Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of QTLs for Rust Resistance in the Peanut Wild Species Arachis magna and the Development of KASP Markers for Marker-Assisted Selection

Rust is a major pathogen of the peanut crop. Development and adoption of rust-resistant cultivars is the most cost efficient and effective way to control the spread of the disease and reduce yield losses. Some cultivated peanut germplasm accessions have a degree of resistance, but the secondary gene pool is a source of much stronger resistance alleles. Wild species, however, have undesirable agronomic traits that are a disincentive to their use in breeding. The identification of genomic regions that harbor disease resistance in wild species is the first step in the implementation of marker-assisted selection that can speed the introgression of wild disease resistances and the elimination of linkage drag. In this work, we identify genome regions that control different components of rust resistance in a recombinant inbred line population developed from a cross between two Arachis species, the susceptible most probable B genome ancestor of cultivated peanut, Arachis ipaënsis, and an accession of its closest relative, Arachis magna, which is resistant to rust. Quantitative trait loci for several components of resistance were placed in the same position on linkage group B08. Single-nucleotide polymorphism Kompetitive allele-specific polymerase chain reaction markers for rust resistance region were designed and validated for marker function in both diploid and tetraploid contexts.
Parent and teacher perceptions of ways teachers work with the parents of their students

PARENT AND TEACHER PERCEPTIONS OF WAYS TEACHERS WORK WITH THE PARENTS OF THEIR STUDENTS FEBRUARY 1996 ROBERT R. PUTNAM, B.A., UNIVERSITY OF MASSACHUSETTS AMHERST M.Ed., UNIVERSITY OF MASSACHUSETTS AMHERST Ed.D. , UNIVERSITY OF MASSACHUSETTS AMHERST Directed by: Professor Robert L. Sinclair This descriptive study examined the current practices used by two hundred and twenty-seven elementary school teachers in 23 demographically different schools across the United States to work with the parents of their students. The examination of the perceptions of selected teachers and parents towards the effectiveness of specific ways that teachers work with parents was an additional objective of this research. Further, parent and teacher recommendations for improving parent and teacher collaboration were considered. It is the responsibility of schools to ensure that all children of all families have the opportunity to obtain a quality education. Unfortunately demographic and social changes have made it increasingly difficult for schools to meet that responsibility effectively. Educators are being forced to examine alterable school and nonschool conditions that will help them meet their responsibilities to create more effective schools. Attention has been turning toward the practices teachers use to encourage a parent's involvement in his or her child's education. The practices teachers use to communicate, inform, and influence parents can have profound effects on a parent's attitudes and actions towards working closely with teachers to help youngsters learn well. To understand the factors that affect parental involvement it is necessary to identify the types of practices
Epstein-Barr Virus Latency in B Cells Leads to Epigenetic Repression and CpG Methylation of the Tumour Suppressor Gene Bim

In human B cells infected with Epstein-Barr virus (EBV), latency-associated virus gene products inhibit expression of the pro-apoptotic Bcl-2-family member Bim and enhance cell survival. This involves the activities of the EBV nuclear proteins EBNA3A and EBNA3C and appears to be predominantly directed at regulating Bim mRNA synthesis, although post-transcriptional regulation of Bim has been reported. Here we show that protein and RNA stability make little or no contribution to the EBV-associated repression of Bim in latently infected B cells. However, treatment of cells with inhibitors of histone deacetylase (HDAC) and DNA methyltransferase (DNMT) enzymes indicated that epigenetic mechanisms are involved in the down-regulation of Bim. This was initially confirmed by chromatin immunoprecipitation analysis of histone acetylation levels on the Bim promoter. Consistent with this, methylation-specific PCR (MSP) and bisulphite sequencing of regions within the large CpG island located at the 5′ end of Bim revealed significant methylation of CpG dinucleotides in all EBV-positive, but not EBV-negative B cells examined. Genomic DNA samples exhibiting methylation of the Bim promoter included extracts from a series of explanted EBV-positive Burkitt's lymphoma (BL) biopsies. Subsequent analyses of the histone modification H3K27-Me3 (trimethylation of histone H3 lysine 27) and CpG methylation at loci throughout the Bim promoter suggest that in EBV-positive B cells repression of Bim is initially associated with this repressive epigenetic histone mark gradually followed by DNA methylation at CpG dinucleotides. We conclude that latent EBV initiates a chain of events that leads to epigenetic repression of the tumour suppressor gene Bim in infected B cells and their progeny. This reprogramming of B cells could have important implications for our understanding of EBV persistence and the pathogenesis of EBV-associated disease, in particular BL.
Lack of association of ALOX12 and ALOX15B polymorphisms with psoriasis despite altered urinary excretion of 12(S)‐hydroxyeicosatetraenoic acid

