Miracle-dz/UniFAR-FTUs huggingface dataset:
Cross-species multiple environmental stress responses: An integrated approach to identify candidate genes for multiple stress tolerance in sorghum (Sorghum bicolor (L.) Moench) and related model species

Background Crop response to the changing climate and unpredictable effects of global warming with adverse conditions such as drought stress has brought concerns about food security to the fore; crop yield loss is a major cause of concern in this regard. Identification of genes with multiple responses across environmental stresses is the genetic foundation that leads to crop adaptation to environmental perturbations. Methods In this paper, we introduce an integrated approach to assess candidate genes for multiple stress responses across-species. The approach combines ontology based semantic data integration with expression profiling, comparative genomics, phylogenomics, functional gene enrichment and gene enrichment network analysis to identify genes associated with plant stress phenotypes. Five different ontologies, viz., Gene Ontology (GO), Trait Ontology (TO), Plant Ontology (PO), Growth Ontology (GRO) and Environment Ontology (EO) were used to semantically integrate drought related information. Results Target genes linked to Quantitative Trait Loci (QTLs) controlling yield and stress tolerance in sorghum (Sorghum bicolor (L.) Moench) and closely related species were identified. Based on the enriched GO terms of the biological processes, 1116 sorghum genes with potential responses to 5 different stresses, such as drought (18%), salt (32%), cold (20%), heat (8%) and oxidative stress (25%) were identified to be over-expressed. Out of 169 sorghum drought responsive QTLs associated genes that were identified based on expression datasets, 56% were shown to have multiple stress responses. On the other hand, out of 168 additional genes that have been evaluated for orthologous pairs, 90% were conserved across species for drought tolerance. Over 50% of identified maize and rice genes were responsive to drought and salt stresses and were co-located within multifunctional QTLs. Among the total identified multi-stress responsive genes, 272 targets were shown to be co-localized within QTLs associated with different traits that are responsive to multiple stresses. Ontology mapping was used to validate the identified genes, while reconstruction of the phylogenetic tree was instrumental to infer the evolutionary relationship of the sorghum orthologs. The results also show specific genes responsible for various interrelated components of drought response mechanism such as drought tolerance, drought avoidance and drought escape. Conclusions We submit that this approach is novel and to our knowledge, has not been used previously in any other research; it enables us to perform cross-species queries for genes that are likely to be associated with multiple stress tolerance, as a means to identify novel targets for engineering stress resistance in sorghum and possibly, in other crop species.
Efficacy of Nalbuphine with Flurbiprofen on Multimodal Analgesia with Transverse Abdominis Plane Block in Elderly Patients Undergoing Open Gastrointestinal Surgery: A Randomized, Controlled, Double-Blinded Trial

Objective To assess different doses of nalbuphine with flurbiprofen compared to sufentanil with flurbiprofen in multimodal analgesia efficacy for elderly patients undergoing gastrointestinal surgery with a transverse abdominis plane block (TAPB). Methods 158 elderly patients scheduling for elective open gastrointestinal surgery under general anesthesia and TAPB were randomly assigned to four groups according to different doses of nalbuphine with flurbiprofen in postoperative intravenous analgesia (PCIA). Postoperative pain intensity, effective pressing numbers of PCIA, and adverse effects were recorded at 6, 12, 24, and 48 hours after surgery. Results Postoperative pain intensity, effective pressing numbers, and the incidence of postoperative nausea and vomiting (PONV) were similar among the four groups after surgery, while the severity of PONV was decreased in Group L compared with Group S at 6, 12, and 48 h after surgery. No individual experienced pruritus, respiratory depression, or hypotension. Conclusions Low dose of nalbuphine (15 μg·kg−1·ml−1) combined with flurbiprofen is superior for elderly patients undergoing elective open gastrointestinal surgery with TAPB in terms of the efficient postoperative analgesia and decreased severity of PONV. This trial is registered with NCT02984865.
RuntimeSearch: Ctrl+F for a running program

