Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Multiple Simian Immunodeficiency Virus (SIV)-Specific CTL Epitopes in Sooty Mangabeys with Natural and Experimentally Acquired SIV Infection1

Host immune responses to SIV infection in sooty mangabeys are likely to be an important determinant of how such nonhuman primate species maintain asymptomatic lentivirus infection. We have previously described two patterns of asymptomatic SIV infection in sooty mangabeys: low viral loads with vigorous SIV-specific CTL activity in SIVmac239-infected sooty mangabeys, and high viral loads with generally weak or absent SIV-specific CTL activity in naturally infected sooty mangabeys. To define the specificity of the CTL response in SIV-infected mangabeys, we characterized CTL epitopes in two naturally infected and three SIVmac239-infected sooty mangabeys. Compared with that in SIVmac239-infected mangabeys, the yield of SIV-specific CTL clones was significantly lower in naturally infected sooty mangabeys. All CTL clones were phenotypically CD3+ CD8+, and lysis was MHC restricted. Seven SIV CTL epitopes were identified in five sooty mangabeys: one in Gag and three each in Nef and Envelope (Env). The CTL epitopes mapped to conserved regions in the SIV genome and were immunodominant. Several similar or identical CTL epitopes were recognized by both naturally infected and SIVmac239-infected mangabeys that shared class I MHC alleles. To our knowledge, this is the first report of SIV-specific CTL epitopes in sooty mangabeys. Longitudinal studies of viral load and sequence variation in CTL epitopes may provide useful information on the role of CTL in control or persistence of SIV infection in sooty mangabeys.
A multi-scale assessment of the benthic communities of Bermuda's shallow water platform focusing on existing MPA's & control sites to enhance local management practices

In this report we describe the assessment of benthic ecological data collected across the reef platform as a first step, in order to determine areas of special ecological character that would benefit from additional protection under legislation. We also evaluated the effectiveness of Bermuda's existing MPA's in limiting damage to corals, through the use of comparative digital videography surveys, and highly appropriate recommendations which are of use to local resource managers. A second document reports the concurrent assessment of fish populations across the Bermuda Platform and within MPA versus control sites. Distinct differences were found between fringing reefs, lagoonal patch reef, rim reef and fore reef habitats Additionally, reefs within all types of habitat demonstrated high variability in most measures of coral reef condition and in coral and fish community structure. Lagoonal patch reefs could be broadly categorized into three types based on dominant coral species. These three types were: (1) Madracis Reefs, (2) Montastraea Reefs, and (3) Dipoloria-Porites Reefs. Madracis and Montastraea reefs appear to represent particularly unusual habitat. Fortunately the areas in which these two reef types are found are already benefiting from two levels of legislative protection, in that all corals are protected in Bermuda, and these reef types are located within the Northern Coral Reef Preserve, where no collecting of any benthic organisms are permitted. Rim reefs also can be subdivided into types based on location on the platform, as well as geomorphology. Deeper passes that intersect the shallow rim reef flats are statistically significantly different in coral cover and community structure. Several of these passes are currently protected as MPA sites, but additional passes should be protected as well. MPA sites did NOT differ from environmentally similar control sites in the cover of most benthic functional groups, especially coral cover, in that all sites were quite healthy. A lack of differences is probably due to the hardy nature of the corals that live in the rim habitat where the MPAs were located, as well as low levels of impact by divers or boaters. Chapter One: Introduction Bermuda, a United Kingdom Overseas Territory, is located on a 5560-hectare chain of limestone islands located in the North Atlantic near 32 o N 64 o W (Figure 3.01). Although Bermuda is north of the tropics, prevailing warm oceanic conditions support a limited number of small mangrove forests, extensive seagrass beds and well-developed coral reefs. The Bermuda reef platform …
Factors Associated with Pre-Hypertension Among Tehranian Adults: A Novel Application of Structural Equation Models

Background Pre-hypertension is proposed as an independent risk factor for the incidence of cardiovascular diseases. Objectives This study aimed to explore the main factors associated with pre-hypertension via testing a hypothesized model in Tehranian adults. Methods The study was conducted within the framework of the Tehran Lipid and Glucose Study (TLGS) between 2009 - 2011 on 4640 adults without hypertension, aged ≥ 20 years. Results The mean age of participants was 38.61 ± 12.14 years and 56.6% of them were female. More than one third of the studied participants had pre-hypertension (35.4%) with significantly higher prevalence in males compared to females (46.5% vs. 26.9%; χ2 = 190.7, P < 0.001). Age, waist circumference (WC), and serum triglyceride concentrations (TG) were directly associated with pre-hypertension in both men (β = 0.16, β = 0.25, and β = 0.11, respectively) and women (β = 0.16, β = 0.21 and β = 0.09, respectively). Physical activity, only in men (β = 0.07), and marital status only, in women (β = -0.06), were also directly associated with pre-hypertension. Both healthy and poor dietary patterns showed indirect associations with pre-hypertension in both genders via WC and TG. Higher age and lower education in both genders, being married only in men, and unemployed status only in women, were positively associated with pre-hypertension via behavioral and cardio-metabolic factors. Conclusions Level of TG and WC in both genders are direct modifiable associated factors of pre-hypertension. These findings could be considered in designing future health promotion programs aimed at preventing high blood pressure and its consequences among Tehranian adults.
Blow-analytic equivalence of two variable real analytic function germs

