bluuebunny/crossref_metadata_2025 huggingface dataset:
Fasciotomy and rate of amputation after tibial fracture in adults: a population-based cohort study
Authors: Bihari Aurelia , McClure J. Andrew , Inculet Clayton , Del Balso Christopher , Vinden Christopher , Schemitsch Emil , Sanders David , Lawendy Abdel-Rahman
Published: April 2024

Objectives:

Limb amputation is a possible outcome of acute compartment syndrome. We undertook this study to investigate the occurrence of fasciotomy and amputation in patients with tibial fractures in the Ontario adult population, aiming to evaluate variables that may be associated with each of these outcomes.

Design:

Retrospective, population-based cohort study (April 1, 2003–March 31, 2016).

Setting:

Canadian province of Ontario.

Participants:

Patients with tibial fracture, aged 14 years and older.

Intervention(s):

Fasciotomy after tibial fracture.

Main Outcome(s) and Measure(s):

The primary outcomes were fasciotomy and amputation within 1 year of fasciotomy. Secondary outcomes included repeat surgery, new-onset renal failure, and mortality, all within 30 days of fasciotomy.

Results:

We identified 76,299 patients with tibial fracture; the mean (SD) age was 47 (21) years. Fasciotomy was performed in 1303 patients (1.7%); of these, 76% were male and 24% female. Patients who were younger, male, or experienced polytrauma were significantly more likely to undergo fasciotomy. Limb amputation occurred in 4.3% of patients undergoing fasciotomy, as compared with 0.5% in those without fasciotomy; older age, male sex, presence of polytrauma, and fasciotomy were associated with an increased risk of amputation (age odds ratio [OR] of 1.03 [95% CI, 1.02–1.03], P < 0.0001; sex OR of 2.04 [95% CI, 1.63–2.55], P < 0.0001; polytrauma OR of 9.37 [95% CI, 7.64–11.50], P < 0.0001; fasciotomy OR of 4.35 [95% CI, 3.21–5.90], P < 0.0001), as well as repeat surgery within 30 days (sex OR of 1.54 [95% CI, 1.14–2.07], P = 0.0053; polytrauma OR of 4.24 [95% CI, 3.33–5.38], P < 0.0001).

Conclusions:

Among tibial fracture patients, those who were male and who experienced polytrauma were at significantly higher risk of undergoing fasciotomy and subsequent amputation. Fasciotomy was also significantly associated with risk of amputation, a finding that is likely reflective of the severity of the initial injury.
Effects of multi-month dispensing on viral suppression and continuity in treatment among children living with HIV aged 2 to 9 years: a cohort study in Western Kenya
Authors: Oyuga Roseline , Amadi Emmanuel , Blanco Natalia , Ndaga Angela , Abuya Kepha , Oneya Daniel , Ng'eno Caroline , Koech Emily , Lavoie Marie-Claude C.
Published: April 2024

Background:

In Kenya, of the 82,000 children living with HIV; only 59% of these children are receiving ART, and 67% of these are virally suppressed. Early in the COVID-19 pandemic, the Ministry of Health recommended three multi-month dispensing (3MMD) of ART to all people living with HIV, including children. This study assess the association between 3MMD and clinical outcomes among children in Western Kenya.

Settings

and Methods: We conducted a retrospective cohort study using routinely collected de-identified patient-level data from 43 facilities in Kisii and Migori counties. The study included children 2-9 years old who had been previously initiated on ART and sought HIV services between March 01, 2020, and March 30, 2021. We used generalized linear models with Poisson regression models to assess the association of MMD on retention at 6 months and viral suppression (<1,000 copies/ml).

Results:

Among the 963 children, 65.2% were aged 5-9 years old, and 50.7% were females. Seventy-eight percent received 3MMD at least once during the study period. Children who received 3MMD were 12% [adjusted risk ratio (aRR) (95% CI) =1.12 (1.01-1.24)] more likely to be retained and 22% [aRR =1.22 (1.12-1.34)] more likely to be virally suppressed than those on < 3MMD. When stratified by viral suppression at entry, the association between 3MMD and retention ([aRR= (95% CI) =1.22 (1.02-1.46)]) and viral suppression [aRR= (95% CI) =1.76 (1.30-2.37)] was significant among individuals who were unsuppressed at baseline.

Conclusions:

3MMD was associated with comparable or improved HIV health outcomes among children.
Dose-Response after Low-dose Ionizing Radiation: Evidence from Life Span Study with Data-driven Deep Neural Network Model
Authors: Liu Zhenqiu , Shuryak Igor
Published: April 2024

Accurately evaluating the disease risks after low-dose ionizing radiation (IR) exposure are crucial for protecting public health, setting safety standards, and advancing research in radiation safety. However, while much is known about the disease risks of high-dose irradiation, risk estimates at low dose remains controversial. To date, five different parametric models (supra-linear, linear no threshold, threshold, quadratic, and hormesis) for low doses have been studied in the literature. Different dose-response models may lead to inconsistent or even conflicting results.

In this manuscript, we introduce a data-driven deep neural network (DNN) model designed to evaluate dose-response models at low doses using Life Span Study (LSS) data. DNNs possess the capability to approximate any continuous function with an adequate number of nodes in the hidden layers. Being data-driven, they circumvent the challenges associated with misspecification inherent in parametric models. Our simulation study highlights the effectiveness of DNNs as a valuable tool for precisely identifying dose-response models from available data. New findings from the LSS study provide robust support for a linear quadratic (LQ) dose-response model at low doses.

