Miracle-dz/UniFAR-FTUs huggingface dataset:
Systematic Review of Success Factors for Scaling Agile Methods in Global Software Development Environment: A Client-Vendor Perspective

Presently, global software development(GSD) is gaining a much attention from the softwaredevelopment organizations. In GSD, the agile developmentbecomes more challenging due to the geographically,socio-cultural and temporal boundaries.Several frameworks have been developed to managethe agile development programs in large scale softwaredevelopment organizations e.g. scaled agile framework(SAFe), large-scale scrum (LeSS) and disciplined agiledelivery (DAD). However, these frameworks arelacking to provide the detail information about theagile development programs in GSD environment. Inthis study, the mentioned research gap has been triedto fill by conducting a systematic literature review(SLR) study to identify the key factors that couldpositively impact the agile development activities inGSD environment. Using SLR approach, a total of 15success factors were identified that could positivelyaffect the agile development in GSD environment.The identified success factors were further categorizedinto two broad categories of client and vendor GSDorganizations. Client-vendor classification was used toprovide a broad picture of agile programs, and theirrespective success factors. Moreover, the identifiedfactors were also mapped into six different categoriesbased on a model of process improvement.
Comparative phylogeography of Aedes mosquitoes and the role of past climatic change for evolution within Africa

Abstract The study of demographic processes involved in species diversification and evolution ultimately provides explanations for the complex distribution of biodiversity on earth, indicates regions important for the maintenance and generation of biodiversity, and identifies biological units important for conservation or medical consequence. African and forest biota have both received relatively little attention with regard to understanding their diversification, although one possible mechanism is that this has been driven by historical climate change. To investigate this, we implemented a standard population genetics approach along with Approximate Bayesian Computation, using sequence data from two exon‐primed intron‐crossing (EPIC) nuclear loci and mitochondrial cytochrome oxidase subunit I, to investigate the evolutionary history of five medically important and inherently forest dependent mosquito species of the genus Aedes. By testing different demographic hypotheses, we show that Aedes bromeliae and Aedes lilii fit the same model of lineage diversification, admixture, expansion, and recent population structure previously inferred for Aedes aegypti. In addition, analyses of population structure show that Aedes africanus has undergone lineage diversification and expansion while Aedes hansfordi has been impacted by population expansion within Uganda. This congruence in evolutionary history is likely to relate to historical climate‐driven habitat change within Africa during the late Pleistocene and Holocene epoch. We find differences in the population structure of mosquitoes from Tanzania and Uganda compared to Benin and Uganda which could relate to differences in the historical connectivity of forests across the continent. Our findings emphasize the importance of recent climate change in the evolution of African forest biota.
Detection of a Cis eQTL Controlling BMCO1 Gene Expression Leads to the Identification of a QTG for Chicken Breast Meat Color

Classical quantitative trait loci (QTL) analysis and gene expression QTL (eQTL) were combined to identify the causal gene (or QTG) underlying a highly significant QTL controlling the variation of breast meat color in a F2 cross between divergent high-growth (HG) and low-growth (LG) chicken lines. Within this meat quality QTL, BCMO1 (Accession number GenBank: AJ271386), encoding the β-carotene 15, 15′-monooxygenase, a key enzyme in the conversion of β-carotene into colorless retinal, was a good functional candidate. Analysis of the abundance of BCMO1 mRNA in breast muscle of the HG x LG F2 population allowed for the identification of a strong cis eQTL. Moreover, reevaluation of the color QTL taking BCMO1 mRNA levels as a covariate indicated that BCMO1 mRNA levels entirely explained the variations in meat color. Two fully-linked single nucleotide polymorphisms (SNP) located within the proximal promoter of BCMO1 gene were identified. Haplotype substitution resulted in a marked difference in BCMO1 promoter activity in vitro. The association study in the F2 population revealed a three-fold difference in BCMO1 expression leading to a difference of 1 standard deviation in yellow color between the homozygous birds at this haplotype. This difference in meat yellow color was fully consistent with the difference in carotenoid content (i.e. lutein and zeaxanthin) evidenced between the two alternative haplotypes. A significant association between the haplotype, the level of BCMO1 expression and the yellow color of the meat was also recovered in an unrelated commercial broiler population. The mutation could be of economic importance for poultry production by making possible a gene-assisted selection for color, a determining aspect of meat quality. Moreover, this natural genetic diversity constitutes a new model for the study of β-carotene metabolism which may act upon diverse biological processes as precursor of the vitamin A.
Determining Text Databases to Search in the Internet

