bluuebunny/crossref_metadata_2025_split huggingface dataset:
Classifying native versus foreign speech perception from EEG using linguistic speech features
Authors: Puffay Corentin , Vanthornhout Jonas , Gillis Marlies , De Clercq Pieter , Accou Bernd , Van hamme Hugo , Francart Tom 
Published: April 2024

AbstractWhen a person listens to natural speech, the relation between features of the speech signal and the corresponding evoked electroencephalogram (EEG) is indicative of neural processing of the speech signal. Using linguistic representations of speech, we investigate the differences in neural processing between speech in a native and foreign language that is not understood. We conducted experiments using three stimuli: a comprehensible language, an incomprehensible language, and randomly shuffled words from a comprehensible language, while recording the EEG signal of native Dutch-speaking participants. We modeled the neural tracking of linguistic features of the speech signals using a deep-learning model in a match-mismatch task that relates EEG signals to speech, while accounting for lexical segmentation features reflecting acoustic processing. The deep learning model effectively classifies languages. We also observed significant differences in tracking patterns between comprehensible and incomprehensible speech stimuli within the same language. It demonstrates the potential of deep learning frameworks in measuring speech understanding objectively.
An effector XopL enhances ethylene biosynthesis to promoteXanthomonas fragariaeinfection in strawberry
Authors: Cai Xiaolin , Zhang Wenyao , Luo Jinnan , Li Wei , Chen Rui-hong , Xu Xiang-nan , Wen Ying-qiang , Feng Jia-yue 
Published: April 2024

AbstractXanthomonas fragariae(Xaf) is the cause for strawberry crown dry cavity rot and strawberry leaf angular spots. Despite having a long evolutionary history with strawberries, the plant-pathogen connection is poorly understood. Pathogenicity for the majority of plant pathogens is mostly dependent on the type-III secretion system, which introduces virulence type III effectors (T3Es) into eukaryotic hosts cells. For most of these T3Es, the subcellular targets are yet unclear. Here, We used the yeast-two-hybrid (Y2H) technique to construct an interaction network of strawberry-XafT3Es. Multiple T3Es were discovered to converge onto the strawberry 1-aminocyclopropane-1-carboxylic acid oxidases (ACOs), which are the last rate-limited step in the production of ethylene. We then concentrated on the connection between XopL and FveACO9. Strawberry plants that overexpressed XopL accumulated higher levels of ethylene and exhibited more severeXafinfection. XopL boosted ethylene production by stabilizing the accumulation of FveACO9 protein and enhancing ACO enzyme activity. Additionally, strawberries treated with ACC or overexpressing FveACO9 were particularly vulnerable toXafinfection. On the other hand, pre-treatment with α-aminoinoisobutyric acid (AIB), an ACO inhibitor, effectively reducedXafinfection. Our research indicates thatXafutilizes a distinct approach to regulate the ethylene production of host plants in order to promote infection.
Neural correlates of individual facial recognition in a social wasp
Authors: Jernigan Christopher M. , Freiwald Winrich A. , Sheehan Michael J. 
Published: April 2024

AbstractIndividual recognition is critical for social behavior across species. Whether recognition is mediated by circuits specialized for social information processing has been a matter of debate. Here we examine the neurobiological underpinning of individual visual facial recognition inPolistes fuscatuspaper wasps. Front-facing images of conspecific wasps broadly increase activity across many brain regions relative to other stimuli. Notably, we identify a localized subpopulation of neurons in the protocerebrum which show specialized selectivity for front-facing wasp images, which we termwasp cells. Thesewasp cellsencode information regarding the facial patterns, with ensemble activity correlating with facial identity.Wasp cellsare strikingly analogous to face cells in primates, indicating that specialized circuits are likely an adaptive feature of neural architecture to support visual recognition.One-Sentence SummaryWe identify a localized population of neurons specifically tuned to wasp faces in a social wasp that has independently evolved individual facial recognition analogous to the face cells of primates.
Effects of antiretroviral treatment on central and peripheral immune response in mice with EcoHIV infection
Authors: Xie Qiaowei , Namba Mark D , Buck Lauren A , Park Kyewon , Jackson Joshua G , Barker Jacqueline M 
Published: April 2024