While the linear no threshold (LNT) model tends to overestimate disease risk at very low doses and underestimate health risk at relatively high doses, it remains a reasonable approximation for the LQ model, given the minor impact of the quadratic term at low doses. Our demonstration underscores the power of DNNs in facilitating comprehensive investigations into dose-response associations.
Precise Timing Matters: Modulating Human Memory by Synchronizing Hippocampal Stimulation to Saccadic Event Related Potentials
Authors: Katz C.N , Patel K. , Schjetnan A.G. , Barkley V. , Groppe David , Zariffa J , Duncan K.D. , Valiante T.A
Published: April 2024

Episodic memory, the ability to record and relive experiences, is intricately connected to visual exploration in most humans. This study explores the possibility that eye movements create physiological states relevant for memory, analogous to those associated with hippocampal theta. Previous work has demonstrated that saccadic eye movements, which occur roughly at theta frequency, elicit hippocampal event-related potentials (ERPs). Building on the Separate Phases of Encoding and Retrieval (SPEAR) model, we asked if the peaks and troughs of this saccadic ERP are differentially important for memory formation. Specifically, we applied saccade-contingent hippocampal electrical stimulation at estimated ERP peaks and troughs while individuals with epilepsy visually explored natural scenes across 59 sessions. We subsequently assessed their recognition memory for scenes and their recall of associated targets. Results indicate that memory is robust when stimulation precisely targets the peak or trough, contrasting with impairments observed with random stimulation. Moreover, memory impairment is prominent when stimulation is applied within 100 ms of saccade initiation, a time that reflects high medial temporal lobe inhibition. Our findings suggest that the hippocampus rapidly evolves through memory-relevant states following each eye movement, while also challenging the assumption that human saccadic ERP peaks and troughs mirror the encoding and retrieval phases of theta rhythms studied in rodents. The study sheds light on the dynamic interplay between eye movements, hippocampal activity, and memory formation, offering theoretical insights with potential applications for memory modulation in neurological disorders.

Significance Statement

Why do eye-movements enhance memory formation? Here, we causally tested if eye-movements initiate short-lived states critical for memory formation within the hippocampus, a brain region known to support memory. We built a system that could precisely apply hippocampal electrical stimulation at key moments after eye-movements to test how the timing of this stimulation influenced people’s ability to form memories. We found that stimulation was particularly disruptive to memory formation when applied within 100 ms of initiating an eye movement. By contrast, memory was robust to stimulation precisely timed to the peak and trough of hippocampal eye-movement responses. We interpret this temporal evolution of memory-relevant states within a prominent model of how theta phases relate to rodent memory.
An ascending vagal sensory-central noradrenergic pathway modulates retrieval of passive avoidance memory
Authors: Edwards Caitlyn M. , Guerrero Inge Estefania , Thompson Danielle , Dolezel Tyla , Rinaman Linda
Published: April 2024

Background

Visceral feedback from the body is often subconscious, but plays an important role in guiding motivated behaviors. Vagal sensory neurons relay “gut feelings” to noradrenergic (NA) neurons in the caudal nucleus of the solitary tract (cNTS), which in turn project to the anterior ventrolateral bed nucleus of the stria terminalis (vlBNST) and other hypothalamic-limbic forebrain regions. Prior work supports a role for these circuits in modulating memory consolidation and extinction, but a potential role in retrieval of conditioned avoidance remains untested.

Results

To examine this, adult male rats underwent passive avoidance conditioning. We then lesioned gut-sensing vagal afferents by injecting cholecystokinin-conjugated saporin toxin (CSAP) into the vagal nodose ganglia (Experiment 1), or lesioned NA inputs to the vlBNST by injecting saporin toxin conjugated to an antibody against dopamine-beta hydroxylase (DSAP) into the vlBNST (Experiment 2). When avoidance behavior was later assessed, rats with vagal CSAP lesions or NA DSAP lesions displayed significantly increased conditioned passive avoidance.

Conclusions

These new findings support the view that a gut vagal afferent-to-cNTSNA-to-vlBNST circuit plays a role in modulating the expression/retrieval of learned passive avoidance. Overall, our data suggest a dynamic modulatory role of vagal sensory feedback to the limbic forebrain in integrating interoceptive signals with contextual cues that elicit conditioned avoidance behavior.
Deep learning models to predict mammographic density jointly on standard dose and low dose images
Authors: Squires Steven , Mackenzie Alistair , Evans D. Gareth , Howell Sacha J , Astley Susan M
Published: April 2024

Objectives

Mammographic density is associated with increased risk of developing breast cancer. Automated estimation of density in women below normal screening age would enable earlier risk stratification. We are piloting the use of low dose mammograms combined with models that can make accurate mammographic density estimates.

Methods

Three models were trained on a joint set (107,619) of standard dose mammograms with associated density scores and their simulated low dose counterparts such that the models made predictions on standard and low dose mammograms. A second set of models was trained separately on the standard and simulated low dose mammograms. All models were tested on a held-out set from the training data and an independent dataset with 294 pairs of standard and real low dose mammograms.

