Miracle-dz/UniFAR-FTUs huggingface dataset:
Differential Immunodominance Hierarchy of CD8+ T-Cell Responses in HLA-B*27:05- and -B*27:02-Mediated Control of HIV-1 Infection

ABSTRACT The well-characterized association between HLA-B*27:05 and protection against HIV disease progression has been linked to immunodominant HLA-B*27:05-restricted CD8+ T-cell responses toward the conserved Gag KK10 (residues 263 to 272) and polymerase (Pol) KY9 (residues 901 to 909) epitopes. We studied the impact of the 3 amino acid differences between HLA-B*27:05 and the closely related HLA-B*27:02 on the HIV-specific CD8+ T-cell response hierarchy and on immune control of HIV. Genetic epidemiological data indicate that both HLA-B*27:02 and HLA-B*27:05 are associated with slower disease progression and lower viral loads. The effect of HLA-B*27:02 appeared to be consistently stronger than that of HLA-B*27:05. In contrast to HLA-B*27:05, the immunodominant HIV-specific HLA-B*27:02-restricted CD8+ T-cell response is to a Nef epitope (residues 142 to 150 [VW9]), with Pol KY9 subdominant and Gag KK10 further subdominant. This selection was driven by structural differences in the F pocket, mediated by a polymorphism between these two HLA alleles at position 81. Analysis of autologous virus sequences showed that in HLA-B*27:02-positive subjects, all three of these CD8+ T-cell responses impose selection pressure on the virus, whereas in HLA-B*27:05-positive subjects, there is no Nef VW9-mediated selection pressure. These studies demonstrate that HLA-B*27:02 mediates protection against HIV disease progression that is at least as strong as or stronger than that mediated by HLA-B*27:05. In combination with the protective Gag KK10 and Pol KY9 CD8+ T-cell responses that dominate HIV-specific CD8+ T-cell activity in HLA-B*27:05-positive subjects, a Nef VW9-specific response is additionally present and immunodominant in HLA-B*27:02-positive subjects, mediated through a polymorphism at residue 81 in the F pocket, that contributes to selection pressure against HIV. IMPORTANCE CD8+ T cells play a central role in successful control of HIV infection and have the potential also to mediate the eradication of viral reservoirs of infection. The principal means by which protective HLA class I molecules, such as HLA-B*27:05 and HLA-B*57:01, slow HIV disease progression is believed to be via the particular HIV-specific CD8+ T cell responses restricted by those alleles. We focus here on HLA-B*27:05, one of the best-characterized protective HLA molecules, and the closely related HLA-B*27:02, which differs by only 3 amino acids and which has not been well studied in relation to control of HIV infection. We show that HLA-B*27:02 is also protective against HIV disease progression, but the CD8+ T-cell immunodominance hierarchy of HLA-B*27:02 differs strikingly from that of HLA-B*27:05. These findings indicate that the immunodominant HLA-B*27:02-restricted Nef response adds to protection mediated by the Gag and Pol specificities that dominate anti-HIV CD8+ T-cell activity in HLA-B*27:05-positive subjects.
A method for segmenting DNA

The variability of the nucleotide composition along DNA has been documented for a long time [2], notably for GC composition (the isochores) [1]. In particular the eucaryotic DNA sequences can be seen as a mosaic of regions having distinct homogeneous GC-proportions. In this work we present a method to infer such regions using the GC-proportions distribution of overlapping windows. The rest of this paper is divided into three parts, one for each step of the approach. Each step is computed in a time linear with the length of the sequence, which allows us to parse whole genomes.
Monopyrroles in porphyria and related disorders

