bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reconstructing Voice Identity from Noninvasive Auditory Cortex Recordings
Authors: Lamothe Charly , Thoret Etienne , Trapeau Régis , Giordano Bruno L. , Sein Julien , Takerkart Sylvain , Ayache Stéphane , Artières Thierry , Belin Pascal 
Published: February 2024

AbstractThe cerebral processing of voice information is known to engage, in human as well as non-human primates, “temporal voice areas” (TVAs) that respond preferentially to conspecific vocalizations. However, how voice information is represented by neuronal populations in these areas, particularly speaker identity information, remains poorly understood. Here, we used a deep neural network (DNN) to generate a high-level, small-dimension representational space for voice identity—the ‘voice latent space’ (VLS)—and examined its linear relation with cerebral activity via encoding, representational similarity, and decoding analyses. We find that the VLS maps onto fMRI measures of cerebral activity in response to tens of thousands of voice stimuli from hundreds of different speaker identities and better accounts for the representational geometry for speaker identity in the TVAs than in A1. Moreover, the VLS allowed TVA-based reconstructions of voice stimuli that preserved essential aspects of speaker identity as assessed by both machine classifiers and human listeners. These results indicate that the DNN-derived VLS provides high-level representations of voice identity information in the TVAs.
Transcriptomic characterization of recombinantClostridium beijerinckiiNCIMB 8052 expressing methylglyoxal synthase and glyoxal reductase fromClostridium pasteurianumATCC 6013
Authors: Kumar Santosh , Agyeman-Duah Eric , Ujor Victor C. 
Published: February 2024

ABSTRACTBioconversion of abundant lactose-replete whey permeate to value added chemicals holds promise for valorization of this increasing food processing waste. Efficient conversion of whey-permeate-borne lactose requires adroit microbial engineering to funnel carbon to the desired chemical. Having engineered a strain ofClostridium beijerinckiiNCIMB 8052 (C. beijerinckii_mgsA+mgR) that produces 87% more butanol on lactose than the control strain, in this study, we deployed RNA sequencing to profile the global transcriptome ofC. beijerinckii_mgsA+mgR. The results revealed broadly contrasting gene expression patterns inC. beijerinckii_mgsA+mgR relative to the control strain. These were characterized by widespread downregulation of Fe-S proteins inC. beijerinckii_mgsA+mgR, coupled with increased expression of lactose uptake and catabolic genes, iron and phosphate uptake genes, two component signal transduction and motility genes, and genes involved in the biosynthesis of vitamin B5and B12, aromatic amino acids, particularly tryptophan; arginine, and pyrimidines. Conversely, L-aspartate-dependentde novobiosynthesis of NAD as well as biosynthesis/metabolism of glycine, threonine, lysine, isoleucine and asparagine were downregulated. Furthermore, genes involved in cysteine and methionine biosynthesis and metabolism, including cysteine desulfurase—a central player in Fe-S cluster biosynthesis—were equally downregulated. Genes involved in biosynthesis of capsular polysaccharides and stress response were also downregulated inC. beijerinckii_mgsA+mgR. The results suggest that remodeling of cellular and metabolic networks inC. beijerinckii_mgsA+mgR to counter likely effect of methylglyoxal production following heterologous expression of methyl glyoxal synthase led to enhanced growth and butanol production inC. beijerinckii_mgsA+mgR.IMPORTANCEBiological production of commodity chemicals from abundant waste streams such as whey permeate represents a rational approach for decarbonizing chemical production. Whey permeate remains a vastly underutilized feedstock for bioproduction purposes. Thus, enhanced understanding of the cellular and metabolic repertoires of lactose-mediated production of chemicals such as butanol, promises to arm researchers with new engineering targets that can be fine-tuned in recombinant and native microbial strains to engender stronger coupling of whey permeate-borne lactose to value-added chemicals. Our results highlight new genetic targets for future engineering ofC. beijerinckii_mgsA+mgR and indeed,C. beijerinckiifor improved butanol production on lactose, and ultimately in whey permeate.
New approaches to the Single-Interval Adjustment Matrix (SIAM) Yes-No task
Authors: Shepherd Daniel , Hautus Michael J. 
Published: February 2024

