Miracle-dz/UniFAR-FTUs huggingface dataset:
Compliance with antiretroviral regimens to prevent perinatal HIV-1 transmission in Kenya

Objective: To compare compliance and infant HIV-1 infection risk at 6 weeks with the Thai-CDC and HIVNET-012 antiretroviral regimens in a field setting. Design: Randomized clinical trial. Setting: Tertiary hospital antenatal clinic in Nairobi, Kenya. Participants: HIV-1 infected women referred from primary care clinics. Interventions: Thai-CDC zidovudine regimen or HIVNET-012 nevirapine regimen. Main outcome measures: Women were considered compliant if they used ⩾ 80% of the doses. Infants were tested for HIV-1 at 6 weeks. Results: Seventy women were randomized to Thai-CDC and 69 to HIVNET-012 regimens. More women were compliant with the antenatal (86%) than the intrapartum (44%) Thai-CDC regimen doses (P = 0.001). Ninety-seven per cent took the maternal and 91% gave the infant dose of the HIVNET-012 regimen (P = 0.2). Overall, 41% were compliant with the Thai-CDC regimen and 87% with the HIVNET-012 regimen (P < 0.001). Compliance with the Thai-CDC regimen was associated with partner support of antiretroviral use [odds ratio (OR), 3.0;, 95% confidence interval (CI), 1.0–9.1] and knowledge at recruitment that antiretroviral drugs could prevent infant HIV-1 (OR, 2.9; 95% CI, 1.0–8.1). Compliance with the HIVNET-012 regimen was associated with partner notification (OR, 8.0; 95% CI, 1.5–50) and partner willingness to have HIV-1 testing (OR, 7.5; 95% CI, 1.4–40). There was a trend for a higher risk of transmission with the HIVNET-012 regimen than with the Thai-CDC regimen (22% versus 9%; P = 0.07). Conclusion: Compliance with the Thai-CDC and HIVNET-012 regimens was comparable to that in efficacy trials. Partner involvement, support and education on perinatal HIV-1 prevention may improve compliance and increase the number of infants protected from HIV-1 infection.
Hemispheric dominance and cell phone use.

IMPORTANCE A thorough understanding of why we hold a cell phone to a particular ear may be of importance when studying the impact of cell phone safety. OBJECTIVE To determine if there is an obvious association between sidedness of cell phone use and auditory hemispheric dominance (AHD) or language hemispheric dominance (LHD). It is known that 70% to 95% of the population are right-handed, and of these, 96% have left-brain LHD. We have observed that most people use their cell phones in their right ear. DESIGN An Internet survey was e-mailed to individuals through surveymonkey.com. The survey used a modified Edinburgh Handedness Inventory protocol. Sample questions surveyed which hand was used to write with, whether the right or left ear was used for phone conversations, as well as whether a brain tumor was present. SETTING General community. PARTICIPANTS An Internet survey was randomly e-mailed to 5000 individuals selected from an otology online group, patients undergoing Wada testing and functional magnetic resonance imaging, as well as persons on the university listserv, of which 717 surveys were completed. MAIN OUTCOME AND MEASURE Determination of hemispheric dominance based on preferred ear for cell phone use. RESULTS A total of 717 surveys were returned. Ninety percent of the respondents were right handed, and 9% were left handed. Sixty-eight percent of the right-handed people used the cell phone in their right ear, 25% in the left ear, and 7% had no preference. Seventy-two of the left-handed respondents used their left ear, 23% used their right ear, and 5% had no preference. Cell phone use averaged 540 minutes per month over the past 9 years. CONCLUSIONS AND RELEVANCE An association exists between hand dominance laterality of cell phone use (73%) and our ability to predict hemispheric dominance. Most right-handed people have left-brain LHD and use their cell phone in their right ear. Similarly, most left-handed people use their cell phone in their left ear. Our study suggests that AHD may differ from LHD owing to the difference in handedness and cell phone ear use. Literature suggests a possible relationship between cell phone use and cancer. The fact that few tumors were identified in this population does not rule out an association.
Evaluation of software dependability based on stability test data