Text data in the Internet can be partitioned into many databases naturally. Efficient retrieval of desired data can be achieved if we can accurately predict the usefulness of each database, because with such information, we only need to retrieve potentially useful documents from useful databases. In this paper, we propose two new methods for estimating the usefulness of text databases. For a given query, the usefulness of a text database in this paper is defined to be the number of documents in the database that are sufficiently similar to the query. Such a usefulness measure enables naive-users to make informed decision about which databases to search. We also consider the collection fusion problem. Because local databases may employ similarity functions that are different from that used by the global database, the threshold used by a local database to determine whether a document is potentially useful may be different from that used by the global database. We provide techniques that determine the best threshold for a given local database.
A Comparative Study of Health Status and Quality of Life of Elderly People Living in Old Age Homes and within Family Setup in Raigad District, Maharashtra

Background: The traditional concept of family in India to provide support to the elderly is changing soon with disintegration of joint families. In this scenario the concept of old age homes (OAHs) is gaining momentum and the number of people seeking OAH care is rapidly increasing. However, not much is known about the quality of life (QOL) of Indian elderly staying in the OAH setup. Objectives: To assess and compare the Health status, Quality of Life and Depression in elderly people living in OAHs & within family using WHOQOL –OLD questionnaire & Geriatric Depression Scale Methods: A cross sectional study was conducted in elderly aged above 60 years of age. After taking a written consent and matching for age and sex & socioeconomic status, 60 elderly from OAHs & 120 elderly living within family setup were selected randomly. The WHOQOL-OLD standard questionnaire & GDS were used to assess quality of life & depression in elderly. Result: The QOL of elderly in domains of autonomy, past present & future activities, social participation and intimacy was better in family setup (60.62, 70.62, 66.14 and 58.43) as compared to OAHs (51.35, 62.91, 59.47and 41.16) (p<0.05). There was statistically significant difference in mean geriatric depression scores of both the group (3.96 within family setup and 5.76 in OAH's). Conclusion: Quality of life of elderly within family setup was better as compared to elderly in OAHs.
The Tolerability and Efficacy of Oral Isotonic Solution versus Plain Water in Dengue Patients: A Randomized Clinical Trial

Background: Plasma leakage plays an important role in dengue infection, and this condition can lead to hemoconcentration, hypovolemia, and shock. Fluid replacement is the main treatment for dengue. There is a lack of evidence to support certain oral fluid therapy as a treatment for dengue patients. Objectives: The objective of this study is to evaluate tolerability and efficacy of oral isotonic solution (OIS) compared to plain water as a fluid replacement in dengue patients. Materials and Methods: A randomized, clinical trial with single-blinded groups was conducted to compare tolerability and efficacy of OIS and plain water in dengue patients. We evaluated gastrointestinal disturbances (nausea, vomiting, and bloating), body temperature, mean arterial pressure (MAP), fluid balance, hematocrit, Na+, and K+ levels. Data were analyzed with SPSS 20.0, and figures were made with GraphPad Prism version 5.01. Results: Twenty four subjects were included and divided equally into two groups. Our results showed that there are no significant differences but indicate several noteworthy trends. The intervention group (OIS) experienced less nausea, less vomiting, had positive fluid balance and higher MAP, and became afebrile faster compared to the control group (plain water). Conclusion: Although not statistically significant, this study shows the trend that OIS is well-tolerated and effective for dengue patients compared to plain water.
Interferon-&ggr; Treatment of Human Laryngotracheal Stenosis–Derived Fibroblasts