AbstractHIV infection is an ongoing global health issue despite increased access to antiretroviral therapy (ART). People living with HIV (PLWH) who are virally suppressed through ART still experience negative health outcomes, including neurocognitive impairment. It is increasingly evident that ART may act independently or in combination with HIV infection to alter immune state, though this is difficult to disentangle in the clinical population. Thus, these experiments used multiplexed chemokine/cytokine arrays to assess peripheral (plasma) and brain (nucleus accumbens; NAc) expression of immune targets in the presence and absence of ART treatment in the EcoHIV mouse model. The findings identify effects of EcoHIV infection and of treatment with bictegravir (B), emtricitabine (F) and tenofovir alafenamide (TAF) on expression of numerous immune targets. In the NAc, this included EcoHIV-induced increases in IL-1α and IL-13 expression and B/F/TAF-induced reductions in KC/CXCL1. In the periphery, EcoHIV suppressed IL-6 and LIF expression, while B/F/TAF reduced IL-12p40 expression. In absence of ART, IBA-1 expression was negatively correlated with CX3CL1 expression in the NAc of EcoHIV-infected mice. These findings identify distinct effects of ART and EcoHIV infection on peripheral and central immune factors and emphasize the need to consider ART effects on neural and immune outcomes.
In search of a conditioned place preference test to assess the severity of experimental procedures
Authors: Jaap Anne , Kahnau Pia , Lewejohann Lars 
Published: April 2024

AbstractTo compare the severity of experimental procedures and behavioural tests from an animal’s perspective novel methods are needed. In theory, one feasible approach could be the use of a conditioned place preference test (CPP). In this test the preference for a certain area in a test apparatus is associated with an experimental treatment.Traditionally, the CPP is used to investigate, for example, the effects of drugs. Here, we wanted to develop a protocol, which instead would enable us to compare the effects of different experimental procedures conducted with mice.Nine experiments with C57BL/6J mice were performed, varying the setup, the procedure duration, the neutral to be conditioned stimuli (NS→CS; visual and/or textual), and the unconditioned stimuli (US; fixation, food reward, or weighing) as well as the presentation order (NS before, after, or parallel to US).Unfortunately, none of the tested protocol resulted in a distinct preference. Moreover, even simple protocols using food reward as a treatment failed to result in a conditioned place preference. Overall, none of the protocols was sufficient to form a reliable association between NS and US. We have scrutinized the experimental setup in detail, and we cannot present a solution yet. However, hopefully, our findings will help to create a working CPP to compare the severity of different experimental procedures for mice.
A registration strategy to characterize DTI-observed changes in skeletal muscle architecture due to passive shortening
Authors: Hooijmans Melissa T. , Lockard Carly A. , Zhou Xingyu , Coolbaugh Crystal , Guzman Roberto Pineda , Kersh Mariana E. , Damon Bruce M. 
Published: April 2024

AbstractSkeletal muscle architecture is a key determinant of muscle function. Architectural properties such as fascicle length, pennation angle, and curvature can be characterized using Diffusion Tensor Imaging (DTI), but acquiring these data during a contraction is not currently feasible. However, an image registration-based strategy may be able to convert muscle architectural properties observed at rest to their contracted state. As an initial step toward this long-term objective, the aim of this study was to determine if an image registration strategy could be used to convert the whole-muscle average architectural properties observed in the extended joint position to those of a flexed position, following passive rotation. DTI and high-resolution fat/water scans were acquired in the lower leg of seven healthy participants on a 3T MR system in +20° (plantarflexion) and −10° (dorsiflexion) foot positions. The diffusion and anatomical images from the two positions were used to propagate DTI fiber-tracts from seed points along a mesh representation of the aponeurosis of fiber insertion. The −10° and +20° anatomical images were registered and the displacement fields were used to transform the mesh and fiber-tracts from the +20° to the −10° position. Student’s pairedt-tests were used to compare the mean architectural parameters between the original and transformed fiber-tracts. The whole-muscle average fiber-tract length, pennation angle, curvature, and physiological cross-sectional areas estimates did not differ significantly. DTI fiber-tracts in plantarflexion can be transformed to dorsiflexion position without significantly affecting the average architectural characteristics of the fiber-tracts. In the future, a similar approach could be used to evaluate muscle architecture in a contracted state.
Distinct mechanisms of visual and sound adaptation in the cat visual cortex
Authors: Belkacemi Yassine Yahia , Hospital Solène , Chanauria Nayan , Flouty Oliver , Molotchnikoff Stéphane , Bharmauria Vishal 
Published: April 2024

