bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global Genotype by Environment Prediction Competition Reveals That Diverse Modeling Strategies Can Deliver Satisfactory Maize Yield Estimates
Authors: Washburn Jacob D. , Varela José Ignacio , Xavier Alencar , Chen Qiuyue , Ertl David , Gage Joseph L. , Holland James B. , Lima Dayane Cristina , Romay Maria Cinta , Lopez-Cruz Marco , de los Campos Gustavo , Barber Wesley , Zimmer Cristiano , Trucillo Silva Ignacio , Rocha Fabiani , Rincent Renaud , Ali Baber , Hu Haixiao , Runcie Daniel E , Gusev Kirill , Slabodkin Andrei , Bax Phillip , Aubert Julie , Gangloff Hugo , Mary-Huard Tristan , Vanrenterghem Theodore , Quesada-Traver Carles , Yates Steven , Ariza-Suárez Daniel , Ulrich Argeo , Wyler Michele , Kick Daniel R. , Bellis Emily S. , Causey Jason L. , Soriano Chavez Emilio , Wang Yixing , Piyush Ved , Fernando Gayara D. , Hu Robert K , Kumar Rachit , Timon Annan J. , Venkatesh Rasika , Segura Abá Kenia , Chen Huan , Ranaweera Thilanka , Shiu Shin-Han , Wang Peiran , Gordon Max J. , Amos B K. , Busato Sebastiano , Perondi Daniel , Gogna Abhishek , Psaroudakis Dennis , Chen C. P. James , Al-Mamun Hawlader A. , Danilevicz Monica F. , Upadhyaya Shriprabha R. , Edwards David , de Leon Natalia 
Published: September 2024

AbstractPredicting phenotypes from a combination of genetic and environmental factors is a grand challenge of modern biology. Slight improvements in this area have the potential to save lives, improve food and fuel security, permit better care of the planet, and create other positive outcomes. In 2022 and 2023 the first open-to-the-public Genomes to Fields (G2F) initiative Genotype by Environment (GxE) prediction competition was held using a large dataset including genomic variation, phenotype and weather measurements and field management notes, gathered by the project over nine years. The competition attracted registrants from around the world with representation from academic, government, industry, and non-profit institutions as well as unaffiliated. These participants came from diverse disciplines include plant science, animal science, breeding, statistics, computational biology and others. Some participants had no formal genetics or plant-related training, and some were just beginning their graduate education. The teams applied varied methods and strategies, providing a wealth of modeling knowledge based on a common dataset. The winner’s strategy involved two models combining machine learning and traditional breeding tools: one model emphasized environment using features extracted by Random Forest, Ridge Regression and Least-squares, and one focused on genetics. Other high-performing teams’ methods included quantitative genetics, classical machine learning/deep learning, mechanistic models, and model ensembles. The dataset factors used, such as genetics; weather; and management data, were also diverse, demonstrating that no single model or strategy is far superior to all others within the context of this competition.
A Comparative Study of Radiomic and Connectomic Approaches to Classification of IDH1 Status and 1p/19q Co-deletion in Lower Grade Gliomas
Authors: Paradkar Rohit V. , Alterman Ron L. 
Published: September 2024

AbstractPurposeGrade III and IV brain tumors are labeled “high grade”, or malignant. Lower grade tumors (grade II and III) can progress to high grade and must be closely monitored. In lower grade gliomas, the presence of a specific IDH1 gene mutation and the 1p/19q chromosomal co-deletion confer favorable prognosis and alternative treatment strategy. Presently, these markers are evaluated using surgically obtained tissue specimens. In this study, we evaluate noninvasive approaches to classification of these genetic markers. We hypothesized that connectomic and radiomic approaches to classification would perform similarly. We also tested combined classification, incorporating radiomics and connectomics.MethodsBinary classifiers used radiomic and connectomic features from MRI to classify IDH1 and 1p/19q co-deletion status. Radiomic features were calculated to characterize tumor gray-level, texture, and shape. Voxel-based morphometry was performed to create gray-matter structural connectomes. Nodal efficiencies of brain regions, number of nodes and connections were computed. Binary classifiers predicted IDH1 and 1p/19q co-deletion status. Statistical analysis quantified differences in model performance.ResultsConnectomic and radiomic features had insignificant difference in classification of IDH1 status. Radiomic and connectomic classification of 1p/19q co-deletion status had no significant accuracy difference, however, radiomics had significantly higher AUC score. The combined approach had no significant difference to radiomics and connectomics except for a significantly higher AUC score than connectomics in 1p/19q co-deletion classification.ConclusionAltogether, the study shows that radiomics, connectomics, and a combination of the two are viable classification approaches for these markers. Future studies could incorporate these methods to improve diagnostic performance.
Carboxy-terminal blockade of sortilin binding enhances progranulin gene therapy, a potential treatment for frontotemporal dementia
Authors: Kashyap Shreya N. , Fox Stephanie N. , Wilson Katherine I. , Murchison Charles F. , Ambaw Yohannes A. , Walther Tobias C. , Farese Robert V. , Arrant Andrew E. , Roberson Erik D. 
Published: September 2024