Results

The root mean squared errors (RMSE) between the model predictions and density scores on standard and simulated low dose images were 8.26 (8.16-8.36) and 8.27 (8.17-8.38) respectively. The RMSE between predictions on standard and simulated low dose images for the jointly trained models was 1.91 (1.88-1.96). The RMSE of the predictions on the real low dose images compared to the standard dose images is 3.79 (2.75-4.99).

Conclusions

Deep learning models make density predictions on low dose images with similar quality as on standard dose images. Such automated analysis of low dose mammograms could contribute to accurate breast cancer risk estimation in younger women enabling stratification for further monitoring and preventative therapy.

Advances in knowledge

Mammographic density can be estimated in low dose mammograms with similar quality to standard dose mammograms.
Interrater agreement of annotations of epileptiform discharges and its impact on deep learning – A pilot study
Authors: Svantesson Mats , Eklund Anders , Thordstein Magnus
Published: April 2024

1.

Background

Expert interrater agreement for epileptiform discharges can be moderate. This reasonably will affect the performance when developing classifiers based on annotations performed by experts. In addition, evaluation of classifier performance will be difficult since the ground truth will have a variability. In this pilot study, these aspects were investigated to evaluate the feasibility of conducting a larger study on the subject.

Methods

A multi-channel EEG of 78 minutes duration with abundant periodic discharges was independently annotated for epileptiform discharges by two experts. Based on this, several deep learning classifiers were developed which in turn produced new annotations. The agreements of all annotations were evaluated by pairwise comparisons using Cohen’s kappa and Gwet’s AC1. A cluster analysis was performed on all periodic discharges using a newly developed version of parametric t-SNE to assess the similarity between annotations.

Results

The Cohen’s kappa values were 0.53 for the experts, 0.52–0.65 when comparing the experts to the classifiers, and 0.67–0.82 for the classifiers. The Gwet’s AC1 values were 0.92 for the experts, 0.92–0.94 when comparing the experts to the classifiers, and 0.94–0.96 for the classifiers. Although there were differences between all annotations regarding which discharges that had been selected as epileptiform, the selected discharges were mostly similar according to the cluster analysis. Almost all identified epileptiform discharges by the classifiers were also periodic discharges.

Conclusions

There was a discrepancy between agreement scores produced by Cohen’s kappa and Gwet’s AC1. This was probably due to the skewed prevalence of epileptiform discharges, which only constitutes a small part of the whole EEG. Gwet’s AC1 is often considered the better option and the results would then indicate an almost perfect agreement. However, this conclusion is questioned when considering the number of differently classified discharges. The difference in annotation between experts affected the learning of the classifiers, but the cluster analysis indicates that all annotations were relatively similar. The difference between experts and classifiers is speculated to be partly due to intrarater variability of the experts, and partly due to underperformance of the classifiers. For a larger study, in addition to using more experts, intrarater agreement should be assessed, the classifiers can be further optimized, and the cluster method hopefully be further improved.
Implicit Adaptation is Fast, Robust and Independent from Explicit Adaptation
Authors: D’Amario Sebastian , Ruttle Jennifer E. , ’t Hart Bernard Marius , Henriques Denise Y. P.
Published: April 2024

During classical visuomotor adaptation, the implicit process is believed to emerge rather slowly; however, recent evidence has found this may not be true. Here, we further quantify the time-course of implicit learning in response to diverse feedback types, rotation magnitudes, feedback timing delays, and the role of continuous aiming on implicit learning. Contrary to conventional beliefs, we affirmed that implicit learning unfolds at a high rate in all feedback conditions. Increasing rotation size not only raises asymptotes, but also generally heightens explicit awareness, with no discernible difference in implicit rates. Cursor-jump and terminal feedback, with or without delays, predominantly enhance explicit adaptation while slightly diminishing the extent or the speed of implicit adaptation. In a continuous aiming reports condition, there is no discernible impact on implicit adaptation, and implicit and explicit adaptation progress at indistinguishable speeds. Finally, investigating the assumed negative correlation as an indicator of additivity of implicit and explicit processes, we consistently observe a weak association across conditions. Our observation of implicit learning early in training in all tested conditions signifies how fast and robust our innate adaptation system is.
Cross-reactivity of rPvs48/45, a recombinantPlasmodium vivaxprotein, with sera fromPlasmodium falciparumendemic areas of Africa
Authors: Balam Saidou , Miura Kazutoyo , Ayadi Imen , Konaté Drissa , Incandela Nathan C. , Agnolon Valentina , Guindo Merepen A , Diakité Seidina A.S. , Olugbile Sope , Nebie Issa , Herrera Sonia M , Long Carole , Kajava Andrey V. , Diakité Mahamadou , Corradin Giampietro , Herrera Socrates , Arevalo Herrera Myriam
Published: April 2024

Background

Ps48/45, aPlasmodiumgametocyte surface protein, is a promising candidate for malaria transmission-blocking (TB) vaccine. Due to its relevance for a multispecies vaccine, we explored the cross-reactivity and TB activity of a recombinantP. vivax Ps48/45 protein (rPvs48/45) with sera fromP. falciparum-exposed African donors.