Blow-analytic equivalence is a notion for real analytic function germs, introduced by Tzee-Char Kuo in order to develop real analytic equisingularity theory. In this paper we give complete characterisations of blow-analytic equivalence in the two dimensional case: in terms of the real tree model for the arrangement of real parts of Newton-Puiseux roots and their Puiseux pairs, and in terms of minimal resolutions. These characterisations show that in the two dimensional case the blow-analytic equivalence is a natural analogue of topological equivalence of complex analytic function germs. Moreover, we show that in the two-dimensional case the blow-analytic equivalence can be made cascade, and hence satisfies several geometric properties. It preserves, for instance, the contact orders of real analytic arcs. In the general $n$-dimensional case, we show that a singular real modification satisfies the arc-lifting property.
How replicated data management in the cloud can benefit from a data grid protocol: the Re:GRIDiT Approach

Cloud computing has recently received considerable attention both in industry and academia. Due to the great success of the first generation of Cloud-based services, providers have to deal with larger and larger volumes of data. Quality of service agreements with customers require data to be replicated across data centers in order to guarantee a high degree of availability. In this context, Cloud Data Management has to address several challenges, especially when replicated data are concurrently updated at different sites or when the system workload and the resources requested by clients change dynamically. Mostly independent from recent developments in Cloud Data Management, Data Grids have undergone a transition from pure file management with read-only access to more powerful systems. In our recent work, we have developed the Re:GRIDiT protocol for managing data in the Grid which provides concurrent access to replicated data at different sites without any global component and supports the dynamic deployment of replicas. Since it is independent from the underlying Grid middleware, it can be seamlessly transferred to other environments like the Cloud. In this paper, we compare Data Management in the Grid and the Cloud, briefly introduce the Re:GRIDiT protocol and show its applicability for Cloud Data Management.
Derivation of the Rabi Equation by Means of the Pauli Matrices

The general quantum-mechanical properties of two-level systems are very relevant for the study of different physical subjects of great interest, as, for instance, magnetic resonance, nuclear physics, molecular dynamics, masers, neutrino oscillations, quantum computation, etc. In this work we present a nonperturbative approach to the study of the oscillations among two quantum states when an interaction term is considered. First, we show that using a simple parametrization for the superposition of the two states, it is possible to derive easily the Rabi equation. Next, we show that the Pauli matrices can be conveniently used to write the Hamiltonian operator and to derive the Rabi equation, directly applying the time evolution operator to the initial state of the system. c
Dealing with the deluge of historical weather data: the example of the TEMPEST database

People have long been interested in the history of weather, particularly extremes, and chronologies of past events drawing on information from written records have been compiled and published throughout history. In recent years, concern over current and future weather and climate has triggered a new level of interest in past weather events and their impacts. This interest, alongside the development of digital humanities research methods, has resulted in a rapid growth in the number of online databases relating to historic weather and climate around the world. This paper documents the design, creation and content of one such database, TEMPEST, an online repository for extreme weather history in the UK. TEMPEST has been created as the major output of the AHRC funded project ‘Spaces of Experience and Horizons of Expectation: The Implications of Extreme Weather in the UK, Past, Present and Future’ (2013-2017). Unlike the majority of existing databases that rely on published materials, TEMPEST's records are drawn from primary research into original documentary sources held in archives around the UK. The c. 18,000 records that TEMPEST currently contains offer personalised and geo-referenced insights into the relationship between society and extreme weather in the UK spanning a period of over 400 years. In this paper we outline potential applications for TEMPEST and suggest directions for future research and resources in historical weather. We also consider broader issues for the digital humanities relating to the storage, archiving, ownership, and usage of data and the need to ensure connectivity between complementary datasets.
Expression of fibroblast growth factor 21 in the liver of dairy cows in the transition period and during lactation.