AbstractFrontotemporal dementia is commonly caused by loss-of-function mutations in the progranulin gene. Potential therapies for this disorder have entered clinical trials, including progranulin gene therapy and drugs that reduce progranulin interactions with sortilin. Both approaches ameliorate functional and pathological abnormalities in mouse models of progranulin insufficiency. Here we investigated whether modifying the progranulin carboxy terminus to block sortilin interactions would improve the efficacy of progranulin gene therapy. We compared the effects of treating progranulin-deficient mice with gene therapy vectors expressing progranulin with intact sortilin interactions, progranulin with the carboxy terminus blocked to reduce sortilin interactions, or GFP control. We found that expressing carboxy-terminally blocked progranulin generated higher levels of progranulin both at the injection site and in more distant regions. Carboxy-terminally blocked progranulin was also more effective at ameliorating microgliosis, microglial lipofuscinosis, and lipid abnormalities including ganglioside accumulation and loss of bis(monoacylglycero)phosphate lipids. Finally, only carboxy-terminally blocked progranulin reduced plasma neurofilament light chain, a biomarker of neurodegeneration, in progranulin-deficient mice. These results demonstrate that modifying the progranulin cargo to block sortilin interactions may be important for increasing the effectiveness of progranulin gene therapy.One-sentence SummaryThe effectiveness of progranulin gene therapy in models of FTD is improved by blocking the protein’s carboxy terminus, which prevents sortilin binding
Automated speech artefact removal from MEG data utilizing facial gestures and mutual information
Authors: Tuomaala Sara , Autti Salla , Cotroneo Silvia Federica , Lioumis Pantelis , Renvall Hanna , Liljeström Mia 
Published: September 2024

AbstractThe ability to speak is one of the most crucial human skills, motivating neuroscientific studies of speech production and speech-related neural dynamics. Increased knowledge in this area, allows e.g., for development of rehabilitation protocols for language-related disorders. While our understanding of speech-related neural processes has greatly enhanced owing to non-invasive neuroimaging techniques, the interpretations have been limited by speech artefacts caused by the activation of facial muscles that mask important languagerelated information. Despite earlier approaches applying independent component analysis (ICA), the artefact removal process continues to be time-consuming, poorly replicable and affected by inconsistencies between different observers, typically requiring manual selection of artefactual components. The artefact component selection criteria have been variable, leading to non-standardized speech artefact removal processes. To address these issues, we propose here a pipeline for automated speech artefact removal from MEG data. We developed an ICA-based speech artefact removal routine by utilizing EMG data measured from facial muscles during a facial gesture task for isolating the speech-induced artefacts. Additionally, we used mutual information (MI) as a similarity measure between the EMG signals and the ICA-decomposed MEG to provide a feasible way to identify the artefactual components. Our approach efficiently and in an automated manner removed speech artefacts from MEG data. The method can be feasibly applied to improve the understanding of speech-related cortical dynamics, while transparently evaluating the removed and preserved MEG activation.
TRPC3 suppression ameliorates synaptic dysfunctions and memory deficits in Alzheimer’s disease
Authors: Wang Jiaxing , Chen Ling , Wang Zhengjun , Zhang Sicheng , Ding Dongyi , Lin Geng , Zhang Hua , Boda Vijay K. , Kong Dehui , Ortyl Tyler C. , Wang Xusheng , Lu Lu , Zhou Fu-Ming , Bezprozvanny Ilya , Du Jianyang , Wu Zhongzhi , Li Wei , Liao Francesca-Fang 
Published: September 2024

