Miracle-dz/UniFAR-FTUs huggingface dataset:
HIV-1 outcompetes HIV-2 in dually infected Senegalese individuals with low CD4+ cell counts

Objective:Dual infection with HIV-1 and HIV-2, which is not uncommon in West Africa, has implications for transmission, progression, and antiretroviral therapy (ART). Few studies have examined viral dynamics in this setting. Our objective was to directly compare HIV-1 and HIV-2 viral loads and to examine whether this relationship is associated with CD4+ cell count. Study design:This is a retrospective analysis of data from observational cohort studies. Methods:We compared HIV-1 and HIV-2 viral loads from 65 dually infected, ART-naive Senegalese individuals. Participants provided blood, oral fluid, and cervicovaginal lavage (CVL) or semen samples for virologic and immunologic testing. We assessed relationships between HIV-1 and HIV-2 levels using linear regression with generalized estimating equations to account for multiple study visits. Results:After adjusting for CD4+ cell count, age, sex, and commercial sex work, HIV-1 RNA levels were significantly higher than HIV-2 levels in semen, CVL, and oral fluids. Despite similar peripheral blood mononuclear cell DNA levels among individuals with CD4+ cell counts above 500 cells/&mgr;l, individuals with CD4+ cell counts below 500 cells/&mgr;l had higher HIV-1 and lower HIV-2 DNA levels. Individuals with high CD4+ cell counts had higher mean HIV-1 plasma RNA viral loads than HIV-2, with HIV-1 levels significantly higher and HIV-2 levels trending toward lower mean viral loads among individuals with low CD4+ cell counts. Conclusion:Our data are consistent with the hypothesis that with disease progression, HIV-1 outcompetes HIV-2 in dually infected individuals. This finding helps explain differences in prevalence and outcomes between HIV-1, HIV-2, and HIV-dual infection.
Half-Octave Shift in Mammalian Hearing Is an Epiphenomenon of the Cochlear Amplifier

The cochlear amplifier is a hypothesized positive feedback process responsible for our exquisite hearing sensitivity. Experimental evidence for or against the positive feedback hypothesis is still lacking. Here we apply linear control theory to determine the open-loop gain and the closed-loop sensitivity of the cochlear amplifier from available measurements of basilar membrane vibration in sensitive mammalian cochleae. We show that the frequency of peak closed-loop sensitivity is independent of the stimulus level and close to the characteristic frequency. This implies that the half-octave shift in mammalian hearing is an epiphenomenon of the cochlear amplifier. The open-loop gain is consistent with positive feedback and suggests that the high-frequency cut-off of the outer hair cell transmembrane potential in vivo may be necessary for cochlear amplification.
Similarity of Bacteriocin Activity Profiles of Mutans Streptococci within the Family When the Children Acquire the Strains After the age of 5

It has been shown that there is a window of infectivity for mutans streptococci between the ages of 19 and 31 months, when many children acquire mutans streptococci transmitted from their mothers. Part of the children that escape this window acquire mutans streptococci at a later age. In this group, maternal transmission is expected to be less prevalent. The present study compared the bacteriocin activity profiles of mutans streptococci isolated from mothers, fathers and children when the children acquired the mutans streptococci between the ages of 5 and 11. Twelve families were randomly selected from a group of 11–year–old children who were known to have acquired mutans streptococci during this age period. From the saliva of the mothers (n = 12), fathers (n = 8) and children (n = 12) approximately 30 mutans streptococci strains were isolated. All isolates were tested twice for bacteriocin activity against 21 indicator strains with a double–layer technique. Bacteriocin activity of strains was considered to be different when the number of strains against which bacteriocin was produced differed >1 or when the width of one or more inhibition zones differed ≥4 mm. In 7/12 mother–child pairs similar profiles were found. In the 8 father–child pairs similar profiles were only found on 2 occasions. In these 2 families, all 3 ( mother, father and child) harboured strains with a similar profile. In 4/8 father–mother pairs similar profiles were found. There was no correlation between the prevalence of mutans streptococci strains, the number of indicator strains against which the strains made bacteriocin, nor the mean size of the inhibition zones and the presence of similarity of bacteriocin activity profiles of mutans streptococci within the family members. The results show that even when a child acquires mutans streptococci after the age of 5, there may be similarity between mutans streptococci in mother, father and child, indicating that transmission between the family members occurs.
Risk Score Model for Predicting Sonographic Non-alcoholic Fatty Liver Disease in Children and Adolescents

