bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bayesian Unsupervised Machine Learning Approach to Segment Arctic Sea Ice Using SMOS Data
Authors: Herbert Christoph , Camps Adriano , Wellmann Florian , Vall‐llossera Mercedes 
Published: March 2021

AbstractMicrowave radiometry at L‐band is sensitive to sea ice thickness (SIT) up to ∼ 60 cm. Current methods to infer SIT depend on ice‐physical properties and data provided by the ESA’s Soil Moisture and Ocean Salinity (SMOS) mission. However, retrieval accuracy is limited due to seasonally and regionally variable surface conditions during the formation and melting of sea ice. In this work, Arctic sea ice is segmented using a Bayesian unsupervised learning algorithm aiming to recognize spatial patterns by harnessing multi‐incidence angle brightness temperature observations. The approach considers both statistical characteristics and spatial correlations of the observations. The temporal stability and separability of classes are analyzed to distinguish ambiguous from well‐determined regions. Model uncertainty is quantified from class membership probabilities using information entropy. The presented approach opens up a new scope to improve current SIT retrieval algorithms, and can be particularly beneficial to investigate merged satellite products.
Glycolysis reprogramming in cancer-associated fibroblasts promotes the growth of oral cancer through the lncRNA H19/miR-675-5p/PFKFB3 signaling pathway
Authors: Yang Jin , Shi Xueke , Yang Miao , Luo Jingjing , Gao Qinghong , Wang Xiangjian , Wu Yang , Tian Yuan , Wu Fanglong , Zhou Hongmei 
Published: March 2021

AbstractAs an important component of the tumor microenvironment, cancer-associated fibroblasts (CAFs) secrete energy metabolites to supply energy for tumor progression. Abnormal regulation of long noncoding RNAs (lncRNAs) is thought to contribute to glucose metabolism, but the role of lncRNAs in glycolysis in oral CAFs has not been systematically examined. In the present study, by using RNA sequencing and bioinformatics analysis, we analyzed the lncRNA/mRNA profiles of normal fibroblasts (NFs) derived from normal tissues and CAFs derived from patients with oral squamous cell carcinoma (OSCC). LncRNA H19 was identified as a key lncRNA in oral CAFs and was synchronously upregulated in both oral cancer cell lines and CAFs. Using small interfering RNA (siRNA) strategies, we determined that lncRNA H19 knockdown affected proliferation, migration, and glycolysis in oral CAFs. We found that knockdown of lncRNA H19 by siRNA suppressed the MAPK signaling pathway, 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3) and miR-675-5p. Furthermore, the lncRNA H19/miR-675-5p/PFKFB3 axis was involved in promoting the glycolysis pathway in oral CAFs, as demonstrated by a luciferase reporter system assay and treatment with a miRNA-specific inhibitor. Our study presents a new way to understand glucose metabolism in oral CAFs, theoretically providing a novel biomarker for OSCC molecular diagnosis and a new target for antitumor therapy.
A protective role for autophagy in vitiligo
Authors: Bastonini Emanuela , Kovacs Daniela , Raffa Salvatore , delle Macchie Marina , Pacifico Alessia , Iacovelli Paolo , Torrisi Maria Rosaria , Picardo Mauro 
Published: March 2021

AbstractA growing number of studies supports the existence of a dynamic interplay between energetic metabolism and autophagy, whose induction represents an adaptive response against several stress conditions. Autophagy is an evolutionarily conserved and a highly orchestrated catabolic recycling process that guarantees cellular homeostasis. To date, the exact role of autophagy in vitiligo pathogenesis is still not clear. Here, we provide the first evidence that autophagy occurs in melanocytes and fibroblasts from non-lesional skin of vitiligo patients, as a result of metabolic surveillance response. More precisely, this study is the first to reveal that induction of autophagy exerts a protective role against the intrinsic metabolic stress and attempts to antagonize degenerative processes in normal appearing vitiligo skin, where melanocytes and fibroblasts are already prone to premature senescence.
Immune memory in convalescent patients with asymptomatic or mild COVID-19
Authors: Long Quan-Xin , Jia Yan-Jun , Wang Xin , Deng Hai-Jun , Cao Xiao-Xia , Yuan Jun , Fang Liang , Cheng Xu-Rong , Luo Chao , He An-Ran , Tang Xiao-Jun , Hu Jie-li , Hu Yuan , Tang Ni , Cai Xue-Fei , Wang De-Qiang , Hu Jie , Qiu Jing-Fu , Liu Bei-Zhong , Chen Juan , Huang Ai-long 
Published: March 2021

