Miracle-dz/UniFAR-FTUs huggingface dataset:
Use of the breeding technique to estimate the structure of the analysis “ errors of the day ”

A 3D-variational data assimilation scheme for a quasi-geostrophic channel model (Morss, 1998) is used to study the structure of the background error and its relationship to the corresponding bred vectors. The “true” evolution of the model atmosphere is defined by an integration of the model and “rawinsonde observations” are simulated by randomly perturbing the true state at fixed locations. Case studies using different observational densities are considered to compare the evolution of the Bred Vectors to the spatial structure of the background error. In addition, the bred vector dimension (BV-dimension), defined by Patil et al. (2001) is applied to the bred vectors. It is found that after 3–5 days the bred vectors develop well organized structures which are very similar for the two different norms (enstrophy and streamfunction) considered in this paper. When 10 surrogate bred vectors (corresponding to different days from that of the background error) are used to describe the local patterns of the background error, the explained variance is quite high, about 85–88%, indicating that the statistical average properties of the bred vectors represent well those of the background error. However, a subspace of 10 bred vectors corresponding to the time of the background error increased the percentage of explained variance to 96– 98%, with the largest percentage when the background errors are large. These results suggest that a statistical basis of bred vectors collected over time can be used to create an effective constant background error covariance for data assimilation with 3DVar. Including the “errors of the day” through the use of bred vectors corresponding to the background forecast time can bring an additional significant improvement.
The Caenorhabditis elegans Homolog of Gen1/Yen1 Resolvases Links DNA Damage Signaling to DNA Double-Strand Break Repair

DNA double-strand breaks (DSBs) can be repaired by homologous recombination (HR), which can involve Holliday junction (HJ) intermediates that are ultimately resolved by nucleolytic enzymes. An N-terminal fragment of human GEN1 has recently been shown to act as a Holliday junction resolvase, but little is known about the role of GEN-1 in vivo. Holliday junction resolution signifies the completion of DNA repair, a step that may be coupled to signaling proteins that regulate cell cycle progression in response to DNA damage. Using forward genetic approaches, we identified a Caenorhabditis elegans dual function DNA double-strand break repair and DNA damage signaling protein orthologous to the human GEN1 Holliday junction resolving enzyme. GEN-1 has biochemical activities related to the human enzyme and facilitates repair of DNA double-strand breaks, but is not essential for DNA double-strand break repair during meiotic recombination. Mutational analysis reveals that the DNA damage-signaling function of GEN-1 is separable from its role in DNA repair. GEN-1 promotes germ cell cycle arrest and apoptosis via a pathway that acts in parallel to the canonical DNA damage response pathway mediated by RPA loading, CHK1 activation, and CEP-1/p53–mediated apoptosis induction. Furthermore, GEN-1 acts redundantly with the 9-1-1 complex to ensure genome stability. Our study suggests that GEN-1 might act as a dual function Holliday junction resolvase that may coordinate DNA damage signaling with a late step in DNA double-strand break repair.
Synthesis of High Valence Silver-Loaded Mesoporous Silica with Strong Antibacterial Properties

A simple chemical method was developed for preparing high valence silver (Ag)-loaded mesoporous silica (Ag-ethylenediaminetetraacetic acid (EDTA)-SBA-15), which showed strong antibacterial activity. Ag-EDTA-SBA-15 exhibited stronger and more effective antibacterial activity than commercial Ag nanoparticles did, and it offered high stability of high valence silver in the porous matrix and long-lasting antibacterial activity. The synthesized materials were characterized using Fourier transform infrared spectroscopy, powder X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS) analysis, and transmission electron microscopy (TEM). Ag existed in both surface complexation and Ag particles. EDTA anchored within a porous structure chelated Ag ions in higher oxidation states and prevented their agglomeration and oxidation reduction. The XRD results showed that most Ag in the Ag-EDTA-SBA-15 existed in higher oxidation states such as Ag(II) and Ag(III). However, the XPS and TEM results showed that Ag easily reduced in lower oxidation states and agglomerated as Ag particles on the exterior layer of the SBA-15.
Lightweight extraction of object models from bytecode

