bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automated system for training and assessing string-pulling behaviors in rodents
Authors: Jordan Gianna A. , Vishwanath Abhilasha , Holguin Gabriel , Bartlett Mitchell J. , Tapia Andrew K. , Winter Gabriel M. , Sexauer Morgan R. , Stopera Carolyn J. , Falk Torsten , Cowen Stephen L. 
Published: July 2023

AbstractString-pulling tasks have been used for centuries to study coordinated bimanual motor behavior and problem solving. String pulling is rapidly learned, ethologically grounded, and has been applied to many species and disease conditions. Typically, training of string-pulling behaviors is achieved through manual shaping and baiting. Furthermore, behavioral assessment of reaching, grasping, and pulling is often performed through labor intensive manual video scoring. No system, to our knowledge, currently exists for the automated shaping and assessment of string-pulling behaviors.Here we describe the PANDA system (Pulling And Neural Data Analysis), an inexpensive hardware and software system that utilizes a continuous string loop connected to a rotary encoder, feeder, microcontroller, high-speed camera, and analysis software for assessment and training of string-pulling behaviors and synchronization with neural recording data. We demonstrate this system in unimplanted rats and rats implanted with electrodes in motor cortex and hippocampus and show how the PANDA system can be used to assess relationships between paw movements and single-unit and local-field activity. We also found that automating the shaping procedure significantly improved overall performance, with rats regularly pulling >100 meters during a 15-minute session.In conclusion, the PANDA system will be of general use to researchers investigating motor control, motivation, and motor disorders such as Parkinson’s disease, Huntington’s disease, and stroke. It will also support the investigation of neural mechanisms involved in sensorimotor integration.HighlightsHigh-speed tracking of continuous grasping and pulling behaviors.Automated and adaptive reinforcement of string-pulling behavior.Integration with neural recording and video tracking systems.Open-source software and hardware.Supplemental FilesThe supplemental pdf contains additional designs and behavioral data and has been uploaded.Source code and 3D and laser cut design files can be found at:https://github.com/CowenLab/String_Pulling_System/Videos are in the GitHub repository at:https://github.com/CowenLab/String_Pulling_System/tree/main/Videos
Differential expression of tension-sensitiveHOXgenes in fibroblasts is associated with different scar types
Authors: Kang Minwoo , Ko Ung Hyun , Oh Eun-Jung , Kim Hyun Mi , Chung Ho Yun , Shin Jennifer H. 
Published: July 2023

AbstractA scar is considered a natural consequence of the wound-healing process. However, the mechanism by which scars form remains unclear. Here, we suggest a new mechanism of wound healing and scar formation that involves the mechanosensitive regulation ofHOXgenes. RNA-sequencing of fibroblasts from different types of scars revealed differentialHOXgene expression. Computational simulations predicted injury-induced tension loss in the skin, and in vitro experiments revealed a negative correlation between tension and fibroblast proliferation. Remarkably, exogenous tensile stress in fibroblasts has been shown to alterHOXgene expression levels in different scar types. Overall, we propose a model for normal wound healing and scar formation and show that successful wound healing requires tensional homeostasis in the skin tissue, which is regulated by tension-sensitiveHOXgenes.
High resolution imaging and five-year tuberculosis contact outcomes
Authors: Esmail Hanif , Coussens Anna K , Thienemann Friedrich , Sossen Bianca , Mukasa Sandra L , Warwick James , Goliath Rene T. , Davies Nashreen Omar , Douglass Emily , Jackson Amanda , Lakay Francisco , Streicher Elizabeth , Munro Jacob E. , Barrios Marilou H , Heinsohn Torben , Macpherson Liana , Sheerin Dylan , Aziz Saalikha , Serole Keboile , Daroowala Remy , Taliep Arshad , Ahlers Petri , Malherbe Stephanus T. , Bowden Rory , Warren Robin , Walzl Gerhard , Via Laura E. , Bahlo Melanie , Jacobson Karen R. , Horsburgh C. Robert , Salgame Padmini , Alland David , Barry Clifton Earl , Flynn JoAnne L. , Ellner Jerrold J , Wilkinson Robert J 
Published: July 2023

