute to reproductive isolation in this system.
Proline substitutions in the ASIC1 β11-12 linker slow desensitization
Authors: Purohit Rutambhara , Couch Tyler , MacLean David M.
Published: May 2024

Desensitization is a prominent feature of nearly all ligand gated ion channels. Acid-sensing ion channels (ASIC) undergo desensitization within hundreds of milliseconds to seconds upon continual extracellular acidification. The ASIC mechanism of desensitization is primarily due to the isomerization or “flipping” of a short linker joining the 11thand 12thbeta sheets in the extracellular domain. In the resting and active states this β11-12 linker adopts an “upward” conformation while in the desensitized conformation the linker assumes a “downward” state. To accommodate this “downward” state, specific peptide bonds within the linker adopt either trans-like or cis-like conformations. Since proline-containing peptide bonds undergo cis-trans isomerization very slowly, we hypothesized that introducing proline residues in the linker may slow or even abolish ASIC desensitization, potentially providing a valuable research tools. Proline substitutions in the chicken ASIC1 β11-12 linker (L414P and Y416P) slowed desensitization decays approximately 100 to 1000-fold as measured in excised patches. Both L414P and Y416P shifted the steady state desensitization curves to more acidic pHs while activation curves and ion selectivity of these slow-desensitizing currents were largely unaffected. To investigate the functional stoichiometry of desensitization in the trimeric ASIC, we created families of L414P and Y416P concatemers with zero, one, two or three proline substitutions in all possible configurations. Introducing one or two L414P or Y416P mutations only slightly attenuated desensitization, suggesting that conformational changes in the remaining faster wild type subunits were sufficient to desensitize the channel. These data highlight the unusual cis-trans isomerization mechanism of ASIC desensitization and support a model where a single subunit is sufficient to desensitize the entire channel.
Clonal sharing of CD8+ T-cells links skin and joint inflammation in psoriatic arthritis
Authors: Durham Lucy E. , Humby Frances , Ng Nora , Gray Elizabeth H. , Ryan Sarah E. , Ross Rosie , Povoleri Giovanni A. M. , Nuamah Rosamond , Fung Kathy , Kallayil Athul Menon , Dhami Pawan , Kirkham Bruce W. , Taams Leonie S.
Published: May 2024

We hypothesised that skin and joint inflammation in psoriatic arthritis (PsA) is linked in terms of CD8+ T-cell phenotype and clonality. We employed scRNAseq to directly compare the transcriptional signature and T-cell receptor repertoire of memory T-cells from paired skin and synovial tissue and/or fluid from patients with PsA. We identified an enrichment of type-17 CD8+ tissue-resident memory (TRM) T-cells in both skin and joint, with a stronger IL-17 signature in the skin than the joint. Several T-cell clones were shared between the skin and joint and these shared clones tended to have the same signature at both sites, characterised by increased expression of genes associated with a cytotoxic, tissue-resident phenotype. Our findings support the hypothesis that skin and joint inflammation in PsA is linked in terms of T-cell clonality and raises the possibility that specific T-cells migrate between these compartments to propagate inflammation across both sites.
Metagenomic coverage bias at transcription start sites is correlated with gene expression
Authors: Qian Gordon , Coleman Izaak , Korem Tal , Ho Joshua W. K.
Published: May 2024

Metagenomic sequencing is presumed to provide unbiased sampling of all the genetic material in a sample. Downstream analysis methods, such as binning, gene copy number analysis, structural variations, or single nucleotide polymorphism analysis, commonly assume an even distribution across the genome after accounting for known artefacts such as GC content. We discovered coverage bias across gut microbiome species, manifesting as a difference in coverage before and after bacterial transcription start sites. Using matched metatranscriptomic and metagenomic sequencing data, we demonstrate that this bias correlates with gene expression. Potential artefacts such as the sequencing technology, reference genome used for alignment, and mappability bias were investigated across multiple datasets and shown to not be factors for association. While GC bias was found correlated with coverage bias, the association of coverage bias with gene expression remains significant after adjusting for GC bias. Paired-end read mapping demonstrated an enrichment in 5’ read ends immediately downstream of the TSS which was partly a byproduct of unmapped reads upstream of the TSS. Our observations suggest the existence of strain-level variation where sequence variation in the promoter site region is preventing proper read alignment to the reference genome. The correlation of this phenomenon with gene expression may also reflect evolutionary footprints for fine-tuning the regulation of gene expression. Understanding the source of this sequence variation and the biological implications of this artefact will be useful not only to better characterise microbial functions but also to improve interpretations of strain level dynamics.

