bluuebunny/crossref_metadata_2025_split huggingface dataset:
Changing Stimulation Frequency Improves Implanted Peripheral Nerve Stimulator Effects Following Post-Traumatic Total Hip Arthroplasty: A Case Report
Authors: Pierson Chris J. , Velez Natalie , Jain Nitin B. , Konda Chaitanya 
Published: March 2024

Abstract
Total hip arthroplasty (THA) is an effective procedure to improve pain, range of motion, and function for a variety of conditions, including osteoarthritis and post-traumatic arthritis. Up to 28% of patients had persistent pain at the surgical site 12 to 18 months following THA, even in the absence of surgical complications. Currently, there are no widely accepted non-pharmacological treatments for persistent postoperative pain for THA. This case report details the successful management of a 53-year-old man with chronic pain and weakness following post-traumatic THA. He was initially treated with a single-lead percutaneous peripheral nerve stimulator near the right femoral nerve for four weeks with 100 Hz frequency sensory-level parameters. Four weeks after implantation, the frequency was changed to 12 Hz with a goal of motor-level stimulation. During the following three-week time period, his hip flexion strength improved from 10.36 kg to 23.04 kg. His Lower Extremity Functional Scale improved from 35/80 (43.75%) to 54/80 (67.5%) within a five-week time period. This case’s success demonstrates how PNS may help improve post-operative persistent pain and weakness in many patients, including those with post-traumatic arthroplasty.
Inflammatory markers in pregnancy are associated with postpartum weight in South African women living with HIV on antiretroviral therapy
Authors: Madlala Hlengiwe P. , Myer Landon , Geffen Hayli , Rusch Jody , Shey Muki S. , Meyer Demi , Goedecke Julia H. , Malaba Thokozile R. , Gray Clive M. , Newell Marie-Louise , Jao Jennifer 
Published: March 2024

Background:
Postpartum weight (PPW) contributes to long-term obesity, a growing concern in persons with HIV (PWH). We investigated whether inflammatory markers in pregnancy may be involved in postpartum (PP) obesity in PWH.

Setting:
A total of 57 pregnant PWH enrolled at ≤14 weeks gestation (T1) in Gugulethu antenatal care clinic in Cape Town and followed through 48 weeks PP were included.

Methods:
Plasma soluble (s) CD14, sCD163, leptin, tumour necrosis factor receptor 1 (TNFR-1), resistin, adiponectin, and interleukin-6 (IL-6) were assayed in duplicate using the Luminex platform. We considered each inflammatory marker at T1 (n=57) and T3 (29-36 weeks gestation, n=31) as a separate exposure of interest. Linear mixed effects models were fit to examine whether each exposure was associated with average PPW and PPW trajectories; linear regression was used for associations with PPW change between T1 and 48 weeks.

Results:
Median age was 32 years (IQR, 29-35), 98% were multigravida, and 49% had a BMI≥30 kg/m2. Higher T1 sCD14 levels were associated with higher average weight through 48 weeks PP (ß = 0.002, p=0.04), and T3 sCD14 with higher PPW gain (ß = 0.007, p=0.04). Leptin (ß = 0.414, p<0.01), TNFR-1 (ß = 11.048, p<0.01) and resistin (ß = 0.714, p=0.01) at T3 were associated with higher average PPW, and IL-6 (ß = 2.266, p=0.02) with PPW gain.

Conclusion:
These findings suggest that low-grade inflammation in pregnancy may play a role in postpartum obesity, pointing to potential mechanisms with implications for long-term cardiometabolic health in PWH.
18F-Florbetapir PET/CT and 68Ga-FAPI PET/CT in a Case of Light Chain Amyloidosis With Predominant Multiple Tumor-Like Deposits
Authors: Zhang Yuke , Wang Xuezhu , Ren Chao , Shen Kaini , Huo Li 
Published: March 2024

