Miracle-dz/UniFAR-FTUs huggingface dataset:
Precipitation From a Multiyear Database of Convection‐Allowing WRF Simulations

Convection‐allowing models (CAMs) have become frequently used for operational forecasting and, more recently, have been utilized for general circulation model downscaling. CAM forecasts have typically been analyzed for a few case studies or over short time periods, but this limits the ability to judge the overall skill of deterministic simulations. Analysis over long time periods can yield a better understanding of systematic model error. Four years of warm season (April–August, 2010–2013)‐simulated precipitation has been accumulated from two Weather Research and Forecasting (WRF) models with 4 km grid spacing. The simulations were provided by the National Center for Environmental Prediction (NCEP) and the National Severe Storms Laboratory (NSSL), each with different dynamic cores and parameterization schemes. These simulations are evaluated against the NCEP Stage‐IV precipitation data set with similar 4 km grid spacing. The spatial distribution and diurnal cycle of precipitation in the central United States are analyzed using Hovmöller diagrams, grid point correlations, and traditional verification skill scoring (i.e., ETS; Equitable Threat Score). Although NCEP‐WRF had a high positive error in total precipitation, spatial characteristics were similar to observations. For example, the spatial distribution of NCEP‐WRF precipitation correlated better than NSSL‐WRF for the Northern Plains. Hovmöller results exposed a delay in initiation and decay of diurnal precipitation by NCEP‐WRF while both models had difficulty in reproducing the timing and location of propagating precipitation. ETS was highest for NSSL‐WRF in all domains at all times. ETS was also higher in areas of propagating precipitation compared to areas of unorganized diurnal scattered precipitation. Monthly analysis identified unique differences between the two models in their abilities to correctly simulate the spatial distribution and zonal motion of precipitation through the warm season.
Multifactorial Origin of Neurodevelopmental Disorders: Approaches to Understanding Complex Etiologies

A significant body of evidence supports the multifactorial etiology of neurodevelopmental disorders (NDDs) affecting children. The present review focuses on early exposure to environmental chemicals as a risk factor for neurodevelopment, and presents the major lines of evidence derived from epidemiological studies, underlying key uncertainties and research needs in this field. We introduce the exposome concept that, encompassing the totality of human environmental exposures to multiple risk factors, aims at explaining individual vulnerability and resilience to early chemical exposure. In this framework, we synthetically review the role of variable gene backgrounds, the involvement of epigenetic mechanisms as well as the function played by potential effect modifiers such as socioeconomic status. We describe laboratory rodent studies where the neurodevelopmental effects of environmental chemicals are assessed in the presence of either a “vulnerable” gene background or adverse pregnancy conditions (i.e., maternal stress). Finally, we discuss the need for more descriptive and “lifelike” experimental models of NDDs, to identify candidate biomarkers and pinpoint susceptible groups or life stages to be translated to large prospective studies within the exposome framework.
Contribution à l'établissement d'un modèle génétique des gisements d'Imiter (Ag-Hg), Bou Madine (Pb-Zn-Cu-Ag-Au) et Bou Azzer (Co-Ni-As-Au-Ag) dans l'Anti-Atlas marocain