Methods

rPvs48/45 was produced in Chinese hamster ovary cell lines and tested by ELISA for its cross-reactivity with sera from Burkina Faso, Tanzania, Mali, and Nigeria – In addition, BALB/c mice were immunized with the rPvs48/45 protein formulated in Montanide ISA-51 and inoculated with a crude extract ofP. falciparumNF-54 gametocytes to evaluate the parasite-boosting effect on rPvs48/45 antibody titers. Specific anti-rPvs48/45 IgG purified from African sera was used to evaluate theex vivoTB activity onP. falciparum,using standard mosquito membrane feeding assays (SMFA).

Results

rPvs48/45 protein showed cross-reactivity with sera of individuals from all four African countries, in proportions ranging from 94% (Tanzania) to 40% (Nigeria). Also, the level of cross-reactive antibodies varied significantly between countries (p<0.0001), with a higher antibody level in Mali and the lowest in Nigeria. In addition, antibody levels were higher in adults (≥ 17 years) than young children (≤ 5 years) in both Mali and Tanzania, with a higher proportion of responders in adults (90%) than in children (61%) (p<0.0001) in Mali, where male (75%) and female (80%) displayed similar antibody responses. Furthermore, immunization of mice withP. falciparumgametocytes boosted anti-Pvs48/45 antibody responses, recognizingP. falciparumgametocytes in indirect immunofluorescence antibody test. Notably, rPvs48/45 affinity-purified African IgG exhibited a TB activity of 61% againstP. falciparumin SMFA.

Conclusion

African sera (exposed only toP. falciparum)cross-recognized the rPvs48/45 protein. This, together with the functional activity of IgG, warrants further studies for the potential development of aP. vivaxandP. falciparumcross-protective TB vaccine.
Mondrian Abstraction and Language Model Embeddings for Differential Pathway Analysis
Authors: Al Abir Fuad , Chen Jake Y.
Published: April 2024

In this study, we introduce the Mondrian Map, an innovative visualization tool inspired by Piet Mondrian’s abstract art, to address the complexities inherent in visualizing biological networks. By converting intricate biological data into a structured and intuitive format, the Mondrian Map enables clear and meaningful representations of biological pathways, facilitating a deeper understanding of molecular dynamics. Each pathway is represented by a square whose size corresponds to fold change, with color indicating the direction of regulation (up or down) and statistical significance. The spatial arrangement of pathways is derived from language model embeddings, preserving neighborhood relationships and enabling the identification of clusters of related pathways. Additionally, colored lines highlight potential crosstalk between pathways, with distinctions between short- and long-range functional interactions. In a case study of glioblastoma multiforme (GBM), the Mondrian Map effectively revealed distinct pathway patterns across patient profiles at different stages of disease progression. These insights demonstrate the tool’s potential to enhance downstream bioinformatics analysis by providing a more comprehensive and visually accessible overview of pathway interactions, offering new avenues for therapeutic exploration and personalized medicine.
Chronic alcohol consumption alters sex-dependent BNST neuron function in rhesus macaques
Authors: Pleil Kristen E. , Grant Kathleen A. , Cuzon Carlson Verginia C. , Kash Thomas L.
Published: April 2024

Repeated alcohol drinking contributes to a number of neuropsychiatric diseases, including alcohol use disorder and co-expressed anxiety and mood disorders. Women are more susceptible to the development and expression of these diseases with the same history of alcohol exposure as men, suggesting they may be more sensitive to alcohol-induced plasticity in limbic brain regions controlling alcohol drinking, stress responsivity, and reward processing, among other behaviors. Using a translational model of alcohol drinking in rhesus monkeys, we examined sex differences in the basal function and plasticity of neurons in the bed nucleus of the stria terminalis (BNST), a brain region in the extended amygdala shown to be a hub circuit node dysregulated in individuals with anxiety and alcohol use disorder. We performed slice electrophysiology recordings from BNST neurons in male and female monkeys following daily “open access” (22 hr/day) to 4% ethanol and water for more than one year or control conditions. We found that BNST neurons from control females had reduced overall current density, hyperpolarization-activated depolarizing current (Ih), and inward rectification, as well as higher membrane resistance and greater synaptic glutamatergic release and excitatory drive, than those from control males, suggesting that female BNST neurons are more basally excited than those from males. Chronic alcohol drinking produced a shift in these measures in both sexes, decreasing current density, Ih, and inward rectification and increasing synaptic excitation. In addition, network activity-dependent synaptic inhibition was basally higher in BNST neurons of males than females, and alcohol exposure increased this in both sexes, a putative homeostatic mechanism to counter hyperexcitability. Altogether, these results suggest that the rhesus BNST is more basally excited in females than males and chronic alcohol drinking produces an overall increase in excitability and synaptic excitation. These results shed light on the mechanisms contributing to the female-biased susceptibility to neuropsychiatric diseases including co-expressed anxiety and alcohol use disorder.
Individual variability in sensorimotor learning reflects trait-like neurobehavioral subject factors
Authors: Areshenkoff Corson N , de Brouwer Anouk J , Standage Dominic , Nashed Joseph Y. , Gale Daniel J , Flanagan John Randall , Gallivan Jason
Published: April 2024