The hereditary porphyrias are a group of disorders in which the genetic defect results in an abnormality in the biosynthetic pathway leading to the respiratory pigment haem. The characteristic result of this is excessive synthesis and excretion of the tetrapyrrolic porphyrins sind, in the acute porphyrias, their precursors 6-aminolaevulinic acid (ALA.) and porphobilinogen. The acute attacks of acute porphyria show certain similarities to psychiatric disorders and the finding of a pyrrolic metabolite in the urine of patients with acute intermittent porphyria (AIP) and certain psychiatric disorders was the common factor that implicated this metabolite in the aetiology of certain manifestations of these disorders. Identification of the metabolite proved difficult but it was eventually unambiguously identified as 3-ethyl-5-hydroxy-4,5-dimethyl-Δ3-pyrrolin-2-one (OHHPL). The work contained in this thesis describes clinical and biochemical investigations into the occurrence and properties of this compound. Initially a qualitative method was used to detect OEHPL and it was shown to be present in the urine of patients with acute porphyria in attack and remission but to be undetectable in patients who were latent for the disease. Using a gas-liquid chromatography method developed for the quantitative assay of OHHPL, it was shown that in carriers of the AIP gene defect there was no significant difference in OHHPL excretion in latency, attack and remission, but that levels in these patients were significantly greater than in control subjects. No correlation could be shown between OHHPL excretion and clinical condition either in the group of patients or in multiple estimations in single patients. However, a significant association was found between the excretion of OHHPL and that of ALA. and PBG and it was also shown that in the porphyric patients ALA and PBG excretion were related in a linear fashion. Quantitation of OHHPL in groups of psychiatric patients showed that there was a significant elevation of OHHPL excretion in psychotic patients who were undergoing drug therapy and also in groups of patients with schizophrenia and organic brain disease. In the patients with schizophrenia there was a negative correlation between the clinical condition of the patients as assessed on the Hamilton-Lorr rating scale and urinary OHHPL. In an attempt to exatmine further the relationship between OHHPL and PBG and ALA in the patients with porphyria a group of patients, industrial lead workers, with sub-clinical lead poisoning were studied. These patients had raised blood lead and increased urinary excretion of ALA resulting from an inhibition by lead of the enzyme 6-aminolaevulinic acid dehydratase (ALA.D). OKHPL and PBG concentrations in the urine of these workers were within the normal range. It was found that there was a negative association between OHHPL and ALA levels which suggested that the ALA-OHHPL association in the porphyric patients was purely a result of the ALA-PBG relationship.
Zoonotic Tuberculosis: A Concern and Strategies to Combat

Mycobacterium bovis is the main causal agent of bovine tuberculosis that causes zoonotic tuberculosis in humans. The most common routes of transmission of the agent to human are airborne transmission, consumption of unpasteurized milk, direct contact with infected animals or untreated animal products. Conventional diagnostic methods in com- bination with modern molecular and immunological techniques should be used for early and accurate diagnosis of the disease. Some of the challenges to tackle and eradicate zoonotic TB in developing countries are having many hosts, absence of early diagnosis, presence of other acute diseases, being economically unable to implement control strate- gies, and other social and cultural issues. Usually treatment is not recommended in animals but vaccination is carried out in some countries as a preventive measure. Due to the grave consequences of M. bovis infection on animal and human health, it is necessary to introduce accurate control measures to reduce the risk of disease in human and animal populations. Proper food hygiene practices, slaughter of the affected animals in developed countries, and segregation of the suspected animals in developing countries along with stronger intersectoral collaboration between the veterinary and medical professions are important for the control of the disease.
Determination of median effective dose (ED50) of scorpion antivenom against scorpion envenomation using a newly developed formula

About 50 species of scorpions cause fatal scorpionism worldwide. Most of these are members of the Buthidae family, and include, among others, Mesobuthus eupeus, Androctonus crassicauda, Leiurus abdullahbayrami, Leiurus quinquestriatus, Tityus pachyurus and Androctonus australis. Because high doses of scorpion venom and antivenom can cause death and hypersensitive reactions, there is a need to develop a formula that can be used to calculate both lethal and effective doses for scorpion venom and antivenom, respectively, thereby obviating the need for laboratory experiments.
Dysregulation of SPRR3/miR-876-3p Axis Contributes to Tumorigenesis in Non-Small-Cell Lung Cancer