Abstract
A 66-year-old man presented with multiple masses in different regions, including the left groin, back subcutaneous area, and lungs. Pathological examination confirmed localized amyloid deposits after 3 surgeries. Serum-free λ light chains were elevated. To evaluate systemic involvement, the patient underwent 18F-Florbetapir PET/CT and 68Ga-FAPI-04 PET/CT. Both scans showed increased uptake in multiple masses and nodules throughout the body. This report presents a rare case of light chain (AL) amyloidosis, primarily characterized by multiple localized tumor-like deposits with high activity on 18F-Florbetapir PET/CT and 68Ga-FAPI-04 PET/CT.
Making Moral Decisions With Artificial Agents As Advisors. AnfNIRS Study
Authors: Fabre Eve Florianne , Mouratille Damien , Bonnemains Vincent , Palmiotti Grazia Pia , Causse Mickael 
Published: March 2024

AbstractArtificial Intelligence (AI) is on the verge of impacting every domain of our lives. It is increasingly being used as an advisor to assist in making decisions. The present study aimed at investigating the influence of moral arguments provided by AI-advisors (i.e., decision aid tool) on human moral decision-making and the associated neural correlates. Participants were presented with sacrificial moral dilemmas and had to make moral decisions either by themselves (i.e., baseline run) or with AI-advisors that provided utilitarian or deontological arguments (i.e., AI-advised run), while their brain activity was measured using anfNIRS device. Overall, AI-advisors significantly influenced participants. Longer response times and a decrease in right dorsolateral prefrontal cortex activity were observed in response to deontological arguments than to utilitarian arguments. Being provided with deontological arguments by machines appears to have led to a decreased appraisal of the affective response to the dilemmas. This resulted in a reduced level of utilitarianism, supposedly in an attempt to avoid behaving in a less cold-blooded way than machines and preserve their (self-)image. Taken together, these results suggest that motivational power can led to a voluntary up- and down- regulation of affective processes along moral decision-making.
Optimal Placement of High-Channel Visual Prostheses in Human Retinotopic Visual Cortex
Authors: van Hoof Rick , Lozano Antonio , Wang Feng , Klink P. Christiaan , Roelfsema Pieter R. , Goebel Rainer 
Published: March 2024

AbstractObjectiveRecent strides in neurotechnology show potential to restore vision in individuals afflicted with blindness due to early visual pathway damage. As neuroprostheses mature and become available to a larger population, manual placement and evaluation of electrode designs becomes costly and impractical. An automatic method to optimize the implantation process of electrode arrays at large-scale is currently lacking.ApproachHere, we present a comprehensive method to automatically optimize electrode placement for visual prostheses, with the objective of matching pre-defined phosphene distributions. Our approach makes use of retinotopic predictions combined with individual anatomy data to minimize discrepancies between simulated and target phosphene patterns. While demonstrated with a 1000-channel 3D electrode array in V1, our pipeline is versatile, potentially accommodating any electrode design and allowing for design evaluation.Main resultsNotably, our results show that individually optimized placements in 362 brain hemi-spheres outperform average brain solutions, underscoring the significance of anatomical specificity. We further show how virtual implantation of multiple individual brains highlights the challenges of achieving full visual field coverage owing to single electrode constraints, which may be overcome by introducing multiple arrays of electrodes. Including additional surgical considerations, such as intracranial vasculature, in future iterations could refine the optimization process.SignificanceOur open-source software streamlines the refinement of surgical procedures and facilitates simulation studies, offering a realistic exploration of electrode configuration possibilities.
DeST-OT: Alignment of Spatiotemporal Transcriptomics Data
Authors: Halmos Peter , Liu Xinhao , Gold Julian , Chen Feng , Ding Li , Raphael Benjamin J. 
Published: March 2024

AbstractSpatially resolved transcriptomics (SRT) measures mRNA transcripts at thousands of locations within a tissue slice, revealing spatial variations in gene expression and distribution of cell types. In recent studies, SRT has been applied to tissue slices from multiple timepoints during the development of an organism. Alignment of thisspatiotemporaltranscriptomics data can provide insights into the gene expression programs governing the growth and differentiation of cells over space and time. We introduceDeST-OT(DevelopmentalSpatioTemporalOptimalTransport), a method to align SRT slices from pairs of developmental timepoints using the framework of optimal transport (OT).DeST-OTusessemi-relaxedoptimal transport to precisely model cellular growth, death, and differentiation processes that are not well-modeled by existing alignment methods. We demonstrate the advantage ofDeST-OTon simulated slices. We further introduce two metrics to quantify the plausibility of a spatiotemporal alignment: agrowth distortion metricwhich quantifies the discrepancy between the inferred and the true cell type growth rates, and amigration metricwhich quantifies the distance traveled between ancestor and descendant cells.DeST-OToutperforms existing methods on these metrics in the alignment of spatiotemporal transcriptomics data from the development of axolotl brain.Code availabilitySoftware is available athttps://github.com/raphael-group/DeST_OT
Two new qPCR assays for detecting and quantifying theAspergillus flavusandAspergillus parasiticusclades in maize kernels
Authors: Leharanger A. , Paumier D. , Orlando B. , Bailly S. , Valade R. 
Published: March 2024