AbstractIt is important to evaluate the durability of the protective immune response elicited by primary infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we systematically evaluated the SARS-CoV-2-specific memory B cell and T cell responses in healthy controls and individuals recovered from asymptomatic or symptomatic infection approximately 6 months prior. Comparatively low frequencies of memory B cells specific for the receptor-binding domain (RBD) of spike glycoprotein (S) persisted in the peripheral blood of individuals who recovered from infection (median 0.62%, interquartile range 0.48-0.69). The SARS-CoV-2 RBD-specific memory B cell response was detected in 2 of 13 individuals who recovered from asymptomatic infection and 10 of 20 individuals who recovered from symptomatic infection. T cell responses induced by S, membrane (M), and nucleocapsid (N) peptide libraries from SARS-CoV-2 were observed in individuals recovered from coronavirus disease 2019 (COVID-19), and cross-reactive T cell responses to SARS-CoV-2 were also detected in healthy controls.
Model-based deep embedding for constrained clustering analysis of single cell RNA-seq data
Authors: Tian Tian , Zhang Jie , Lin Xiang , Wei Zhi , Hakonarson Hakon 
Published: March 2021

AbstractClustering is a critical step in single cell-based studies. Most existing methods support unsupervised clustering without the a priori exploitation of any domain knowledge. When confronted by the high dimensionality and pervasive dropout events of scRNA-Seq data, purely unsupervised clustering methods may not produce biologically interpretable clusters, which complicates cell type assignment. In such cases, the only recourse is for the user to manually and repeatedly tweak clustering parameters until acceptable clusters are found. Consequently, the path to obtaining biologically meaningful clusters can be ad hoc and laborious. Here we report a principled clustering method named scDCC, that integrates domain knowledge into the clustering step. Experiments on various scRNA-seq datasets from thousands to tens of thousands of cells show that scDCC can significantly improve clustering performance, facilitating the interpretability of clusters and downstream analyses, such as cell type assignment.
A molecular timescale for eukaryote evolution with implications for the origin of red algal-derived plastids
Authors: Strassert Jürgen F. H. , Irisarri Iker , Williams Tom A. , Burki Fabien 
Published: March 2021

AbstractIn modern oceans, eukaryotic phytoplankton is dominated by lineages with red algal-derived plastids such as diatoms, dinoflagellates, and coccolithophores. Despite the ecological importance of these groups and many others representing a huge diversity of forms and lifestyles, we still lack a comprehensive understanding of their evolution and how they obtained their plastids. New hypotheses have emerged to explain the acquisition of red algal-derived plastids by serial endosymbiosis, but the chronology of these putative independent plastid acquisitions remains untested. Here, we establish a timeframe for the origin of red algal-derived plastids under scenarios of serial endosymbiosis, using Bayesian molecular clock analyses applied on a phylogenomic dataset with broad sampling of eukaryote diversity. We find that the hypotheses of serial endosymbiosis are chronologically possible, as the stem lineages of all red plastid-containing groups overlap in time. This period in the Meso- and Neoproterozoic Eras set the stage for the later expansion to dominance of red algal-derived primary production in the contemporary oceans, which profoundly altered the global geochemical and ecological conditions of the Earth.
Manipulating Weyl quasiparticles by orbital-selective photoexcitation in WTe2
Authors: Guan Meng-Xue , Wang En , You Pei-Wei , Sun Jia-Tao , Meng Sheng 
Published: March 2021

AbstractOptical control of structural and electronic properties of Weyl semimetals allows development of switchable and dissipationless topological devices at the ultrafast scale. An unexpected orbital-selective photoexcitation in type-II Weyl material WTe2 is reported under linearly polarized light (LPL), inducing striking transitions among several topologically-distinct phases mediated by effective electron-phonon couplings. The symmetry features of atomic orbitals comprising the Weyl bands result in asymmetric electronic transitions near the Weyl points, and in turn a switchable interlayer shear motion with respect to linear light polarization, when a near-infrared laser pulse is applied. Consequently, not only annihilation of Weyl quasiparticle pairs, but also increasing separation of Weyl points can be achieved, complementing existing experimental observations. In this work, we provide a new perspective on manipulating the Weyl node singularity and coherent control of electron and lattice quantum dynamics simultaneously.
Structure-based design of a Cortistatin analogue with immunomodulatory activity in models of inflammatory bowel disease
Authors: Rol Álvaro , Todorovski Toni , Martin-Malpartida Pau , Escolà Anna , Gonzalez-Rey Elena , Aragón Eric , Verdaguer Xavier , Vallès-Miret Mariona , Farrera-Sinfreu Josep , Puig Eduard , Fernández-Carneado Jimena , Ponsati Berta , Delgado Mario , Riera Antoni , Macias Maria J. 
Published: March 2021