AbstractTransient receptor potential canonical (TRPC) channels are widely expressed in the brain; however, their precise roles in neurodegeneration, such as Alzheimer’s disease (AD) remain elusive. Bioinformatic analysis of the published single-cell RNA-seq data collected from AD patient cohorts indicates that theTrpc3gene is uniquely upregulated in excitatory neurons. TRPC3 expression is also upregulated in post-mortem AD brains, and in both acute and chronic mouse models of AD. Functional screening of TRPC3 antagonists resulted in a lead inhibitor JW-65, which completely rescued Aβ-induced neurotoxicity, impaired synaptic plasticity (e.g., LTP), and learning memory in acute and chronic experimental AD models. In cultured rat hippocampal neurons, we found that treatment with soluble β-amyloid oligomers (AβOs) induces rapid and sustained upregulation of the TRPC3 expression selectively in excitatory neurons. This aberrantly upregulated TRPC3 contributes to AβOs-induced Ca2+overload through the calcium entry and store-release mechanisms. The neuroprotective action of JW-65 is primarily mediated via restoring AβOs-impaired Ca2+/calmodulin-mediated signaling pathways, including calmodulin kinases CaMKII/IV and calcineurin (CaN). The synaptic protective mechanism via TRPC3 inhibition was further supported by hippocampal RNA-seq data from the symptomatic 5xFAD mice after chronic treatment with JW-65. Overall, these findings not only validate TRPC3 as a novel therapeutic target for treating synaptic dysfunction of AD but most importantly, disclose a distinct role of upregulated TRPC3 in AD pathogenesis in mediating Ca2+dyshomeostasis.
Evaluating Best Practices for Isolating Pyrophilous Bacteria and Fungi from Burned Soil
Authors: Enright Dylan J. , Quaal Ryan , Verabeehu Aishwarya , Nguyen Anna , Maddox Jenna , Glassman Sydney I. 
Published: September 2024

AbstractA live microbial culture is invaluable to assess traits and functions via ‘omics and biophysical assays. However, it is not always logistically feasible to culture immediately from freshly obtained soil, and selecting the proper media for culturing is not trivial. While building a culture collection of pyrophilous microbes obtained from burnt soil, we tested the best 1) method of storing soil to retain culturable viability and 2) media to garner the most microbial diversity. We tested four methods of soil storage (dried, stored at 4°C, stored at -80°C alone or in glycerol) and compared to fresh soil obtained 6 months after a severe California chapparal shrubland wildfire. For bacteria, soil frozen at -80°C with glycerol preserved the greatest diversity (25 species, 13 genera) compared to fresh soil (26 species, 13 genera). For fungi, soil stored at -80°C alone preserved the greatest diversity (10 species, 3 genera) compared to fresh soil (13 species, 7 genera). We also tested 3 media types: rich media (Lysogeny Broth (LB) for bacteria; Malt Yeast Agar (MYA) for fungi), oligotrophic media (Reasoner’s 2 Agar (R2A) and media made from pyrogenic organic matter (PyOM). For bacteria, culturing on LB and R2A garnered the greatest diversity (LB = 26 species, 13 genera, R2A = 27 species, 15 genera). For fungi a combination of R2A and PyOM captured the greatest diversity (R2A = 15 species, 8 genera, PyOM = 12 species, 6 genera). For both bacteria and fungi, some species of interest were only captured using the PyOM media. Using a combination of these methods from 2018-2022, we cultured >500 isolates (286 bacteria; 258 fungi) from burned soils of 7 Southern California wildfires.
Glial scar formation by reactive astrocytes derived from oligodendrocyte progenitor cells after closed-head injury
Authors: Matsuda Hinata , Tsuji Erika , Riberu Agnes Antonetta Orchidia , Okano Hideyuki , Morita Mitsuhiro 
Published: September 2024

