bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring Sources of Surface Bias in HRRR Using New York State Mesonet
Authors: Min Lanxi , Fitzjarrald David R. , Du Yuyi , Rose Brian E. J. , Hong Jia , Min Qilong 
Published: September 2021

AbstractIn recent years, there has been increasing demand for applications of short‐term forecasting of renewable energy potential and assessments of the likelihood of extreme weather events using the High‐Resolution Rapid Refresh (HRRR) model. Examining the biases in the newest version of HRRR is necessary to promote further model development. Using data from one of the most comprehensive and dense monitoring networks, New York State Mesonet (NYSM), we evaluate the HRRR version 3 meteorological fields for an entire year. In this work, the land‐atmosphere‐cloud coupling system is evaluated as an integrated whole. We investigate the physical processes influencing the soil hydrological balance and the thermodynamic interactions, from surface fluxes up to the level of boundary layer convection from both temporal (seasonal and diurnal) and spatial perspectives. Results show that the model 2 m temperature and humidity biases are seasonally dependent, with warm and dry bias present during the warm season, and an extreme nocturnal cold bias in winter. The summer warm bias includes both a land‐surface‐induced bias and a cloud‐induced bias. Inaccurate representation of energy partition and soil hydrological process across different land use types as well as a hydrological bias in describing spring snowmelt are identified as the main source of the land‐surface‐induced bias. A feedback loop linking cloud presence, flux changes, and temperature contributes to the cloud‐induced bias. The positive solar radiation bias increases from clear sky to overcast sky conditions. The most significant bias occurs during overcast and thick cloud conditions associated with frontal passage and thunderstorms.
Analyses of oligodontia phenotypes and genetic etiologies
Authors: Zhou Mengqi , Zhang Hong , Camhi Heather , Seymen Figen , Koruyucu Mine , Kasimoglu Yelda , Kim Jung-Wook , Kim-Berman Hera , Yuson Ninna M. R. , Benke Paul J. , Wu Yiqun , Wang Feng , Zhu Yaqin , Simmer James P. , Hu Jan C-C. 
Published: September 2021

AbstractOligodontia is the congenital absence of six or more teeth and comprises the more severe forms of tooth agenesis. Many genes have been implicated in the etiology of tooth agenesis, which is highly variable in its clinical presentation. The purpose of this study was to identify associations between genetic mutations and clinical features of oligodontia patients. An online systematic search of papers published from January 1992 to June 2021 identified 381 oligodontia cases meeting the eligibility criteria of causative gene mutation, phenotype description, and radiographic records. Additionally, ten families with oligodontia were recruited and their genetic etiologies were determined by whole-exome sequence analyses. We identified a novel mutation in WNT10A (c.99_105dup) and eight previously reported mutations in WNT10A (c.433 G > A; c.682 T > A; c.318 C > G; c.511.C > T; c.321 C > A), EDAR (c.581 C > T), and LRP6 (c.1003 C > T, c.2747 G > T). Collectively, 20 different causative genes were implicated among those 393 cases with oligodontia. For each causative gene, the mean number of missing teeth per case and the frequency of teeth missing at each position were calculated. Genotype–phenotype correlation analysis indicated that molars agenesis is more likely linked to PAX9 mutations, mandibular first premolar agenesis is least associated with PAX9 mutations. Mandibular incisors and maxillary lateral incisor agenesis are most closely linked to EDA mutations.
Molecular mechanisms of inhibiting glucosyltransferases for biofilm formation in Streptococcus mutans
Authors: Zhang Qiong , Ma Qizhao , Wang Yan , Wu Hui , Zou Jing 
Published: September 2021

AbstractGlucosyltransferases (Gtfs) play critical roles in the etiology and pathogenesis of Streptococcus mutans (S. mutans)- mediated dental caries including early childhood caries. Gtfs enhance the biofilm formation and promotes colonization of cariogenic bacteria by generating biofilm extracellular polysaccharides (EPSs), the key virulence property in the cariogenic process. Therefore, Gtfs have become an appealing target for effective therapeutic interventions that inhibit cariogenic biofilms. Importantly, targeting Gtfs selectively impairs the S. mutans virulence without affecting S. mutans existence or the existence of other species in the oral cavity. Over the past decade, numerous Gtfs inhibitory molecules have been identified, mainly including natural and synthetic compounds and their derivatives, antibodies, and metal ions. These therapeutic agents exert their inhibitory role in inhibiting the expression gtf genes and the activities and secretion of Gtfs enzymes with a wide range of sensitivity and effectiveness. Understanding molecular mechanisms of inhibiting Gtfs will contribute to instructing drug combination strategies, which is more effective for inhibiting Gtfs than one drug or class of drugs. This review highlights our current understanding of Gtfs activities and their potential utility, and discusses challenges and opportunities for future exploration of Gtfs as a therapeutic target.
Microbial storage and its implications for soil ecology
Authors: Mason-Jones Kyle , Robinson Serina L , Veen G F (Ciska) , Manzoni Stefano , van der Putten Wim H 
Published: September 2021