AbstractBackgroundThe evolution of tuberculosis (TB) disease during the clinical latency period remains incompletely understood.Methods250 HIV-uninfected, adult household contacts of rifampicin-resistant TB with a negative symptom screen underwent baseline18F-Fluorodeoxyglucose positron emission and computed tomography (PET/CT), repeated in 112 after 5-15 months. Following South African and WHO guidelines, participants did not receive preventive therapy. All participants had intensive baseline screening with spontaneous, followed by induced, sputum sampling and were then observed for an average of 4.7 years for culture-positive disease. Baseline PET/CT abnormalities were evaluated in relation to culture-positive disease.ResultsAt baseline, 59 (23.6%) participants had lung PET/CT findings consistent with TB of which 29 (11.6%) were defined as Subclinical TB, and 30 (12%) Subclinical TB-inactive. A further 83 (33.2%) had other lung parenchymal abnormalities and 108 (43.2%) had normal lungs. Over 1107-person years of follow-up 14 cases of culture-positive TB were diagnosed. Six cases were detected by intensive baseline screening, all would have been missed by the South African symptom-based screening strategy and only one detected by a WHO-recommended chest X-Ray screening strategy. Those with baseline Subclinical TB lesions on PET/CT were significantly more likely to be diagnosed with culture-positive TB over the study period, compared to those with normal lung parenchyma (10/29 [34.5%] vs 2/108 [1.9%], Hazard Ratio 22.37 [4.89-102.47, p<0.001]).ConclusionsThese findings challenge the latent/active TB paradigm demonstrating that subclinical disease exists up to 4 years prior to microbiological detection and/or symptom onset. There are important implications for screening and management of TB.
A new Omicron lineage with Spike Y451H mutation that dominated a new COVID-19 wave in Kilifi, Coastal Kenya: March-May 2023
Authors: Mwanga Mike J , Lambisia Arnold W , Morobe John Mwita , Murunga Nickson , Moraa Edidah , Ndwiga Leonard , Cheruiyot Robinson , Mutunga Martin , Guzman-Rincon Laura M , Sande Charles , Mwangangi Joseph , Bejon Philip , Ochola-Oyier Lynette Isabella , Nokes D James , Agoti Charles N , Nyiro Joyce , Githinji George 
Published: July 2023

AbstractWe report a newly emerged SARS-CoV-2 Omicron lineage, named FY.4, that has two unique mutations; spike:Y451H and ORF3a:P42L. FY.4 emergence has coincided with increased SARS-CoV-2 cases in coastal Kenya, April-May 2023. We demonstrate the value of continued SARS-CoV-2 genomic surveillance in the post-acute pandemic era in understanding new COVID-19 outbreaks.
Mating system is associated with seed phenotypes upon loss of RNA-directed DNA Methylation in Brassicaceae
Authors: Dew-Budd Kelly J. , Chow Hiu Tung , Kendall Timmy , David Brandon C. , Rozelle James A. , Mosher Rebecca A. , Beilstein Mark A. 
Published: July 2023

AbstractIn plants,de novoDNA methylation is guided by 24-nt short interfering (si)RNAs in a process called RNA-directed DNA methylation (RdDM). Primarily targeted at transposons, RdDM causes transcriptional silencing and can indirectly influence expression of neighboring genes. During reproduction, a small number of siRNA loci are dramatically upregulated in the maternally-derived seed coat, suggesting that RdDM might have a special function during reproduction. However, the developmental consequence of RdDM has been difficult to dissect because disruption of RdDM does not result in overt phenotypes inArabidopsis thaliana, where the pathway has been most thoroughly studied. In contrast,Brassica rapamutants lacking RdDM have a severe seed production defect, which is determined by the maternal sporophytic genotype. To explore the factors that underlie the different phenotypes of these species, we produced RdDM mutations in three additional members of the Brassicaceae family:Camelina sativa, Capsella rubella, andCapsella grandiflora. Among these three species, only mutations in the obligate outcrosser,C. grandiflora, displayed a seed production defect similar toBrassica rapamutants, suggesting that mating system is a key determinant for reproductive phenotypes in RdDM mutants.
Speech prosody enhances the neural processing of syntax
Authors: Degano Giulio , Donhauser Peter W. , Gwilliams Laura , Merlo Paola , Golestani Narly 
Published: July 2023

