bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Convolutional Autoencoder-based Explainable Clustering Approach for Resting-State EEG Analysis
Authors: Ellis Charles A. , Miller Robyn L. , Calhoun Vince D. 
Published: January 2023

AbstractMachine learning methods have frequently been applied to electroencephalography (EEG) data. However, while supervised EEG classification is well-developed, relatively few studies have clustered EEG, which is problematic given the potential for clustering EEG to identify novel subtypes or patterns of dynamics that could improve our understanding of neuropsychiatric disorders. There are established methods for clustering EEG using manually extracted features that reduce the richness of the feature space for clustering, but only a couple studies have sought to use deep learning-based approaches with automated feature learning to cluster EEG. Those studies involve separately training an autoencoder and then performing clustering on the extracted features, and the separation of those steps can lead to poor quality clustering. In this study, we propose an explainable convolutional autoencoder-based approach that combines model training with clustering to yield high quality clusters. We apply the approach within the context of schizophrenia (SZ), identifying 8 EEG states characterized by varying levels of δ activity. We also find that individuals who spend more time outside of the dominant state tend to have increased negative symptom severity. Our approach represents a significant step forward for clustering resting-state EEG data and has the potential to lead to novel findings across a variety of neurological and neuropsychological disorders in future years.
Distinct prefrontal projections conversely orchestrate social competition and hierarchy
Authors: Choi Tae-Yong , Jeon Hyoungseok , Jeong Sejin , Kim Eum Ji , Kim Jeongseop , Jeong Yun Ha , Kang Byungsoo , Choi Murim , Koo Ja Wook 
Published: January 2023

SummarySocial animals compete for limited resources, resulting in a social hierarchy. Although different neuronal subpopulations in the medial prefrontal cortex (mPFC), a hub brain region of social hierarchy, encode distinct social competition behaviors, their identities and associated molecular underpinnings have not yet been identified. In this study, we found that mPFC neurons projecting to the nucleus accumbens (mPFC-NAc) encode social winning behavior, whereas mPFC neurons projecting to the ventral tegmental area (mPFC-VTA) encode social losing behavior by monitoring and manipulating neural circuit activity. High-throughput single-cell transcriptomic analysis and projection-specific genetic manipulation revealed that the expression level of POU domain, class 3, transcription factor 1 (Pou3f1) in mPFC-VTA neurons controls social hierarchy. Optogenetic activation of mPFC-VTA neurons increasesPou3f1expression and lowers social rank. Together, these data demonstrate that discrete activity and gene expression in separate mPFC projections oppositely orchestrate social competition and hierarchy.
Clinical Characteristics and Outcomes of Laboratory-Confirmed SARS-CoV-2 Cases Infected with Omicron subvariants and XBB recombinant variant
Authors: Karyakarte Rajesh , Das Rashmita , Dudhate Sonali , Agarasen Jeanne , Pillai Praveena , Chandankhede Priyanka , Labshetwar Rutika , Gadiyal Yogita , Rajmane Mansi , Kulkarni Preeti , Nizarudeen Safanah , Joshi Suvarna , Potdar Varsha , Karmodiya Krishanpal 
Published: January 2023