AbstractThe fungi ofAspergillussectionFlavimostly produce carcinogenic mycotoxins — aflatoxins (AFs) — of two types: types B and G (AFBs and AFGs). AF are highly hazardous for human and animal health. Their levels in food and feed are therefore highly regulated, with a low acceptable limit for AF content. In France, global warming has led to the detection of AFs in maize harvests since 2015. Mycoflora analyses have identified two species,A. flavus(producing AFBs) andA. parasiticus(producing both AFBs and AFGs), as responsible for this AF contamination. However, mycoflora analysis is a time-consuming method that cannot readily be applied to large numbers of samples. We propose here an alternative clade-specific functional TaqMan® qPCR method based on the calmodulin gene for distinguishing between theA. flavusclade (AfC) and theA. parasiticusclade (ApC). We applied this method to 553 maize samples collected in three different harvest years (2018 to 2020). Both clades were detected in about 40% of the samples tested. As expected, we observed significant positive correlations between AFBs and AfC DNA (R² =0.708), and between AFGs and ApC DNA (R² =0.885). This method will be useful for the rapid, simple and cheap characterisation of maize grain contamination withAspergillussectionFlavi. This method will make it possible to study the relationship between agroclimatic conditions, AF content and species prevalence, to facilitate the anticipation of AF risks due to global warming in France.
OligoY pipeline for full Y chromosome painting
Authors: Almeida Isabela , Bonilla Bruno Henry Angel , Lisboa Santana Pinheiro Mara Maria , Bernardo Carvalho Antonio , Vibranovski Maria Dulcetti 
Published: March 2024

AbstractMotivationThe standard protocol for designing probes used in full chromosome fluorescent labeling experiments does not include repetitive sequences to avoid off-target hybridization. Due to the Y chromosome’s highly repetitive nature, most assembly nowadays still have heavily fragmented and incomplete Y sequences. Among these, the remaining non-repetitive sequences are insufficient to design probes and efficiently perform FISH Oligopaint assays, since they do not cover most regions of the chromosome. Ergo, cytogenetic studies with the Y are sparse, and analysis such as its function throughout the cell cycle and insights into its evolutionary history and relationships with other regions of the genome remain poorly studied.ResultsIn this work, we introduce a new pipeline for designing FISH Oligopaint probes for the Y chromosome of any species of interest. OligoY pipeline uses open-source tools, enriches the amount of contigs assigned to the Y chromosome from the draft assembly, and effectively uses repetitive sequences unique to the target chromosome to design probes. Throughout all of its steps, the pipeline guarantees the user the autonomy to choose parameters, thus maximizing overall efficiency of cytogenetic experiments. After extensive in silico andin situtests and validations withDrosophila melanogaster, we showed for the first time a pipeline for probe design that significantly increases previous Y chromosome staining with no off-target signal.AvailabilityThe pipeline is available athttps://github.com/isabela42/OligoY.
Genetics-driven Risk Predictions with Differentiable Mendelian Randomization
Authors: Sens Daniel , Gräf Ludwig , Shilova Liubov , Casale Francesco Paolo 
Published: March 2024