Developers often try to find occurrences of a certain term in a software system. Traditionally, a text search is limited to static source code files. In this paper, we introduce a simple approach, RuntimeSearch, where the given term is searched in the values of all string expressions in a running program. When a match is found, the program is paused and its runtime properties can be explored with a traditional debugger. The feasibility and usefulness of RuntimeSearch is demonstrated on a medium-sized Java project.
From Tree House to Barracks

A representative sample of players of a popular massively multiplayer online game (World of Warcraft) was interviewed to map out the social dynamics of guilds. An initial survey and network mapping of players and guilds helped form a baseline. Next, the resulting interview transcripts were reviewed to explore player behaviors, attitudes, and opinions; the meanings they make; the social capital they derive; and the networks they form and to develop a typology of players and guilds. In keeping with current Internet research findings, players were found to use the game to extend real-life relationships, meet new people, form relationships of varying strength, and also use others merely as a backdrop. The key moderator of these outcomes appears to be the game's mechanic, which encourages some kinds of interactions while discouraging others. The findings are discussed with respect to the growing role of code in shaping social interactions.
Modeling of Secure and Dependable Applications Based on a Repository of Patterns: The SEMCO Approach

The requirement for higher quality and seamless development of systems is continuously increasing, even in domains traditionally not deeply involved in such issues. Security and Dependability (S&D) requirements are incorporated to an increasing number of systems. These newer restrictions make the development of those systems more complicated than conventional systems. In our work, we promote a new approach called SEMCO (System and software Engineering with Multi-COncerns) combining Model-Driven Engineering (MDE) with a model-based repository of S&D patterns to support the design and the analysis of pattern-based secure and dependable system and software architectures. The modeling framework to support the approach is based on a set of modeling languages, to specify security and dependability patterns, resources and a set of property models, and a set of model transformation rules to specify some of the analysis activities. As part of the assistance for the development of S&D applications, we have implemented a tool-chain based on the Eclipse platform to support the different activities around the repository, including the analysis activities. The proposed approach was evaluated through a case study from the railway domain.
Image indexing and retrieval using an ART‐2A neural network architecture

Traditional content‐based image retrieval (CBIR) systems use low‐level features such as colors, shapes, and textures of images. Although, users make queries based on semantics, which are not easily related to such low‐level characteristics. Recent works on CBIR confirm that researchers have been trying to map visual low‐level characteristics and high‐level semantics. The relation between low‐level characteristics and image textual information has motivated this article which proposes a model for automatic classification and categorization of words associated to images. This proposal considers a self‐organizing neural network architecture, which classifies textual information without previous learning. Experimental results compare the performance results of the text‐based approach to an image retrieval system based on low‐level features. © 2008 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 18, 202–208, 2008
Epigenome-Wide DNA Methylation in Hearing Ability: New Mechanisms for an Old Problem

Epigenetic regulation of gene expression has been shown to change over time and may be associated with environmental exposures in common complex traits. Age-related hearing impairment is a complex disorder, known to be heritable, with heritability estimates of 57–70%. Epigenetic regulation might explain the observed difference in age of onset and magnitude of hearing impairment with age. Epigenetic epidemiology studies using unrelated samples can be limited in their ability to detect small effects, and recent epigenetic findings in twins underscore the power of this well matched study design. We investigated the association between venous blood DNA methylation epigenome-wide and hearing ability. Pure-tone audiometry (PTA) and Illumina HumanMethylation array data were obtained from female twin volunteers enrolled in the TwinsUK register. Two study groups were explored: first, an epigenome-wide association scan (EWAS) was performed in a discovery sample (n = 115 subjects, age range: 47–83 years, Illumina 27 k array), then replication of the top ten associated probes from the discovery EWAS was attempted in a second unrelated sample (n = 203, age range: 41–86 years, Illumina 450 k array). Finally, a set of monozygotic (MZ) twin pairs (n = 21 pairs) within the discovery sample (Illumina 27 k array) was investigated in more detail in an MZ discordance analysis. Hearing ability was strongly associated with DNA methylation levels in the promoter regions of several genes, including TCF25 (cg01161216, p = 6.6×10−6), FGFR1 (cg15791248, p = 5.7×10−5) and POLE (cg18877514, p = 6.3×10−5). Replication of these results in a second sample confirmed the presence of differential methylation at TCF25 (p(replication) = 6×10−5) and POLE (p(replication) = 0.016). In the MZ discordance analysis, twins' intrapair difference in hearing ability correlated with DNA methylation differences at ACP6 (cg01377755, r = −0.75, p = 1.2×10−4) and MEF2D (cg08156349, r = −0.75, p = 1.4×10−4). Examination of gene expression in skin, suggests an influence of differential methylation on expression, which may account for the variation in hearing ability with age.
Symmetries , Conserved Charges and ( Black ) Holes in Two Dimensional String Theory