ABSTRACTTwo adaptations of the Single-Interval Adjust-Matrix Yes-No (SIAM-YN) task, designed to increase the efficiency of absolute threshold estimation, are described. The first, the SIAM Twin Track (SIAM-TT) task, consists of two interleaved tracks of the standard SIAM-YN that are run in the same trial with a single response. The second new task modifies the binary SIAM-YN task by using a six-point rating-scale (SIAM-Rating). In Experiment 1, data from three tasks estimating absolute thresholds were obtained using a 10-ms tone, the 2-IFC transformed up-down procedure, SIAM-YN task, and the SIAM-TT task. The data support the use of the SIAM-TT as an alternative to the conventional two-interval and one-interval (SIAM-YN) tasks when used to estimate absolute thresholds. By presenting two interleaved SIAM-YN tracks on a single experimental trial, the SIAM-TT task possesses greater efficiency alongside its signal-detection heritage which confers less response bias. Similarly, in Experiment 2, which compared the 2-IFC adaptive, SIAM-YN, and SIAM-Rating tasks, there was no main effect of task upon threshold estimates. The findings replicate previous studies supporting the validity and efficiency of the SIAM-YN task, and extends the SIAM-YN toolbox to efficiently facilitate the generation of psychometric functions (the SIAM-TT task) and Receiver Operating Characteristic Curves (the SIAM-Rating task).
Glucose appetition in C57BL/6J mice: Influence of nonnutritive sweetener experience, food deprivation state and sex differences
Authors: Sclafani Anthony , Ackroff Karen 
Published: February 2024

AbstractIn addition to its sweet taste, glucose has potent and rapid postoral actions (appetition) that enhance its reward value. This has been demonstrated by the experience-induced preference for glucose over initially preferred nonnutritive sweetener solutions in 24-h choice tests. However, some sweetener solutions (e.g., 0.8% sucralose) have inhibitory postoral actions that may exaggerate glucose appetition whereas others (e.g., 0.1% sucralose + 0.1% saccharin, S+S) do not. Experiment 1 revealed that food-restricted (FR) male C57BL/6J mice displayed similar rapid glucose appetition effects (stimulation of glucose licking within minutes) and conditioned flavor preferences following 1-h experience with flavored 0.8% sucralose or 0.1% S+S and 8% glucose solutions. Thus, the inhibitory effects of 0.8% sucralose observed in 24-h tests were not apparent in 1-h tests. Experiment 2 evaluated the effects of food deprivation state on 1-h glucose appetition. Unlike FR female mice, ad libitum (AL) fed mice displayed no or delayed stimulation of glucose licking depending upon the training solutions used (0.1% S+S vs. 8% glucose, or 0.2% S+S vs. 16% glucose). Both AL groups, like the FR group, developed a preference for the glucose-paired flavor over the S+S paired flavor. Thus, food restriction promotes glucose appetition but is not required for a conditioned preference. Overall, male and female mice showed similar glucose appetition responses although females displayed a more rapid initial glucose response.
Meta-analysis of the human gut microbiome uncovers shared and distinct microbial signatures between diseases
Authors: Jin Dong-Min , Morton James T. , Bonneau Richard 
Published: February 2024

ABSTRACTMicrobiome studies have revealed gut microbiota’s potential impact on complex diseases. However, many studies often focus on one disease per cohort. We developed a meta-analysis workflow for gut microbiome profiles and analyzed shotgun metagenomic data covering 11 diseases. Using interpretable machine learning and differential abundance analysis, our findings reinforce the generalization of binary classifiers for Crohn’s disease (CD) and colorectal cancer (CRC) to hold-out cohorts and highlight the key microbes driving these classifications. We identified high microbial similarity in disease pairs like CD vs ulcerative colitis (UC), CD vs CRC, Parkinson’s disease vs type 2 diabetes (T2D), and schizophrenia vs T2D. We also found strong inverse correlations in Alzheimer’s disease vs CD and UC. These findings detected by our pipeline provide valuable insights into these diseases.IMPORTANCEAssessing disease similarity is an essential initial step preceding disease-based approach for drug repositioning. Our study provides a modest first step in underscoring the potential of integrating microbiome insights into the disease similarity assessment. Recent microbiome research has predominantly focused on analyzing individual disease to understand its unique characteristics, which by design excludes comorbidities individuals. We analyzed shotgun metagenomic data from existing studies and identified previously unknown similarities between diseases. Our research represents a pioneering effort that utilize both interpretable machine learning and differential abundance analysis to assess microbial similarity between diseases.
Robust variability of grid cell properties within individual grid modules enhances encoding of local space
Authors: Redman William T. , Acosta-Mendoza Santiago , Wei Xue-Xin , Goard Michael J. 
Published: February 2024