Models of Human motor behaviour often emphasize the computations performed by the motor system during learning. Yet, there is an emerging consensus that the learning of even simple motor actions can be augmented by sophisticated cognitive strategies, which rely upon executive functions implemented throughout the cortex. These executive functions, in turn, have been linked to stable subject differences in intrinsic brain organization function, observable even during rest. Here we show, using behavioural studies in humans, that individual differences in the rate of sensorimotor adaptation are linked to differences in executive function, as assessed using the classic trail-making task. Secondly, using separate train and test functional MRI datasets, we show that specific patterns of resting-state functional connectivity between higher-order cognitive brain networks, which have been previously linked to executive function, subsequently predict more rapid learning during sensorimotor adaptation. Importantly, this relationship was unique to cognitive brain networks, as the functional connectivity between sensorimotor brain networks did not predict subsequent motor learning performance. Together, these findings suggest that individual differences in motor learning reflect, to a substantial degree, trait-like subject differences in cognitive brain network structure. This perspective invites broader consideration as to the origins of motor learning ability, and links motor performance to an expansive literature implicating the coordinated functioning of the default mode, ventral attention, and frontoparietal networks in flexible behavioral control.
Plasmin Cleavage of Beta-2-Glycoprotein I Alters its Structure and Ability to Bind to Pathogenic Antibodies
Authors: Bradford Hannah F. , Lalaurie Christophe J. , Gor Jayesh , Gao Xin , Pericleous Charis , Perkins Stephen J. , Britt Hannah , Thalassinos Konstantinos , Giles Ian , Rahman Anisur , Delcea Mihaela , Dalby Paul A. , McDonnell Thomas C.R.
Published: April 2024

Beta-2-Glycoprotein I (β2GPI) is the main autoantigenic target of antiphospholipid syndrome (APS) with antibodies leading to clinical manifestations. There are two known structural isomers of β2GPI, a J shape and a circular shaped one. The transition between these structures is incompletely understood, with the functional implications unknown. β2GPI is a substrate of the protease plasmin, which cleaves within the fifth domain of β2GPI leading to altered cellular binding. Very little is currently known regarding the structure and function of this protein variant. We present the first comprehensive structural characterisation plasmin-clipped β2GPI and the associated implications for pathogenic antibody binding to this protein.

Methods

β2GPI was purified using a novel acid-free process from healthy control plasma and cleaved with plasmin. Cleavage was confirmed by SDS-PAGE. Structural characterisation was undertaken using dynamic light scattering (DLS), small angle X-ray scattering (SAXS), ion mobility mass spectrometry (IMMS) and molecular dynamics simulation (MD). Activity was tested using inhibition of β2GPI ELISAs with patient samples and cleaved β2GPI in the fluid phase and cellular binding by flow cytometry using HUVEC cells.

Results

DLS revealed a significantly smaller hydrodynamic radius for plasmin-clipped β2GPI (p=0.0043). SAXS and MD analysis indicated a novel S-like structure of β2GPI only present in the plasmin-clipped sample whilst IMMS showed a different structure distributions in plasmin clipped compared to non-clipped B2GPI. The increased binding of autoantibodies was shown for plasmin-clipped β2GPI (p=0.056), implying a greater exposure of pathogenic epitopes following cleavage.

Conclusions

Cleavage of β2GPI by plasmin results in the production of a unique S-shaped structural conformation and higher patient antibody binding. This novel structure may explain the loss of binding to phospholipids and increase in anti-angiogenic potential described previously for plasmin-clipped β2GPI.
Sequencing analysis ofHelicobacter pyloriinfection in gastric mucosa and its progression to gastric mucosa-associated tissue (MALT) lymphoma
Authors: Yoo Seung-Joo , Koh Youngil , Byun Ja Min , Hong Junshik , Shin Dong-Yeop , Chun Jaeyoung , Chung Hyunsoo , Yoon Sung-Soo
Published: April 2024

Introduction

The pathogenesis of gastric mucosa-associated tissue (MALT) lymphoma is associated withHelicobacter pyloriinfection. Although treatment strategies and responsiveness according to the stage of gastric MALT lymphoma have been widely reported, a detailed study of the biological carcinogenic process is still required.

Method

Paired, fresh tumor-adjacent normal and gastric mucosal tissue samples from 13 patients with gastric MALT lymphoma were prospectively collected. Whole exome sequencing (WES) and whole-transcriptome sequencing (WTS) data were generated. The analysis of mutations, gene fusion, gene expression, and the microbiome was stratified byH. pyloriinfection and disease status.

Results

Somatic mutations inTRAF3andTNFAIP3were identified inH. pylori-negative gastric MALT lymphoma. Fusions involvingBIRC3-MALT1(2 samples) andTBL1XR1-TP63(1 sample withH. pyloriinfection) were detected. Stepwise comparative analysis of RNA expression revealed upregulation of immune response, inflammatory responses, and the NF- κB signaling pathway inH. pylori-positive MALT lymphoma cases. Pathways associated with pathogens were upregulated inH. pylori-negative MALT lymphoma cases, suggesting that infections other thanH. pylorimay affect lymphomagenesis. Microbiome analysis revealed thatgenus_Rothiawas negatively correlated with alpha diversity.