AbstractSensory areas exhibit modular selectivity to stimuli, but they can also respond to features outside of their basic modality. Several studies have shown cross-modal plastic modifications between visual and auditory cortices; however, the exact mechanisms of these modifications are yet not completely known. To this aim, we investigated the effect of 12 minutes of visualvs.sound adaptation [forceful application of a non-optimal stimulus to a neuron(s) under observation] on the infra- and supra-granular primary visual neurons (V1) of the cat (Felis catus). Previous reports showed that both protocols induced orientation tuning shifts, but sound increased the bandwidths. Here, we compared visualvs.sound adaptation effects, specifically analysing the raw tuning curves by computing the area under the curve (AUC) on a trial-by-trial basis. We report that sound adaptation elicited broader tuning curves accompanied with increased variance in the supra- and infra-granular layers, compared with visual adaptation. These findings suggest unique modulation of dendritic structure by distinct adaptation protocols, resulting in disparate tunings. We suggest that broader tuning curves after sound adaptation may keep the visual cortex prepared across a spectrum of abstract representations that match with visual stimuli.
Neuropathic pain in a chronic CNS injury model is mediated by CST-targeted spinal interneurons
Authors: Guan Xiaofei , Zhu Yanjie , Zhong Jian , Hollis Edmund 
Published: April 2024

SummaryChronic neuropathic pain is a persistent and debilitating outcome of traumatic central nervous system injury, affecting up to 80% of individuals with chronic injury. Post-injury pain is refractory to clinical treatments due to the limited understanding of the brain-spinal cord circuits that underlie pain signal processing. The corticospinal tract (CST) plays critical roles in sensory modulation during skilled movements and tactile sensation; however, a direct role for the CST in injury-associated neuropathic pain is unclear. Here we show that complete, selective CST transection at the medullary pyramids leads to hyperexcitability within lumbar deep dorsal horn and hindlimb allodynia in chronically injured adult mice. Chemogenetic regulation of CST-targeted lumbar spinal interneurons demonstrates that dysregulation of activity in this circuit underlies the development of tactile allodynia in chronic injury. Our findings shed light on an unrecognized circuit mechanism implicated in CNS injury-induced neuropathic pain and provide a novel target for therapeutic intervention.
A protective role for B-1 cells and oxidation-specific epitope IgM in lung fibrosis
Authors: Sturek Jeffrey M. , Hannan Riley T. , Upadhye Aditi , Otoupalova Eva , Faron Edwin T. , Atya Amr A.E. , Thomas Cassidy , Johnson Vernerdean , Miller Andrew , Garmey James C. , Burdick Marie D. , Barker Thomas H. , Kadl Alexandra , Shim Yun M. , McNamara Coleen A. 
Published: April 2024