A program's object model captures the essence of its design. For some programs, no object model was developed during design; for others, an object model exists but may be out of sync with the code. The paper describes a tool that automatically extracts an object model from the class files of a Java program. Although the tool performs only a simple, heuristic analysis that is almost entirely local, the resulting object model is surprisingly accurate. The paper explains the form of the object model, the assumptions upon which the analysis is based, and its limitations, and evaluates the tool on a suite of sample programs.
Infliximab in inflammatory bowel disease: clinical outcome in a population based cohort from Stockholm County

Background: Several placebo controlled studies have demonstrated the efficacy of infliximab in inflammatory bowel disease (IBD) but the potential toxicity of this new biological compound has been less studied. Aim: To assess the use of infliximab in IBD in a population based cohort, with special emphasis on the occurrence of severe adverse events and mortality. Patients: All patients with IBD treated with infliximab between 1999 and 2001 in Stockholm County were evaluated. Methods: Prospective registration of clinical data was carried out. Retrospective analyses were made of possible adverse events occurring in relation to infliximab treatment. Adverse events requiring pharmacological treatment or hospitalisation were defined as severe. Clinical response was assessed as remission, response, or failure. Results: A cohort comprising 217 patients was assembled: 191 patients had Crohn’s disease (CD), and infliximab was used off label for ulcerative colitis (UC) in 22 patients. Four patients were treated for indeterminate colitis (IC). Mean age was 37.6 (0.9) years (range 8–79). The mean number of infliximab infusions was 2.6 (0.1) (range 1–11). Forty two severe adverse events were registered in 41 patients (CD, n = 35). Eleven of the severe adverse events occurred postoperatively (CD, n = 6). Three patients with CD developed lymphoma (of which two were fatal), opportunistic infections occurred in two patients (one with UC, fatal), and two patients with severe attacks of IBD died due to sepsis (one with CD, one postoperatively with UC). One additional patient with UC died from pulmonary embolism after colectomy. Mean age in the group with fatal outcome was 62.7 years (range 25–79). The overall response rate was 75% and did not differ between the patient groups. Conclusions: Infliximab was efficacious as an anti-inflammatory treatment when assessed in a population based cohort of patients with IBD. However, there appear to be a significant risk of deleterious and fatal adverse events, particularly in elderly patients with severe attacks of IBD. Off label use of infliximab in UC and IC should be avoided until efficacy is proven in randomised controlled trials. The underlying risk of developing malignancies among patients with severe or chronically active CD in need of infliximab treatment is not known but the finding of a 1.5% annual incidence of lymphoma emphasises the need for vigilant surveillance with respect to this malignant complication.
Archival Data in Micro-Organizational Research: A Toolkit for Moving to a Broader Set of Topics

Compared to macro-organizational researchers, micro-organizational researchers have generally eschewed archival sources of data as a means of advancing knowledge. The goal of this paper is to discuss emerging opportunities to use archival research for the purposes of advancing and testing theory in micro-organizational research. We discuss eight specific strengths common to archival micro-organizational research and how they differ from other traditional methods. We further discuss limitations of archival research, as well as strategies for mitigating these limitations. Taken together, we provide a toolkit to encourage micro-organizational researchers to capitalize on archival data.
Prevalence of Loss-of-Function FTO Mutations in Lean and Obese Individuals

OBJECTIVE Single nucleotide polymorphisms (SNPs) in intron 1 of fat mass– and obesity-associated gene (FTO) are strongly associated with human adiposity, whereas Fto−/− mice are lean and Fto+/− mice are resistant to diet-induced obesity. We aimed to determine whether FTO mutations are disproportionately represented in lean or obese humans and to use these mutations to understand structure-function relationships within FTO. RESEARCH DESIGN AND METHODS We sequenced all coding exons of FTO in 1,433 severely obese and 1,433 lean individuals. We studied the enzymatic activity of selected nonsynonymous variants. RESULTS We identified 33 heterozygous nonsynonymous variants in lean (2.3%) and 35 in obese (2.4%) individuals, with 8 mutations unique to the obese and 11 unique to the lean. Two novel mutations replace absolutely conserved residues: R322Q in the catalytic domain and R96H in the predicted substrate recognition lid. R322Q was unable to catalyze the conversion of 2-oxoglutarate to succinate in the presence or absence of 3-methylthymidine. R96H retained some basal activity, which was not enhanced by 3-methylthymidine. However, both were found in lean and obese individuals. CONCLUSIONS Heterozygous, loss-of-function mutations in FTO exist but are found in both lean and obese subjects. Although intron 1 SNPs are unequivocally associated with obesity in multiple populations and murine studies strongly suggest that FTO has a role in energy balance, it appears that loss of one functional copy of FTO in humans is compatible with being either lean or obese. Functional analyses of FTO mutations have given novel insights into structure-function relationships in this enzyme.
Supervisory Control of a Database Unit