The paper discusses a measurement-based approach to dependability evaluation of fault-tolerant, real-time software systems based on failure data collected from stability tests of an air traffic control system under development. Several dependability analysis techniques are illustrated with the data: parameter estimation, availability modeling of software from the task level, applications of the parameter estimation and model evaluation in assessing availability, identifying key problem areas, and predicting required test duration for achieving desired levels of availability and quantification of relationships between software size, the number of faults, and failure rate for a software unit. Although most discussion is focused on a typical subsystem, Sector Suite, the discussed methodology is applicable to other subsystems and the system. The study demonstrates a promising approach to measuring and assessing software availability during the development phase, which has been increasingly demanded by the project management of developing large, critical systems. <<ETX>>
Outcomes and Coping Following Parental Bereavement

1 Background 1 Method 1 Results 1 Conclusions 2 Publications Arising from this Thesis 7 Chapter One Introduction 20 1.0 Abstract 20 1.0. 1 Background 20 1.0. 2 Method 20 1.0. 3 Results 20 1.0. 4 Conclusions 20 1.1 Overview 21 1.1.1 Definition of Bereavement 21 1.2 Historical Perspective on Grief and Bereavement 21 1.2. 1 Freud’s Comparison of Mourning and Melancholia 21 1.2. 2 Engel’s Theory of Grief as a Disease 22 1.2. 3 Bowlby’s Attachment Perspective on Loss 22 1.2. 4 Parkes and Weiss’s Psychosocial Transitions in Bereavement 24 1.3 Contemporary Models of Bereavement 25 1.3. 1 Dual Process Model of Bereavement 25 1.3. 2 Integrative Risk Factor Framework for Coping with Bereavement 27 1.4 Social Theories of Bereavement 28 1.5 Prolonged Grief as a Distinct Diagnostic Condition 28 1.6 Outcomes for Bereaved Parents 32 1.6. 1 Health Outcomes 32 1.6. 2 Changes in Social Functioning 34 1.6. 3 Emotional Consequences 35 1.7 Aims of the Thesis 35 1.8 Thesis Structure 36 Chapter Two – Literature Review of Factors Associated with Differential Outcomes of Parental Bereavement 38 2.0 Abstract 38 2.0. 1 Background 38 2.0. 2 Method 38 2.0. 3 Results 38 2.0. 4 Conclusions 39 2.
Decision support models

Several points of view may be taken if we want to describe a dairy farm. An animal nutritionist would focus on the individual animal and describe how feeds are transformed to meat, bones, tissues, skin, hair, embryos, milk, manure etc. A physiologist would further describe the roles of the various organs in this process and how the transformations are regulated by hormones. A biochemist would even describe the basic processes at molecular level.
Performance augmentation in hybrid bionic systems: techniques and experiment

Recent developments in hybrid biological-technological systems (hybrid bionic systems) has made clear the need for evaluating ergonomic fit in such systems, especially as users first become adjusted to using such systems. This training is accompanied by physiological adaptation, and can be thought of computationally as a relative degree of matching between prosthetic devices, physiology, and behavior. Achieving performance augmentation involves two features of performance: a specific form of learning, memory, and mechanotransduction called sensorimotor learning, and physiological adaptation to novel physical information imposed by the augmented environment of hybrid bionic systems. A method borrowed from environmental medicine involving perturbing the environment for a range of internal physiological conditions was used to induce sensorimotor learning and memory associated physiological changes. In addition, features of the adult phenotype were considered as a mitigator of learning-related adaptations. Using a series of statistical tests and techniques, the results demonstrate than three forms of regulation are at work related to morphological, neural, and muscular control. A discussion of the conceptual relationship between homeostasis and adaptation will then be discussed in addition to potential applications to performance augmentation strategies.
Phylogeny and dating of divergences within the genus Thymallus (Salmonidae: Thymallinae) using complete mitochondrial genomes