ABSTRACTIdiopathic pulmonary fibrosis (IPF) is a morbid fibrotic lung disease with limited treatment options. The pathophysiology of IPF remains poorly understood, and elucidation of the cellular and molecular mechanisms of IPF pathogenesis is key to the development of new therapeutics. B-1 cells are an innate B cell population which play an important role linking innate and adaptive immunity. B-1 cells spontaneously secrete natural IgM and prevent inflammation in several disease states. One class of these IgM recognize oxidation-specific epitopes (OSE), which have been shown to be generated in lung injury and to promote fibrosis. A main B-1 cell reservoir is the pleural space, adjacent to the typical distribution of fibrosis in IPF. In this study, we demonstrate that B-1 cells are recruited to the lung during injury where they secrete IgM to OSE (IgMOSE). We also show that the pleural B-1 cell reservoir responds to lung injury through regulation of the chemokine receptor CXCR4. Mechanistically we show that the transcription factorId3is a novel negative regulator of CXCR4 expression. Using mice with B-cell specific Id3 deficiency, a model of increased B-1b cells, we demonstrate decreased bleomycin-induced fibrosis compared to littermate controls. Furthermore, we show that mice deficient in secretory IgM (sIgM-/-) have higher mortality in response to bleomycin-induced lung injury, which is partially mitigated through airway delivery of the IgMOSEE06. Additionally, we provide insight into potential mechanisms of IgM in attenuation of fibrosis through RNA sequencing and pathway analysis, highlighting complement activation and extracellular matrix deposition as key differentially regulated pathways.
Improved prediction of stabilizing mutations in proteins by incorporation of mutational effects on ligand binding
Authors: Ganesan Srivarshini , Mittal Nidhi , Bhat Akash , Adiga Rachna S. , Ganesan Ananthakrishnan , Nagarajan Deepesh , Varadarajan Raghavan 
Published: April 2024

AbstractWhile many computational methods accurately predict destabilizing mutations, identifying stabilizing mutations has remained a challenge, due to their relative rarity. We tested ΔΔG0predictions from computational predictors such as Rosetta, ThermoMPNN, RaSP, and DeepDDG, using eighty-two mutants of the bacterial toxin CcdB as a test case. On this dataset, the best computational predictor is ThermoMPNN which identifies stabilizing mutations with a precision of 68%. However, the average increase in Tmfor these predicted mutations was only 1°C for CcdB, and predictions were poorer for a more challenging target, influenza neuraminidase. Using data from multiple previously described yeast surface display libraries andin vitrothermal stability measurements, we trained logistic regression models to identify stabilizing mutations with a precision of 90% and an average increase in Tmof 3°C for CcdB. When such libraries contain a population of mutants with significantly enhanced binding relative to the corresponding wild type, there is no benefit in using computational predictors. It is then possible to predict stabilizing mutations without any training, simply by examining the distribution of mutational binding scores. This avoids laborious steps ofin vitroexpression, purification, and stability characterization. When this is not the case, combining data from computational predictors with high-throughput experimental binding data enhances the prediction of stabilizing mutations. However, this requires training on stability data measuredin vitrowith known stabilized mutants. It is thus feasible to predict stabilizing mutations rapidly and accurately for any system of interest that can be subjected to a binding selection or screen.
Sustained Human Outbreak of a New MPXV Clade I Lineage in Eastern Democratic Republic of the Congo
Authors: Vakaniaki Emmanuel H. , Kacita Cris , Kinganda-Lusamaki Eddy , O’Toole Áine , Wawina-Bokalanga Tony , Mukadi-Bamuleka Daniel , Aziza Adrienne Amuri , Malyamungu-Bubala Nadine , Kumbana Franklin Mweshi , Mutimbwa-Mambo Léandre , Belesi-Siangoli Freddy , Mujula Yves , Parker Edyth , Muswamba-Kayembe Pauline-Chloé , Nundu Sabin S. , Lushima Robert S. , Cigolo Jean Claude Makangara , Mulopo-Mukanya Noella , Simbu Elisabeth Pukuta , Akil-Bandali Prince , Kavunga Hugo , Vercauteren Koen , Sam-Agudu Nadia A. , Mills Edward J , Tshiani-Mbaya Olivier , Hoff Nicole A. , Rimoin Anne W. , Hensley Lisa E. , Kindrachuk Jason , Ayouba Ahidjo , Peeters Martine , Delaporte Eric , Ahuka-Mundeke Steve , Nachega Jean B. , Muyembe-Tamfum Jean-Jacques , Rambaut Andrew , Liesenborghs Laurens , Mbala-Kingebeni Placide ,   the Mpox Research Consortium
Published: April 2024