AbstractAccurate predictive models of future disease onset are crucial for effective preventive healthcare, yet longitudinal datasets linking early risk factors to subsequent health outcomes are scarce. To address this challenge, we introduce Differentiable Mendelian Randomization (DMR), an extension of the classical Mendelian Randomization framework to learn risk predictors without longitudinal data. To do so, DMR leverages risk factors and genetic data from a healthy cohort, along with results from genome-wide association studies (GWAS) of diseases of interest. After training, the learned predictor can be used to assess risk for new patients solely based on risk factors. We validated DMR through comprehensive simulations and in future type 2 diabetes predictions in UK Biobank participants without diabetes, using follow-up onset labels for validation. Finally, we apply DMR to predict future Alzheimer’s onset from brain imaging biomarkers. Overall, with DMR we offer a new perspective in predictive modeling, showing it is possible to learn risk predictors leveraging genetics rather than longitudinal data.
Acute, chronic and conditioned effects of intranasal oxytocin in the mu opioid receptor knockout mouse model of autism: social context matters
Authors: Pantouli Fani , Pujol Camille , Derieux Cécile , Fonteneau Mathieu , Pellissier Lucie P , Marsol Claire , Karpenko Julie , Bonnet Dominique , Hibert Marcel , Bailey Alexis , Merrer Julie Le , Becker Jerome AJ 
Published: March 2024

AbstractAutism Spectrum Disorders (ASD) are neurodevelopmental disorders whose diagnosis relies on deficient social interaction and communication together with repetitive behaviours. Multiple studies have highlighted the potential of oxytocin (OT) to ameliorate behavioural abnormalities in animal models and subjects with ASD. Clinical trials, however, yielded disappointing results. Our study aimed at challenging hypotheses accounting for such negative results by assessing the behavioural effects of different regimens of OT administration in theOprm1null mouse model of ASD. We assessed the effects of intranasal OT injected once at different doses and time points following administration, or chronically, on ASD-related behaviours inOprm1+/+and Oprm1-/-mice. We then tested whether pairing intranasal OT injection with social experience would influence its outcome on ASD-like core symptoms, and measured gene expression in several regions of the reward/social circuit. Acute intranasal OT improved social behaviour inOprm1-/-mice at a moderate dose (0.3 IU) shortly after administration (5 min). Effects on non-social behaviours were limited. Chronic OT at this dose maintained beneficial effects inOprm1null mice but was deleterious in wild-type mice. Finally, improvements in the social behaviour ofOprm1-/-mice were greater and longer lasting when OT was administered in a social context, while the expression of OT and vasopressin receptor genes, as well as marker genes of striatal projection neurons, was suppressed. Our results highlight the importance of considering dosage and social context when evaluating the effects of OT treatment in ASD.HighlightsAcute intranasal oxytocin improved social behaviour shortly after administrationEffects of oxytocin on non-social behaviours were limitedChronic oxytocin maintained beneficial effects in mutant mice but was deleterious in wild-type miceOxytocin triggers greater and longer-lasting improvements in social behaviour when administered within a social contextChronic oxytocin suppresses the expression of its own receptor gene and key striatal neuron gene markers
metaRange: A framework to build mechanistic range models
Authors: Fallert Stefan , Li Lea , Sarmento Cabral Juliano 
Published: March 2024

1AbstractMechanistic or process-based models offer great insights into the range dynamics of species facing non-equilibrium conditions, such as climate and land-use changes or invasive species. Their consideration of underlying mechanisms relaxes the species-environment equilibrium assumed by correlative approaches, while also generating conservation-relevant indicators, such as range-wide abundance time-series and migration rates if demographically explicit. However, the computational complexity of mechanistic models limits their development and applicability to large spatiotemporal extents.We developed the R package ‘metaRange’ that is a modular framework to build population-based and metabolically constrained range models. It provides a function catalogue for users to calculate niche-based suitability, metabolic scaling, population dynamics, biotic interactions, and kernel-based dispersal, which may include directed movement. The framework’s modularity enables the user to combine, extend, or replace these functions, making it possible to customize the model to the ecology of the study system. The package supports an unlimited number of static or dynamic environmental factors as input, including climate and land use.As an example, we simulated 100 virtual species in Germany on a 1 km2resolution over 110 years under realistic environmental fluctuations in three scenarios: without competition, with competition, and with competition and a generalist-specialist trade-off. The results are in accordance with theoretical expectations. Due to the population-level, the package can execute such extensive simulation experiments on regular enduser hardware in a short amount of time. We provide detailed technical documentation, both for the individual functions in the package as well as instructions on how to set up different types of model structures and experimental designs.The metaRange framework enables process-based simulations of range dynamic of multiple interacting species on a high resolution and low computational demand. We believe that it allows for theoretical insights and hypotheses testing about future range dynamics of real-world species, which may better support conservation policies targeting biodiversity loss mitigation.
Longevity and environmental temperature modulate mitochondrial DNA evolution in fishes
Authors: Cam Sabrina Le , Mortz Mathieu , Blier Pierre 
Published: March 2024