Conclusion

A stepwise approach using diverse stages of WTS data revealed detailed pathogenic mechanisms of gastric MALT lymphoma. Chronic inflammation following infection contributes to gastric MALT lymphomagenesis in bothH. pyloripositive and negative cases.
Molecular responses of chicken embryos to maternal heat stress through DNA methylation and gene expression
Authors: Karami Keyvan , Sabban Jules , Cerutti Chloé , Devailly Guillaume , Foissac Sylvain , Gourichon David , Hubert Alexandre , Hubert Jean-Noël , Leroux Sophie , Zerjal Tatiana , Lagarrigue Sandrine , Pitel Frédérique
Published: April 2024

Climate change, with its repercussions on agriculture, is one of the most important adaptation challenges for livestock production. Poultry production is a major source of proteins for human consumption all over the world. With a growing human population, improving poultry’s adaptation to environmental constraints becomes critical. Extensive evidence highlights the influence of environmental variations on epigenetic modifications. The aim of this paper is therefore to explore chickens’ molecular response to maternal heat stress. We employed Reduced Representation Bisulfite Sequencing (RRBS) to generate genome-wide single-base resolution DNA methylation profiling and RNA sequencing (RNA-seq) to profile the transcriptome of the brains of embryos hatched from dams reared under either heat stress (32 °C) or thermoneutrality (22°C). We detected 289 significant differentially methylated CpG sites (DMCs) and one differentially methylated region (DMR) between heat stressed and control groups. These DMCs were associated with 357 genes involved in processes such as cellular response to stimulus, developmental processes and immune function. In addition, we identified 11 genes differentially expressed between the two groups of embryos, and identified ATP9A as a target gene of maternal heat stress on offspring. This study provides a body of fundamental knowledge on adaptive mechanisms concerning heat tolerance in chickens.
A sequence- and structure-based characterization of microbial enzymes identifies P. stutzeri as a plastic-degrading species
Authors: Hong Alexander , Turner Serafina , Glazer Rita , Weishampel Zachary A. , Vispute Atharva , Huang Ashley , Holmes Zachary A. , Schleupner Beatrice , Dunphy-Daly Meagan M. , Eward William C. , Somarelli Jason A.
Published: April 2024

Plastic waste has accumulated rapidly in the past century and is now found throughout every ecosystem on Earth. Its ubiquitous presence means that plastic is routinely ingested by countless organisms, with potential negative consequences for organismal health. New solutions are urgently needed to combat plastic pollution. Among the many strategies required to curb the plastic pollution crisis, the bioremediation of plastic via enzymatic activity of microbial species represents a promising approach. Diverse microbes harbor enzymes capable of degrading plastic polymers and utilizing the polymers as a carbon source. Herein, we characterize the landscape of microbial protein-coding sequences with potential plastic degrading capability. Using the two enzyme systems of PETase and MHETase as a guide, we combined sequence motif analysis, phylogenetic inference, and machine learning-guided 3D protein structure prediction to pinpoint potential plastic-degrading enzymes. Our analysis platform identified hundreds of enzymes from diverse microbial taxa with similarity to known PETases, and far fewer enzymes with similarity to known MHETases. Phylogenetic reconstruction revealed that the plastic degrading enzymes formed distinct clades from the sequences of ancestral enzymes. Among the potential candidate sequences, we pinpointed both a PETase-like and MHETase-like enzyme within the bacteriumPseudomonas stutzeri. Using plate clearing assays, we demonstrated thatP. stutzeriis capable of degrading both polyurethane (Impranil®) and polycaprolactone (PCL).Pseudomonas stutzerialso grew on carbon-free agar supplemented with polystyrene, suggesting this organism can utilize synthetic polymers as a carbon source. Overall, our integrated bioinformatics and experimental approach provides a rapid and low-cost solution to identify and test novel polymer-degrading enzymes for use in the development of plastic bioremediation technologies.
Traction Force Microscopy with DNA FluoroCubes
Authors: Mortazavi Armina , Jiang Jianfei , Laric Philip , Helmerich Dominic A. , Seifert Rick , Sauer Markus , Sabass Benedikt
Published: April 2024

From cell differentiation to morphogenesis and cell migration, a multitude of processes are coordinated by mechanical forces that cells generate. Among diverse techniques to assess the mechanical properties of the cell, traction force microscopy (TFM) has emerged as one of the most popular methods for quantifying cell-generated stresses. Standard TFM procedures rely on fiducial markers in the extracellular environment to measure the deformations that are caused by cellular forces. Typically, fluorescent beads are used as fiducials. However, the replacement of beads with fluorescently labeled DNA structures can have numerous advantages, including a smaller size of the markers and the possibility of customizing the DNA structures, for example to read out orthogonal information or to realize a switchable surface functionalization. Here, we develop a multi-purpose platform for combining such setups with TFM. As fiducials we employ FluoroCubes – nanometer-sized DNA constructs - for TFM. These constructs are grafted to a high refractive index polyethylene siloxane surface for the precise tracking of displacements resulting from cell-generated forces. To ensure a local transmission of traction forces from the adhesion ligands to the substrate, we also graft RGD peptides, which represent the smallest ligands of the extracellular matrix, onto our elastic substrates. To further enhance the spatial resolution of the TFM, FluoroCubes can be supplemented with densely packed fluorescent beads as fiducials. We propose a modification of the Kanade-Lucas-Tomasi (KLT) optical flow tracking (OFT) algorithm for optimal, simultaneous tracking of FluoroCubes and beads. Together, the developed experimental setup and tracking algorithm yield highly resolved maps of traction forces that correlate well with the spatial distribution of kindlin at focal adhesions.
Defining mononuclear phagocyte distribution and behaviour in the zebrafish heart
Authors: Moyse Bethany , Moss Joanna , Bevan Laura , Scott Aaron , Wittamer Valérie , Richardson Rebecca J.
Published: April 2024