Two dimensional string theory is known to have an infinite dimensional symmetry, both in the continuum formalism as well as in the matrix model formalism. We develop a systematic procedure for computing the conserved charges associated with these symmetries for any configuration of D-branes in the continuum description. We express these conserved charges in terms of the boundary state associated with the D-brane, and also in terms of the asymptotic field configurations produced by this D-brane. Comparison of the conserved charges computed in the continuum description with those computed in the matrix model description facilitates identification of the states between these two formalisms. Using this we put constraints on the continuum description of the hole states in the matrix model, and matrix model description of the black holes solutions of the continuum theory. We also discuss possible generalization of the construction of the conserved charges to the case of D-branes in critical string theory.
The impact of leadership behaviour and organisational culture on job satisfaction and its relationship among organisational commitment and turnover intentions. A case study on an Egyptian company

Purpose – The purpose of this paper is to explore the relationship among leadership behaviour, organisational culture, job satisfaction, organisational commitment and turnover intentions through a case analysis on one of the biggest Egyptian company. Design/methodology/approach – A structured questionnaire was developed. The hypotheses were simultaneously tested on a sample of 455 employees out of 700 distributed, giving a response rate of 65 per cent. Several analytical techniques were used to assess the relationships among the variables under investigation such as Pearson correlation, chi-square, and multiple linear regressions. Findings – The findings of this study have shown significant relationships among the variables under investigation. Practical Implications – It is imperative to better understand how one of the biggest Egyptian companies can effectively and efficiently manage a skilled workforce within the Egyptian context. Research Limitations – The research was limited to one of the biggest Egyptian companies in Egypt. Also the use of cross-sectional design restricts inferences being drawn regarding casualty. Originality/Value – Despite the significant academic interest in leadership behaviour and organisational culture, this study contributes in adding to the body of the Egyptian culture knowledge. Also, to the best of the authors’ knowledge there is no study published that explores the influence of leadership behaviour and organisational culture on staff job satisfaction, commitment and turnover intention within the Egyptian context.
Overexpression of a Triticum aestivum Calreticulin gene (TaCRT1) Improves Salinity Tolerance in Tobacco

Calreticulin (CRT) is a highly conserved and abundant multifunctional protein that is encoded by a small gene family and is often associated with abiotic/biotic stress responses in plants. However, the roles played by this protein in salt stress responses in wheat (Triticum aestivum) remain obscure. In this study, three TaCRT genes were identified in wheat and named TaCRT1, TaCRT2 and TaCRT3-1 based on their sequence characteristics and their high homology to other known CRT genes. Quantitative real-time PCR expression data revealed that these three genes exhibit different expression patterns in different tissues and are strongly induced under salt stress in wheat. The calcium-binding properties of the purified recombinant TaCRT1 protein were determined using a PIPES/Arsenazo III analysis. TaCRT1 gene overexpression in Nicotiana tabacum decreased salt stress damage in transgenic tobacco plants. Physiological measurements indicated that transgenic tobacco plants showed higher activities of superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) than non-transgenic tobacco under normal growth conditions. Interestingly, overexpression of the entire TaCRT1 gene or of partial TaCRT1 segments resulted in significantly higher tolerance to salt stress in transgenic plants compared with their WT counterparts, thus revealing the essential role of the C-domain of TaCRT1 in countering salt stress in plants.
Comparative Analysis of the Intestinal Bacterial and RNA Viral Communities from Sentinel Birds Placed on Selected Broiler Chicken Farms