AbstractThe diversity of reactive astrocytes is key to understanding complicated pathological processes in the brain. The accumulation of reactive astrocytes expressing the neural stem/precursor cell marker Nestin is common after brain injury, but the pathological implications of this reactive astrocyte subpopulation remain elusive. This study initially aimed to determine the origin and fate of these reactive astrocytes expressing Nestin by characterizing cells labeled with green fluorescent protein (GFP) after closed-head injury, using aNestinpromoter region widely utilized to study neural stem/precursor cells. Unexpectedly, oligodendrocyte progenitor cells (OPCs), rather than astrocytes, were robustly and selectively labeled with GFP. A fraction of these cells showed a subsequent upregulation of astrocyte markers and were incorporated into glial scars. These glial scars are aggregates of reactive astrocytes that form between lesion cores and the perilesional recovering region. Deletion of theStat3gene, which is essential for astrocyte activation, using aNestinpromoter reduced glial scars, further confirming that OPCs are involved in glial scar formation. Reactive astrocytes labeled with aglial fibrillary acidic proteinpromoter differed in morphology and distribution from astrocytes derived from OPCs. This confirms that astrocytes and OPCs produce distinct reactive astrocyte subpopulations. Some GFP-labeled OPCs lacking astrocyte markers were found to distribute in perilesional recovering regions. The reduced expression of Nestin and OPC markers in these non-astrocytic descendants of OPCs, coupled with a significant fraction of these cells remaining olig2-positive, suggests that OPCs give rise to both reactive astrocytes and oligodendrocytes. These findings suggest that OPCs are activated by a novel process after brain injury.
A Potential Method for Identifying Milk Adulteration and Pb(II) Contamination Scenarios Using Principal Component Analysis From Smartphone Photographs
Authors: Chandra Alicia Catelyn , Lianto Cheralyn Clarecia , Sulimro Felicia Liem , Santoso Gabriella Anna , Wang Michelle Aiko , Miah Lie , Prabowo Norbertus Krisnu 
Published: September 2024

ABSTRACTHeavy metal contaminants and adulteration in cow milk products are major issues affecting milk safety and quality, posing health risks to consumers of all ages. These contaminants are sometimes difficult to detect with the naked eye and can potentially pass sensory tests, particularly in white cow milk. This research explores the detection of lead(II) poisoning in milk post-production and the adulteration of different milk samples using an alternative approach through chemometric techniques based on RGB and Grey Area image analysis. A controlled photography environment was used. We analyzed over 105 samples of control, adulterated, and lead(II)-added milk in this study using image processing software. Each photograph was analyzed to provide triplicate Regions of Interest (ROI), resulting in a total of 315 statistical datasets. We found that Principal Component Analysis (PCA) effectively clustered control white milk and Pb(II)-contaminated milk. Clusters of different adulterants were recognized simply by feeding RGB and Grey Area data into PCA. However, some clusters, such as mixed chocolate milk and white milk with lead(II) contamination, were not well distinguished. In this early-stage method, a comparison study with infrared spectra will be required in future research. This alternative method shows potential promise for deployment in limited settings for real-world food quality surveillance and regulation.
FEATURE-SPECIFIC ANTICIPATORY PROCESSING FADES DURING HUMAN SLEEP
Authors: Topalidis Pavlos I. , Reisinger Lisa , Shubert Juliane , Ameen Mohamed S. , Weisz Nathan , Schabus Manuel 
Published: September 2024

SUMMARYImagine you are listening to a familiar song on the radio. As the melody and rhythm unfold, you can often anticipate the next note or beat, even before it plays. This ability demonstrates the brain’s capacity to extract statistical regularities from sensory input and to generate predictions about future sensory events. It is considered automatic, requiring no conscious effort or attentional resources (1–4). But to what extent does this predictive ability operate when our attention is greatly reduced, such as during sleep? Experimental findings from animal and human studies reveal a complex picture of how the brain engages in predictive processing during sleep (5–13). Although evidence suggests that the brain differentially reacts to unexpected stimuli and rhythmic music (5,7,13), there is a notable disruption in feedback processing, which is essential for generating accurate predictions of upcoming stimuli (10). Here, for the first time, we examine the brain’s ability during sleep to predict or pre-activate low-level features of expected stimuli before presentation. We use sequences of predictable or unpredictable/random tones in a passive-listening paradigm while recording simultaneous electroencephalography (EEG) and magnetoencephalography (MEG) during wakefulness and sleep. We found that during wakefulness, N1 sleep and N2 sleep, subtle changes in tone frequencies elicit unique/distinct neural activations. However, these activations are less distinct and less sustained during sleep than during wakefulness. Critically, replicating previous work in wakefulness (4), we find evidence that neural activations specific to the anticipated tone occur before its presentation. Extending previous findings, we show that such predictive neural patterns fade as individuals fall into sleep.In BriefThe extent to which predictive processing takes place in sleep is yet to be determined. Using a passive-listening EEG/MEG paradigm, Topalidis et al. show that auditory representations in sleep are brief and unstable, easily overwritten by subsequent inputs, which possibly hinders the tracking and extraction of sensory associations.HighlightsParticipants passively listened to random and predictable sequences of tones during both wakefulness and sleep, without being made aware of the underlying pattern.The brain retains the ability to process basic low-level features during sleep.While these feature-specific responses are preserved during sleep, they are less distinct and sustained than in wakefulness.Unlike in wakefulness, during sleep, the brain does not predict or anticipate upcoming sounds, despite continuing to process basic auditory information.
Distinct H3K9me3 heterochromatin maintenance dynamics govern different gene programs and repeats in pluripotent cells
Authors: Zhang Jingchao , Donahue Greg , Gilbert Michael B. , Lapidot Tomer , Nicetto Dario , Zaret Kenneth S. 
Published: September 2024