To effectively enhance service availability, this paper proposes a redundancy configuration for a database unit residing in a command and control (C2) system that supports air operations. The results of modeling, supervisory control, and performance analysis of the database unit are presented. The unit is modeled as a closed Markovian queuing network. State variable feedback is used to implement the functions of restoration and routing upon the identification of the failure of one of the database servers in the unit. Several control policies are evaluated in terms of the resulting mean time to unit failure, the steady state availability, the expected response time, and the service overhead of the database unit.
International Journal of Pure and Applied Sciences and Technology Determination of Heavy Metals in Forage Grasses (carpet Grass (axonopus Ompressus), Guinea Grass (panicum Maximum) and Elephant Grass (pennisetum Purpureum)) in the Vicinity of Itakpe Iron Ore Mine, Nigeria

The role of Livestock in the production of safe food has underlined its impacts on public health and food security. Samples of grasses Carpet Grass (Axonopus lompressus), Guinea Grass (Panicum maximum) and Elephant grass (Pennisetum purpureum) used as fodder grown on the vicinity of iron mine of Itakpe, Nigeria were analyzed for Cd, Cu, Mg, Ni, Pb and Zn. Samples from Ossara 12 kilometers away from Itakpe was used for comparison. All elements were determined by AAS. Mean concentration of total metal content of agricultural soils investigated gave 0. Pb and Zn respectively. Total concentrations of the elements examined were within ranges normally encountered in soils and the observed metallic levels of the grasses were below the FAO/WHO limit guideline values for heavy metal levels in food.
Association of parental psychopathology to the comorbid disorders of boys with attention deficit-hyperactivity disorder.

This study examined whether particular forms of parental psychopathology are related to similar forms of comorbid psychopathology in offspring with attention deficit-hyperactivity disorder (ADHD). Parental disorders were assessed using maternal interviews, and child disorders were assessed using multiple-informant interviews for 111 clinic-referred boys (aged 7-12) with Diagnostic and Statistical Manual of Mental Disorders (3rd ed., rev.; American Psychiatric Association, 1987) ADHD. Associations between parental and child internalizing disorders and between parental and child externalizing disorders were found, but associations across categories of disorder (i.e., internalizing and externalizing) were not. Similar relationships were observed in 66 clinic-referred boys without ADHD. These findings support specific modes of familial transmission, in contrast to theories that comorbidity simply reflects more severe psychopathology in children with ADHD.
HBPR: History Based Prediction for Routing in Infrastructure-less Opportunistic Networks

In Opportunistic Networks (OppNets), the existence of an end-to-end connected path between the sender and the receiver is not possible. Thus routing in this type of networks is different from the traditional Mobile Adhoc Networks (MANETs). MANETs assume the existence of a fixed route between the sender and the receiver before the start of the communication and till its completion. Routes are constructed dynamically as the source node or an intermediate node can choose any node as next hop from a group of neighbors assuming that it will take the message closer to the destination node or deliver to the destination itself. In this paper, we proposed a novel History Based Prediction Routing (HBPR) protocol for infrastructure-less OppNets which utilizes the behavioral information of the nodes to find the best next node for routing. The proposed protocol was compared with the Epidemic routing protocol. Through simulations it was found that the HBPR performs better in terms of number of messages delivered and the overhead ratio than the Epidemic protocol.
Pattern Colored Hamilton Cycles in Random Graphs

We consider the existence of patterned Hamilton cycles in randomly colored random graphs. Given a string $\Pi$ over a set of colors $\{1,2,\ldots,r\}$, we say that a Hamilton cycle is $\Pi$-colored if the pattern repeats at intervals of length $|\Pi|$ as we go around the cycle. We prove a hitting time for the existence of such a cycle. We also prove a hitting time result for a related notion of $\Pi$-connected.
Clinical illness and outcomes in patients with Ebola in Sierra Leone.