ABSTRACTBackgroundSARS-CoV-2 has evolved to produce new variants causing successive waves of infection. Currently, six variants are being monitored by the World Health Organization that are replacing BA.5. These include BF.7 (BA.5 + R346T in spike), BQ.1 (and BQ.1.1, with BA.5 + R346T, K444T, N460K mutations in spike), BA.2.75 (including BA.2.75.2 and CH.1.1), and XBB (including XBB.1.5). BQ.1 and XBB variants are more immune evasive and have spread quickly throughout the world. With the concern of the potential severity of infections caused by these variants, the present study describes the clinical characteristics and outcomes of these major variants in Maharashtra.Material and MethodsA total of 1141 Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR) positive SARS-CoV-2 samples, with a cycle threshold value (Ct) less than 25, were processed for SARS-CoV-2 whole genome sequencing between 10th July 2022 and 12th January 2023. All corresponding demographic and clinical data were recorded and analysed using Microsoft® Excel and Epi Info™.ResultsOut of 1141 samples sequenced, BA.2.75* (63.78%) was the predominant Omicron variant, followed by the XBB* (18.88%), BA.2.38* (4.94%), BA.5* (4.06%), BA.2.10* (3.51%) and BQ.1* (1.65%). A total of 540 cases were contacted telephonically, of which 494 (91.48%) were symptomatic with mild symptoms. Fever (77.73%) was the most common symptom, followed by cold (47.98%), cough (42.31%), myalgia and fatigue (18.83%). Of the 540 cases, 414 (76.67%) cases recovered at home, and 126 (23.33%) were institutionally quarantined/hospitalised. Among the home-isolated and hospitalised cases, 416 (99.76%) and 108 (87.80%), respectively, recovered with symptomatic treatment, while one (0.24%) and 15 (12.20%), respectively, succumbed to the disease. In all, 491 (90.93%) cases were vaccinated with at least one dose of the COVID-19 vaccine, 41 (7.59%) were unvaccinated, and for 08 (1.48%), vaccine data was not available.ConclusionThe current study indicates that the XBB* variant is causing mild disease in India. However, as XBB* possess both immune-escape and infectivity-enhancing mutations, it has the potential to spread to other parts of the world rapidly.
Primary Blastic Plasmacytoid Dendritic Cell Neoplasm: a US Population-Based Study
Authors: Wang Fan 
Published: January 2023

AbstractBackgroundBlastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare and poorly understood hematopoietic malignancy. This study aimed to investigate the clinical characteristics and prognostic factors in patients with primary BPDCN.MethodsPatients diagnosed with primary BPDCN from 2000 to 2019 were extracted from the Surveillance, Epidemiology and End Results (SEER) database. Independent prognostic factors were evaluated based on the univariate and multivariate Cox regression analysis. The nomogram was then constructed to predict the overall survival of primary BPDCN patients at 3, 5 and 10 years after diagnosis.ResultsA total of 668 primary BPDCN patients were included in this study. The average age was 35.7 ± 25.4 years, with 68.7% being male. The mostly affected sites were lymph nodes (59.9%). Most patients (69.9%) received chemotherapy or radiation therapy. For all the patients, the 1-year, 3-year, 5-year, and 10-year overall survival (OS) were 78.0%, 62.6%, 59.0%, and 56.3%, respectively, and the corresponding disease-specific survival (DSS) were 80.6%, 66.8%, 63.5, and 61.8%, respectively. Multivariate cox analysis indicated that age and marital status of other (divorced, widowed and separated) at diagnosis were independent prognostic factors for DSS, but only age was for OS. The 5-year OS rate significantly declined with increasing age: age <15, 89.3%; age 15-39, 57.9%; age 40-64, 51.2%; age ≥65, 26.1%. Nomograms were further constructed to predict the possibility of OS and DSS with good performances.ConclusionsPrimary BPDCN is a rare disease, age and marital status were associated with survival of primary BPDCN patients, and age was an independent prognostic factor for OS.
Direct comparison of clinical diagnostic sensitivity of saliva from buccal swabs versus combined oro-/nasopharyngeal swabs in the detection of SARS-CoV-2 B.1.1.529 Omicron
Authors: Puyskens Andreas , Michel Janine , Stoliaroff-Pépin Anna , Bayram Fatimanur , Sesver Akin , Wichmann Ole , Harder Thomas , Schaade Lars , Nitsche Andreas , Peine Caroline 
Published: January 2023

AbstractWhile current guidelines recommend the use of respiratory tract specimens for the direct detection of SARS-CoV-2 infection, saliva has recently been suggested as preferred sample type for the sensitive detection of SARS-CoV-2 B.1.1.529 (Omicron). Here, we compare the clinical diagnostic sensitivity of paired buccal saliva swabs and combined oro-/nasopharyngeal swabs from hospitalized, symptomatic COVID-19 patients collected at median six days after symptom onset by real-time polymerase chain reaction (PCR) and antigen test. Of the tested SARS-CoV-2 positive sample pairs, 55.8% were identified as Omicron BA.1 and 44.2% as Omicron BA.2. Real-time PCR from buccal swabs generated significantly higher quantification cycle (Cq) values compared to those from matched combined oro-/nasopharyngeal swabs and resulted in an increased number of false-negative PCR results. Reduced diagnostic sensitivity of buccal swabs by real-time PCR was observed already at day one after symptom onset. Similarly, detection rates using the Abbott COVID-19 Ag Rapid Test Device were reduced in buccal swabs compared to those using combined oro-/nasopharyngeal swabs. Our results suggest reduced clinical diagnostic sensitivity of saliva from buccal swabs in comparison to combined oro-/nasopharyngeal swabs in the detection of Omicron in symptomatic individuals.
Malaria diagnosis in rural healthcare facilities and treatment-seeking behavior in malaria endemic settings in western Kenya
Authors: Omondi Collince J. , Odongo David , Otambo Wilfred O. , Ochwedo Kevin O. , Otieno Antony , Lee Ming-Chieh , Kazura James W. , Githeko Andrew K. , Yan Guiyun 
Published: January 2023