Importance Laryngotracheal stenosis (LTS) is a fibroproliferative disorder of the glottis, subglottis, and trachea. In models of fibrosis from other organ systems, the CD4+ T-cell response has been shown to regulate extracellular matrix deposition. Specifically, helper T cell 2 (TH2) promotes fibrosis, whereas TH1 and associated cytokines have been shown to be antifibrotic. However, this antifibrotic effect of the TH1 response has not been demonstrated in LTS. Objective To determine whether the TH1 cytokine interferon-&ggr; inhibits the function of LTS-derived fibroblasts in vitro. Design, Setting, and Participants This in vitro controlled study included 6 patients with iatrogenic LTS undergoing routine surgical subglottic and tracheal dilation at a single institution. Fibroblasts were isolated from biopsy specimens of laryngotracheal scar and normal-appearing trachea. The presence of fibroblasts was confirmed by an immunohistochemical analysis. Laryngotracheal stenosis–derived fibroblasts were treated with interferon-&ggr; and compared with untreated controls (2 sets of untreated, LTS-derived fibroblasts [media did not contain interferon-&ggr;]) and normal airway fibroblasts (fibroblasts isolated from normal trachea). Data were collected from August 2015 through June 2016. Interventions Treatment with interferon-&ggr;, 10 ng/mL. Main Outcomes and Measures Cellular proliferation, fibrosis gene expression (using quantitative reverse transcription polymerase chain reaction analysis), soluble collagen, and cellular histologic features were assessed. Results Among the 6 patients (6 women; mean [SD] age, 38.3 [17.2] years), LTS-derived fibroblast proliferation was reduced in patients who received interferon-&ggr; treatment compared with untreated controls on days 3 (mean difference, −6515 cells; 95% CI, −10 630 to −2600 cells) to 6 (mean difference, −47 521 cells; 95% CI, −81 285 to −13 757 cells). Interferon-&ggr; treatment reduced collagen types I and III gene expression by 86% and 68%, respectively, and resulted in lower total collagen production (10.94 vs 14.89 &mgr;g/mL). In addition, interferon-&ggr; treatment resulted in a 32% reduction in expression of transforming growth factor &bgr; in LTS-derived fibroblasts. Conclusions and Relevance Interferon-&ggr; reduced proliferation, soluble collagen production, and collagen expression in LTS-derived fibroblasts while also reducing the expression of the profibrotic cytokine transforming growth factor &bgr;. These findings suggest that therapeutics aimed at increasing interferon-&ggr; and the TH1 response could attenuate LTS.
Cyclic Di-GMP Signaling Contributes to Pseudomonas aeruginosa-Mediated Catheter-Associated Urinary Tract Infection

ABSTRACT Bis-(3′-5′) cyclic dimeric GMP (c-di-GMP) controls the lifestyle transition between the sessile and motile states in many Gram-negative bacteria, including the opportunistic human pathogen Pseudomonas aeruginosa. Under laboratory conditions, high concentrations of c-di-GMP decrease motility and promote biofilm formation, while low concentrations of c-di-GMP promote motility and decease biofilm formation. Here we sought to determine the contribution of c-di-GMP signaling to biofilm formation during P. aeruginosa-mediated catheter-associated urinary tract infection (CAUTI). Using a murine CAUTI model, a decrease in CFU was detected in the bladders and kidneys of mice infected with strains overexpressing the phosphodiesterases (PDEs) encoded by PA3947 and PA2133 compared to those infected with wild-type P. aeruginosa. Conversely, overexpression of the diguanylate cyclases (DGCs) encoded by PA3702 and PA1107 increased the number of bacteria in bladder and significantly increased dissemination of bacteria to the kidneys compared to wild-type infection. To determine which of the DGCs and PDEs contribute to c-di-GMP signaling during infection, a panel of PA14 in-frame deletion mutants lacking DGCs and PDEs were tested in the CAUTI model. Results from these infections revealed five mutants, three containing GGDEF domains (ΔPA14_26970, ΔPA14_72420, and ΔsiaD) and two containing dual GGDEF-EAL domains (ΔmorA and ΔPA14_07500), with decreased colonization of the bladder and dissemination to the kidneys. These results indicate that c-di-GMP signaling influences P. aeruginosa-mediated biofilms during CAUTI. IMPORTANCE Biofilm-based infections are an important cause of nosocomial infections, since they resist the immune response and traditional antibiotic treatment. Cyclic di-GMP (c-di-GMP) is a second messenger that promotes biofilm formation in many Gram-negative pathogens, including Pseudomonas aeruginosa. Here we determined the contribution of c-di-GMP signaling to catheter-associated urinary tract infection (CAUTI), an animal model of biofilm-based infection. P. aeruginosa with elevated levels of c-di-GMP during the initial infection produces an increased bacterial burden in the bladder and kidneys. Conversely, low concentrations of c-di-GMP decreased the bacterial burden in the bladder and kidneys. We screened a library of mutants with mutations in genes regulating c-di-GMP signaling and found several mutants that altered colonization of the urinary tract. This study implicates c-di-GMP signaling during CAUTI.
SSOScan: Automated Testing of Web Applications for Single Sign-On Vulnerabilities