BACKGROUND Limited clinical and laboratory data are available on patients with Ebola virus disease (EVD). The Kenema Government Hospital in Sierra Leone, which had an existing infrastructure for research regarding viral hemorrhagic fever, has received and cared for patients with EVD since the beginning of the outbreak in Sierra Leone in May 2014. METHODS We reviewed available epidemiologic, clinical, and laboratory records of patients in whom EVD was diagnosed between May 25 and June 18, 2014. We used quantitative reverse-transcriptase-polymerase-chain-reaction assays to assess the load of Ebola virus (EBOV, Zaire species) in a subgroup of patients. RESULTS Of 106 patients in whom EVD was diagnosed, 87 had a known outcome, and 44 had detailed clinical information available. The incubation period was estimated to be 6 to 12 days, and the case fatality rate was 74%. Common findings at presentation included fever (in 89% of the patients), headache (in 80%), weakness (in 66%), dizziness (in 60%), diarrhea (in 51%), abdominal pain (in 40%), and vomiting (in 34%). Clinical and laboratory factors at presentation that were associated with a fatal outcome included fever, weakness, dizziness, diarrhea, and elevated levels of blood urea nitrogen, aspartate aminotransferase, and creatinine. Exploratory analyses indicated that patients under the age of 21 years had a lower case fatality rate than those over the age of 45 years (57% vs. 94%, P=0.03), and patients presenting with fewer than 100,000 EBOV copies per milliliter had a lower case fatality rate than those with 10 million EBOV copies per milliliter or more (33% vs. 94%, P=0.003). Bleeding occurred in only 1 patient. CONCLUSIONS The incubation period and case fatality rate among patients with EVD in Sierra Leone are similar to those observed elsewhere in the 2014 outbreak and in previous outbreaks. Although bleeding was an infrequent finding, diarrhea and other gastrointestinal manifestations were common. (Funded by the National Institutes of Health and others.).
Psychosocial functioning in adolescents with and without borderline personality disorder.

OBJECTIVE Little is known about the psychosocial functioning of adolescents with borderline personality disorder (BPD). The main objective of this paper is to compare the psychosocial functioning of a group of adolescents with BPD to a group of psychiatrically healthy adolescents. METHODS The present cross-sectional study included 104 adolescent inpatients with BPD, compared with 60 age-matched psychiatrically healthy comparison subjects. All participants were rigorously diagnosed using three semi-structured interviews: the Structured Clinical Interview for DSM-IV Childhood Diagnoses, the Revised Diagnostic Interview for Borderlines and the Childhood Interview for DSM-IV Borderline Personality. All subjects were also interviewed using the adolescent version of the Background Information Schedule to assess multiple facets of psychosocial functioning. RESULTS Adolescents with BPD rated their relationships with their parents as significantly less positive, were more likely to date, but spent more time alone than their healthy counterparts. In addition, adolescents with BPD reported significantly more problems at work and school (i.e. lower frequency of having a good work or school history, higher frequency of being suspended or expelled from school) and significantly lower rates of participation in extra-curricular activities than their healthy counterparts. CONCLUSIONS Taken together, the results of this study suggest that adolescents with BPD are more impaired in both the social and vocational areas of functioning than psychiatrically healthy comparison subjects. They might also suggest that an overlooked area of strength concerns their relationships with peers. Copyright © 2017 John Wiley & Sons, Ltd.
Lactobacillus plantarum TWK10 Supplementation Improves Exercise Performance and Increases Muscle Mass in Mice