ABSTRACTBackgroundMonkeypox virus (MPXV) attracted global attention in 2022 during a widespread outbreak linked primarily to sexual contact. Clade I MPXV is prevalent in Central Africa and characterized by severe disease and high mortality, while Clade II is confined to West Africa and associated with milder illness. A Clade IIb MPXV emerged in Nigeria in 2017, with protracted human-to-human transmission a forerunner of the global Clade II B.1 lineage outbreak in 2022. In October 2023, a large mpox outbreak emerged in the Kamituga mining region of the Democratic Republic of the Congo (DRC), of which we conducted an outbreak investigation.MethodsSurveillance data and hospital records were collected between October 2023 and January 2024. Blood samples and skin/oropharyngeal swabs were obtained for molecular diagnosis at the National Institute of Biomedical Research, Kinshasa. MPXV genomes were sequenced and analyzed using Illumina NextSeq 2000 and bioinformatic tools.ResultsThe Kamituga mpox outbreak spread rapidly, with 241 suspected cases reported within 5 months of the first reported case. Of 108 confirmed cases, 29% were sex workers, highlighting sexual contact as a key mode of infection. Genomic analysis revealed a distinct MPXV Clade Ib lineage, divergent from previously sequenced Clade I strains in DRC. Predominance of APOBEC3-type mutations and estimated time of emergence around mid-September 2023 suggest recent human-to-human transmission.ConclusionsUrgent measures, including reinforced, expanded surveillance, contact tracing, case management support, and targeted vaccination are needed to contain this new pandemic-potential Clade Ib outbreak.
Prevalence and impact of foot peripheral neuropathy in Sytemic Sclerosis (SSc): results from a single centre cross-sectional study
Authors: Alcacer-Pitarch Begonya , Di Battista Marco , Redmond Anthony C. , Keenan Anne-Maree , Di Donato Stefano , Buch Maya H. , Del Galdo Francesco 
Published: April 2024

AbstractIntroductionPeripheral Sensory Neuropathy (PSN) is an under-recognized feature in systemic sclerosis (SSc). Moreover, SSc foot involvement is frequent but poorly investigated. We aimed to provide a detailed characterization of foot peripheral neuropathy in a large cohort of SSc patients, describing its associations with disease-specific features, physical disability and Quality of Life (QoL).MethodsSSc patients and healthy controls (HC) comparable for age and gender, were enrolled in a cross-sectional observational case-control study. All subjects underwent a detailed quantitative sensory testing (QST) of feet evaluating touch, vibratory, thermal, and pain sensitivity; ultimately investigating the presence of large and small fiber neuropathy. Neuroptahtic symptoms were captured through a numerical rating scale assessing the presence of paraesthesia, numbness, burning, and stabbing pain. While the Manchester Foot Pain and Disability Index (MFPDI), SSc Health Assessment Questionnaire Disability Index (HAQ-DI), and the Systemic Sclerosis Quality of Life (SScQoL) needs-based questionnaire were used to capture the impact of the PSN on foot disability and QoL.Results109 SSc patients (88.1% female, median age 59.0 years) and 51 HC were enrolled. SSc patients presented with a significant median reduction of areas with preserved tactile sensitivity (14 IQR 4; p<0.001), and a delayed vibration perception threshold (1.7 µm IQR 3.0; p=0.01). Regarding thermoreceptor impairment, they presented with signifiantlly higer cold and warm thresholds (27.0 °C, IQR 3.0; vs 28.2 °C, p<0.001; 38.4 °C IQR 4.6, p=0.003 respectivelly), greater warm-cold threshold range (11.2 °C, IQR 6.9, p<0.001), and higher heat-induced pain threshold (44.8 °C, IQR 3.5; p<0.001),. At group level, 85.3% patients showed PSN on the feet, with 80% having small fibre involvement and 57% having large fiber neuropathy; while the coexistence of the two was present in 51.4% of the cases. Leaving only 14% without neuropathy. From those patients with PSN, 80.6% reported at least one neuropathic symptom, while 18% were asymptomatic. PSN was associated with age, smoking, foot ulceration,disease duration and corticosteroids use. Patients with neuropathic symptoms reported worse physical function, worse foot disability, and poorer QoL.ConclusionFoot PSN presents as common and disabling manifestation in patients with SSc, involving both large and small fibers, often co-existing. Clinically, the presence of neuropathic symptoms might serve as an indicator of PSN, although it can have a subclinical presentation. Hence, PSN assessment should be included as part of the workup of the SSc patient .