Pro‐ and anti‐inflammatory metabolites of arachidonic acid – eicosanoids – participate in skin homeostasis, affecting the growth and differentiation of keratinocytes. Alterations of 12‐lipoxygenase (LOX) and 15‐LOX and their metabolites have been described in the epidermis of patients with psoriasis, but systemic production of 12‐LOX and 15‐LOX eicosanoids has not been studied in the disease.
Learning Stochastic Feedforward Neural Networks

Multilayer perceptrons (MLPs) or neural networks are popular models used for nonlinear regression and classification tasks. As regressors, MLPs model the conditional distribution of the predictor variables Y given the input variables X. However, this predictive distribution is assumed to be unimodal (e.g. Gaussian). For tasks involving structured prediction, the conditional distribution should be multi-modal, resulting in one-to-many mappings. By using stochastic hidden variables rather than deterministic ones, Sigmoid Belief Nets (SBNs) can induce a rich multimodal distribution in the output space. However, previously proposed learning algorithms for SBNs are not efficient and unsuitable for modeling real-valued data. In this paper, we propose a stochastic feedforward network with hidden layers composed of both deterministic and stochastic variables. A new Generalized EM training procedure using importance sampling allows us to efficiently learn complicated conditional distributions. Our model achieves superior performance on synthetic and facial expressions datasets compared to conditional Restricted Boltzmann Machines and Mixture Density Networks. In addition, the latent features of our model improves classification and can learn to generate colorful textures of objects.
Comparison of a computerized anesthesia device with a traditional syringe in preschool children.

PURPOSE The purpose of this investigation was to evaluate the efficacy of a computerized injection device (Wand) on reducing pain behavior during injections with preschool-aged children. METHODS Subjects consisted of 40 patients between the ages of 2 and 5 requiring local anesthesia for dental restorations in the maxilla. Patients were randomly assigned to either the Wand or the traditional anesthetic delivery system. A palatal approach to the anterior and middle superior alveolar nerves and the anterior superior alveolar nerve was used with the Wand injections. Buccal infiltration and palatal injections were used for the traditional method. Pain behavior was observed and coded. RESULTS Results of Fisher Exact tests found that using the Wand to deliver anesthetic lead to significantly fewer (P < .01) disruptive behaviors in preschool-aged children when compared with a traditional injection regimen. In addition, none of the preschool-aged children exposed to the Wand required restraint during the initial interval, while nearly half of the children receiving a traditional injection required some type of immediate restraint. CONCLUSIONS These results demonstrate that the Wand can significantly reduce disruptive behaviors in a population of young children who are traditionally more difficult to manage and may be one method of creating a more positive experience for the young child and the practitioner.
Cytokine Indexes in Pemphigus Vulgaris: Perception of Its Immunpathogenesis and Hopes for Non-Steroidal Treatment

Pemphigus vulgaris (PV) is a chronic autoimmune blistering disease of the skin, in which loss of adhesion between keratinocytes is caused by autoantibodies. It has been hypothesized that cytokines play an essential role in the pathogenesis of PV. This study aimed to investigate the other immunopathological aspects of PV by determining the serum levels of cytokines in PV patients to find another treatment strategy except corticosteroid therapy. Twenty-three patients with PV and a control group consisting of 24 healthy subjects were studied. Interleukin (IL)-2, IL-4, IL-6, IL10, IL-12, IL-17 and interferon-gamma (IFN-γ) were measured in the sera of patients by the enzyme-linked immunosorbent assay (ELISA) method. The serum levels of IL-2, IL-4, IL-17 and IFN-γ in most patients and controls were undetectable. The serum concentrations of IL-10 in the patients and controls were undetectable, nevertheless, the mean serum levels of this cytokine was 64.375 pg/mL in four patients. The mean serum levels of pro-inflammatory cytokine IL-6 increased significantly in the patients, compared to the controls (169.50 vs. 75.62 pg/mL) (P < 0.05). The same was observed for another pro-inflammatory cytokine, IL-12 (135.33 vs. 86.28 pg/mL) (P < 0.05). Based on the results of this study it can be concluded that the Type 2 T helper cytokine (IL-6) and macrophage-derived cytokine (IL-12) have essential roles in PV pathophysiology. In addition, the potential clinical application of Th1/Th2 type cytokine-based therapy in PV should be considered in next studies.
Active Learning for Black-Box Semantic Role Labeling with Neural Factors