L’analyse structurale de la zone de faille du gisement Ag-Hg d’Imiter confirme la superposition de deux regimes tectoniques, synchrones de l’episode argentifere, successivement extensif N-S a gangue siliceuse puis transtensif senestre. Un reseau filonien rhyolitique caracterise par des injections dans les plans d’ouverture E-W du premier regime extensif, est associe au depot des mineralisations. Les mesures in situ U/Pb sur mono zircon a microsonde ionique CAMECA IMS 1270 ont permis de dater deux evenements magmatiques distincts a 572 ± 5 Ma (granodiorite de Taouzzakt) et 550 ± 3 Ma (rhyolite de Takhatert). Les analyses 40Ar/39Ar ont fourni des resultats qui confirment l’existence des deux evenements magmatiques et hydrothermaux a Imiter associes a un episode de mineralisation a metaux de base (563 a 577 Ma) puis epithermal argentifere. Les isotopes du soufre suggerent deux reservoirs pour cet element, un reservoir magmatique et un autre metasedimentaire. Les donnees Re/Os indiquent sans ambiguite une origine mantellique du stock metal. Les mineralisations Ag-Hg d’Imiter sont interpretees dans le cadre d’un modele epithermal neutre dont les deux parametres essentiels sont la presence d’une extension de direction N-S permettant le piegeage des mineralisations et l’injection de magmas rhyolitiques. Ceux-ci fournissent egalement l’energie necessaire au developpement des circulations hydrothermales. La datation de la mineralisation des gisements de Bou Madine (553 Ma, U/Pb sur zircon) et de Bou Azzer (533 Ma U/Pb sur zircon du trachyte d’Aghbar et 218 Ma 39Ar/40Ar sur adulaire) montre l’importance de l’evenement metallogenique lors de la transition Precambrien/Cambrien et l’existence probable de mineralisations post-cambriennes. L’integration de l’ensemble de ces resultats dans un modele geodynamique met en evidence, lors de la transition Precambrien/Cambrien l’evolution de l’Anti-Atlas d’un contexte de marge continentale active a celui d’une marge continentale passive.
Mammalian MicroRNA Prediction through a Support Vector Machine Model of Sequence and Structure

Background MicroRNAs (miRNAs) are endogenous small noncoding RNA gene products, on average 22 nt long, found in a wide variety of organisms. They play important regulatory roles by targeting mRNAs for degradation or translational repression. There are 377 known mouse miRNAs and 475 known human miRNAs in the May 2007 release of the miRBase database, the majority of which are conserved between the two species. A number of recent reports imply that it is likely that many mammalian miRNAs remain to be discovered. The possibility that there are more of them expressed at lower levels or in more specialized expression contexts calls for the exploitation of genome sequence information to accelerate their discovery. Methodology/Principal Findings In this article, we describe a computational method-mirCoS-that uses three support vector machine models sequentially to discover new miRNA candidates in mammalian genomes based on sequence, secondary structure, and conservation. mirCoS can efficiently detect the majority of known miRNAs and predicts an extensive set of hairpin structures based on human-mouse comparisons. In total, 3476 mouse candidates and 3441 human candidates were found. These hairpins are more similar to known miRNAs than to negative controls in several aspects not considered by the prediction algorithm. A significant fraction of predictions is supported by existing expression evidence. Conclusions/Significance Using a novel approach, mirCoS performs comparably to or better than existing miRNA prediction methods, and contributes a significant number of new candidate miRNAs for experimental verification.
Cooperative spectrum sensing using random matrix theory

In this paper, using tools from asymptotic random matrix theory, a new cooperative scheme for frequency band sensing is introduced for both AWGN and fading channels. Unlike previous works in the field, the new scheme does not require the knowledge of the noise statistics or its variance and is related to the behavior of the largest and smallest eigenvalue of random matrices. Remarkably, simulations show that the asymptotic claims hold even for a small number of observations (which makes it convenient for time-varying topologies), outperforming classical energy detection techniques.
A Fasciclin-Like Arabinogalactan-Protein (FLA) Mutant of Arabidopsis thaliana, fla1, Shows Defects in Shoot Regeneration

Background The fasciclin-like arabinogalactan-proteins (FLAs) are an enigmatic class of 21 members within the larger family of arabinogalactan-proteins (AGPs) in Arabidopsis thaliana. Located at the cell surface, in the cell wall/plasma membrane, they are implicated in many developmental roles yet their function remains largely undefined. Fasciclin (FAS) domains are putative cell-adhesion domains found in extracellular matrix proteins of organisms from all kingdoms, but the juxtaposition of FAS domains with highly glycosylated AGP domains is unique to plants. Recent studies have started to elucidate the role of FLAs in Arabidopsis development. FLAs containing a single FAS domain are important for the integrity and elasticity of the plant cell wall matrix (FLA11 and FLA12) and FLA3 is involved in microspore development. FLA4/SOS5 with two FAS domains and two AGP domains has a role in maintaining proper cell expansion under salt stressed conditions. The role of other FLAs remains to be uncovered. Method/Principal Findings Here we describe the characterisation of a T-DNA insertion mutant in the FLA1 gene (At5g55730). Under standard growth conditions fla1-1 mutants have no obvious phenotype. Based on gene expression studies, a putative role for FLA1 in callus induction was investigated and revealed that fla1-1 has a reduced ability to regenerate shoots in an in vitro shoot-induction assay. Analysis of FLA1p:GUS reporter lines show that FLA1 is expressed in several tissues including stomata, trichomes, the vasculature of leaves, the primary root tip and in lateral roots near the junction of the primary root. Conclusion The results of the developmental expression of FLA1 and characterisation of the fla1 mutant support a role for FLA1 in the early events of lateral root development and shoot development in tissue culture, prior to cell-type specification.
Topology control of multihop wireless networks using transmit power adjustment