AbstractH3K9me3-heterochromatin, established by lysine methyltransferases (KMTs) and compacted by HP1 isoforms, represses alternative lineage genes and DNA repeats. Our understanding of H3K9me3-heterochromatin stability is presently limited to individual domains and DNA repeats. We engineeredSuv39h2KO mouse embryonic stem cells to degrade remaining two H3K9me3- KMTs within one hour and found that both passive dilution and active removal contribute to H3K9me3 decay within 12-24 hours. We discovered four different H3K9me3 decay rates across the genome and chromatin features and transcription factor binding patterns that predict the stability classes. A “binary switch” governs heterochromatin compaction, with HP1 rapidly dissociating from heterochromatin upon KMTs’ depletion and a particular threshold level of HP1 limiting pioneer factor binding, chromatin opening, and exit from pluripotency within 12 hr. Unexpectedly, receding H3K9me3 domains unearth residual HP1β peaks enriched with heterochromatin-inducing proteins. Our findings reveal distinct H3K9me3-heterochromatin maintenance dynamics governing gene networks and repeats that together safeguard pluripotency.
Striatal indirect pathway mediates hesitation
Authors: Geramita Matthew A , Ahmari Susanne E , Yttri Eric A 
Published: September 2024

AbstractDetermining the best possible action in an uncertain situation is often challenging, and organisms frequently need extra time to deliberate. This pause in behavior in response to uncertainty – also known as hesitation – commonly occurs in many aspects of daily life, yet its neural circuits are poorly understood. Here we present the first experimental paradigm that reliably evokes hesitation in mice. Using cell-type specific electrophysiology and optogenetics, we show that indirect, but not direct, pathway spiny projection neurons specifically in the dorsomedial striatum mediate hesitation. These data indicate that the basal ganglia circuits controlling the pausing involved in cognitive processes like hesitation are distinct from those that control other types of behavioral inhibition, such as cue-induced stopping.
Synaptic Specializations at Dopamine Release Sites Orchestrate Efficient and Precise Neuromodulatory Signaling
Authors: Bulumulla Chandima , Walpita Deepika , Iyer Nirmala , Eddison Mark , Patel Ronak , Alcor Damien , Ackerman David , Beyene Abraham G. 
Published: September 2024

AbstractDopamine is a key chemical neuromodulator that plays vital roles in various brain functions. Traditionally, neuromodulators like dopamine are believed to be released in a diffuse manner and are not commonly associated with synaptic structures where pre- and postsynaptic processes are closely aligned. Our findings challenge this conventional view. Using single-bouton optical measurements of dopamine release, we discovered that dopamine is predominantly released from varicosities that are juxtaposed against the processes of their target neurons. Dopamine axons specifically target neurons expressing dopamine receptors, forming synapses to release dopamine. Interestingly, varicosities that were not directly apposed to dopamine receptor-expressing processes or associated with neurons lacking dopamine receptors did not release dopamine, regardless of their vesicle content. The ultrastructure of dopamine release sites share common features of classical synapses. We further show that the dopamine released at these contact sites induces a precise, dopamine-gated biochemical response in the target processes. Our results indicate that dopamine release sites share key characteristics of conventional synapses that enable relatively precise and efficient neuromodulation of their targets.