Importance

Sequencing coverage calculated from metagenomic sequencing data is extensively used in the microbiome field, providing valuable information about microbial abundances, gene (functional) abundances, growth rates, and genomic variations. Understanding factors that impact the distribution of coverage along genomes is therefore important for multiple applications. In this study, we report on uneven read coverage across the transcription start sites of bacterial genomes that is correlated with gene expression levels. We determine that this bias is independent of multiple factors including GC bias, and arises due to higher strain divergence from reference genomes upstream of the transcript start site. We propose that evolutionary finetuning of gene expression in competitive microbial ecosystems can drive genetic mutations at the promoter site. Our findings suggest the potential to glean gene regulatory information from metagenomic data, and better understand how ecological factors shape genomes in the microbiome and their sequencing coverage.
Exportin-1 functions as an adaptor for transcription factor-mediated docking of chromatin at the nuclear pore complex
Authors: Ge Tiffany , Brickner Donna Garvey , Zehr Kara , VanBelzen D. Jake , Zhang Wenzhu , Caffalette Christopher , Ungerleider Sara , Marcou Nikita , Chait Brian , Rout Michael P. , Brickner Jason H.
Published: May 2024

Nuclear pore proteins (Nups) in yeast, flies and mammals physically interact with hundreds or thousands of chromosomal sites, which impacts transcriptional regulation. In budding yeast, transcription factors mediate interaction of Nups with enhancers of highly active genes. To define the molecular basis of this mechanism, we exploited a separation-of-function mutation in the Gcn4 transcription factor that blocks its interaction with the nuclear pore complex (NPC) without altering its DNA binding or activation domains. SILAC mass spectrometry revealed that this mutation reduces the interaction of Gcn4 with the highly conserved nuclear export factor Crm1/Xpo1. Crm1 both interacts with the same sites as Nups genome-wide and is required for Nup2 to interact with the yeast genome.In vivo, Crm1 undergoes extensive and stable interactions with the NPC.In vitro, Crm1 binds to Gcn4 and these proteins form a complex with the nuclear pore protein Nup2. Importantly, the interaction between Crm1 and Gcn4 does not require Ran-GTP, suggesting that it is not through the nuclear export sequence binding site. Finally, Crm1 stimulates DNA binding by Gcn4, supporting a model in which allosteric coupling between Crm1 binding and DNA binding permits docking of transcription factor-bound enhancers at the NPC.
T-ChIC: multi-omic detection of histone modifications and full-length transcriptomes in the same single cell
Authors: Zeller Peter , Blotenburg Marloes , Bhardwaj Vivek , de Barbanson Buys Anton , Salmén Fredrik , van Oudenaarden Alexander
Published: May 2024

Epigenetic mechanisms, such as histone modifications, are key regulators of transcription and maintenance of cell identity. While our knowledge concerning cell type-specific histone modifications has constantly increased, we still know little about the interplay between epigenetics and transcription at the level of the individual cell. To gain an understanding of this process, we developed T-ChIC (Transcriptome + Chromatin ImmunoCleavage), a method allowing for the detection of full-length transcripts and histone modifications in the same single cell. We applied this technique to anin vitromodel of gastrulation and monitored the coordinated dynamics of the transcriptome and active and repressive histone modifications as mouse embryonic stem cells differentiate into the three germ layers. Our analysis reveals a germ layer-dependent coupling between chromatin regulation and transcriptional states.
Evaluation of Hi-C sequencing for the detection of gene fusions in hematologic and solid pediatric cancer samples
Authors: Schmitt Anthony D. , Sikkink Kristin , Ahmed Atif A. , Melnyk Shadi , Reid Derek , Van Meter Logan , Guest Erin M. , Lansdon Lisa A. , Pastinen Tomi , Pushel Irina , Yoo Byunggil , Farooqi Midhat S.
Published: May 2024