Active learning is a useful technique for tasks for which unlabeled data is abundant but manual labeling is expensive. One example of such a task is semantic role labeling (SRL), which relies heavily on labels from trained linguistic experts. One challenge in applying active learning algorithms for SRL is that the complete knowledge of the SRL model is often unavailable, against the common assumption that active learning methods are aware of the details of the underlying models. In this paper, we present an active learning framework for black-box SRL models (i.e., models whose details are unknown). In lieu of a query strategy based on model details, we propose a neural query strategy model that embeds both language and semantic information to automatically learn the query strategy from predictions of an SRL model alone. Our experimental results demonstrate the effectiveness of both this new active learning framework and the neural query strategy model.
Bilateral Intravitreal Dexamethasone Implant for Retinitis Pigmentosa-Related Macular Edema

Purpose: To report the efficacy of intravitreal dexamethasone implant in a patient with retinitis pigmentosa and bilateral cystoid macular edema unresponsive to topical carbonic anhydrase inhibitors. Case Report: A 36-year-old man with bilateral cystoid macular edema associated with retinitis pigmentosa that was unresponsive to topical carbonic anhydrase inhibitors underwent bilateral 0.7-mg intravitreal dexamethasone implants two weeks apart. Spectral domain optical coherence tomography revealed resolution of macular edema one week following each injection in both eyes and his visual acuity improved. However, macular edema recurred two months later in OS and three months later in OD. Second implant was considered for both eyes. No implant-related complication was experienced during the follow-up of seven months. Conclusion: Inflammatory process seems to play a role in retinitis pigmentosa. Intravitreal dexamethasone implant may offer retina specialists a therapeutic option especially in cases unresponsive to other treatment regimens in eyes with retinitis pigmentosa-related macular edema.
A qualitative exploration of organizational culture and workplace stressors : a competing values approach

This study sought to investigate the extent to which differing organizational cultures might be associated with different types of work stressors, and whether manifestations and perceptions of work stressors varied as a function of organizational culture. Researchers have not yet extensively considered this question in the context of a theoretical framework of organizational culture. Interviews were conducted with 77 employees representing the four Competing Values Framework culture types. Results revealed that work stressors within organizational cultures were manifested as a function of the primary organizational values, and that human relations culture stressors were additionally related to others not abiding by the primary workplace values. Further, results revealed that several employees (within the flexible-type cultures especially) described workplace events more as a challenge than stressful, and that these employees tended to report a similarity between themselves and the organization. These findings suggested that a person’s fit with the organizational culture has importance in the investigation of organizational culture and perceptions of work stressors.
Addressing Childhood Overweight: Strategies Learned From One Latino Community

The purpose of this study is to understand one Latino community's perspectives about childhood overweight within this high-risk ethnic group. Three focus groups, consisting of 12 mothers, 12 fathers, and 8 boys and 4 girls ages 10-12, participated. Transcripts of interviews were coded using N-VIVO and analyzed thematically. Several themes emerge: parents' demanding work schedules, lack of time, transportation issues, opportunities for physical activities, and lack of meal preparation. Participants knew good nutrition and exercise help prevent obesity. Nursing interventions must address multiple challenges with childhood obesity at the family and community levels.
AS04, an Aluminum Salt- and TLR4 Agonist-Based Adjuvant System, Induces a Transient Localized Innate Immune Response Leading to Enhanced Adaptive Immunity1