There is a great deal of interest in characterizing the complex microbial communities in the poultry gut, and in understanding the effects of these dynamic communities on poultry performance, disease status, animal welfare, and microbes with human health significance. Investigations characterizing the poultry enteric virome have identified novel poultry viruses, but the roles these viruses play in disease and performance problems have yet to be fully characterized. The complex bacterial community present in the poultry gut influences gut development, immune status, and animal health, each of which can be an indicator of overall performance. The present metagenomic investigation was undertaken to provide insight into the colonization of specific pathogen free chickens by enteric microorganisms under field conditions and to compare the pre-contact intestinal microbiome with the altered microbiome following contact with poultry raised in the field. Analysis of the intestinal virome from contact birds (“sentinels”) placed on farms revealed colonization by members of the Picornaviridae, Picobirnaviridae, Reoviridae, and Astroviridae that were not present in pre-contact birds or present in proportionally lower numbers. Analysis of the sentinel gut bacterial community revealed an altered community in the post-contact birds, notably by members of the Lachnospiracea/Clostridium and Lactobacillus families and genera. Members of the avian enteric Reoviridae and Astroviridae have been well-characterized and have historically been implicated in poultry enteric disease; members of the Picobirnaviridae and Picornaviridae have only relatively recently been described in the poultry and avian gut, and their roles in the recognized disease syndromes and in poultry performance in general have not been determined. This metagenomic analysis has provided insight into the colonization of the poultry gut by enteric microbes circulating in commercial broiler flocks, and has identified enteric viruses and virus communities that warrant further study in order to understand their role(s) in avian gut health and disease.
A bioengineered retinal pigment epithelial monolayer for advanced, dry age-related macular degeneration

Implantation of a human embryonic stem cell–derived retinal pigment epithelial monolayer is feasible in human subjects with advanced, dry age-related macular degeneration. Treating vision loss, a goal within sight Non-neovascular age-related macular degeneration (NNAMD) is a progressive blinding disease primarily due to loss of the retinal pigment epithelium (RPE) of the eye. Currently, there is no effective treatment for NNAMD. Now, Kashani and colleagues have developed a clinical-grade retinal implant made of human embryonic stem cell (hESC)–derived RPE grown on a synthetic substrate. In a first-in-human phase 1 clinical trial in five patients with advanced NNAMD, the implant was shown to be safe and well tolerated. Preliminary results reported potential therapeutic effects on visual acuity, suggesting that this approach might be useful for treating retinal disorders involving RPE loss. Retinal pigment epithelium (RPE) dysfunction and loss are a hallmark of non-neovascular age-related macular degeneration (NNAMD). Without the RPE, a majority of overlying photoreceptors ultimately degenerate, leading to severe, progressive vision loss. Clinical and histological studies suggest that RPE replacement strategies may delay disease progression or restore vision. A prospective, interventional, U.S. Food and Drug Administration–cleared, phase 1/2a study is being conducted to assess the safety and efficacy of a composite subretinal implant in subjects with advanced NNAMD. The composite implant, termed the California Project to Cure Blindness–Retinal Pigment Epithelium 1 (CPCB-RPE1), consists of a polarized monolayer of human embryonic stem cell–derived RPE (hESC-RPE) on an ultrathin, synthetic parylene substrate designed to mimic Bruch’s membrane. We report an interim analysis of the phase 1 cohort consisting of five subjects. Four of five subjects enrolled in the study successfully received the composite implant. In all implanted subjects, optical coherence tomography imaging showed changes consistent with hESC-RPE and host photoreceptor integration. None of the implanted eyes showed progression of vision loss, one eye improved by 17 letters and two eyes demonstrated improved fixation. The concurrent structural and functional findings suggest that CPCB-RPE1 may improve visual function, at least in the short term, in some patients with severe vision loss from advanced NNAMD.
Class I ADP-Ribosylation Factors Are Involved in Enterovirus 71 Replication