Fibroblast growth factor 21 (FGF21) has been identified as a novel hormonal factor involved in the regulation of metabolic adaptations during energy deprivation. The present study aimed to investigate the expression of the FGF21 gene in the liver of dairy cows during the transition from pregnancy to lactation. Therefore, the relative mRNA abundance of FGF21 in liver biopsy samples of 20 dairy cows in late pregnancy (3 weeks pre-partum) and early lactation (1, 5, 14 weeks post-partum) was determined. It was observed that hepatic mRNA abundance of FGF21 at 1 week post-partum was dramatically increased (110-fold) compared to 3 weeks pre-partum (p < 0.001). With progress of lactation, mRNA concentration of FGF21 was declining; nevertheless, mRNA abundance at 5 and 14 weeks post-partum remained 25- and 10-fold increased compared to 3 weeks pre-partum (p < 0.001). Using a gene array technique, it was found that many genes involved in fatty acid oxidation, gluconeogenesis and ketogenesis were up-regulated during early lactation compared to late pregnancy. Moreover, there were positive linear correlations between hepatic mRNA concentration of FGF21 and mRNA concentrations of genes involved in ketogenesis as well as carnitine synthesis and carnitine uptake at various time-points during lactation, indicating that FGF21 could play a role in ketogenesis and carnitine metabolism in the liver of dairy cows (p < 0.05). In overall, the present study shows that expression of the FGF21 gene is strongly up-regulated during the transition period. It is assumed that the up-regulation of FGF21 might play an important role in the adaptation of liver metabolism during early lactation in dairy cows such as in other species.
Mixtures of Bayesian joint factor analyzers for noise robust automatic speech recognition

This paper investigates a noise robust approach to automatic speech recognition based on a mixture of Bayesian joint factor analyzers. In this approach, noisy features are modeled by two joint groups of factors accounting for speaker and noise variabilities which are estimated by clean and noisy speech respectively. The factors form an overcomplete dictionary with a redundant representation. Automatic relevance determination (ARD) is carried out by the relevance vector machine (RVM) where sparsity-promoting priors are applied on two factor loading matrices. Experiments on large vocabulary continuous speech recognition (LVCSR) tasks show good improvements by this approach.
Oxidative Damage and Antioxidative Therapy in Systemic Sclerosis

Systemic sclerosis (SSc) is an autoimmune connective tissue disorder of unknown etiology. This disease is characterized by a large variety of clinical patterns, which include the fibrosis of skin and visceral organs causing a variety of clinical manifestations. Genetic and environmental factors participate in the etiology of this disease; however, recently many studies underline the oxidative background influencing the course and complications of this disease. Reactive oxygen species (ROS) synthesized in SSc can mediate extra- and intracellular oxidative processes affecting endothelial cells and fibroblasts. The estimation of prooxidative markers in the pathogenesis of SSc can enable the identification of useful markers for disease activity and, thus, may help in planning appropriate therapy focusing on the fibrotic or vascular pattern. Recently, many attempts have been made to find antioxidative molecules (nutritional and pharmacological) reducing the prooxidant state in a variety of cells—mainly in endothelium and proliferating fibroblasts. This paper presents both the background of oxidative stress processes in systemic sclerosis mediated by different mechanisms and the evidence suggesting which of the dietary and pharmacological antioxidants can be used as therapeutic targets for this disease.
A real-time tracking system for in vivo endofunctional capsule using magnetic sensors

This paper presents a real-time magnetic tracking system to be used for tracking an endofunctional capsule intended to aid in the delivery of biomarkers to specific areas in the gastrointestinal (GI) tract. Magnetic technology is chosen due to its significant advantages over others like RF and Ultrasonics. The tracking system is designed to be used with eight magnetic sensors making it less complex than the other proposed systems. The paper describes a new mathematical model which is more accurate than the existing ones, a linear tracking algorithm and system's performance evaluation for three sensor configurations. The algorithm copes with the problem of magnetic field strength drop due to varying orientation of magnet. The minimum average error obtained is 1.37cm/6.85% in a 20×20×20 cm3 volume for two dimensional sensor configuration.
The Perception of Corporate Social Responsibility among Consumers in a Developing Nation

Corporate social responsibility is getting more and more attention from academia and managers, particularly in terms of how consumers perceive and react to corporate social responsibility or CSR. Nonetheless, the majority of this research was carried out from the perspective of advanced nations. It demonstrates the need for more research on how consumers in emerging nations perceive corporate social responsibility. This study will look at the perception of consumers of Pakistan being a developing country. The study's contradictory findings imply that CSR is still an idea that has to be implemented in underdeveloped nations. Consumers often have little knowledge of and are unsupportive of CSR. This finding is contrary to consumers’ perception in developed nations, who are willing to support corporate social responsibility (CSR) initiatives launched by organizations.
Myelin Basic Protein Priming Reduces the Expression of Foxp3 in T Cells via Nitric Oxide