AbstractAlthough grid cells are one of the most well studied functional classes of neurons in the mammalian brain, whether there is a single orientation and spacing value per grid module has not been carefully tested. We analyze a recent large-scale recording of medial entorhinal cortex to characterize the presence and degree of heterogeneity of grid properties within individual modules. We find evidence for small, but robust, variability and hypothesize that this property of the grid code could enhance the encoding of local spatial information. Performing analysis on synthetic populations of grid cells, where we have complete control over the amount heterogeneity in grid properties, we demonstrate that grid property variability of a similar magnitude to the analyzed data leads to significantly decreased decoding error. This holds even when restricted to activity from a single module. Our results highlight how the heterogeneity of the neural response properties may benefit coding and opens new directions for theoretical and experimental analysis of grid cells.
Synchronized photoactivation of T4K rhodopsin causes a chromophore-dependent retinal degeneration that is moderated by interaction with phototransduction cascade components
Authors: Tam Beatrice M. , Burns Paloma , Chiu Colette N. , Moritz Orson L. 
Published: February 2024

AbstractMultiple mutations in theRhodopsingene cause sector retinitis pigmentosa in humans and a corresponding light-exacerbated retinal degeneration (RD) in animal models. Previously we have shown that therhodopsinmutation T4K requires photoactivation to exert its toxic effect. Here we further investigated the mechanisms involved in rod cell death caused by T4K rhodopsin inXenopus laevis. In this model, RD was prevented by rearing animals in constant darkness but surprisingly also in constant light. RD was maximized by light cycles containing at least one hour of darkness and 20 minutes of light exposure, light of intensity 750 lux or greater, and by sudden light onset. Under conditions of frequent light cycling, RD occured rapidly and synchronously, with massive shedding of ROS fragments into the RPE initiated within hours, and subsequent death and phagocytosis of rod cell bodies. RD was minimized by reduced light levels, pre-treatment with constant light, and gradual light onset. RD was prevented by genetic ablation of the retinal isomerohydrolase RPE65, and exacerbated by ablation of phototransduction components GNAT1, SAG, and GRK1. Our results indicate that photoactivated T4K rhodopsin is toxic, that cell death requires synchronized photoactivation of T4K rhodopsin, and that toxicity is mitigated by interaction with other rod outer segment proteins regardless of whether they participate in activation or shutoff of phototransduction. In contrast, RD caused by P23H rhodopsin does not require photoactivation of the mutant protein, as it was exacerbated by RPE65 ablation, suggesting that these phenotypically similar disorders may benefit from different treatment strategies.SignificanceA large number ofrhodopsinmutations are linked to the inherited degenerative disease retinitis pigmentosa. Although the end result in each case is the loss of photoreceptor cells and blindness, not all of these mutations cause cell death via the same mechanism. In order to design and test treatment therapies that target the disease at points as upstream as possible in the process, we require detailed understanding of the range and nature of these disease mechanisms. This study using a transgenicXenopus laevismodel has extended our understanding of how T4K rhodopsin and related mutations cause rod cell photoreceptor death via a phototoxic product, and how this mechanism differs from the more extensively researched protein misfolding mechanism underlying cell death caused by P23H rhodopsin.
Failed stopping transiently suppresses the electromyogram in task-irrelevant muscles
Authors: Mills Isaiah , Fisher Mitchell , Wadsley Corey , Greenhouse Ian 
Published: February 2024