HiC sequencing is a DNA-based next-generation sequencing method that preserves the 3D conformation of the genome and has shown promise in detecting genomic rearrangements in translational research studies. To evaluate HiC as a potential clinical diagnostic platform, analytical concordance with routine laboratory testing was assessed using primary pediatric leukemia and sarcoma specimens previously positive for clinically significant genomic rearrangements. Archived specimen types tested included viable and nonviable frozen leukemic cells, as well as formalin-fixed paraffin-embedded (FFPE) tumor tissues. Initially, pediatric acute myeloid leukemia (AML) and alveolar rhabdomyosarcoma (A-RMS) specimens with known genomic rearrangements were subjected to HiC analysis to assess analytical concordance. Subsequently, a discovery cohort consisting of AML and acute lymphoblastic leukemia (ALL) cases with no known genomic rearrangements based on prior clinical diagnostic testing were evaluated to determine whether HiC could detect rearrangements. Using a standard sequencing depth of 50 million raw read-pairs per sample, or approximately 5X raw genomic coverage, 100% concordance was observed between HiC and previous clinical cytogenetic and molecular testing. In the discovery cohort, a clinically relevant gene fusion was detected in 45% of leukemia cases (5/11). This study demonstrates the value of HiC sequencing to medical diagnostic testing as it identified several clinically significant rearrangements, including those that might have been missed by current clinical testing workflows.

Key points

HiC sequencing is a DNA-based next-generation sequencing method that preserves the 3D conformation of the genome, facilitating detection of genomic rearrangements.

HiC was 100% concordant with clinical diagnostic testing workflows for detecting clinically significant genomic rearrangements in pediatric leukemia and rhabdomyosarcoma specimens.

HiC detected clinically significant genomic rearrangements not previously detected by prior clinical cytogenetic and molecular testing.

HiC performed well with archived non-viable and viable frozen leukemic cell samples, as well as archived formalin-fixed paraffin-embedded tumor tissue specimens.
A new form of hereditary iron overload unlinked to known hereditary haemochromatosis genes
Authors: Wallace Daniel F. , Subramaniam V. Nathan
Published: May 2024

Hereditary iron overload conditions are normally caused by mutations in theHFEgene or other genes involved in the regulation of iron homeostasis. We describe a family with an iron overload condition with apparent autosomal dominant inheritance and phenotypic similarities to the classical form of ferroportin disease. The condition is characterised by elevated serum ferritin levels with normal or mildly elevated transferrin saturation and prominent iron deposition in both Kupffer cells and hepatocytes. Serum hepcidin levels were elevated in affected members of the pedigree and correlated with serum ferritin concentration. No pathogenic variants were identified inHFEorSLC40A1, the gene encoding ferroportin. Whole genome linkage analysis showed maximal linkage of the iron overload phenotype to regions on chromosomes 1, 3, 12, 18 and 19, indicating that affected members of this family do not have a variant form of ferroportin disease and are likely to have a new form of hereditary iron overload due to defects in another gene.
CLINICOPATHOLOGIC FEATURES OF URINARY BLADDER CANCER AT A TERTIARY HOSPITAL IN WESTERN KENYA
Authors: Oduor Charles Sore , Mugalo Edward , Kirongo Geoffrey
Published: May 2024

Background

Urinary bladder cancer is the ninth leading cause of morbidity and mortality globally, with a prevalence of 3% of all cancer diagnoses. Its local prevalence in Kenya is 1.89 per 100, 000 persons with previously documented studies describing it as a disease of the elderly. Local anecdotal data indicate that younger patients have begun presenting with bladder cancer.

Objectives

To establish the clinicopathological features of urinary bladder cancer.

Methods

A prospective descriptive hospital-based study among participants with bladder cancer at MTRH Urology department, sampled using a census sampling technique. Socio-demographic and clinical characteristics as well as predisposing factors were obtained through both interviews and a review of medical records. Disease staging was based on radiological imaging findings and histopathology reports. Statistical tests of association between socio-demographic characteristics, predisposing factors as well as the histological type, and Tumor, Node, Metastasis (TNM) stage of urinary bladder cancer were conducted using Pearson chi-square test with a critical value of ≤0.05.

Results

Forty-five (45) adults aged between 21 to 85 years with a mean age of 61.84 (±14.46) years and diagnosed with urinary bladder cancer were enrolled. Majority were male (68.9%; n=31) commonly presenting with painless hematuria, exposure to agrochemicals (60%; n=27), history of cigarette smoking (31.1%; n=14) with an average pack year of 9.43 (±6.198). The most common (71.1%; n=32) clinical stage was T1while 6.7% (n=3) had metastatic disease. More than half (55.6%) had stage I according to the TNM system while 91.1% had low-grade tumors. Transitional cell carcinoma (51.1%) was the most common histological type, followed by adenocarcinoma (29%), and squamous cell carcinoma (20%).