Regulatory T cells (Tregs) play a vital role in autoimmune disorders. Among several markers, forkhead box p3 (Foxp3) is the most specific with regard to Treg activity. Therefore, understanding mechanisms that regulate Foxp3 expression is a critical step for unraveling the complicacy of autoimmune pathophysiology. The present study was undertaken to investigate the crosstalk between NO and Tregs. Interestingly, after myelin basic protein (MBP) priming, the expression of Foxp3 decreased in MBP-primed T cells. However, blocking NO either by inhibiting inducible NO synthase with l-N6-(1-iminoethyl)-lysine hydrochloride or through scavenging with PTIO or by pharmacological drugs, such as pravastatin, sodium benzoate, or gemfibrozil, restored the expression of Foxp3 in MBP-primed T cells. However, this restoration of Foxp3 by pharmacological drugs was reversed by S-nitrosoglutathione, an NO donor. Similarly, NO also decreased the populations of Tregs characterized by CD4+CD25+ and CD25+FoxP3+ phenotypes. We have further confirmed this inverse relationship between NO and Foxp3 by analyzing the mRNA expression of Foxp3 and characterizing CD25+FoxP3+ or CD4+Foxp3+ phenotypes from inducible NO synthase knockout mice. Moreover, this inverse relation between NO and Foxp3 also was observed during priming with myelin oligodendrocyte glycoprotein, another target neuroantigen in multiple sclerosis, as well as collagen, a target autoantigen in rheumatoid arthritis. Finally, we demonstrate that NO inhibited the expression of Foxp3 in MBP-primed T cells via soluble guanylyl cyclase-mediated production of cGMP. Taken together, our data imply a novel role of NO in suppressing Foxp3+ Tregs via the soluble guanylyl cyclase pathway.
Treatment decision-making in cancer care: the role of the carer.

AIMS AND OBJECTIVES This study explores the role of the carer in treatment decision-making in cancer care. BACKGROUND Literature about involvement in treatment decision-making tends to focus on patients and clinicians, with the carer rarely included. The absence of carers is problematic because the management of illness is often carried out in the context of complex networks of relationships. Although current policy encourages health care practitioners to work in partnership with family members, implementation is troubled by a lack of understanding of the significance of interpersonal relationships and interactions and the role of the relationship throughout the course of the illness experience. Despite awareness, there is little systematic, coherent analysis of the complexity of these interactional dynamics and, in particular, consideration of the implications for involvement and treatment decision-making. DESIGN Qualitative, longitudinal. METHODS Three serial semi-structured interviews with 66 patients and 43 carers within the first year following a diagnosis of cancer. A descriptive and thematic approach to data analysis was adopted. RESULTS Carers are involved in treatment decision-making in cancer care and contribute to the involvement of patients through their actions during, before and after consultations with clinicians. Carers can act as conduits for information from patient to clinician and from clinician to patient. They can also act as facilitators during deliberations, helping patients to consider whether to have treatment or not and which treatment. CONCLUSIONS Our study has highlighted the deficiency of models that fail to acknowledge the role of the carer in the treatment decision-making process. We propose the adoption of a relational approach by the inclusion of the carer in conceptual frameworks and recommend triadic (patient, carer and professional) models of involvement. RELEVANCE TO CLINICAL PRACTICE Cancer care clinicians should recognise and actively involve the carer as well as the patient in treatment decision-making.
Anesthesia, Outcomes, and Public Health: Changing Health Care While “Asleep”

Abstract More than 50 million surgical procedures are performed annually in the United States, with perioperative complications and related long-term adverse outcomes profoundly affecting the nation’s health. A growing number of studies recognize that type of anesthesia, a main determinant of perioperative care, is associated with perioperative morbidity and mortality. Emerging data suggest, for example, that anesthesia may be a determinant of cancer recurrence after surgery. Further research is needed to elucidate the impact of anesthesia-related factors on short- and long-term health outcomes. Progress in this area of medicine and its public-health consequences will depend largely on the interest of the public, researchers, and health care policy makers.
Computational Prediction of an Antimony-Based n-Type Transparent Conducting Oxide: F-Doped Sb2O5

Transparent conducting oxides (TCOs) possess a unique combination of optical transparency and electrical conductivity, making them indispensable in optoelectronic applications. However, their heavy dependence on a small number of established materials limits the range of devices that they can support. The discovery and development of additional wide bandgap oxides that can be doped to exhibit metallic-like conductivity are therefore necessary. In this work, we use hybrid density functional theory to identify a binary Sb(V) system, Sb2O5, as a promising TCO with high conductivity and transparency when doped with fluorine. We conducted a full point defect analysis, finding F-doped Sb2O5 to exhibit degenerate n-type transparent conducting behavior. The inherently large electron affinity found in antimony oxides also widens their application in organic solar cells. Following our previous work on zinc antimonate, this work provides additional support for designing Sb(V)-based oxides as cost-effective TCOs for a broader range of applications.