Adjuvant System 04 (AS04) combines the TLR4 agonist MPL (3-O-desacyl-4′-monophosphoryl lipid A) and aluminum salt. It is a new generation TLR-based adjuvant licensed for use in human vaccines. One of these vaccines, the human papillomavirus (HPV) vaccine Cervarix, is used in this study to elucidate the mechanism of action of AS04 in human cells and in mice. The adjuvant activity of AS04 was found to be strictly dependent on AS04 and the HPV Ags being injected at the same i.m. site within 24 h of each other. During this period, AS04 transiently induced local NF-κB activity and cytokine production. This led to an increased number of activated Ag-loaded dendritic cells and monocytes in the lymph node draining the injection site, which further increased the activation of Ag-specific T cells. AS04 was also found to directly stimulate those APCs in vitro but not directly stimulate CD4+ T or B lymphocytes. These AS04-induced innate responses were primarily due to MPL. Aluminum salt appeared not to synergize with or inhibit MPL, but rather it prolonged the cytokine responses to MPL at the injection site. Altogether these results support a model in which the addition of MPL to aluminum salt enhances the vaccine response by rapidly triggering a local cytokine response leading to an optimal activation of APCs. The transient and confined nature of these responses provides further supporting evidence for the favorable safety profile of AS04 adjuvanted vaccines.
Receptor, Ligand and Transducer Contributions to Dopamine D2 Receptor Functional Selectivity

Functional selectivity (or biased agonism) is a property exhibited by some G protein-coupled receptor (GPCR) ligands, which results in the modulation of a subset of a receptor’s signaling capabilities and more precise control over complex biological processes. The dopamine D2 receptor (D2R) exhibits pleiotropic responses to the biogenic amine dopamine (DA) to mediate complex central nervous system functions through activation of G proteins and β-arrestins. D2R is a prominent therapeutic target for psychological and neurological disorders in which DA biology is dysregulated and targeting D2R with functionally selective drugs could provide a means by which pharmacotherapies could be developed. However, factors that determine GPCR functional selectivity in vivo may be multiple with receptors, ligands and transducers contributing to the process. We have recently described a mutagenesis approach to engineer biased D2R mutants in which G protein-dependent ([Gprot]D2R) and β-arrestin-dependent signaling ([βarr]D2R) were successfully separated (Peterson, et al. PNAS, 2015). Here, permutations of these mutants were used to identify critical determinants of the D2R signaling complex that impart signaling bias in response to the natural or synthetic ligands. Critical residues identified in generating [Gprot]D2R and [βarr]D2R conferred control of partial agonism at G protein and/or β-arrestin activity. Another set of mutations that result in G protein bias was identified that demonstrated that full agonists can impart unique activation patterns, and provided further credence to the concept of ligand texture. Finally, the contributions and interplay between different transducers indicated that G proteins are not aberrantly activated, and that receptor kinase and β-arrestin activities are inextricably linked. These data provide a thorough elucidation of the feasibility and malleability of D2R functional selectivity and point to means by which novel in vivo therapies could be modeled.
Comparative Transcriptomic Analysis Reveals Novel Insights into the Adaptive Response of Skeletonema costatum to Changing Ambient Phosphorus

Phosphorus (P) is a limiting macronutrient for diatom growth and productivity in the ocean. Much effort has been devoted to the physiological response of marine diatoms to ambient P change, however, the whole-genome molecular mechanisms are poorly understood. Here, we utilized RNA-Seq to compare the global gene expression patterns of a marine diatom Skeletonema costatum grown in inorganic P-replete, P-deficient, and inorganic- and organic-P resupplied conditions. In total 34,942 unique genes were assembled and 20.8% of them altered significantly in abundance under different P conditions. Genes encoding key enzymes/proteins involved in P utilization, nucleotide metabolism, photosynthesis, glycolysis, and cell cycle regulation were significantly up-regulated in P-deficient cells. Genes participating in circadian rhythm regulation, such as circadian clock associated 1, were also up-regulated in P-deficient cells. The response of S. costatum to ambient P deficiency shows several similarities to the well-described responses of other marine diatom species, but also has its unique features. S. costatum has evolved the ability to re-program its circadian clock and intracellular biological processes in response to ambient P deficiency. This study provides new insights into the adaptive mechanisms to ambient P deficiency in marine diatoms.
Redefining overweight and obesity in rheumatoid arthritis patients