AbstractAccurate diagnosis and timely treatment are central requirements for effective malaria management in communities. However, in resource-constrained settings, healthcare facilities are likely to be few, inaccessible, and ill-equipped with frequent drug or rapid diagnostic test kit (RDT) shortages. This may jeopardize much-needed quality care for patients and may have an impact on treatment-seeking behavior among the local population. The study’s goal is to determine treatment-seeking behavior, malaria diagnosis and treatment, and likely treatment-seeking determinants in the local population. Passive case detection, which targeted all patients with suspected malaria cases, was conducted in ten public healthcare facilities over a three-month period. Monthly malaria cases, methods of diagnosis and antimalarial drug availability were assessed. A household-based survey was also carried out. Structured questionnaires were used to collect data from household heads. Malaria knowledge, treatment seeking behavior, and predictors of malaria treatment-seeking were all determined. Three of the seven dispensaries lacked a laboratory to conduct microscopy-based diagnosis. These three dispensaries also experienced frequent RDT stock-outs, which resulted in a clinical diagnosis of malaria. The majority of local residents with fever (50.3%) purchased antimalarial drugs from a chemist. About 37% of fever patients sought treatment at healthcare facility while the remaining 12.7% did nothing. In irrigated areas, 45.5% (46/64) of fever patients sought treatment at healthcare facilities, compared to 25% (18/64) in non-irrigated areas (p = 0.009). Most children aged below 5 who had fever (77.7%) were taken to healthcare facility for treatment compared to 31.4% of older children or 20.9% of adults (0.0001). Predictors of treatment seeking included access to healthcare facility (OR = 16.23, 95% CI: 2.74-96.12), and ability to pay hospital bill (OR = 10.6, 95% CI: 1.97-57). Other factors that influenced health-seeking behavior included the severity of symptoms, the age of the fever patient and knowledge of malaria symptoms.
Evaluating Evasion Strategies in Zebrafish Larvae
Authors: Jiao Yusheng , Colvert Brendan , Man Yi , McHenry Matthew J. , Kanso Eva 
Published: January 2023

AbstractAn effective evasion strategy allows prey to survive encounters with predators. Prey are generally thought to escape in a direction that is either random or serves to maximize the minimum distance from the predator. Here we introduce a comprehensive approach to determine the most likely evasion strategy among multiple hypotheses and the role of biomechanical constraints on the escape response of prey fish. Through a consideration of six strategies with sensorimotor noise and previous kinematic measurements, our analysis shows that zebrafish larvae generally escape in a direction orthogonal to the predator’s heading. By sensing only the predator’s heading, this orthogonal strategy maximizes the distance from fast-moving predators, and, when operating within the biomechanical constraints of the escape response, it provides the best predictions of prey behavior among all alternatives. This work demonstrates a framework for resolving the strategic basis of evastion in predator-prey interactions, which could be applied to a broad diversity of animals.
Microbial strong organic ligand production is tightly coupled to iron in hydrothermal plumes
Authors: Hoffman Colleen L. , Monreal Patrick J. , Albers Justine B. , Lough Alastair J.M. , Santoro Alyson E. , Mellett Travis , Buck Kristen N. , Tagliabue Alessandro , Lohan Maeve C. , Resing Joseph A. , Bundy Randelle M. 
Published: January 2023