AbstractUlcerative colitis and Crohn’s disease are forms of inflammatory bowel disease whose incidence and prevalence are increasing worldwide. These diseases lead to chronic inflammation of the gastrointestinal tract as a result of an abnormal response of the immune system. Recent studies positioned Cortistatin, which shows low stability in plasma, as a candidate for IBD treatment. Here, using NMR structural information, we design five Cortistatin analogues adopting selected native Cortistatin conformations in solution. One of them, A5, preserves the anti-inflammatory and immunomodulatory activities of Cortistatin in vitro and in mouse models of the disease. Additionally, A5 displays an increased half-life in serum and a unique receptor binding profile, thereby overcoming the limitations of the native Cortistatin as a therapeutic agent. This study provides an efficient approach to the rational design of Cortistatin analogues and opens up new possibilities for the treatment of patients that fail to respond to other therapies.
Clonal analysis and dynamic imaging identify multipotency of individual Gallus gallus caudal hindbrain neural crest cells toward cardiac and enteric fates
Authors: Tang Weiyi , Li Yuwei , Li Ang , Bronner Marianne E. 
Published: March 2021

AbstractNeural crest stem cells arising from caudal hindbrain (often called cardiac and posterior vagal neural crest) migrate long distances to form cell types as diverse as heart muscle and enteric ganglia, abnormalities of which lead to common congenital birth defects. Here, we explore whether individual caudal hindbrain neural crest precursors are multipotent or predetermined toward these particular fates and destinations. To this end, we perform lineage tracing of chick neural crest cells at single-cell resolution using two complementary approaches: retrovirally mediated multiplex clonal analysis and single-cell photoconversion. Both methods show that the majority of these neural crest precursors are multipotent with many clones producing mesenchymal as well as neuronal derivatives. Time-lapse imaging demonstrates that sister cells can migrate in distinct directions, suggesting stochasticity in choice of migration path. Perturbation experiments further identify guidance cues acting on cells in the pharyngeal junction that can influence this choice; loss of CXCR4 signaling results in failure to migrate to the heart but no influence on migration toward the foregut, whereas loss of RET signaling does the opposite. Taken together, the results suggest that environmental influences rather than intrinsic information govern cell fate choice of multipotent caudal hindbrain neural crest cells.
Membrane type 1 matrix metalloproteinase promotes LDL receptor shedding and accelerates the development of atherosclerosis
Authors: Alabi Adekunle , Xia Xiao-Dan , Gu Hong-Mei , Wang Faqi , Deng Shi-Jun , Yang Nana , Adijiang Ayinuer , Douglas Donna N. , Kneteman Norman M. , Xue Yazhuo , Chen Li , Qin Shucun , Wang Guiqing , Zhang Da-Wei 
Published: March 2021

AbstractPlasma low-density lipoprotein (LDL) is primarily cleared by LDL receptor (LDLR). LDLR can be proteolytically cleaved to release its soluble ectodomain (sLDLR) into extracellular milieu. However, the proteinase responsible for LDLR cleavage is unknown. Here we report that membrane type 1-matrix metalloproteinase (MT1-MMP) co-immunoprecipitates and co-localizes with LDLR and promotes LDLR cleavage. Plasma sLDLR and cholesterol levels are reduced while hepatic LDLR is increased in mice lacking hepatic MT1-MMP. Opposite effects are observed when MT1-MMP is overexpressed. MT1-MMP overexpression significantly increases atherosclerotic lesions, while MT1-MMP knockdown significantly reduces cholesteryl ester accumulation in the aortas of apolipoprotein E (apoE) knockout mice. Furthermore, sLDLR is associated with apoB and apoE-containing lipoproteins in mouse and human plasma. Plasma levels of sLDLR are significantly increased in subjects with high plasma LDL cholesterol levels. Thus, we demonstrate that MT1-MMP promotes ectodomain shedding of hepatic LDLR, thereby regulating plasma cholesterol levels and the development of atherosclerosis.
The effect of SARS-CoV-2 D614G mutation on BNT162b2 vaccine-elicited neutralization
Authors: Zou Jing , Xie Xuping , Fontes-Garfias Camila R. , Swanson Kena A. , Kanevsky Isis , Tompkins Kristin , Cutler Mark , Cooper David , Dormitzer Philip R. , Shi Pei-Yong 
Published: March 2021