We consider the problem of adjusting the transmit powers of nodes in a multihop wireless network (also called an ad hoc network) to create a desired topology. We formulate it as a constrained optimization problem with two constraints-connectivity and biconnectivity, and one optimization objective-maximum power used. We present two centralized algorithms for use in static networks, and prove their optimality. For mobile networks, we present two distributed heuristics that adaptively adjust node transmit powers in response to topological changes and attempt to maintain a connected topology using minimum power. We analyze the throughput, delay, and power consumption of our algorithms using a prototype software implementation, an emulation of a power-controllable radio, and a detailed channel model. Our results show that the performance of multihop wireless networks in practice can be substantially increased with topology control.
The olfactory neuron AWC promotes avoidance of normally palatable food following chronic dietary restriction

Changes in metabolic state alter foraging behavior and food preference in animals. Here, I show that normally attractive food becomes repulsive to Caenorhabditis elegans if animals are chronically undernourished as a result of alimentary tract defects. This behavioral plasticity is achieved in two ways: increased food leaving and induction of aversive behavior towards food. A particularly strong food avoider is defective in the chitin synthase that makes the pharyngeal lining. Food avoidance induced by underfeeding is mediated by cGMP signaling in the olfactory neurons AWC and AWB, and the gustatory neurons ASJ and ASK. Food avoidance is enhanced by increased population density and is reduced if the animals are unable to correctly interpret their nutritional state as a result of defects in the AMP kinase or TOR/S6kinase pathways. The TGF-β/DBL-1 pathway suppresses food avoidance and the cellular basis for this is distinct from its role in aversive olfactory learning of harmful food. This study suggests that nutritional state feedback via nutrient sensors, population size and olfactory neurons guides food preference in C. elegans.
Humoral regulation of cell-mediated immunity to syngeneic tumor.

Inoculation i.p. of C57BL/6 mice with FBL-3 cells, a syngeneic Friend virus-induced leukemia, results in progressive growth of ascitic tumors; in contrast, s.c. inoculation of FBL-3 cells produces transient, localized tumor growth; the recipients are then subsequently resistant to further i.p. challenge of this tumor. Experiments were performed to study the effects of humoral factors that might be present in the ascitic fluid and that could affect the growth of the tumors and the host immune response. It was found that ascitic fluids obtained from various murine tumors could indeed promote the s.c. growth of FBL-3 cells. Furthermore, administration of these ascitic fluids was found to suppress the induction of both the primary and secondary cell-mediated cytotoxic responses to FBL-3 cells in vivo and in vitro and to inhibit the effector phase of these cell-mediated cytotoxic reactions in vitro. These studies indicate that the ascitic fluids obtained from tumor-bearing hosts contain humoral factors that can promote tumor growth and suppress immune responses.
Blockade of T-cell activation by dithiocarbamates involves novel mechanisms of inhibition of nuclear factor of activated T cells