Background SPRR3, also known as esophagin, has been shown to be involved in the initiation and progression of numerous types of tumor. However, the biological function of SPRR3 that contributes to non-small-cell lung cancer (NSCLC) growth and migration is largely unknown. Methods The expression of SPRR3 and its association with EZH2 and miR-876-3p in NSCLC cells were determined by real-time PCR. Protein levels were measured by immunohistochemistry (IHC) and Western blot. Cell functions were studied by CCK-8, transwell assay, flow cytometry and dual-luciferase reporter assay. The effect of SPRR3 on tumor growth in vivo was evaluated in patient-derived xenograft (PDX) models. Results SPRR3 was up-regulated in most NSCLC cell lines and clinical tissues. Also, the correlation between SPRR3 expression and clinical features was significant. Functional studies confirmed that SPRR3 modulates cell proliferation, invasion and cell apoptosis in NSCLC via regulating EZH2, which is a well-known oncogene in NSCLC. Furthermore, SPRR3 was found to be a direct target of miR-876-3p that also plays a suppressor role in NSCLC. Conclusion These findings indicated that miR-876-3p/SPRR3/EZH2 signaling cascade exerts important roles in the regulation of NSCLC, suggesting that this pathway can serve as a potential therapeutic target in NSCLC.
Treatment fidelity in Model of Human Occupation research

Introduction Treatment fidelity is an important consideration in occupational therapy efficacy research. It involves methodological strategies that enhance quantitative rigor and improves confidence in research outcomes. This study examines treatment fidelity in Model of Human Occupation efficacy literature because it is a widely used, occupation-focused theory with a substantial evidence base. Method Relevant articles (n = 17) were coded for treatment fidelity with the Treatment Fidelity Measure. Percentages of articles reporting treatment fidelity strategies and mean adherence to fidelity strategies were calculated. One-way analysis of variance was used to examine fidelity over time. Results Only one study reported provider training strategies and measured nonspecific treatment effects. Overall mean adherence to treatment fidelity strategies for Model of Human Occupation research was 0.57; one study demonstrated high fidelity with a score of ≥0.80. Model of Human Occupation efficacy literature trends toward higher levels of treatment fidelity over time. Conclusion Model of Human Occupation research demonstrates a moderate level of treatment fidelity overall; it has stronger treatment fidelity from 2001 to the present. As the model progresses toward more outcomes studies, Model of Human Occupation scholars should report provider training and strategies that monitor treatment delivery to improve the quality and applicability of research outcomes.
A gait generation mechanism for leg rehabilitation therapy

A GAIT GENERATION MECHANISM FOR LEG REHABILITATION THERAPY by Yazan Ahmad Manna While most take their ability to walk for granted, some are unable to walk secondary to any number of pathologies, such as traumatic brain injury (TBI), spinal cord injury (SCI), cerebrovascular accidents (CVA), cerebral palsy (CP), multiple sclerosis (MS), Parkinson's disease, as well as various orthopedic conditions. Decreased activity has been shown to be associated with rapidly deconditioning and other co-morbidities. Rehabilitation techniques that afford patients the ability to begin reconditioning through walking sooner may ultimately enhance their return to a better quality of life. The overall goal of this study is to design a gait generation mechanism for rehabilitation of paralyzed legs. This mechanism should provide an appropriate afferent input to the spinal cord by moving the legs in a physiological way. This thesis focuses on the dimensional synthesis of a four-bar linkage to reproduce the desired ankle trajectory in the sagittal plane. The data of sagittal flexion/extension at the hip and knee joints from healthy people are used to define the desired ankle trajectory during normal gait cycle. A path generation four-bar mechanism is then synthesized to obtain proper link and coupler dimensions. The resulted coupler curve matches well with the desired ankle trajectory. A GAIT GENERATION MECHANISM FOR LEG REHABILITATION THERAPY by Yazan Ahmad Manna A Thesis Submitted to the Faculty of New Jersey Institute of Technology in Partial Fulfillment of the Requirements for the Degree of Master of Science in Mechanical Engineering Department of Mechanical Engineering
Silages prepared from different maize hybrids effect in-vitro rumen fermentation parameters and growth performance in crossbred calves