Correctly integrating third-party services into web applications is challenging, and mistakes can have grave consequences when third-party services are used for security-critical tasks such as authentication and authorization. Developers often misunderstand integration requirements and make critical mistakes when integrating services such as single sign-on APIs. Since traditional programming techniques are hard to apply to programs running inside black-box web servers, we propose to detect vulnerabilities by probing behaviors of the system. This paper describes the design and implementation of SSOScan, an automatic vulnerability checker for applications using Facebook Single Sign-On (SSO) APIs. We used SSOScan to study the twenty thousand top-ranked websites for five SSO vulnerabilities. Of the 1660 sites in our study that employ Facebook SSO, over 20% were found to suffer from at least one serious vulnerability.
The complete mitochondrial genome sequence of Zebrias crossolepis (pleuronectiformes: soleidae) and Acrossocheilus monticola (cypriniformes: cyprinidae) and phylogenetic studies

Abstract In this study, two complete mitogenome sequences of Zebrias crossolepis and Acrossocheilus monticola were determined and the phylogenetic relationship were constructed based on concatenated nucleotide sequences of 12 mitochondrial protein-coding genes. The length of the complete mitogenome sequence are 16 775 bp and 16 605 bp in Z. crossolepis and A. monticola, respectively, both containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes, a putative control region (CR), and a light-strand replication origin (OL). The overall base composition is 28.3% A, 26.3% T, 30.0% C, 15.5% G, with a slight AT bias (54.6%) in Z. crossolepis, while 31.4% A, 24.5% T, 28.2% C, 15.9% G, with an slight AT bias (55.9%) in A. monticola. All the protein-coding genes use the initiation codon ATG except COI uses GTG. Most of them have TAA or TAG as the stop codon, while ND4 and Cytb in Z. crossolepis and COII, ND4, and Cytb in A. monticola use an incomplete stop codon T. These results are expected to provide useful molecular data for species identification and further phylogenetic studies.
New Elements To Consider When Modeling the Hazards Associated with Botulinum Neurotoxin in Food

ABSTRACT Botulinum neurotoxins (BoNTs) produced by the anaerobic bacterium Clostridium botulinum are the most potent biological substances known to mankind. BoNTs are the agents responsible for botulism, a rare condition affecting the neuromuscular junction and causing a spectrum of diseases ranging from mild cranial nerve palsies to acute respiratory failure and death. BoNTs are a potential biowarfare threat and a public health hazard, since outbreaks of foodborne botulism are caused by the ingestion of preformed BoNTs in food. Currently, mathematical models relating to the hazards associated with C. botulinum, which are largely empirical, make major contributions to botulinum risk assessment. Evaluated using statistical techniques, these models simulate the response of the bacterium to environmental conditions. Though empirical models have been successfully incorporated into risk assessments to support food safety decision making, this process includes significant uncertainties so that relevant decision making is frequently conservative and inflexible. Progression involves encoding into the models cellular processes at a molecular level, especially the details of the genetic and molecular machinery. This addition drives the connection between biological mechanisms and botulism risk assessment and hazard management strategies. This review brings together elements currently described in the literature that will be useful in building quantitative models of C. botulinum neurotoxin production. Subsequently, it outlines how the established form of modeling could be extended to include these new elements. Ultimately, this can offer further contributions to risk assessments to support food safety decision making.
Human Neutral Genetic Variation and Forensic STR Data