Objective This study aimed to develop and test the validity of a risk score to be used as a simple tool to identify those children at high risk of sonographic non-alcoholic fatty liver disease (NAFLD). Methods This cross-sectional study was conducted among 962 participants aged 6–18 years in Isfahan, Iran. They consisted of three groups of nearly equal number of normal-weight, overweight and obese individuals. Coefficients of the logistic regression models were used to assign a score value for each variable and the composite sonographic NAFLD risk score was calculated as the sum of those scores. Performance of model was assessed by receiver operating characteristic (ROC) curve procedure. Findings Data of 931 participants was included in the analysis. The sonographic findings of 16.8% of participants were compatible with NAFLD. Age, sex, body mass index, waist circumference and serum triglycerides level were diagnosed as factors associated with NAFLD. The risk score was calculated as 50 for sonographic NAFLD. Conclusion This study, to the best of our knowledge is the first of its kind in the pediatric age group, focuses on predicting sonographic NAFLD from easily-measured factors. It may suggest an association of hypertriglyceridemic-waist phenotype with NAFLD in the pediatric age group.
Photon number localization of ground states in nonrelativistic QED

One electron system minimally coupled to a quantized radiation field is considered. It is assumed that the quantized radiation field is massless, and no infrared cutoff is imposed. The Hamiltonian, H, of this system is defined as a self-adjoint operator acting on L2(R3) ⊗ F , where F is the Boson Fock space over L2(R3 × {1, 2}). It is shown that the ground state, ψg, of H belongs to ∩k=1D(1 ⊗Nk), where N denotes the photon number operator of F . Moreover it is shown that, for almost every electron position variable x ∈ R3 and for arbitrary k ≥ 0, ‖(1⊗N)ψg(x)‖F ≤ Dke m+1 with some constants m, Dk, and δ independent of k In particular ψg ∈ ∩k=1D(e m+1 ⊗Nk) for 0 < β < δ/2 is obtained.
Parameterization of Mixed Layer and Deep-Ocean Mesoscales including Nonlinearity

AbstractIn 2011, Chelton et al. carried out a comprehensive census of mesoscales using altimetry data and reached the following conclusions: “essentially all of the observed mesoscale features are nonlinear” and “mesoscales do not move with the mean velocity but with their own drift velocity,” which is “the most germane of all the nonlinear metrics. ” Accounting for these results in a mesoscale parameterization presents conceptual and practical challenges since linear analysis is no longer usable and one needs a model of nonlinearity. A mesoscale parameterization is presented that has the following features: 1) it is based on the solutions of the nonlinear mesoscale dynamical equations, 2) it describes arbitrary tracers, 3) it includes adiabatic (A) and diabatic (D) regimes, 4) the eddy-induced velocity is the sum of a Gent and McWilliams (GM) term plus a new term representing the difference between drift and mean velocities, 5) the new term lowers the transfer of mean potential energy to mesoscales, 6) th.
Deaths from pesticide poisoning: a global response

Summary Self-poisoning with pesticides accounts for about a third of all suicides worldwide. To tackle this problem, the World Health Organization announced a global public health initiative in the second half of 2005. Planned approaches were to range from government regulatory action to the development of new treatments for pesticide poisoning. With broad-based support, this strategy should have a major impact on the global burden of suicide.
Obstructive Sleep Apnea Syndrome: From Phenotype to Genetic Basis

Obstructive sleep apnea syndrome (OSAS) is a complex chronic clinical syndrome, characterized by snoring, periodic apnea, hypoxemia during sleep, and daytime hypersomnolence. It affects 4-5% of the general population. Racial studies and chromosomal mapping, familial studies and twin studies have provided evidence for the possible link between the OSAS and genetic factors and also most of the risk factors involved in the pathogenesis of OSAS are largely genetically determined. A percentage of 35-40% of its variance can be attributed to genetic factors. It is likely that genetic factors associated with craniofacial structure, body fat distribution and neural control of the upper airway muscles interact to produce the OSAS phenotype. Although the role of specific genes that influence the development of OSAS has not yet been identified, current researches, especially in animal model, suggest that several genetic systems may be important. In this chapter, we will first define the OSAS phenotype, the pathogenesis and the risk factors involved in the OSAS that may be inherited, then, we will review the current progress in the genetics of OSAS and suggest a few future perspectives in the development of therapeutic agents for this complex disease entity.
Identification of Genes That Promote or Antagonize Somatic Homolog Pairing Using a High-Throughput FISH–Based Screen