Dithiocarbamates (DTCs) have recently been reported as powerful inhibitors of NF-kappaB activation in a number of cell types. Given the role of this transcription factor in the regulation of gene expression in the inflammatory response, NF-kappaB inhibitors have been suggested as potential therapeutic drugs for inflammatory diseases. We show here that DTCs inhibited both interleukin 2 (IL-2) synthesis and membrane expression of antigens which are induced during T-cell activation. This inhibition, which occurred with a parallel activation of c-Jun transactivating functions and expression, was reflected by transfection experiments at the IL-2 promoter level, and involved not only the inhibition of NF-kappaB-driven reporter activation but also that of nuclear factor of activated T cells (NFAT). Accordingly, electrophoretic mobility shift assays (EMSAs) indicated that pyrrolidine DTC (PDTC) prevented NF-kappaB, and NFAT DNA-binding activity in T cells stimulated with either phorbol myristate acetate plus ionophore or antibodies against the CD3-T-cell receptor complex and simultaneously activated the binding of AP-1. Furthermore, PDTC differentially targeted both NFATp and NFATc family members, inhibiting the transactivation functions of NFATp and mRNA induction of NFATc. Strikingly, Western blotting and immunocytochemical experiments indicated that PDTC promoted a transient and rapid shuttling of NFATp and NFATc, leading to their accelerated export from the nucleus of activated T cells. We propose that the activation of an NFAT kinase by PDTC could be responsible for the rapid shuttling of the NFAT, therefore transiently converting the sustained transactivation of this transcription factor that occurs during lymphocyte activation, and show that c-Jun NH2-terminal kinase (JNK) can act by directly phosphorylating NFATp. In addition, the combined inhibitory effects on NFAT and NF-KB support a potential use of DTCs as immunosuppressants.
Improving Detection of Prediabetes in Children and Adults: Using Combinations of Blood Glucose Tests

Highlights The combined use of fasting plasma glucose and hemoglobin A1c test is associated with significantly higher diagnostic rates of prediabetes across age, race/ethnicity, and BMI than using only one test. Combined use of fasting plasma glucose, hemoglobin A1c, and oral glucose tolerance test do not improve the overall and gender-specific prediabetes prevalence beyond what is observed using a combination fasting plasma glucose and hemoglobin A1c test. A redefined hemoglobin A1c test that incorporates racial/ethnic, gender, age, and BMI differences may provide a better way to use hemoglobin A1c test in population-based and clinical settings. Aim To determine combinations of blood glucose tests: oral glucose tolerance (OGT), fasting plasma glucose (FPG), and hemoglobin A1C (HbA1C) that are associated with highest diagnostic rates of prediabetes in non-diabetic American children and adults. Methods The 2007–2008 U.S. National Health and Nutrition Examination Surveys data were used for this study. Overall and specific prevalence of prediabetes (defined using OGT + FPG, OGT + HbA1C, HbA1C + FPG, and OGT + FPG + HbA1C tests) were determined across age, race/ethnicity, sex, and BMI categories. Results FPG + HbA1C test was associated with significantly higher diagnostic rates of prediabetes across age, race/ethnicity, and BMI. Estimates of overall prevalence of prediabetes using OGT + FPG, OGT + HbA1C, HbA1C + FPG, and OGT + FPG + HbA1C tests were 20.3, 24.2, 33, and 34.3%, respectively. Compared to OGT + FPG, the use of HbA1C + FPG test in screening was associated with 44.8, 135, 38.6, and 35.9% increased prevalence of prediabetes in non-Hispanic White, non-Hispanic Black, Mexican-American, and other racial/ethnic men, respectively. The corresponding values in women were 67.8, 140, 37.2, and 42.6%, respectively. Combined use of all blood glucose tests did not improve the overall and gender-specific prediabetes prevalence beyond what was observed using HbA1C + FPG test. Conclusion HbA1C criteria were associated with higher diagnosis rates of prediabetes than FPG and OGT tests in non-diabetic American children and adults. Using a combination of HbA1C and FPG test in screening for prediabetes reduces intrinsic systematic bias in using just HbA1C testing and offers the benefits of each test. A well-defined HbA1C that takes into consideration race/ethnicity, gender, age, and body mass index may improve detection of prediabetes in population and clinical settings.
Efficient group key management for secure big data in predictable large‐scale networks

It is challenging to secure group communications among large‐scale networks due to their network scale. We observe that in many large‐scale networks, the scale of actual group communication is nevertheless predicable and not very large. For instance, although the entire social network (e.g., Facebook) may have billions of users, the members in a concrete group are usually about tens to hundreds. We manage to secure group communication in such scenarios with efficient group management protocols. Technically, we achieve this goal by using a novel dual‐ring approach in which two rings of nodes are established, one active and one dummy. When some nodes leave, the remaining nodes can replace these nodes with dummy nodes, minimizing the required communications and computations after the protocol is set up and thus providing significant advantage over existing group key management protocols. Formal security arguments show that our protocols are secure under standard computational assumptions. Thorough analysis confirms that our protocols are efficient in computation and communication. Copyright © 2015 John Wiley & Sons, Ltd.
Origin and status of the Great Lakes wolf