The experiment was conducted to evaluate the effects of silages prepared from different maize varieties/hybrids on fermentation characteristics, microbiological characteristics, and growth performance in growing crossbred calves. Female crossbred calves (18) of 4–5.5 months of age were selected and distributed randomly into 3 treatment groups of 6 animals each, based on their body weight. All the calves of 3 groups were offered silages prepared from different varieties/hybrids (control - Vijay composite, T1 - DKC 9108 and T2 - 900M Gold) and concentrate in 70: 30 ratio in 105 days of experimental period. Metabolism trial was conducted to assess feed intake, nutrients utilization and N balance. In vitro gas/methane production and digestibility trials were carried out for 24 h and 48 h respectively. In vitro methane production was higher in T1 than control and T2. The total DMI (kg/day) as well as body weight change in crossbred calves was similar in 3 groups throughout the experimental period. TDNI (kg/day) and NDF digestibility was significantly higher in T1 than control and T2 groups. CP digestibility was higher in control and T1 than T2. The results showed that DMI and growth performance of calves were similar in 3 groups notwithstanding the different chemical composition as well as different microbial characteristics of silages prepared from different maize varieties/hybrids. However methane production differed significantly among the groups which can be an area of interest for further mitigation studies.
Risk of deterioration among general ward patients: Nurses’ ability in assessing early warning signs

Background The challenge of recognizing ward-based patients at risk of deterioration is discussed frequently within the relevant literature. Nurses in particular hold the prime position to identify problems at an early stage using systematic patient assessment. However, general ward nurses’ perceived knowledge, attitudes, and practice related to assessment of the risk of deterioration are not well understood. Failures to recognize or act upon the deterioration of general ward patients has sometimes resulted in the implementation of early warning scoring systems and Critical Care Outreach teams. Aim: The study aim to explore general ward nurses’ perceived knowledge, attitude, and practice (KAP) in assessing patients at risk of deteriorating in general wards. Method A Cross-sectional study design with Modified Early Warning Score questionnaire for general ward nurses was done in one tertiary hospital in Malaysia in 2013 and 2014. Results: General ward nurses perceived that they struggled with knowledge and attitude, but they feel they performed good practice in assessing patients at risk for deterioration. Nevertheless, the study finding shows otherwise. Only one respondent achieved ‘grade B’ (85%) and the remainder scored in the band ‘grade F’ (very poor). The respondents’ attitude was measured by their perception of their levels of confidence and concern. The mean confidence level was greater than six out of 10 for all categories. The attitudes mean score ± SD was set at 42.02 ±7.76. The data showed that 51% (N=50) scored below mean core of 42.02. However, participants’ overall mean score ±SD for perceptions of practice (risk of deterioration assessment) was 90.27 ± 21.87 (6.94+/-1.683). The majority of participants awarded themselves a score between eight and nine, which is in the ‘good’ range for the scale (0-2 weak; 3-5 moderate; 6-8 good; 9-10 excellent). Those who scored above it were classified as having a good attitude. Conclusion: A need exists for general ward nurses to gain a knowledge foundation in detecting abnormality to address lack of confidence, poor attitude and alertness, and concern.
Is Good Health Contagious? The Impact of BMI Environment on Individual BMI

Increasing trends in obesity have driven policymakers around the US to examine factors associated with lower Body Mass Index (BMI) and improved health. Our research examines the relationship between an individual's health and their environment. Specifically, we examine whether moving to a state with a different statewide average BMI than the state of origin leads to changes in individual BMI. Combining individual data from the 1997 cohort of the National Longitudinal Survey of Youth with state-level data on average BMI from the Centers for Disease Control, we find that individuals experience changes in BMI that move their individual BMI based on the BMI of their destination state relative to their state of origin. The effect is largely due to female moving to states with much higher BMI than their state of origin. These individuals see an increase in their average BMI of approximately 2.5 percent and an increase in the likelihood of being overweight of approximately 9.8 percentage points.
Interspecific competition and species co - occurrence patterns on islands: null models and the evalu

A tracking band-pass filter useful for locking onto, and passing, an input signal which changes rapidly in frequency. The filter has a frequency pass band controlled by a rectangular voltage waveform which is derived from the output signal passed by the filter. The filter output signal is translated from a sine wave to a pulse wave. The period between each two successive pulses is measured by counting the cycles of an oscillator during each respective period. The time-representing count is inverted to a frequency-representing count which controls the duty cycle of a rectangular wave used to make the filter track the changing frequency of the input signal.
Effects of the Janani Suraksha Yojana on maternal and newborn care practices: Women's experiences in Rajasthan