AbstractSelectively stopping individual parts of planned or ongoing movements is an everyday motor skill. For example, while walking in public you may stop yourself from waving at a stranger who you mistook for a friend while continuing to walk. Despite its ubiquity, our ability to selectively stop actions is limited. Canceling one action can delay the execution of other simultaneous actions. This stopping-interference effect on continuing actions during selective stopping may be attributed to a global inhibitory mechanism with widespread effects on the motor system. Previous studies have characterized a transient global reduction in corticomotor excitability by combining brain stimulation with electromyography (EMG). Here, we examined whether global motor inhibition during selective stopping can be measured peripherally and with high temporal resolution using EMG alone. Eighteen participants performed a bimanual anticipatory response inhibition task with their index fingers while maintaining a tonic contraction of the task-irrelevant abductor digiti minimi (ADM) muscles. A time series analysis of the ADM EMG signal revealed transient inhibition during failed stopping compared to go response trials 150 ms to 203 ms following the stop signal. The pattern was observed in both hands during bimanual stop-all trials as well as selective stop-left and stop-right trials of either hand. These results indicate that tonic muscle activity is sensitive to the effects of global motor suppression even when stopping fails. Therefore, EMG can provide a physiological marker of global motor inhibition to probe the time course and extent of stopping processes.Key PointsSuccessfully stopping an initiated response globally suppresses the motor system.Using electromyography of tonic muscle activity, we show inhibition spills over to task-irrelevant muscles during failed stopping.The electromyographic pattern of inhibition is transient, lasting from approximately 150 to 203 ms following a stop signal when stopping fails.The time course of the peripheral suppression of muscle activity may be leveraged to more precisely examine candidate neural mechanisms.This non-invasive measure of motor system inhibition may be useful for tracking inhibitory control deficits in clinical populations.
A computational and multi-brain signature for aberrant social coordination in schizophrenia
Authors: Wang Ya-Jie , Wen Yalan , Zheng Leilei , Chen Ji , Lin Zheng , Pan Yafeng 
Published: February 2024

AbstractSocial functioning impairment is a core symptom of schizophrenia (SCZ). Yet, the computational and neural mechanisms of social coordination in SCZ under real-time and naturalistic settings are poorly understood. Here, we instructed patients with SCZ to coordinate with a healthy control (HC) in a joint finger-tapping task, during which their brain activity was measured by functional near-infrared spectroscopy simultaneously. The results showed that patients with SCZ exhibited poor rhythm control ability and unstable tapping behaviour, which weakened their interpersonal synchronization when coordinating with HCs. Moreover, the dynamical systems modelling revealed disrupted between-participant coupling when SCZ patients coordinated with HCs. Importantly, increased inter-brain synchronization was identified within SCZ-HC dyads, which positively correlated with behavioural synchronization and successfully predicted dimensions of psychopathology. Our study suggests that SCZ individuals may require stronger neural alignment to compensate for deficiency in their coordination ability. This hyperalignment may be relevant for developing inter-personalized treatment strategies.
Effectiveness of DiabeText, a mHealth intervention to support diabetes self-management: randomized controlled trial in primary care
Authors: Zamanillo-Campos Rocío , Fiol-Deroque Maria Antonia , Serrano-Ripoll Maria Jesús , Llobera-Canaves Joan , Taltavull-Aparicio Joana María , Leiva-Rus Alfonso , Ripoll-Amengual Joana , Angullo-Martínez Escarlata , Socias-Buades Isabel Maria , Masmiquel Luis , Konieczna Jadwiga , Zaforteza-Dezcallar María , Boronat-Moreiro Maria Asunción , Mira-Martínez Sofía , Gervilla-García Elena , Ricci-Cabello Ignacio 
Published: February 2024

AbstractBackgroundComplications arising from uncontrolled Type 2 Diabetes (T2D) poses a significant burden on individuals’ well-being and healthcare resources. Digital interventions may play a key role in mitigating such complications by supporting patients to adequately self-manage their condition.AimTo assess the impact of DiabeText, a new theory-based, patient-centered, mobile health intervention integrated with electronic health records to send tailored short text messages to support T2D self-management.Design and settingPragmatic, phase III, 12-month, two-arm randomized clinical trial with T2D primary care patients in Spain.Method742 participants with suboptimal glycemic control (HbA1c>7.5) were randomly allocated to a control (usual care) or intervention (DiabeText) group. The DiabeText group received, in addition to usual care, 165 messages focused on healthy lifestyle and medication adherence. Primary outcome: glycated hemoglobin (HbA1c). Secondary outcomes: medication possession ratio, quality of life (EQ-5D-5L), diabetes self-efficacy (DSES); and self-reported adherence to medication, Mediterranean diet (MEDAS-14), and physical activity (IPAQ).ResultsAt 12 months follow-up, no statistically significant differences in mean HbA1c were observed between the intervention (7.5 [95%CI 6.7 to 8.2]) and control groups (7.4 [6.7 to 8.3]). In comparison with the control group, the DiabeText group showed significant (p<0.05) improvements in self-reported medication adherence (OR=1.4; 95%CI: 1.0 to 1.9), DSES (Cohen’s d=0.4), and EQ5D-5L (Cohen’s d=0.2) scores; but not in the rest of secondary outcomes.ConclusionDiabeText successfully improved quality of life, diabetes self-management, and self-reported medication adherence in primary care patients with T2D. Further research is needed to enhance its effects on physiological outcomes.
Sleep Hygiene Index: Dimensionality, internal consistency, and nomological validity among Colombian medical students
Authors: Campo-Arias Adalberto , Pedrozo-Pupo John Carlos , Caballero-Domínguez Carmen Cecilia 
Published: February 2024