AbstractHydrothermal vents have emerged as an important source of iron to seawater, yet only a subset of iron is soluble and persists long enough to be available for surface biological uptake. The longevity and solubility of iron in seawater is governed by strong organic ligands, like siderophores, that are produced by marine microorganisms and are a part of the ocean’s dissolved iron-binding ligand pool. These ligands have been hypothesized to aid in the persistence of dissolved iron in hydrothermal environments. To explore this hypothesis, we measured iron, iron-binding ligands, and siderophores from 11 geochemically distinct sites along a 1,700 km section of the Mid-Atlantic Ridge. Siderophores were found in hydrothermal plumes at all sites, with proximity to the vent playing an important role in dictating siderophore types and diversity. The notable presence of amphiphilic siderophores may point to microbial utilization of siderophores to access particulate hydrothermal iron, and the exchange of dissolved and particulate iron. The tight coupling between strong ligands and dissolved iron within neutrally buoyant plumes across six distinct hydrothermal environments, and the presence of dissolved siderophores with siderophore-producing microbial genera, suggests that biological production of siderophores exerts a key control on hydrothermal dissolved iron concentrations.
CartoCell, a high-content pipeline for 3D image analysis, unveils cell morphology patterns in epithelia
Authors: Andrés-San Román Jesús A. , Gordillo-Vázquez Carmen , Franco-Barranco Daniel , Morato Laura , Fernández-Espartero Cecilia H. , Baonza Gabriel , Tagua Antonio , Vicente-Munuera Pablo , Palacios Ana M. , Gavilán María P. , Martín-Belmonte Fernando , Annese Valentina , Gómez-Gálvez Pedro , Arganda-Carreras Ignacio , Escudero Luis M. 
Published: January 2023

SUMMARYDecades of research have not yet fully explained the mechanisms of epithelial self-organization and 3D packing. Single-cell analysis of large 3D epithelial libraries is crucial for understanding the assembly and function of whole tissues. Combining 3D epithelial imaging with advanced deep learning segmentation methods is essential for enabling this high-content analysis. We introduce CartoCell, a deep learning-based pipeline that uses small datasets to generate accurate labels for hundreds of whole 3D epithelial cysts. Our method detects the realistic morphology of epithelial cells and their contacts in the 3D structure of the tissue. CartoCell enables the quantification of geometric and packing features at the cellular level. Our Single-cell Cartography approach then maps the distribution of these features on 2D plots and 3D surface maps, revealing cell morphology patterns in epithelial cysts. Additionally, we show that CartoCell can be adapted to other types of epithelial tissues.MOTIVATIONA major bottleneck in developing neural networks for cell segmentation is the need for labor-intensive manual curation in order to develop a training dataset. The present work addresses this limitation by developing an automated image analysis pipeline that utilizes small datasets to generate accurate labels of cells in complex, 3D epithelial contexts. The overall goal is to provide an automatic and feasible method to achieve high-quality epithelial reconstructions and to enable high-content analysis of morphological features, which can improve our understanding of how these tissues self-organize.
Distinct functions of TIR1 and AFB1 receptors in auxin signalling
Authors: Chen Huihuang , Li Lanxin , Zou Minxia , Qi Linlin , Friml Jiří 
Published: January 2023

AbstractAuxin is the major plant hormone regulating growth and development (Friml, 2022). Forward genetic approaches in the model plantArabidopsis thalianahave identified major components of auxin signalling and established the canonical mechanism mediating transcriptional and thus developmental reprogramming. In this textbook view, TRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN-SIGNALING F-BOX (AFBs) are auxin receptors, which act as F-box subunits determining the substrate specificity of the Skp1-Cullin1-F box protein (SCF) type E3 ubiquitin ligase complex. Auxin acts as a “molecular glue” increasing the affinity between TIR1/AFBs and the Aux/IAA repressors. Subsequently, Aux/IAAs are ubiquitinated and degraded, thus releasing auxin transcription factors from their repression making them free to mediate transcription of auxin response genes (Yuet al., 2022). Nonetheless, accumulating evidence suggests existence of rapid, non-transcriptional responses downstream of TIR1/AFBs such as auxin-induced cytosolic calcium (Ca2+) transients, plasma membrane depolarization and apoplast alkalinisation, all converging on the process of root growth inhibition and root gravitropism (Liet al., 2022). Particularly, these rapid responses are mostly contributed by predominantly cytosolic AFB1, while the long-term growth responses are mediated by mainly nuclear TIR1 and AFB2-AFB5 (Liet al., 2021; Priggeet al., 2020; Serreet al., 2021). How AFB1 conducts auxin-triggered rapid responses and how it is different from TIR1 and AFB2-AFB5 remains elusive. Here, we compare the roles of TIR1 and AFB1 in transcriptional and rapid responses by modulating their subcellular localization in Arabidopsis and by testing their ability to mediate transcriptional responses when part of the minimal auxin circuit reconstituted in yeast.Short summaryAuxin receptors TIR1 and AFB1 have distinct functions in mediating transcriptional and non-transcriptional responses, respectively. Manipulation of their subcellular localizations revealed that these functional differences cannot be attributed to nuclear versus cytosolic enrichment of TIR1 and AFB1 but to different, specific properties of these proteins, not least to their ability to associate with ubiquitin ligase components.
Identification and characterization of metabolic subtypes of endometrial cancer using systems-level approach
Authors: Srivastava Akansha , Vinod P K 
Published: January 2023