AbstractHuman language relies on the correct processing of syntactic information, as it is essential for successful communication between speakers. As an abstract level of language, syntax has often been studied separately from the physical form of the speech signal, thus often masking the interactions that can promote better syntactic processing in the human brain. We analyzed a MEG dataset to investigate how acoustic cues, specifically prosody, interact with syntactic representations. We examined whether prosody enhances the cortical encoding of syntactic representations. We decoded syntactic phrase boundaries directly from brain activity, and evaluated possible modulations of the decoding by the presence of prosodic boundaries. Our findings demonstrate that the presence of a prosodic boundary improves the representation of phrase boundaries, indicating the facilitative role of prosodic cues in processing abstract linguistic features. This study gives neurobiological evidence for the boosting of syntactic processing via interactions with prosody.
Extracellular vesicles promote autophagy in human microglia through lipid raft-dependent mechanisms
Authors: Romenskaja Diana , Jonavičė Ugnė , Pivoriūnas Augustas 
Published: July 2023

AbstractAutophagy dysfunction has been closely related with pathogenesis of many neurodegenerative diseases and therefore represents a potential therapeutic target. Extracellular vesicles (EVs) may act as a potent anti-inflammatory agents and also modulators of autophagy in target cells. However, the molecular mechanisms by which EVs modulate autophagy flux in human microglia remain largely unexplored.In the present study we investigated the effects of EVs derived from human oral mucosa stem cells on the autophagy in human microglia. We demonstrate that EVs promoted autophagy and autophagic flux in human microglia and that this process was dependent on the integrity of lipid rafts. LPS also activated autophagy, but combined treatment with EVs and LPS suppressed autophagy response indicating interference between these signalling pathways. Blockage of Toll-like receptor 4 (TLR4) with anti-TLR4 antibody suppressed EV- induced autophagy. Furthermore, blockage of EV- asscoiated HSP70 chaperone which is one of the endogenous ligands of the TLR4 also suppressed EV- induced lipid raft formation and autophagy. Pre-treatment of microglia with selective inhibitor of αvβ3/αvβ5 integrins cilengitide inhibited EV-induced autophagy. Finally, blockage of purinergic P2X4 receptor (P2X4R) with selective inhibitor 5-BDBD also suppressed of EV-induced autophagy.In conclusion, we demonstrate that EVs activate autophagy in human microglia through interaction with HSP70/TLR4, αVβ3/αVβ5, and P2X4R signalling pathways and that these effects depend on the integrity of lipid rafts.Our findings could be used for development of new therapeutic strategies targeting disease-associated microglia.
Assessing RNAi feasibility and susceptibility to environmental RNAi inTrichogramma dendrolimi(Hymenoptera: Trichogrammatidae)
Authors: Yan Zhichao , Li Fangyi , Wang Aokai , Wang Chengxing , Wang Haiyan , Yu Zeqi , Wang Kepeng , Wang Yihan , Luo Yuanyuan , Li Yuanxi 
Published: July 2023