Abstract
Organisms throughout the tree of life accumulate chemical resources, in particular forms or compartments, to secure their availability for future use. Here we review microbial storage and its ecological significance by assembling several rich but disconnected lines of research in microbiology, biogeochemistry, and the ecology of macroscopic organisms. Evidence is drawn from various systems, but we pay particular attention to soils, where microorganisms play crucial roles in global element cycles. An assembly of genus-level data demonstrates the likely prevalence of storage traits in soil. We provide a theoretical basis for microbial storage ecology by distinguishing a spectrum of storage strategies ranging from surplus storage (storage of abundant resources that are not immediately required) to reserve storage (storage of limited resources at the cost of other metabolic functions). This distinction highlights that microorganisms can invest in storage at times of surplus and under conditions of scarcity. We then align storage with trait-based microbial life-history strategies, leading to the hypothesis that ruderal species, which are adapted to disturbance, rely less on storage than microorganisms adapted to stress or high competition. We explore the implications of storage for soil biogeochemistry, microbial biomass, and element transformations and present a process-based model of intracellular carbon storage. Our model indicates that storage can mitigate against stoichiometric imbalances, thereby enhancing biomass growth and resource-use efficiency in the face of unbalanced resources. Given the central roles of microbes in biogeochemical cycles, we propose that microbial storage may be influential on macroscopic scales, from carbon cycling to ecosystem stability.
Bacillus velezensis stimulates resident rhizosphere Pseudomonas stutzeri for plant health through metabolic interactions
Authors: Sun Xinli , Xu Zhihui , Xie Jiyu , Hesselberg-Thomsen Viktor , Tan Taimeng , Zheng Daoyue , Strube Mikael L , Dragoš Anna , Shen Qirong , Zhang Ruifu , Kovács Ákos T 
Published: September 2021

Abstract
Trophic interactions play a central role in driving microbial community assembly and function. In gut or soil ecosystems, successful inoculants are always facilitated by efficient colonization; however, the metabolite exchanges between inoculants and resident bacteria are rarely studied, particularly in the rhizosphere. Here, we used bioinformatic, genetic, transcriptomic, and metabonomic analyses to uncover syntrophic cooperation between inoculant (Bacillus velezensis SQR9) and plant-beneficial indigenous Pseudomonas stutzeri in the cucumber rhizosphere. We found that the synergistic interaction of these two species is highly environmental dependent, the emergence of syntrophic cooperation was only evident in a static nutrient-rich niche, such as pellicle biofilm in addition to the rhizosphere. Our results identified branched-chain amino acids (BCAAs) biosynthesis pathways are involved in syntrophic cooperation. Genome-scale metabolic modeling and metabolic profiling also demonstrated metabolic facilitation among the bacterial strains. In addition, biofilm matrix components from Bacillus were essential for the interaction. Importantly, the two-species consortium promoted plant growth and helped plants alleviate salt stress. In summary, we propose a mechanism in which synergic interactions between a biocontrol bacterium and a partner species promote plant health.
Increased somatic mutation burdens in normal human cells due to defective DNA polymerases
Authors: Robinson Philip S. , Coorens Tim H. H. , Palles Claire , Mitchell Emily , Abascal Federico , Olafsson Sigurgeir , Lee Bernard C. H. , Lawson Andrew R. J. , Lee-Six Henry , Moore Luiza , Sanders Mathijs A. , Hewinson James , Martin Lynn , Pinna Claudia M. A. , Galavotti Sara , Rahbari Raheleh , Campbell Peter J. , Martincorena Iñigo , Tomlinson Ian , Stratton Michael R. 
Published: September 2021