AbstractThe link between longevity and mitochondrial function has been documented for years. Since mitochondrial DNA (mtDNA) encodes for electron transport system (ETS) proteins, we could suspect that its evolution is linked with that of longevity. A negative relationship has been documented between the synonymous substitution rate and lifespan when analyzing the whole mitochondrial genome in animals. In this study, we aimed to confirm this negative correlation for each of the mitochondrial protein coding genes (mtPCGs) and explore potential relationships between adaptation to extreme temperatures and the evolution of mtDNA. To this end, we selected 112 species of fish with a wide range of longevity as well as divergences in environmental temperature, which is a good proxy for energy metabolism in these animals. Our results 1) challenge the “rate of living” theory by not showing any correlation between longevity and environmental temperature, 2) confirm the negative relationship between substitution rate and longevity for each of the 13 mtPCGs, and 3) highlight for the first time a link between high conservation of the three COX genes and adaptation to warmer temperatures in fish. By challenging a paradigm and extending the conclusions made for mtDNA to individual genes, our study opens a wide field to be explored concerning study of the aging process. Moreover, the specific link between the evolution of COX genes and temperature tolerance confirms the importance of complex IV in adaptation to extreme temperatures and, more generally, the importance of distinguishing gene families when studying mtDNA evolution in animals.
hAMRonization: Enhancing antimicrobial resistance prediction using the PHA4GE AMR detection specification and tooling
Authors: Mendes Inês , Griffiths Emma , Manuele Alex , Fornika Dan , Tausch Simon H , Le-Viet Thanh , Phelan Jody , Meehan Conor J. , Raphenya Amogelang R. , Alcock Brian , Culp Elizabeth , Lorenzo Federico , Haim Maria Sol , Witney Adam , Black Allison , Katz Lee , Oluniyi Paul , Olawoye Idowu , Timme Ruth , Neoh Hui-min , Lam Su Datt , Jamaluddin Tengku Zetty Maztura Tengku , Nathan Sheila , Ang Mia Yang , Di Gregorio Sabrina , Vandelannoote Koen , Dusadeepong Rutaiwan , Chindelevitch Leonid , Nasar Muhammad Ibtisam , Aanensen David , Afolayan Ayorinde Oluwatobiloba , Odih Erkison Ewomazino , McArthur Andrew Grant , Feldgarden Michael , Galas Marcelo M , Campos Josefina , Okeke Iruka N. , Underwood Anthony , Page Andrew J. , MacCannell Duncan , Maguire Finlay 
Published: March 2024

AbstractThe detection of antimicrobial resistance (AMR) markers directly from genomic or metagenomic data is becoming a standard clinical and public health procedure. This has resulted in the development of a number of different bioinformatic AMR prediction tools. Although many may implement similar principles, these tools differ significantly in their supported inputs, search algorithms, parameterisation, and underlying reference databases. Each of these tools generates a report of detected AMR genes or variants in a distinct, non-standard, format. This presents a huge barrier to the comparison of results and to the modularity of tools for AMR gene prediction within bioinformatic workflows.In collaboration with 17 public health laboratories across 10 countries, the Public Health Alliance for Genomic Epidemiology (PHA4GE) (https://pha4ge.org) data structures working group has developed and piloted a standardized output specification for the bioinformatic detection of AMR from microbial genomes. In this report, we discuss hAMRonization, a python package and command-line utility, which implements PHA4GE’s AMR specification to combine the outputs of disparate antimicrobial resistance gene detection tools into a single unified format. hAMRonization can be easily extended and currently supports 18 different tools (both species-agnostic and species-specific) for the detection of genes and/or variants conferring AMR. The harmonized reports are available in tabular form, JSON format or through an interactive HTML file (e.g.,https://maguire-lab.github.io/assets/interactive_report_demo.html) that can be opened within the browser for navigable data exploration. As of 2024-03-07 hAMRonization has been downloaded ∼12,500 times, incorporated into >9 public bioinformatic tools and workflows, and been internally adopted by several national and international public health groups. The hAMRonization tool and underlying specification are open-source and freely available through PyPI, conda and GitHub (https://github.com/pha4ge/hAMRonization).