Objectives: To assess whether body mass index (BMI) and body fat (BF) differ between rheumatoid arthritis (RA) patients, patients with non-inflammatory arthritis (osteoarthritis, OA) and healthy individuals, and whether disease specific measures of adiposity are required to accurately reflect BF in these groups. Methods: 641 individuals were assessed for BMI (kg/m2) and BF (bioelectrical impedance). Of them, 299 (174 RA, 43 OA and 82 healthy controls (HC)) formed the observation group and 342 (all RA) the validation group. RA disease characteristics were collected. Results: ANOVA revealed significant differences between disease groups for BMI (p<0.05) and BF (p<0.001). ANCOVA showed that age accounted for the differences in BMI (F1,294 = 5.10, p<0.05); age (F1,293 = 22.43, p<0.001), sex (F1,293 = 380.90, p<0.001) and disease (F2, 293 = 18.7, p<0.001) accounted for the differences in BF. For a given BF, patients with RA exhibited BMI levels reduced by 1.83 kg/m2 (p<0.001) compared to HC; there were no significant differences between OA and HC. A predictive model for BF was developed (R2 = 0.769, p<0.001) and validated using limits of agreement Analysis against measured BF in the validation group (95%LIMAG = 6.17; CV = 8.94). Conclusions: In individuals with RA, BMI cut-off points should be reduced by 2 kg/m2 (that is, to 23 kg/m2 for overweight and 28 kg/m2 for obesity). The equation developed can be used to accurately predict BF from BMI in RA patients. These findings may be important in the context of the cardiovascular comorbidity of RA.
Probability-Based Prediction and Sleep Scheduling for Energy-Efficient Target Tracking in Sensor Networks

A surveillance system, which tracks mobile targets, is one of the most important applications of wireless sensor networks. When nodes operate in a duty cycling mode, tracking performance can be improved if the target motion can be predicted and nodes along the trajectory can be proactively awakened. However, this will negatively influence the energy efficiency and constrain the benefits of duty cycling. In this paper, we present a Probability-based Prediction and Sleep Scheduling protocol (PPSS) to improve energy efficiency of proactive wake up. We start with designing a target prediction method based on both kinematics and probability. Based on the prediction results, PPSS then precisely selects the nodes to awaken and reduces their active time, so as to enhance energy efficiency with limited tracking performance loss. We evaluated the efficiency of PPSS with both simulation-based and implementation-based experiments. The experimental results show that compared to MCTA algorithm, PPSS improves energy efficiency by 25-45 percent (simulation based) and 16.9 percent (implementation based), only at the expense of an increase of 5-15 percent on the detection delay (simulation based) and 4.1 percent on the escape distance percentage (implementation based), respectively.
Oropharyngeal and oesophageal candidiasis in HIV infected patients

Candidiasis is a common infection caused by yeast-like fungus. Oropharyngeal candidiasis occurs when CD4 count is 200-500 cell/mm3, with fall in CD4 count to <200 cells/mm3 oesophageal candidiasis occur in HIV infected patients. Aim- To identify and characterize Candida species (oropharyngeal and oesophageal) in HIV infected patients and to correlate them with CD4+ T lymphocyte count. Method- Two hundred HIV positive cases were selected for this study. Identification of Candida species was done by conventional standard techniques using Gram’s stain, cultural character on Saboraud dextrose agar, germ tube test, morphology on corn meal agar, colour difference on CHROM agar and sugar assimilation test. Findings- The prevalence of candidiasis was 72.5% with majority of the patients belonged to age group 16 - 45 years. Male to female ratio was 1.64:1 with male preponderance. 58.62% of patients belonged to Stage 4 of WHO clinical staging. Majority of species (60.67%) were C. albicans. The non-Candida albicans isolated were C. dublinienses (25.33%), C. krusei (12.00%), C. tropicalis (1.33%) and C. glabrata (0.67%). Conclusion- Though Candida albicans continues to be the common and important pathogen among the Candida species there is a increase in the incidence of non- Candida albicans species like Candida dublinienses, Candida krusei, Candida tropicalis and Candida glabrata.