AbstractMutation accumulation in somatic cells contributes to cancer development and is proposed as a cause of aging. DNA polymerases Pol ε and Pol δ replicate DNA during cell division. However, in some cancers, defective proofreading due to acquired POLE/POLD1 exonuclease domain mutations causes markedly elevated somatic mutation burdens with distinctive mutational signatures. Germline POLE/POLD1 mutations cause familial cancer predisposition. Here, we sequenced normal tissue and tumor DNA from individuals with germline POLE/POLD1 mutations. Increased mutation burdens with characteristic mutational signatures were found in normal adult somatic cell types, during early embryogenesis and in sperm. Thus human physiology can tolerate ubiquitously elevated mutation burdens. Except for increased cancer risk, individuals with germline POLE/POLD1 mutations do not exhibit overt features of premature aging. These results do not support a model in which all features of aging are attributable to widespread cell malfunction directly resulting from somatic mutation burdens accrued during life.
Parallel subgenome structure and divergent expression evolution of allo-tetraploid common carp and goldfish
Authors: Li Jiong-Tang , Wang Qi , Huang Yang Mei-Di , Li Qing-Song , Cui Ming-Shu , Dong Zai-Jie , Wang Hong-Wei , Yu Ju-Hua , Zhao Yu-Jie , Yang Chen-Ru , Wang Ya-Xin , Sun Xiao-Qing , Zhang Yan , Zhao Ran , Jia Zhi-Ying , Wang Xi-Yin 
Published: September 2021

AbstractHow two subgenomes in allo-tetraploids adapt to coexistence and coordinate through structure and expression evolution requires extensive studies. In the present study, we report an improved genome assembly of allo-tetraploid common carp, an updated genome annotation of allo-tetraploid goldfish and the chromosome-scale assemblies of a progenitor-like diploid Puntius tetrazona and an outgroup diploid Paracanthobrama guichenoti. Parallel subgenome structure evolution in the allo-tetraploids was featured with equivalent chromosome components, higher protein identities, similar transposon divergence and contents, homoeologous exchanges, better synteny level, strong sequence compensation and symmetric purifying selection. Furthermore, we observed subgenome expression divergence processes in the allo-tetraploids, including inter-/intrasubgenome trans-splicing events, expression dominance, decreased expression levels, dosage compensation, stronger expression correlation, dynamic functionalization and balancing of differential expression. The potential disorders introduced by different progenitors in the allo-tetraploids were hypothesized to be alleviated by increasing structural homogeneity and performing versatile expression processes. Resequencing three common carp strains revealed two major ecotypes and uncovered candidate genes relevant to growth and survival rate.
High-resolution structural and functional deep brain imaging using adaptive optics three-photon microscopy
Authors: Streich Lina , Boffi Juan Carlos , Wang Ling , Alhalaseh Khaleel , Barbieri Matteo , Rehm Ronja , Deivasigamani Senthilkumar , Gross Cornelius T. , Agarwal Amit , Prevedel Robert 
Published: September 2021

AbstractMultiphoton microscopy has become a powerful tool with which to visualize the morphology and function of neural cells and circuits in the intact mammalian brain. However, tissue scattering, optical aberrations and motion artifacts degrade the imaging performance at depth. Here we describe a minimally invasive intravital imaging methodology based on three-photon excitation, indirect adaptive optics (AO) and active electrocardiogram gating to advance deep-tissue imaging. Our modal-based, sensorless AO approach is robust to low signal-to-noise ratios as commonly encountered in deep scattering tissues such as the mouse brain, and permits AO correction over large axial fields of view. We demonstrate near-diffraction-limited imaging of deep cortical spines and (sub)cortical dendrites up to a depth of 1.4 mm (the edge of the mouse CA1 hippocampus). In addition, we show applications to deep-layer calcium imaging of astrocytes, including fibrous astrocytes that reside in the highly scattering corpus callosum.
Image-guided MALDI mass spectrometry for high-throughput single-organelle characterization
Authors: Castro Daniel C. , Xie Yuxuan Richard , Rubakhin Stanislav S. , Romanova Elena V. , Sweedler Jonathan V. 
Published: September 2021