Mononuclear phagocytes (MNPs) are recognised as highly plastic, multifunctional cells that influence multiple physiological and pathophysiological states. In the heart, they support homeostatic functions, contribute to disease progression and play multiple roles in reparative and regenerative processes following tissue damage. Understanding the heterogeneous populations of cells that contribute to these diverse functions is crucial to facilitating beneficial, and limiting adverse, cardiac outcomes. However, characterisation of precise populations of cardiac immune cells remains incomplete in vertebrate models capable of endogenous regeneration, such as adult zebrafish. Here, we use a combination of transgenic lines to identify distinct MNPs in the zebrafish heart. We show that larval macrophage populations have different origins and a sub-population ofcsf1raexpressing cells are maintained on the surface of the adult heart. MNPs are differently distributed in the myocardium, exhibit different behaviours and are distinguished via expression level ofcsf1raandmpeg1.1. Following injury, tissue resident macrophages rapidly proliferate potentially contributing to reduced scarring. The adult zebrafish heart contains multiple populations of MNPs that can be defined by existing tools. This new understanding of innate immune cell populations in the heart of adult zebrafish sheds light on the composition of a pro-regenerative cardiac microenvironment.
Circadian desynchronization desensitizes insulin-producing cells to cytokine-mediated transcriptomic remodeling and cell death: a novel beta-cell anti-apoptotic response to inflammation
Authors: Andersen Phillip Alexander Keller , Reeh Rasmus Henrik , Sanders Isabel , Overlund Emilie Bender , Mandrup-Poulsen Thomas
Published: April 2024

Perturbation of the circadian clock is a risk factor for metabolic diseases. Beta-Cell specific clock disruption causes glucose intolerance in mice, associated with oxidative stress and secretory failure in beta-cells. Proinflammatory cytokines alter the expression of core-clock machinery in human and rodent beta-cells, but the molecular mechanisms and consequences for cell viability are unclear. We hypothesized that cytokine-mediated clock perturbation in beta-cells is NF-kappaB driven, concomitant with cytokine-induced apoptosis, and depends on the cellular synchronization status. Cytokine-mediated changes of core-clock mRNA expression observed in non-synchronized INS-1 cells were potentiated in synchronized cells. These transcriptional changes differentially translated into alterations in core-clock protein levels. Interestingly, synchronization also sensitized INS-1 cells to cytokine-mediated cytotoxicity, associated with potentiation in the expression of inducible (ind) proteasomal catalytic subunits, ER stress markers, NF-kappaB activity, and activation of the intrinsic apoptotic pathway. Small-molecule NF-kappaB inhibition abrogated cytokine-mediated regulation of clock gene expression in both synchronized and non-synchronized INS-1 cells and reversed cytokine-mediated alterations in circadian parameters in INS-1 reporter cells at non-cytotoxic concentrations. However, at cytotoxic cytokine concentrations, NF-kappaB inhibition caused a loss of circadian rhythmicity while still reducing the cytotoxic effects of cytokines, indicating a differential effect of NF-kappaB signaling in controlling beta-cell viability and clock regulation. We propose that in synchronized cells, the proinflammatory transcriptional activity of NF-kappaB is enhanced by interaction with clock transcription factors, as has been suggested for the clock activator Brain and muscle Arnt-like protein-1 (Bmal1). Thus, desynchronization provides a novel anti-apoptotic defense mechanism in response to cytokine assault, similar to that provided by beta-cell phenotypic de-differentiation.
Fetal protection against bovine viral diarrhea virus types 1 and 2 after vaccination of the dam with the DIVENCE vaccine
Authors: Taberner Ester , Gibert Marta , Montbrau Carlos , Muñoz Irene , Mallorquí Joaquim , Tomas Héctor Santo , Prenafeta Antoni , March Ricard
Published: April 2024

The aim of this study was to demonstrate the efficacy of DIVENCE, a vaccine against BVDV types 1 and 2 (BVDV-1 and BVDV-2) transplacental infection, following a booster regimen in heifers. Calves of two-to-three months of age were given two intramuscular doses three weeks apart and a booster vaccine six months later. Efficacy was evaluated by means of a challenge with virulent BVDV-1 or BVDV-2 administered via the intranasal route at 85 days of gestation. Clinical signs, serology, viral shedding, WBC count and viremia were monitored after the challenge. Sixty-six days post-challenge, the fetuses were assessed for BVDV to detect transplacental infection. The results demonstrate a reduction in hyperthermia, leukopenia, viral shedding, and viremia in vaccinated animals post-challenge with BVDV-1 and BVDV-2. Most importantly, DIVENCE administered prior to breeding protected 94% of the fetuses against BVDV transplacental infection overall across both challenge trials (BVDV-1 and BVDV-2).
Glial state changes and neuroinflammatory RIPK1 signaling are a key feature of ALS pathogenesis
Authors: Zelic Matija , Blazier Anna , Pontarelli Fabrizio , LaMorte Michael , Huang Jeremy , Tasdemir-Yilmaz Ozge E. , Ren Yi , Ryan Sean K. , Krishnaswami Pavithra , Levit Mikhail , Sood Disha , Chen Yao , Gans Joseph , Tang Xinyan , Hsiao-Nakamoto Jennifer , Huang Fen , Zhang Bailin , Gaglia Giorgio , Ofengeim Dimitry , Hammond Timothy R.
Published: April 2024