ABSTRACTBackground and purposeA new version of the Sleep Hygiene Index (SHI-10) has recently been introduced, and the psychometric performance in other populations is unknown. This study aimed to determine the dimensionality, internal consistency, and nomological validity of the SHI-10 among medical students at a Colombian university.MethodsA psychometric study was designed to determine indicators of validity (construct and nomological) and reliability (internal consistency) in which 309 medical students between 18 and 39 years (M=20.83, SD=2.68), and 54.69% were female. Construct validity (dimensionality) was tested through confirmatory factor analysis, internal consistency with Cronbach’s alpha and McDonald’s omega coefficients, and nomological validity through correlations with the Athens Insomnia Scale, Epworth Somnolence Scale, Generalized Anxiety Disorder (GAD)-7) and Patient Health Questionnaire (PHQ-9).ResultsThe four-dimensional structure of the SHI-10 showed adequate indicators of goodness of fit (Satorra-Bentler’s chi-square of 43.30 [df of 29, p=.04], chi-square/df of 1.49, RMSEA of .04 [90%CI .01-.06], CFI of .97, TLI of .96 and SRMR .04). The four dimensions of the SHI-10 showed values less than .70 and limited nomological validity (most Pearson correlations were less than .30).ConclusionsThe SHI-10 shows a four-dimensional structure of SHI-10; however, the four dimensions of the SHI-10 present low internal consistency and limited nomological validity. More studies are needed to show the psychometric performance of the SHI-10.
Phylogenetic signal in primate tooth enamel proteins and its relevance for paleoproteomics
Authors: Zazueta Ricardo Fong , Krueger Johanna , Alba David M. , Aymerich Xènia , Beck Robin M. D. , Cappellini Enrico , Martín Guillermo Carrillo , Cirilli Omar , Clark Nathan , Cornejo Omar E. , Farh Kyle Kai-How , Ferrández-Peral Luis , Juan David , Kelley Joanna L. , Kuderna Lukas F. K. , Little Jordan , Orkin Joseph D. , Paterson Ryan S. , Pawar Harvinder , Marques-Bonet Tomas , Lizano Esther 
Published: February 2024

AbstractAncient tooth enamel, and to some extent dentin and bone, contain characteristic peptides that persist for long periods of time. In particular, peptides from the enamel proteome (enamelome) have been used to reconstruct the phylogenetic relationships of fossil specimens and to estimate divergence times. However, the enamelome is based on only about 10 genes, whose protein products undergo fragmentationpost mortem. Moreover, some of the enamelome genes are paralogous or may coevolve. This raises the question as to whether the enamelome provides enough information for reliable phylogenetic inference. We address these considerations on a selection of enamel-associated proteins that has been computationally predicted from genomic data from 232 primate species. We created multiple sequence alignments (MSAs) for each protein and estimated the evolutionary rate for each site and examined which sites overlap with the parts of the protein sequences that are typically isolated from fossils. Based on this, we simulated ancient data with different degrees of sequence fragmentation, followed by phylogenetic analysis. We compared these trees to a reference species tree. Up to a degree of fragmentation that is similar to that of fossil samples from 1-2 million years ago, the phylogenetic placements of most nodes at family level are consistent with the reference species tree. We found that the composition of the proteome influences the phylogenetic placement of Tarsiiformes. For the inference of molecular phylogenies based on paleoproteomic data, we recommend characterizing the evolution of the proteomes from the closest extant relatives to maximize the reliability of phylogenetic inference.