This report is the result of a large-scale evaluation of the Janani Suraksha Yojana in rural and urban settings of the northwestern state of Rajasthan, India. The study explored recently delivered women's awareness and perceptions of the JSY, the reach of the scheme among the most vulnerable women, and the effects of the scheme on the utilisation of maternal health services, the adoption of best practices in newborn care and the quality of maternal health services. The Population Council is an international, non-profit, non-governmental organisation that seeks to improve the well-being and reproductive health of current and future generations around the world and to help achieve a humane, equitable and sustainable balance between people and resources. The Council conducts biomedical, social science and public health research, and helps build research capacities in developing countries.
A review of the impact of exercise on treatment-related fatigue among patients receiving adjuvant radiotherapy for breast cancer

Abstract Purpose To evaluate the use of exercise in managing fatigue in breast cancer patients undergoing adjuvant radiotherapy. To explore the effectiveness of different exercise practices and explore how optimum management of fatigue might be achieved. Method A CINAHL (Cumulative Index to Nursing and Allied Health Literature) database search of literature was undertaken and publications screened for retrieval with 24 qualifying for inclusion in the review. Results There is evidence to support various forms of exercise including aerobic, resistance, alternative and combination exercise in the management of fatigue in early stage breast cancer patients undergoing adjuvant radiotherapy. The benefits of exercise for patients with later stage and metastatic disease is less clear and there is a lack of published research related to this category of patient. Conclusion Exercise is considered a safe, non-pharmacological intervention for early stage breast cancer patients receiving adjuvant radiotherapy. Further investigation is required into optimum exercise interventions and the effectiveness and viability of supervised and unsupervised models. Patient centred tailored advice and guidance needs to be developed and effectively promoted by therapeutic radiographers in order for patients to fully realise the benefit.
Application of ICF Model to a Patient With Home Mechanical Ventilation: A Case Report With 1-Year Follow-up

Introduction:Physical therapy (PT) imparts positive benefits to patients using invasive mechanical ventilation. However, there is a paucity of literature detailing PT interventions for patients who require home mechanical ventilation (HMV). The purpose of this case report is to describe PT management of a patient using HMV using the International Classification of Functioning, Disability and Health (ICF) framework. Case Presentation:A 62-year-old woman with severe chronic obstructive pulmonary disease and a 6-year history of invasive HMV by tracheostomy was referred to home-based PT after an 11-day hospitalization in the intensive care unit. She participated in 8 weeks of PT to address activity and participation restrictions in her home environment. PT included progressive resistance training (PRT) and aerobic interval training (AIT). A 1-year follow-up was conducted to assess maintenance of gains. Conclusions:Home-based PT including PRT and AIT is feasible and safe for a patient undergoing HMV and resulted in improved participation in her activities of daily living. These improvements were partially maintained over the course of 1 year.
MRI for Crohn's disease : From quantification to automation

MRI has become an important technique for diagnosis and monitoring of Crohn’s disease. As there is increasing reliance on MRI to guide therapeutic decisions, accurate and reproducible tools for grading of disease activity are imperative. In this thesis, we show that MRI and CT can both be used to accurately grade Crohn’s disease activity, although MRI has the added benefit of not using ionizing radiation. We compare several available MRI scores, which are found to be similar in accuracy, reproducibility and diagnostic performance. However, considerable variability between radiologists remains an issue. To overcome this problem, we have developed and validated a semiautomatic MRI score, which increases the agreement between radiologists by automating parts of the radiologic evaluation. This includes newly developed MRI features, such as bowel wall volume and a dynamic contrast enhancement feature. In addition, we compare diffusion-weighted imaging (DWI) to contrast-enhanced MRI and show that DWI can be an acceptable alternative in patients with contraindications to intravenous contrast. Another technique called motility imaging is investigated and shows promise as a new biomarker for disease activity. Finally, we show that radiologists retain long-term performance, after being trained to grade Crohn’s disease on MRI.