Enterovirus 71 is one of the major causative agents of hand, foot, and mouth disease in infants and children. Replication of enterovirus 71 depends on host cellular factors. The viral replication complex is formed in novel, cytoplasmic, vesicular compartments. It has not been elucidated which cellular pathways are hijacked by the virus to create these vesicles. Here, we investigated whether proteins associated with the cellular secretory pathway were involved in enterovirus 71 replication. We used a loss-of-function assay, based on small interfering RNA. We showed that enterovirus 71 RNA replication was dependent on the activity of Class I ADP-ribosylation factors. Simultaneous depletion of ADP-ribosylation factors 1 and 3, but not three others, inhibited viral replication in cells. We also demonstrated with various techniques that the brefeldin-A-sensitive guanidine nucleotide exchange factor, GBF1, was critically important for enterovirus 71 replication. Our results suggested that enterovirus 71 replication depended on GBF1-mediated activation of Class I ADP-ribosylation factors. These results revealed a connection between enterovirus 71 replication and the cellular secretory pathway; this pathway may represent a novel target for antiviral therapies.
A Quantitative Model Proposal for the Assesment of Project Performance: The Bridge Model

Project performance models should serve as managerial measurement tools that evaluate the various aspects of projects with a holistic approach. However, predate models in the literature generally focus on limited performance indicators of projects - such as budget and time - for performance assessment and they lack broad perspective. In this respect, we aimed to introduce and propose a new model for the quantitative, effective and holistic evaluation of projects. The proposed model is originally developed as a conceptual approach by Livvarcin (2013) and entitled as The Bridge Model. In this study we enlarged the study and embodied the project performance parameters. In this study, we examine project performance by focusing on two different parameter groups: Process parameters and indicator parameters. Process parameters include seven elements of The Bridge Model, these are preparation phase, initiation phase, implementation phase, closing phase, post-project phase, project atmosphere and project actors. Indicator parameters are measures that are similar to the project parameters used in existing project performance models and they include cost, time, quality, performance of outcomes, motivation, development and competitiveness. We also performed a pilot study to figure out the performance of 42 different projects by using the performance parameters of the proposed model. We proved the validity and reliability of our model by using both quantitaive and qualitative methodologies.
Effect of Surgical Weight Loss on Plantar Fasciitis and Health-Care Use.

BACKGROUND: Plantar fasciitis (PF) is one of the most common causes of heel pain. Obesity is recognized as a major factor in PF development, possibly due to increased mechanical loading of the foot due to excess weight. The benefit of bariatric surgery is documented for other comorbidities but not for PF. METHODS: A retrospective medical record review was performed for patients with PF identified from a prospectively maintained database of the Cleveland Clinic Bariatric and Metabolic Institute. Age, sex, surgery, excess weight loss, body mass index (BMI), and health-care use related to PF treatment were abstracted. Comparative analyses were stratified by surgery type. RESULTS: Two hundred twenty-eight of 10,305 patients (2.2%) had a documented diagnosis of PF, of whom 163 underwent bariatric surgery and were included in the analysis. Eighty-five percent of patients were women, mean ± SD age was 52.2 ± 9.9 years, and mean ± SD preintervention BMI was 45 ± 7.7. Postoperatively, mean ± SD BMI and excess weight loss were 34.8 ± 7.8 and 51.0% ± 20.4%, respectively. One hundred forty-six patients (90%) achieved resolution of PF and related symptoms. The mean ± SD number of treatment modalities used for PF per patient preoperatively was 1.9 ± 1.0 ( P = .25). After surgery, the mean ± SD number of treatment modalities used per patient was reduced to 0.3 ± 0.1 ( P = .01). CONCLUSIONS: We present new evidence suggesting that reductions in BMI after bariatric surgery may be associated with decreasing the number of visits for PF and may contribute to symptomatic improvement.