AbstractTrichogramma, a genus of egg parasitoid wasps, are widely used as biological control agents and serve as model organisms in parasitoid research. Despite their significance, the understanding of RNA interference (RNAi) inTrichogrammaremains very limited. In this study, we investigated RNAi-associated genes by bioinformatic approaches and experimentally assessed the feasibility of RNAi and the susceptibility of environmental RNAi inTrichogramma. We found thatTrichogrammagenomes contain a complete set of genes in the RNAi pathway and exhibit extensive gene expansion of dsRNase, which may influence RNAi efficiency by degrading dsRNA. We demonstrated successful RNAi through pupal microinjection inT. dendrolimiMatsumura, providing a technical approach for future gene functional studies. In addition, we observed no evidence of susceptibility to environmental RNAi in eitherT. dendrolimiadults or larvae, which might be attributed to the extensive expansion of dsRNase. This low environmental RNAi sensitivity inTrichogrammacould suggest a reduced risk of RNAi-based pest management strategies affecting nontargetTrichogrammapopulations. Overall, this study presents a technical approach for conducting gene functional studies inTrichogrammaand provides a foundation for evaluating the nontarget effects of RNAi-based pest control strategies onTrichogramma.
Reconstructing the Transcriptional Regulatory Network of ProbioticL. reuteriis Enabled by Transcriptomics and Machine Learning
Authors: Josephs-Spaulding Jonathan , Rajput Akanksha , Hefner Ying , Szubin Richard , Balasubramanian Archana , Li Gaoyuan , Zielinski Daniel C. , Jahn Leonie , Sommer Morten , Phaneuf Patrick , Palsson Bernhard O. 
Published: July 2023

IAbstractLimosilactobacillus reuteri, a probiotic microbe instrumental to human health and sustainable food production, adapts to diverse environmental shifts via dynamic gene expression. We applied independent component analysis to 117 high-quality RNA-seq datasets to decode its transcriptional regulatory network (TRN), identifying 35 distinct signals that modulate specific gene sets. This study uncovers the fundamental properties ofL. reuteri’sTRN, deepens our understanding of its arginine metabolism, and the co-regulation of riboflavin metabolism and fatty acid biosynthesis. It also sheds light on conditions that regulate genes within a specific biosynthetic gene cluster and the role of isoprenoid biosynthesis inL. reuteri’sadaptive response to environmental changes. Through the integration of transcriptomics and machine learning, we provide a systems-level understanding ofL. reuteri’sresponse mechanism to environmental fluctuations, thus setting the stage for modeling the probiotic transcriptome for applications in microbial food production.Graphical AbstractComprehensive iModulon Workflow Overview. Our innovative workflow is grounded in the analysis of the LactoPRECISE compendium, a curated dataset containing 117 internally sequenced RNA-seq samples derived from a diversity of 50 unique conditions, encompassing an extensive range of 13 distinct condition types. We employ the power of Independent Component Analysis (ICA), a cutting-edge machine learning algorithm, to discern the underlying structure of iModulons within this wealth of data. In the subsequent stage of our workflow, the discovered iModulons undergo detailed scrutiny to uncover media-specific regulatory mechanisms governing metabolism, illuminate the context-dependent intricacies of gene expression, and predict pathways leading to the biosynthesis of probiotic secondary metabolites. Our workflow offers an invaluable and innovative lens through which to view probiotic strain design while simultaneously highlighting transformative approaches to data analytics in the field.
MesenchymalVanglfacilitates airway elongation and widening independently of the planar cell polarity complex
Authors: Paramore Sarah V. , Goodwin Katharine , Devenport Danelle , Nelson Celeste M. 
Published: July 2023

AbstractA hallmark of mammalian lungs is the fractal nature of the bronchial tree. In the adult, each successive generation of airways is a fraction of the size of the parental branch. This fractal structure is physiologically beneficial, as it minimizes the energy needed for breathing. Achieving this pattern likely requires precise control of airway length and diameter, as the branches of the embryonic airways initially lack the fractal scaling observed in those of the adult lung. In epithelial monolayers and tubes, directional growth can be regulated by the planar cell polarity (PCP) complex. Here, we comprehensively characterized the roles of PCP-complex components in airway initiation, elongation, and widening during branching morphogenesis of the murine lung. Using tissue-specific knockout mice, we surprisingly found that branching morphogenesis proceeds independently of PCP-component expression in the developing airway epithelium. Instead, we found a novel,Celsr1-independent role for the PCP componentVanglin the pulmonary mesenchyme. Specifically, mesenchymal loss ofVangl1/2leads to defects in branch initiation, elongation, and widening. At the cellular level, we observe changes in the shape of smooth muscle cells that indicate a potential defect in collective mesenchymal rearrangements, which we hypothesize are necessary for lung morphogenesis. Our data thus reveal an explicit function forVanglthat is independent of the core PCP complex, suggesting a functional diversification of PCP components in vertebrate development. These data also reveal an essential role for the embryonic mesenchyme in generating the fractal structure of airways of the mature lung.
Movement-related modulation in mouse auditory cortex is widespread yet locally diverse
Authors: Morandell Karin , Yin Audrey , Del Rio Rodrigo Triana , Schneider David M. 
Published: July 2023