AbstractPeptidergic dense-core vesicles are involved in packaging and releasing neuropeptides and peptide hormones—critical processes underlying brain, endocrine and exocrine function. Yet, the heterogeneity within these organelles, even for morphologically defined vesicle types, is not well characterized because of their small volumes. We present image-guided, high-throughput mass spectrometry-based protocols to chemically profile large populations of both dense-core vesicles and lucent vesicles for their lipid and peptide contents, allowing observation of the chemical heterogeneity within and between these two vesicle populations. The proteolytic processing products of four prohormones are observed within the dense-core vesicles, and the mass spectral features corresponding to the specific peptide products suggest three distinct dense-core vesicle populations. Notable differences in the lipid mass range are observed between the dense-core and lucent vesicles. These single-organelle mass spectrometry approaches are adaptable to characterize a range of subcellular structures.
A genome-wide association study identifies a novel candidate locus at the DLGAP1 gene with susceptibility to resistant hypertension in the Japanese population
Authors: Takahashi Yasuo , Yamazaki Keiko , Kamatani Yoichiro , Kubo Michiaki , Matsuda Koichi , Asai Satoshi 
Published: September 2021

AbstractNumerous genetic variants associated with hypertension and blood pressure are known, but there is a paucity of evidence from genetic studies of resistant hypertension, especially in Asian populations. To identify novel genetic loci associated with resistant hypertension in the Japanese population, we conducted a genome-wide association study with 2705 resistant hypertension cases and 21,296 mild hypertension controls, all from BioBank Japan. We identified one novel susceptibility candidate locus, rs1442386 on chromosome 18p11.3 (DLGAP1), achieving genome-wide significance (odds ratio (95% CI) = 0.85 (0.81–0.90), P = 3.75 × 10−8) and 18 loci showing suggestive association, including rs62525059 of 8q24.3 (CYP11B2) and rs3774427 of 3p21.1 (CACNA1D). We further detected biological processes associated with resistant hypertension, including chemical synaptic transmission, regulation of transmembrane transport, neuron development and neurological system processes, highlighting the importance of the nervous system. This study provides insights into the etiology of resistant hypertension in the Japanese population.
First results of undersea muography with the Tokyo-Bay Seafloor Hyper-Kilometric Submarine Deep Detector
Authors: Tanaka Hiroyuki K. M. , Aichi Masaatsu , Bozza Cristiano , Coniglione Rosa , Gluyas Jon , Hayashi Naoto , Holma Marko , Kamoshida Osamu , Kato Yasuhiro , Kin Tadahiro , Kuusiniemi Pasi , Leone Giovanni , Presti Domenico Lo , Matsushima Jun , Miyamoto Hideaki , Mori Hirohisa , Nomura Yukihiro , Oláh László , Steigerwald Sara , Shimazoe Kenji , Sumiya Kenji , Takahashi Hiroyuki , Thompson Lee F. , Yokota Yusuke , Paling Sean , Varga Dezső 
Published: September 2021

AbstractTidal measurements are of great significance since they may provide us with essential data to apply towards protection of coastal communities and sea traffic. Currently, tide gauge stations and laser altimetry are commonly used for these measurements. On the other hand, muography sensors can be located underneath the seafloor inside an undersea tunnel where electric and telecommunication infrastructures are more readily available. In this work, the world’s first under-seafloor particle detector array called the Tokyo-bay Seafloor Hyper-Kilometric Submarine Deep Detector (TS-HKMSDD) was deployed underneath the Tokyo-Bay seafloor for conducting submarine muography. The resultant 80-day consecutive time-sequential muographic data were converted to the tidal levels based on the parameters determined from the first-day astronomical tide height (ATH) data. The standard deviation between ATH and muographic results for the rest of a 79-day measurement period was 12.85 cm. We anticipate that if the length of the TS-HKMSDD is extended from 100 m to a full-scale as large as 9.6 km to provide continuous tidal information along the tunnel, this muography application will become an established standard, demonstrating its effectiveness as practical tide monitor for this heavy traffic waterway in Tokyo and in other important sea traffic areas worldwide.
A new humanized antibody is effective against pathogenic fungi in vitro
Authors: Di Mambro Tomas , Vanzolini Tania , Bruscolini Pierpaolo , Perez-Gaviro Sergio , Marra Emanuele , Roscilli Giuseppe , Bianchi Marzia , Fraternale Alessandra , Schiavano Giuditta Fiorella , Canonico Barbara , Magnani Mauro 
Published: September 2021