AbstractBackgroundEndometrial cancer(EC) is the most common gynaecological cancer worldwide. Understanding the metabolic adaptation and its heterogeneity in tumor tissues may provide new insights and help in cancer diagnosis, prognosis, and treatment. In this study, we investigated metabolic alterations of EC to understand the variations in the metabolism within tumor samples.MethodsWe integrated the TCGA transcriptomics data of EC (RNA-Seq) with the human genome-scale metabolic model (HMR2.0) and performed unsupervised learning to identify the metabolic subtypes of EC and uncover the underlying dysregulated metabolic pathways and reporter metabolites in each subtype. The relationship between metabolic subtypes and clinical variables was explored. Further, we characterized each subtype at the molecular level and correlated the subtype-specific metabolic changes occurring at the transcriptome level with the genomic alterations.ResultsEC patients are stratified into two robust metabolic subtypes (cluster-1 and cluster-2) that significantly correlate to patient survival, tumor stages, mutation, and copy number variations. We observed coactivation of pentose phosphate pathway and one-carbon metabolism along with genes involved in controlling estrogen levels in cluster-2, which is linked to poor survival. PNMT and ERBB2 are also upregulated in cluster-2 samples and present in the same chromosome locus 17q12, which is amplified. PTEN and TP53 mutations show mutually exclusive behavior between subtypes and display a difference in survival.ConclusionThis work identifies metabolic subtypes with distinct characteristics at the transcriptome and genome levels, highlighting the metabolic heterogeneity within EC.
Resilience of genetic diversity in forest trees over the Quaternary
Authors: Milesi Pascal , Kastally Chedly , Dauphin Benjamin , Cervantes Sandra , Bagnoli Francesca , Budde Katharina B. , Cavers Stephen , Fady Bruno , Faivre-Rampant Patricia , González-Martínez Santiago C. , Grivet Delphine , Gugerli Felix , Jorge Véronique , Kupin Isabelle Lesur , Ojeda Dario I. , Olsson Sanna , Opgenoorth Lars , Pinosio Sara , Plomion Christophe , Rellstab Christian , Rogier Odile , Scalabrin Simone , Scotti Ivan , Vendramin Giovanni G. , Westergren Marjana , Lascoux Martin ,   GenTree Consortium, Pyhäjärvi Tanja 
Published: January 2023

AbstractThe effect of past environmental changes on the demography and genetic diversity of natural populations remains a contentious issue and has rarely been investigated across multiple, phylogenetically distant species. Here, we performed comparative population genomic analyses and demographic inferences for seven widely distributed and ecologically contrasted European forest tree species based on concerted sampling of 164 populations across their natural ranges. For all seven species, the effective population size,Ne, increased or remained stable over many glacial cycles and up to 15 million years in the most extreme cases. Hence, surprisingly, the drastic environmental changes associated with the Pleistocene glacial cycles have had little impact on the level of genetic diversity of dominant forest tree species, despite major shifts in their geographic ranges. Based on their trajectories ofNeover time, the seven tree species can be divided into three major groups, highlighting the importance of life history and range size in determining synchronous variation in genetic diversity, over time. Altogether, our results indicate that forest trees were able to retain their evolutionary potential over very long periods of time despite strong environmental changes.One-Sentence SummaryPopulation genomic analyses reveal that forest trees retained their evolutionary potential over the Quaternary.