AbstractInitial COVID-19 vaccine candidates were based on the original sequence of SARS-CoV-2. However, the virus has since accumulated mutations, among which the spike D614G is dominant in circulating virus, raising questions about potential virus escape from vaccine-elicited immunity. Here, we report that the D614G mutation modestly reduced (1.7–2.4-fold) SARS-CoV-2 neutralization by BNT162b2 vaccine-elicited mouse, rhesus, and human sera, concurring with the 95% vaccine efficacy observed in clinical trial.
EORNA, a barley gene and transcript abundance database
Authors: Milne Linda , Bayer Micha , Rapazote-Flores Paulo , Mayer Claus-Dieter , Waugh Robbie , Simpson Craig G. 
Published: March 2021

AbstractA high-quality, barley gene reference transcript dataset (BaRTv1.0), was used to quantify gene and transcript abundances from 22 RNA-seq experiments, covering 843 separate samples. Using the abundance data we developed a Barley Expression Database (EORNA*) to underpin a visualisation tool that displays comparative gene and transcript abundance data on demand as transcripts per million (TPM) across all samples and all the genes. EORNA provides gene and transcript models for all of the transcripts contained in BaRTV1.0, and these can be conveniently identified through either BaRT or HORVU gene names, or by direct BLAST of query sequences. Browsing the quantification data reveals cultivar, tissue and condition specific gene expression and shows changes in the proportions of individual transcripts that have arisen via alternative splicing. TPM values can be easily extracted to allow users to determine the statistical significance of observed transcript abundance variation among samples or perform meta analyses on multiple RNA-seq experiments. * Eòrna is the Scottish Gaelic word for Barley.
Polypill eligibility and equivalent intake in a Swiss population-based study
Authors: Castioni Julien , Abolhassani Nazanin , Vollenweider Peter , Waeber Gérard , Marques-Vidal Pedro 
Published: March 2021

AbstractThe polypill has been advocated for cardiovascular disease (CVD) management. The fraction of the population who could benefit from the polypill in Switzerland is unknown. Assess (1) the prevalence of subjects (a) eligible for the polypill and (b) already taking a polypill equivalent; and (2) the determinants of polypill intake in the first (2009–2012) and second follow-ups (2014–2017) of a population-based prospective study conducted in Lausanne, Switzerland. The first and the second follow-ups included 5038 and 4596 participants aged 40–80 years, respectively. Polypill eligibility was defined as having a high CVD risk as assessed by an absolute CVD risk ≥ 5% with the SCORE equation for Switzerland and/or presenting with CVD. Four polypill equivalents were defined: statin + any antihypertensive with (A) or without (B) aspirin; statin + calcium channel blocker (CCB) (C); and statin + CCB + angiotensin-converting enzyme inhibitor (D). The prevalence of polypill eligibility was 20.6% (95% CI 19.5–21.8) and 27.7% (26.5–29.1) in the first and second follow-up, respectively. However, only around one-third of the eligible 29.5% (95% CI 26.7–32.3) and 30.4% (27.9–33.0) respectively, already took the polypill equivalents. All polypill equivalents were more prevalent among men, elderly and in presence of CVD. After multivariable adjustment, in both periods, male gender was associated with taking polypill equivalent A (OR: 1.93; 95% CI 1.45–2.55 and OR: 1.67; 95% CI 1.27–2.19, respectively) and polypill equivalent B (OR: 1.52; 95% CI 1.17–1.96 and OR: 1.41; 95% CI 1.07–1.85, respectively). Similarly, in both periods, age over 70 years, compared to middle-age, was associated with taking polypill equivalent A (OR: 11.71; CI 6.74–20.33 and OR: 9.56; CI 4.13–22.13, respectively) and equivalent B (OR: 13.22; CI 7.27–24.07 and OR: 20.63; CI 6.51–56.36, respectively). Former or current smoking was also associated with a higher likelihood of taking polypill equivalent A in both periods. A large fraction of the population is eligible for the polypill, but only one-third of them actually benefits from an equivalent, and this proportion did not change over time.
A 3D analysis of growth trajectory and integration during early human prenatal facial growth
Authors: Katsube Motoki , Yamada Shigehito , Utsunomiya Natsuko , Yamaguchi Yutaka , Takakuwa Tetsuya , Yamamoto Akira , Imai Hirohiko , Saito Atsushi , Vora Siddharth R. , Morimoto Naoki 
Published: March 2021