The forensic genetics field is generating extensive population data on polymorphism of short tandem repeats (STR) markers in globally distributed samples. In this study we explored and quantified the informative power of these datasets to address issues related to human evolution and diversity, by using two online resources: an allele frequency dataset representing 141 populations summing up to almost 26 thousand individuals; a genotype dataset consisting of 42 populations and more than 11 thousand individuals. We show that the genetic relationships between populations based on forensic STRs are best explained by geography, as observed when analysing other worldwide datasets generated specifically to study human diversity. However, the global level of genetic differentiation between populations (as measured by a fixation index) is about half the value estimated with those other datasets, which contain a much higher number of markers but much less individuals. We suggest that the main factor explaining this difference is an ascertainment bias in forensics data resulting from the choice of markers for individual identification. We show that this choice results in average low variance of heterozygosity across world regions, and hence in low differentiation among populations. Thus, the forensic genetic markers currently produced for the purpose of individual assignment and identification allow the detection of the patterns of neutral genetic structure that characterize the human population but they do underestimate the levels of this genetic structure compared to the datasets of STRs (or other kinds of markers) generated specifically to study the diversity of human populations.
Design and development of gripping assistive device for post — Stroke rehabilitation

Report from The National Stroke Association of Malaysia (NASAM), the disease that cause most deaths is stroke which comes after cancer and heart attack. Even though most of the stroke cases is avoidable, rehabilitation will be in high demand. Devices as such has not been created and looking into since the therapist could not fulfil the demand. This project addresses a device to help post — stroke patients to grip and release their fingers as a rehabilitation working process. The system uses leap motion sensor as the input and the output is a servomotor-based exoskeleton. At the moment the system is based on a master-slave mechanism which needs a healthy hand to control the weak hand. The exoskeleton is still being tested on using linear-like actuator mechanisms to perform grasping and extension.
Virtual High-Throughput Screening Identifies Mycophenolic Acid as a Novel RNA Capping Inhibitor

The RNA guanylyltransferase (GTase) is involved in the synthesis of the m7Gppp-RNA cap structure found at the 5′ end of eukaryotic mRNAs. GTases are members of the covalent nucleotidyl transferase superfamily, which also includes DNA and RNA ligases. GTases catalyze a two-step reaction in which they initially utilize GTP as a substrate to form a covalent enzyme-GMP intermediate. The GMP moiety is then transferred to the diphosphate end of the RNA transcript in the second step of the reaction to form the Gppp-RNA structure. In the current study, we used a combination of virtual database screening, homology modeling, and biochemical assays to search for novel GTase inhibitors. Using this approach, we demonstrate that mycophenolic acid (MPA) can inhibit the GTase reaction by preventing the catalytic transfer of the GMP moiety onto an acceptor RNA. As such, MPA represents a novel type of inhibitor against RNA guanylyltransferases that inhibits the second step of the catalytic reaction. Moreover, we show that the addition of MPA to S. cerevisiae cells leads to a reduction of capped mRNAs. Finally, biochemical assays also demonstrate that MPA can inhibit DNA ligases through inhibition of the second step of the reaction. The biological implications of these findings for the MPA-mediated inhibition of members of the covalent nucleotidyl superfamily are discussed.
The complete mitochondrial genome of the phytopathogenic fungus Phomopsis longicolla

Abstract The complete mitochondrial genome of the ascomycete fungus Phomopsis longicolla was sequenced using Illumina HiSeq platform. It consists of 53,439 bp with high (65.6%) A + T content and includes 14 conserved protein subunits of the mitochondrial oxidative phosphorylation system, two ribosomal RNAs and 25 tRNA genes. To our knowledge, this is the first complete mitochondrial genome of the Diaporthales member.