Abstract The genus Thymallus has attracted increasing attention in recent years because of its sharp demographic decline. In this study, we reported four complete mitochondrial genomes in the Thymallus genus: Baikal-Lena grayling (T. arcticus baicalolenensis), lower Amur grayling (T. tugarinae), Yalu grayling (T. a. yaluensis), and Mongolian grayling (T. brevirostris). The total length of the four new grayling mtDNAs ranged from 16 658 to 16 663 bp, all of which contained 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region. The results suggested that mitochondrial genomes could be a powerful marker for resolving the phylogeny within Thymallinae. Our study validated that the Yalu grayling should be a synonym of the Amur grayling (T. grubii) at the whole mitogenome level. The phylogenetic and dating analyses placed the Amur grayling at the deepest divergence node within Thymallus, diverging at ∼14.95 Ma. The lower Amur grayling diverged at the next deepest node (∼12.14 Ma). This was followed by T. thymallus, which diverged at ∼9.27 Ma. The Mongolian grayling and the ancestor of the sister species, T. arcticus and T. arcticus baicalolenensis, diverged at ∼7.79 Ma, with T. arcticus and T. arcticus baicalolenensis separating at ∼6.64 Ma. Our study provides far better resolution of the phylogenetic relationships and divergence dates of graylings than previous studies.
NATIONAL CONTEXT, SOCIAL CHANGE, AND SEX DIFFERENCES IN SUICIDE RATES

Rejecting claims of either convergence or divergence in male and female suicide rates associated with changes in gender equality, I examine a hypothesis of institutional adjustment in which the sex differential in suicide rates first narrows and then widens with continued societal change. Further, I argue that among high-income nations, the degree of institutional adjustment varies with national context. Using aggregate data on age-specific suicide rates for men and women in 18 nations from 1953 to 1992, the analysis shows curvilinear effects of age, time, the female labor force participation rate, the divorce rate, and the marriage rate consistent with the institutional adjustment hypothesis. The analysis also shows that adjustment occurs more quickly among nations with collectivist rather than individualist institutions of social protection.
A Restricted Role for TYK2 Catalytic Activity in Human Cytokine Responses Revealed by Novel TYK2-Selective Inhibitors

TYK2 is a JAK family protein tyrosine kinase activated in response to multiple cytokines, including type I IFNs, IL-6, IL-10, IL-12, and IL-23. Extensive studies of mice that lack TYK2 expression indicate that the IFN-α, IL-12, and IL-23 pathways, but not the IL-6 or IL-10 pathways, are compromised. In contrast, there have been few studies of the role of TYK2 in primary human cells. A genetic mutation at the tyk2 locus that results in a lack of TYK2 protein in a single human patient has been linked to defects in the IFN-α, IL-6, IL-10, IL-12, and IL-23 pathways, suggesting a broad role for TYK2 protein in human cytokine responses. In this article, we have used a panel of novel potent TYK2 small-molecule inhibitors with varying degrees of selectivity against other JAK kinases to address the requirement for TYK2 catalytic activity in cytokine pathways in primary human cells. Our results indicate that the biological processes that require TYK2 catalytic function in humans are restricted to the IL-12 and IL-23 pathways, and suggest that inhibition of TYK2 catalytic activity may be an efficacious approach for the treatment of select autoimmune diseases without broad immunosuppression.
Arterial‐Venous Nitroglycerin Gradient During Intravenous Infusion in Man

We assessed the concentration of nitroglycerin (GTN) measured in plasma at different sampling sites in the circulation during a constant i.v. infusion. Twenty patients with chronic congestive cardiac failure underwent hemodynamic monitoring during i.v. GTN infusion. Our end point was a reduction in pulmonary capillary wedge pressure by at least 25% of its control value or a 10‐fold increment over the initial infusion rate. Nitroglycerin infusion produced no change in heart rate, a reduction in mean arterial pressure from 90 ± 21 (± SD) to 83 ± 17 mm Hg (p< 0.001), a fall in total peripheral resistance from 24.3 ± 10.8 to 20.8 ± 7.0 units (p < 0.02), and a substantial reduction in both pulmonary capillary wedge pressure (from 27 ± 6 to 20 ± 6 mm Hg, p < 0.001) and right atrial pressure (from 12 ± 4 to 8 ± 4mm Hg, p < 0.001). The concentrations of GTN in the pulmonary artery and systemic artery were similar (29.8 ng/ml ± 52.8 and 25.1 ± 48.4 ng/ml, respectively) and considerably higher than the concentration in the peripheral vein (7.3 ± 15.4 ng/ml). There was a 17.4 ± 19.1% extraction of GTN across the pulmonary vascular bed and a 60.8 ± 27.2% extraction across the arterial-venous bed (p < 0.001). There was norelationship between the arterial-venous extraction and the magnitude of arterial plasma GTN concentration, the duration of the infusion of GTN or the total dose administered. These data show that a better understanding of GTN pharmacokinetics is provided by simultaneous arterial and venous samples.
Primary Sclerosing Cholangitis with Inflammatory Bowel Disease in Korean Children