AbstractSignificant shape changes in the human facial skeleton occur in the early prenatal period, and understanding this process is critical for studying a myriad of congenital facial anomalies. However, quantifying and visualizing human fetal facial growth has been challenging. Here, we applied quantitative geometric morphometrics (GM) to high-resolution magnetic resonance images of human embryo and fetuses, to comprehensively analyze facial growth. We utilized non-linear growth estimation and GM methods to assess integrated epigenetic growth between masticatory muscles and associated bones. Our results show that the growth trajectory of the human face in the early prenatal period follows a curved line with three flexion points. Significant antero-posterior development occurs early, resulting in a shift from a mandibular prognathic to relatively orthognathic appearance, followed by expansion in the lateral direction. Furthermore, during this time, the development of the zygoma and the mandibular ramus is closely integrated with the masseter muscle.
Classification of unlabeled online media
Authors: Prakash Sakthi Kumar Arul , Tucker Conrad 
Published: March 2021

AbstractThis work investigates the ability to classify misinformation in online social media networks in a manner that avoids the need for ground truth labels. Rather than approach the classification problem as a task for humans or machine learning algorithms, this work leverages user–user and user–media (i.e.,media likes) interactions to infer the type of information (fake vs. authentic) being spread, without needing to know the actual details of the information itself. To study the inception and evolution of user–user and user–media interactions over time, we create an experimental platform that mimics the functionality of real-world social media networks. We develop a graphical model that considers the evolution of this network topology to model the uncertainty (entropy) propagation when fake and authentic media disseminates across the network. The creation of a real-world social media network enables a wide range of hypotheses to be tested pertaining to users, their interactions with other users, and with media content. The discovery that the entropy of user–user and user–media interactions approximate fake and authentic media likes, enables us to classify fake media in an unsupervised learning manner.
Generalized chest CT and lab curves throughout the course of COVID-19
Authors: Kassin Michael T. , Varble Nicole , Blain Maxime , Xu Sheng , Turkbey Evrim B. , Harmon Stephanie , Yang Dong , Xu Ziyue , Roth Holger , Xu Daguang , Flores Mona , Amalou Amel , Sun Kaiyun , Kadri Sameer , Patella Francesca , Cariati Maurizio , Scarabelli Alice , Stellato Elvira , Ierardi Anna Maria , Carrafiello Gianpaolo , An Peng , Turkbey Baris , Wood Bradford J. 
Published: March 2021

AbstractA better understanding of temporal relationships between chest CT and labs may provide a reference for disease severity over the disease course. Generalized curves of lung opacity volume and density over time can be used as standardized references from well before symptoms develop to over a month after recovery, when residual lung opacities remain. 739 patients with COVID-19 underwent CT and RT-PCR in an outbreak setting between January 21st and April 12th, 2020. 29 of 739 patients had serial exams (121 CTs and 279 laboratory measurements) over 50 ± 16 days, with an average of 4.2 sequential CTs each. Sequential volumes of total lung, overall opacity and opacity subtypes (ground glass opacity [GGO] and consolidation) were extracted using deep learning and manual segmentation. Generalized temporal curves of CT and laboratory measurements were correlated. Lung opacities appeared 3.4 ± 2.2 days prior to symptom onset. Opacity peaked 1 day after symptom onset. GGO onset was earlier and resolved later than consolidation. Lactate dehydrogenase, and C-reactive protein peaked earlier than procalcitonin and leukopenia. The temporal relationships of quantitative CT features and clinical labs have distinctive patterns and peaks in relation to symptom onset, which may inform early clinical course in patients with mild COVID-19 pneumonia, or may shed light upon chronic lung effects or mechanisms of medical countermeasures in clinical trials.