An extensive debate concerning the origin and taxonomic status of wolf‐like canids in the North American Great Lakes region and the consequences for conservation politics regarding these enigmatic predators is ongoing. Using maternally, paternally and biparentally inherited molecular markers, we demonstrate that the Great Lakes wolves are a unique population or ecotype of gray wolves. Furthermore, we show that the Great Lakes wolves experienced high degrees of ancient and recent introgression of coyote and western gray wolf mtDNA and Y‐chromosome haplotypes, and that the recent demographic bottleneck caused by persecution and habitat depletion in the early 1900s is not reflected in the genetic data.
HER 2-Directed Therapy for Metastatic Breast Cancer

The human epidermal growth factor receptor 2 (HER2) is a transmembrane tyrosine kinase that is overexpressed in approximately 20% of invasive breast cancers, primarily due to gene amplification. [1] HER2 overexpression is clearly associated with more aggressive disease and worse clinical outcomes. [2] Importantly, HER2 overexpression strongly predicts response to HER2-targeted therapies, highlighting the importance of accurately defining the level of HER2 expression in both primary and metastatic tumors. Multiple studies have shown discordance in HER2 expression levels in up to 25% of paired primary and metastatic breast cancers,[3-5] and a substantial proportion of women with HER2-negative primary tumors acquire HER2 protein overexpression in their tumors at the time of relapse. [6-8] In patients with metastatic breast cancer (MBC), accurate determination of HER2 status is thus critical for guiding treatment decisions. The National Comprehensive Cancer Network (NCCN) guidelines recommend HER2 testing at relapse, particularly if HER2 expression was originally unknown or negative. [9]
Virulence Factors of Escherichia coli from Cellulitis or Colisepticemia Lesions in Chickens

SUMMARY. This study was designed to compare virulence factors of cellulitis-derived Escherichia coli to colisepticemic E. coli in order to clarify whether E. coli associated with cellulitis comprise a unique subset of pathogenic E. coli. Isolates were tested for serotype, capsule, aerobactin production, colicin production, the presence of the iss gene, and serum resistance. Untypable isolates made up the greatest percentage of each group. Serotypes O2 and O78 were the most commonly identified among both groups of isolates. No statistical differences in the distribution of aerobactin or colicin production, capsule, or iss gene were observed between groups. Cluster analysis showed that 90% of the E. coli isolates had greater than 42% livability in serum-resistance tests. No separation of colisepticemic vs. cellulitis E. coli isolates was observed on the basis of SR. Colicin production by E. coli was highly correlated with serum resistance (P = 0.0029). These data suggest that cellulitis E. coli have virulence traits similar to those of colisepticemic E. coli.
Network modules and hubs in plant-root fungal biomes

Terrestrial plants host phylogenetically and functionally diverse groups of below-ground microbes, whose community structure controls plant growth/survival in both natural and agricultural ecosystems. Therefore, understanding the processes by which whole root-associated microbiomes are organized is one of the major challenges in ecology and plant science. We here report that diverse root-associated fungi can form highly compartmentalized networks of coexistence within host roots and that the structure of the fungal symbiont communities can be partitioned into semi-discrete types even within a single host plant population. Illumina sequencing of root-associated fungi in a monodominant south beech forest revealed that the network representing symbiont–symbiont co-occurrence patterns was compartmentalized into clear modules, which consisted of diverse functional groups of mycorrhizal and endophytic fungi. Consequently, terminal roots of the plant were colonized by either of the two largest fungal species sets (represented by Oidiodendron or Cenococcum). Thus, species-rich root microbiomes can have alternative community structures, as recently shown in the relationships between human gut microbiome type (i.e. ‘enterotype’) and host individual health. This study also shows an analytical framework for pinpointing network hubs in symbiont–symbiont networks, leading to the working hypothesis that a small number of microbial species organize the overall root–microbiome dynamics.