ABSTRACTNeurons in the mouse auditory cortex are strongly influenced by behavior, including both suppression and enhancement of sound-evoked responses during movement. The mouse auditory cortex comprises multiple fields with different roles in sound processing and distinct connectivity to movement-related centers of the brain. Here, we asked whether movement-related modulation might differ across auditory cortical fields, thereby contributing to the heterogeneity of movement-related modulation at the single-cell level. We used wide-field calcium imaging to identify distinct cortical fields followed by cellular-resolution two-photon calcium imaging to visualize the activity of layer 2/3 excitatory neurons within each field. We measured each neuron’s responses to three sound categories (pure tones, chirps, and amplitude modulated white noise) as mice rested and ran on a non-motorized treadmill. We found that individual neurons in each cortical field typically respond to just one sound category. Some neurons are only active during rest and others during locomotion, and those that are responsive across conditions retain their sound-category tuning. The effects of locomotion on sound-evoked responses vary at the single cell level, with both suppression and enhancement of neural responses, and the net modulatory effect of locomotion is largely conserved across cortical fields. Movement-related modulation in auditory cortex also reflects more complex behavioral patterns, including instantaneous running speed and non-locomotor movements such as grooming and postural adjustments, with similar patterns seen across all auditory cortical fields. Our findings underscore the complexity of movement-related modulation throughout the mouse auditory cortex and indicate that movement related modulation is a widespread phenomenon.SIGNIFICANCE STATEMENTThroughout the sensory cortex, neural activity is influenced by behavior. It remains unknown whether primary and higher-order sensory cortical centers are similarly or differentially influenced by movement. We show that movement-related modulation in the mouse auditory cortex is locally complex and heterogeneous, but that at a more macroscopic level, the net effect of movement on primary and higher-order auditory cortex is largely conserved. These data highlight the widespread nature of movement-related modulation and suggest that movement signals may inform neural computations throughout multiple nodes of the sensory cortex.
Cognitive biases and financial decisions of potential investors during Covid-19: an exploration
Authors: Mohanty Stutee , Patnaik B.C.M. , Satpathy Ipseeta , Sahoo Suresh Kumar 
Published: July 2023

PurposeThis paper aims to identify, examine, and present an empirical research design of behavioral finance of potential investors during Covid-19.Design/methodology/approachA well-structured questionnaire was designed; a survey was conducted among potential investors using convenience sampling, and 200 valid responses were collected. The research work uses multiple regression and discriminant function analysis to evaluate the influence of cognitive factors on the financial decision-making of investors.FindingsRecency and familiarity bias are proven to have the highest significant impact on the financial decisions of investors followed by confirmation bias. Overconfidence bias had a negligible effect on the decision-making process of the respondents and found insignificant.Research limitations/implicationsCovid-19 is a temporary phase that may lead to changes in financial behavior and investors’ decisions in the near future.Practical implicationsThe paper will help academicians, scholars, analysts, practitioners, policymakers and firms dealing with capital markets to execute their job responsibilities with respect to the cognitive bias in terms of taking financial decisions.Originality/valueThe present investigation attempts to fill the gap in the literature on the intended topic because it is evident from literature on the chosen subject that no study has been undertaken to evaluate the impact of cognitive biases on financial behavior of investors during Covid-19.