Conclusions

Patients diagnosed with bladder cancer in this study were mainly males with a mean age of 61.8 years. Majority of the participants had a history of smoking cigarettes or exposure to agrochemicals, and all presented with painless hematuria. Most patients had low-grade tumors diagnosed early.
Virome Sequencing Identifies H5N1 Avian Influenza in Wastewater from Nine Cities
Authors: Tisza Michael J. , Hanson Blake M. , Clark Justin R. , Wang Li , Payne Katelyn , Ross Matthew C. , Mena Kristina D. , Gitter Anna , Javornik-Cregeen Sara J. , Cormier Juwan , Avadhanula Vasanthi , Terwilliger Austen , Balliew John , Wu Fuqing , Rios Janelle , Deegan Jennifer , Piedra Pedro A. , Petrosino Joseph F. , Boerwinkle Eric , Maresso Anthony W.
Published: May 2024

Avian influenza (serotype H5N1) is a highly pathogenic virus that emerged in domestic waterfowl in 1996. Over the past decade, zoonotic transmission to mammals, including humans, has been reported. Although human to human transmission is rare, infection has been fatal in nearly half of patients who have contracted the virus in past outbreaks. The increasing presence of the virus in domesticated animals raises substantial concerns that viral adaptation to immunologically naïve humans may result in the next flu pandemic. Wastewater-based epidemiology (WBE) to track viruses was historically used to track polio and has recently been implemented for SARS-CoV2 monitoring during the COVID-19 pandemic. Here, using an agnostic, hybrid-capture sequencing approach, we report the detection of H5N1 in wastewater in nine Texas cities, with a total catchment area population in the millions, over a two-month period from March 4thto April 25th, 2024. Sequencing reads uniquely aligning to H5N1 covered all eight genome segments, with best alignments to clade 2.3.4.4b. Notably, 19 of 23 monitored sites had at least one detection event, and the H5N1 serotype became dominant over seasonal influenza over time. A variant analysis suggests avian or bovine origin but other potential sources, especially humans, could not be excluded. We report the value of wastewater sequencing to track avian influenza.
A cross sectional study on “Behavioral risk factors of cardiovascular disease among adolescents of secondary level school in a sub-metropolitan city of Nepal”
Authors: Bista Sita , Puri Bishow , Maharjan Sanju , Bhandari Buna
Published: May 2024

Background

Cardiovascular diseases (CVDs) are the leading cause of death and disability globally, where one-third of adolescents are affected. There is plenty of evidence that behavioral factors like physical inactivity, unhealthy diet, smoking, and alcohol use are major risks associated with CVDs among adolescents/school-going children.

Objective(s)

The main aim of this study was to assess the prevalence of behavioral risk factors of cardiovascular disease among adolescents of secondary-level schools in Tulsipur Sub Metropolitan City, Nepal.

Methods

It was a school-based cross-sectional study among 361 adolescents of grades 11 and 12 between the ages of 16 and 19. The school was selected by using a stratified proportionate sampling method. Data were collected through a self-administered structured and validated questionnaire containing socio-demographic characteristics, behavioral risk factors of CVDs and respective parent’s information. Data were analyzed using both descriptive and analytical statistics.

Results

The most prevalent behavioral risk factor was consumption of calorie drinks (99%); followed by sedentary behavior (60%), insufficient fruit and vegetable intake (57%), physical inactivity (35%), intake of processed food high in salt (33%), refined vegetable oil use in meal preparation (19%) and added salt intake (15.5%). Similarly, the prevalence of current smoking tobacco, alcohol use and smokeless tobacco use was 12%, 10% and 9%, respectively. Mother education, ethnicity, education system were associated factors of majority of behavioral risk factors of CVDs among adolescents. Mother education, parent’s smoking habit and parent’s smokeless tobacco use were associated factors of current tobacco smoking. Parent’s smokeless tobacco use and parent’s alcohol use were associated factors of current alcohol use.

Conclusions

This study provided evidence of high prevalence of CVD risk factors among adolescents in Nepal. It demands an urgent need to effectively design appropriate interventions in household and school settings to address the risk factors at the municipal level of Nepal.