Purpose Primary sclerosing cholangitis (PSC) is a rare condition that can be associated with inflammatory bowel disease (IBD). The aim of this study was to evaluate PSC and its association with IBD in children. Methods We retrospectively enrolled 13 pediatric patients (<18 years) with PSC treated at Asan Medical Center between June 1989 and December 2013. Clinical findings and long-term outcomes were investigated. During the same period, the incidence of PSC among IBD patients was evaluated among 600 Crohn disease (CD) and 210 ulcerative colitis (UC) patients. Results All 13 study patients diagnosed with PSC also presented with IBD. Eleven boys and two girls with a median age of 15.0 years old (9.0-17.8 years) were included. The cumulative incidence of PSC for UC was 5.7% (12 of 210) and 0.2% for CD (1 of 600), respectively. PSC occurred during follow-up for IBD for five patients (38.5%) whereas, IBD developed during follow-up for PSC for two patients (15.4%), and was diagnosed during the initial work-up for PSC for 6 patients (46.2%). For the 77.3 month median follow-up period, 9/13 patients (69.2%), neither the clinical symptoms nor blood test results worsened. Two cases (15.4%) developed liver cirrhosis and underwent liver transplantation. Among 13 PSC patients with IBD, two (15.4%) developed colorectal cancer, and no one developed cholangiocarcinoma. Conclusion All patients with PSC in this study had associated IBD. The incidence of PSC was not rare compared to reports in adults. PSC should be considered during the management of IBD and vice versa in children.
Predicting Peptide Binding Affinities to MHC Molecules Using a Modified Semi-Empirical Scoring Function

The Major Histocompatibility Complex (MHC) plays an important role in the human immune system. The MHC is involved in the antigen presentation system assisting T cells to identify foreign or pathogenic proteins. However, an MHC molecule binding a self-peptide may incorrectly trigger an immune response and cause an autoimmune disease, such as multiple sclerosis. Understanding the molecular mechanism of this process will greatly assist in determining the aetiology of various diseases and in the design of effective drugs. In the present study, we have used the Fresno semi-empirical scoring function and modify the approach to the prediction of peptide-MHC binding by using open-source and public domain software. We apply the method to HLA class II alleles DR15, DR1, and DR4, and the HLA class I allele HLA A2. Our analysis shows that using a large set of binding data and multiple crystal structures improves the predictive capability of the method. The performance of the method is also shown to be correlated to the structural similarity of the crystal structures used. We have exposed some of the obstacles faced by structure-based prediction methods and proposed possible solutions to those obstacles. It is envisaged that these obstacles need to be addressed before the performance of structure-based methods can be on par with the sequence-based methods.
Environmental and Public Health Implications of Water Reuse: Antibiotics, Antibiotic Resistant Bacteria, and Antibiotic Resistance Genes