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease that causes motor neuron loss in the brain and spinal cord. Neuroinflammation driven by activated microglia and astrocytes is prominent in ALS, but an understanding of cell state dynamics and which pathways contribute to the disease remains unclear. Single nucleus RNA sequencing of ALS spinal cords demonstrated striking changes in glial cell states, including increased expression of inflammatory and glial activation markers. Many of these signals converged on RIPK1 and the necroptotic cell death pathway. Activation of the necroptosis pathway in ALS spinal cords was confirmed in a large bulk RNA sequencing dataset and at the protein level. Blocking RIPK1 kinase activity delayed symptom onset and motor impairment and modulated glial responses in SOD1G93Amice. We used a human iPSC-derived motor neuron, astrocyte, and microglia tri-culture system to identify potential biomarkers secreted upon RIPK1 activation, inhibited pharmacologicallyin vitro, and modulated in the CSF of people with ALS treated with a RIPK1 inhibitor. These data reveal ALS-enriched glial populations associated with inflammation and suggest a deleterious role for neuroinflammatory signaling in ALS pathogenesis.
In Silico Vaccine Design: Targeting Highly Epitopic Regions ofClostridium perfringensType D Epsilon Toxin andClostridium novyiType B Alpha Toxin for Optimal Immunogenicity
Authors: Ashoori Nastaran , Ranjbar Mohammad Mehdi , Schirhagl Romana
Published: April 2024

Livestock infections caused by highly toxic bacteria pose significant challenges in veterinary medicine, often requiring complex and elusive treatment regimens. Developing effective vaccines tailored to combat these specific pathogens remains a pressing need within the field. Among the most formidable culprits areClostridium perfringenstype D andClostridium novyitype B, notorious for their extreme toxicity and the difficulty in culturing them for vaccine production. In response to this challenge, our study endeavors to engineer a vaccine candidate capable of concurrently neutralizing the virulence of both bacterial strains. Leveraging computational techniques, we meticulously identified highly epitopic regions withinC. perfringensEpsilon Toxin (ETX) andC. novyiAlpha Toxin (ATX), crucial targets for effective immunization. Through innovative fusion gene design, we integrated these epitopic regions alongside the PADRE-peptide sequence, serving as a universal adjuvant to bolster immune response. The culmination of our efforts materialized in the creation of Recombinant Fusion Protein D (rFPD), a novel vaccine construct poised to elicit robust and specific immune defenses against both bacterial species. By harnessing the power of in silico design and molecular engineering, our study heralds a promising stride towards mitigating the deleterious impact of livestock infections caused by these formidable pathogens.
Predicting chromatin conformation contact maps
Authors: Min Alan , Schreiber Jacob , Kundaje Anshul , Noble William Stafford
Published: April 2024

Over the past 15 years, a variety of next-generation sequencing assays have been developed for measuring the 3D conformation of DNA in the nucleus. Each of these assays gives, for a particular cell or tissue type, a distinct picture of 3D chromatin architecture. Accordingly, making sense of the relationship between genome structure and function requires teasing apart two closely related questions: how does chromatin 3D structure change from one cell type to the next, and how do different measurements of that structure differ from one another, even when the two assays are carried out in the same cell type? In this work, we assemble a collection of chromatin 3D datasets—each represented as a 2D contact map— spanning multiple assay types and cell types. We then build a machine learning model that predicts missing contact maps in this collection. We use the model to systematically explore how genome 3D architecture changes, at the level of compartments, domains, and loops, between cell type and between assay types.
Excitatory neurons of the anterior cingulate cortex encode chosen actions and their outcomes rather than cognitive state
Authors: Jendryka Martin M. , Lewin Uwe , Kapanaiah Sampath K.T. , Dermutz Hartmut , Liss Birgit , Pekcec Anton , Akam Thomas , Grewe Benjamin F. , Kätzel Dennis
Published: April 2024

The anterior cingulate cortex (ACC) causally influences cognitive control of goal-directed behaviour. However, it is unclear whether ACC directly encodes cognitive variables like attention or impulsivity, or implements goal-directed action selection mechanisms that are modulated by them. We recorded ACC activity with miniature endoscopic microscopes in mice performing the 5-choice-serial-reaction time task, and applied decoding and encoding analyses. ACC pyramidal cells represented specific actions before and during the behavioural response, whereas the response type (e.g. correct/incorrect/premature) – indicating the state of attentional and impulse control – could only be decoded during and after the response with high reliability. Devaluation and extinction experiments further revealed that action encoding depended on reward expectation. Our findings support a role for ACC in goal-directed action selection and monitoring, that is modulated by cognitive state, rather than in tracking levels of attention or impulsivity directly in individual trials.