Lactobacillus plantarum (L. plantarum) is a well-known probiotic among the ingested-microorganism probiotics (i.e., ingested microorganisms associated with beneficial effects for the host). However, few studies have examined the effects of L. plantarum TWK10 (LP10) supplementation on exercise performance, physical fatigue, and gut microbial profile. Male Institute of Cancer Research (ICR) strain mice were divided into three groups (n = 8 per group) for oral administration of LP10 for six weeks at 0, 2.05 × 108, or 1.03 × 109 colony-forming units/kg/day, designated the vehicle, LP10-1X and LP10-5X groups, respectively. LP10 significantly decreased final body weight and increased relative muscle weight (%). LP10 supplementation dose-dependently increased grip strength (p < 0.0001) and endurance swimming time (p < 0.001) and decreased levels of serum lactate (p < 0.0001), ammonia (p < 0.0001), creatine kinase (p = 0.0118), and glucose (p = 0.0151) after acute exercise challenge. The number of type I fibers (slow muscle) in gastrocnemius muscle significantly increased with LP10 treatment. In addition, serum levels of albumin, blood urea nitrogen, creatinine, and triacylglycerol significantly decreased with LP10 treatment. Long-term supplementation with LP10 may increase muscle mass, enhance energy harvesting, and have health-promotion, performance-improvement, and anti-fatigue effects.
Disability and Risk of Recent Sexual Violence in the United States.

OBJECTIVES To examine the relative prevalence of recent (past 12 months) penetrative and nonpenetrative sexual violence comparing men and women with and without a disability. METHODS Data are from the 2010 National Intimate Partner and Sexual Violence Survey, a national telephone survey of US adults, and includes an expansive measure of sexual violence victimization. A total of 9086 women and 7421 men completed the telephone survey in 2010. RESULTS Compared with persons without a disability, persons with a disability were at increased risk for recent rape for women (adjusted odds ratio = 3.3; 95% confidence interval = 1.6, 6.7), and being made to penetrate a perpetrator for men (adjusted odds ratio = 4.2; 95% confidence interval = 1.6, 10.8). An estimated 39% of women raped in the 12 months preceding the survey had a disability at the time of the rape. For women and men, having a disability was associated with an increased risk of sexual coercion and noncontact unwanted sexual experiences. CONCLUSIONS In this nationally representative sample, men and women with a disability were at increased risk for recent sexual violence, compared to those without a disability.
Altered Proteome of Burkholderia pseudomallei Colony Variants Induced by Exposure to Human Lung Epithelial Cells

Burkholderia pseudomallei primary diagnostic cultures demonstrate colony morphology variation associated with expression of virulence and adaptation proteins. This study aims to examine the ability of B. pseudomallei colony variants (wild type [WT] and small colony variant [SCV]) to survive and replicate intracellularly in A549 cells and to identify the alterations in the protein expression of these variants, post-exposure to the A549 cells. Intracellular survival and cytotoxicity assays were performed followed by proteomics analysis using two-dimensional gel electrophoresis. B. pseudomallei SCV survive longer than the WT. During post-exposure, among 259 and 260 protein spots of SCV and WT, respectively, 19 were differentially expressed. Among SCV post-exposure up-regulated proteins, glyceraldehyde 3-phosphate dehydrogenase, fructose-bisphosphate aldolase (CbbA) and betaine aldehyde dehydrogenase were associated with adhesion and virulence. Among the down-regulated proteins, enolase (Eno) is implicated in adhesion and virulence. Additionally, post-exposure expression profiles of both variants were compared with pre-exposure. In WT pre- vs post-exposure, 36 proteins were differentially expressed. Of the up-regulated proteins, translocator protein, Eno, nucleoside diphosphate kinase (Ndk), ferritin Dps-family DNA binding protein and peptidyl-prolyl cis-trans isomerase B were implicated in invasion and virulence. In SCV pre- vs post-exposure, 27 proteins were differentially expressed. Among the up-regulated proteins, flagellin, Eno, CbbA, Ndk and phenylacetate-coenzyme A ligase have similarly been implicated in adhesion, invasion. Protein profiles differences post-exposure provide insights into association between morphotypic and phenotypic characteristics of colony variants, strengthening the role of B. pseudomallei morphotypes in pathogenesis of melioidosis.