Water scarcity is a global problem, and is particularly acute in certain regions like Africa, the Middle East, as well as the western states of America. A breakdown on water usage revealed that 70% of freshwater supplies are used for agricultural irrigation. The use of reclaimed water as an alternative water source for agricultural irrigation would greatly alleviate the demand on freshwater sources. This paradigm shift is gaining momentum in several water scarce countries like Saudi Arabia. However, microbial problems associated with reclaimed water may hinder the use of reclaimed water for agricultural irrigation. Of particular concern is that the occurrence of antibiotic residues in the reclaimed water can select for antibiotic resistance genes among the microbial community. Antibiotic resistance genes can be associated with mobile genetic elements, which in turn allow a promiscuous transfer of resistance traits from one bacterium to another. Together with the pathogens that are present in the reclaimed water, antibiotic resistant bacteria can potentially exchange mobile genetic elements to create the “perfect microbial storm”. Given the significance of this issue, a deeper understanding of the occurrence of antibiotics in reclaimed water, and their potential influence on the selection of resistant microorganisms would be essential. In this review paper, we collated literature over the past two decades to determine the occurrence of antibiotics in municipal wastewater and livestock manure. We then discuss how these antibiotic resistant bacteria may impose a potential microbial risk to the environment and public health, and the knowledge gaps that would have to be addressed in future studies. Overall, the collation of the literature in wastewater treatment and agriculture serves to frame and identify potential concerns with respect to antibiotics, antibiotic resistant bacteria, and antibiotic resistance genes in reclaimed water.
Detecting False Data Injection Attacks on DC State Estimation

State estimation is an important power system application that is used to estimate the state of the power transmission networks using (usually) a redundant set of sensor measurements and network topology information. Many power system applications such as contingency analysis rely on the output of the state estimator. Until recently it was assumed that the techniques used to detect and identify bad sensor measurements in state estimation can also thwart malicious sensor measurement modification. However, recent work by Liu et al. [1] demonstrated that an adversary, armed with the knowledge of network configuration, can inject false data into state estimation that uses DC power flow models without being detected. In this work, we explore the detection of false data injection attacks of [1] by protecting a strategically selected set of sensor measurements and by having a way to independently verify or measure the values of a strategically selected set of state variables. Specifically, we show that it is necessary and sufficient to protect a set of basic measurements to detect such attacks.
Real-World Drug Costs of Treating Hepatitis C Genotypes 1-4 with Direct-Acting Antivirals: Initiating Treatment at Fibrosis 0-2 and 3-4

BACKGROUND: Direct-acting antivirals (DAA) for the treatment of hepatitis C virus (HCV) have drastically improved outcomes but are also very costly. For this reason, priority for treatment is often given to patients with a higher fibrosis score at baseline by payers and providers rather than treating all eligible patients. Simulation studies have suggested that waiting to treat patients until fibrosis 3-4 may be more costly and result in worse outcomes; however, real-world implications are unknown. OBJECTIVE: To determine drug costs and outcomes for treating hepatitis C in patients with fibrosis scores of 0-2 and 3-4 at baseline in a real-world ambulatory care setting. METHODS: A total of 322 patients at 36 clinical sites in Massachusetts with HCV genotype 1-4 and a prescription for at least 1 DAA medication between May 2011 and October 2015 were included. Retrospective and prospective chart reviews were completed by the primary investigator. Data were collected through April 2016. The primary outcome for the study was to determine the mean drug cost per sustained virologic response (SVR) achieved for patients with fibrosis scores of 0-2 and 3-4. Drug costs were calculated using average wholesale price and only included the cost of HCV medications, not for adjunctive medications, blood work, hospitalizations, anticipated complications, or any other projected medical costs. RESULTS: The mean ± SD (median) drug cost per patient was $130,391 ± 46,787 (113,400) and completed treatment duration was 15.0 ± 8.9 (12) weeks. The mean drug cost per SVR was $155,662 for all patients with a mean drug cost per SVR of $122,452 and $178,401 for patients with fibrosis scores of 0-2 and 3-4, respectively. SVR rates were 83.5% (269/322) for all patients and 92.2% (107/116) and 78.6% (162/206) for patients with fibrosis scores of 0-2 and 3-4, respectively. Ledipasvir/sofosbuvir; sofosbuvir + ribavirin; ledipasvir/sofosbuvir + ribavirin; sofosbuvir + interferon + ribavirin; boceprevir + interferon + ribavirin; sofosbuvir + simeprevir; and telaprevir + interferon + ribavirin had a mean drug cost per SVR of $123,559; $153,347; $157,969; $184,800; $248,640; $251,550; and $373,333; respectively. CONCLUSIONS: Real-world knowledge about outcomes and drug costs may influence future decisions. Further studies are needed to evaluate emerging treatment options and to reflect changes in treatment guidelines.