AbstractInvasive fungal infections mainly affect patients undergoing transplantation, surgery, neoplastic disease, immunocompromised subjects and premature infants, and cause over 1.5 million deaths every year. The most common fungi isolated in invasive diseases are Candida spp., Cryptococcus spp., and Aspergillus spp. and even if four classes of antifungals are available (Azoles, Echinocandins, Polyenes and Pyrimidine analogues), the side effects of drugs and fungal acquired and innate resistance represent the major hurdles to be overcome. Monoclonal antibodies are powerful tools currently used as diagnostic and therapeutic agents in different clinical contexts but not yet developed for the treatment of invasive fungal infections. In this paper we report the development of the first humanized monoclonal antibody specific for β-1,3 glucans, a vital component of several pathogenic fungi. H5K1 has been tested on C. auris, one of the most urgent threats and resulted efficient both alone and in combination with Caspofungin and Amphotericin B showing an enhancement effect. Our results support further preclinical and clinical developments for the use of H5K1 in the treatment of patients in need.
Karyotype analysis of amniotic fluid cells and report of chromosomal abnormalities in 15,401 cases of Iranian women
Authors: Younesi Sarang , Taheri Amin Mohammad Mahdi , Hantoushzadeh Sedigheh , Saadati Pourandokht , Jamali Soudabeh , Modarressi Mohammad-Hossein , Savad Shahram , Delshad Saeed , Amidi Saloomeh , Geranorimi Taraneh , Navidpour Fariba , Ghafouri-Fard Soudeh 
Published: September 2021

AbstractThe aim of present study was to assess the karyotypes of amniotic fluid cells and find the frequency of chromosomal abnormalities and their significance in clinical setting. A total of 15,401 pregnant women were assessed from March 2016 to May 2019, and 14,968 amniotic fluid samples were successfully cultured. These fetuses were grouped according to different indications including advanced maternal age, abnormal nuchal translucency (NT) values, positive first/second trimester screening results, high risk NIPT results, very low PAPP-A and free β-hCG multiples of the normal median (MoM) results, abnormal ultrasound findings or previous history of chromosomal abnormalities. Results indicated the presence of normal karyotype in 90.2% (13,497/14,968) of fetuses. Totally, 46.4% (6945/14,968) of fetuses were 46,XX and 43.8% (6552/14,968) had 46,XY chromosome pattern. A total of 1077 abnormal karyotypes were found among 14,968 fetuses, thus the rate of abnormal fetuses was calculated to be 7.2% (1072/14,968). Meanwhile, a total of 394 cases (2.8%) had a normal polymorphism in their karyotype. In other words, abnormal karyotypes were detected in one of 13.9 cases of patients underwent amniocentesis. Down syndrome, Edward’s syndrome, abnormal mosaicisms and Patau’s syndrome were detected in 4.4% (659/14,968), 0.57% (85/14,968), 0.49% (74/14,968) and 0.24% (36/14,968) of cases, respectively. Sex chromosomal abnormalities including Klinefelter syndrome, Turner syndrome and 47,XXX karyotype were detected in 64 cases (0.43%). In this article, the rates of chromosomal abnormalities are compared between different groups of patients based on the advanced maternal age, abnormal NT values, very low PAPP-A and free β-hCG MoMs results, and positive FTS results. The current investigation provides insight into the most appropriate indications for amniocentesis in Iran.
Role of Cattaneo–Christov heat flux in an MHD Micropolar dusty nanofluid flow with zero mass flux condition
Authors: Ramzan Muhammad , Gul Hina , Baleanu Dumitru , Nisar Kottakkaran Sooppy , Malik M. Y. 
Published: September 2021

AbstractThis investigation aims to look at the thermal conductivity of dusty Micropolar nanoliquid with MHD and Cattaneo–Christov heat flux flow over an elongated sheet. The novelty of the envisioned mathematical model is augmented with the added impacts of the heat source/sink, chemical reaction with slip, convective heat, and zero mass flux boundary conditions. The salient feature of the existing problem is to discuss the whole scenario with liquid and dust phases. The graphical depiction is attained for arising pertinent parameters by using bvp4c a built-in MATLAB function. It is noticed that the thermal profile and velocity field increases for greater values of liquid particle interaction parameter in the case of the dust phase. An escalation in the thermal profile of both liquid and dust phases is noticed for the magnetic parameter. The rate of mass transfer amplifies for large estimates of the Schmidt number. The thickness of the boundary layer and the fluid velocity are decreased as the velocity slip parameter is augmented. In both dust and liquid phases, the thermal boundary layer thickness is lessened for growing estimates of thermal relaxation time. The attained results are verified when compared with a published result.