The pairing of homologous chromosomes is a fundamental feature of the meiotic cell. In addition, a number of species exhibit homolog pairing in nonmeiotic, somatic cells as well, with evidence for its impact on both gene regulation and double-strand break (DSB) repair. An extreme example of somatic pairing can be observed in Drosophila melanogaster, where homologous chromosomes remain aligned throughout most of development. However, our understanding of the mechanism of somatic homolog pairing remains unclear, as only a few genes have been implicated in this process. In this study, we introduce a novel high-throughput fluorescent in situ hybridization (FISH) technology that enabled us to conduct a genome-wide RNAi screen for factors involved in the robust somatic pairing observed in Drosophila. We identified both candidate “pairing promoting genes” and candidate “anti-pairing genes,” providing evidence that pairing is a dynamic process that can be both enhanced and antagonized. Many of the genes found to be important for promoting pairing are highly enriched for functions associated with mitotic cell division, suggesting a genetic framework for a long-standing link between chromosome dynamics during mitosis and nuclear organization during interphase. In contrast, several of the candidate anti-pairing genes have known interphase functions associated with S-phase progression, DNA replication, and chromatin compaction, including several components of the condensin II complex. In combination with a variety of secondary assays, these results provide insights into the mechanism and dynamics of somatic pairing.
Economic impact of converting from 10-mL insulin vials to 3-mL vials and pens in a hospital setting.

PURPOSE The economic impact associated with the conversion from 10-mL vials of insulin to 3-mL vials and pens at a community hospital was assessed. METHODS Pharmacy purchasing and administrative data from Providence St. Vincent Hospital in Portland, Oregon, were used in this analysis. The hospital converted floor-stock 10-mL vials of insulin in October 2010 to individual patient supply (IPS) 3-mL vials and pens. Insulin acquisition costs from the nine-month preconversion period were compared with those during the nine-month postconversion period. RESULTS Before the conversion, total acquisition costs were $168,783 for 5,086,500 units of insulin. After the conversion, total acquisition costs were reduced by 8.6% (to $154,303) and units purchased were reduced by 33.1% (to 3,404,900 units of insulin). The analyses also examined the results of converting to 3-mL vials of rapid-, short-, or intermediate-acting insulin to 3-mL pens of long-acting insulin analog. Conversion from 10- to 3-mL vials was associated with a 37.6% reduction in units of insulin and a 23.5% reduction in acquisition costs. In contrast, switching from 10-mL vials to 3-mL pens was associated with a 10.1% increase in costs, despite the fact that there was a 11.5% reduction in units purchased. CONCLUSION Conversion from floor-stock 10-mL insulin vials to IPS 3-mL insulin vials or pens reduced the number of units of insulin purchased and expenditures for insulin. The overall cost savings was driven by the conversion from 10- to 3-mL vials, whereas cost increased for the conversion of 10-mL vials to 3-mL pens for long-acting insulin analogs.
Exposure to Political Discussion in College is Associated With Higher Rates of Political Participation Over Time

While individuals who are exposed to political discussion are more politically active, analytical biases make it difficult to show evidence of causation. It is also uncertain how long the relationship between discussion and participation lasts. Here both questions are addressed with panel data collected from individuals who were randomly assigned to their college dormitories. The data show that exposure to political discussion in college leads to higher levels of participation, immediately while still in college and years into the future after graduation. As political behavior is habitual, the initial increase in participation after being exposed to political discussion is a mechanism underlying the long-run relationship between discussion and participation.
Effect of smoking on breast cancer in carriers of mutant BRCA1 or BRCA2 genes.

BACKGROUND Smoking has carcinogenic effects, and possibly antiestrogenic effects as well, but it has not been found to be a risk factor for breast cancer in women in the general population. However, hereditary breast cancer is primarily a disease of premenopausal women, and interactions between genes and hormonal and environmental risk factors may be particularly important in this subgroup. METHODS We conducted a matched case-control study of breast cancer among women who have been identified to be carriers of a deleterious mutation in either the BRCA1 or the BRCA2 gene. These women were assessed for genetic risk at one of several genetic counseling programs for cancer in North America. Information about lifetime smoking history was derived from a questionnaire routinely administered to women who were found to carry a mutation in either gene. Smoking histories of case subjects with breast cancer and age-matched healthy control subjects were compared. Odds ratios for developing breast cancer were determined for smokers versus nonsmokers by use of conditional logistic regression for matched sets after adjustment for other known risk factors. RESULTS Subjects with BRCA1 or BRCA2 gene mutations and breast cancer were significantly more likely to have been nonsmokers than were subjects with mutations and without breast cancer (two-sided P = .007). In a multivariate analysis, subjects with BRCA1 or BRCA2 mutations who had smoked cigarettes for more than 4 pack-years (i.e., number of packs per day multiplied by the number of years of smoking) were found to have a lower breast cancer risk (odds ratio = 0.46, 95% confidence interval = 0.27-0.80; two-sided P = .006) than subjects with mutations who never smoked. CONCLUSIONS This study raises the possibility that smoking reduces the risk of breast cancer in carriers of BRCA1 or BRCA2 gene mutations.
A Theory of Interfaces and Modules I-Composition Theorem

We model a system as a directed acyclic graph where nodes represent modules and arcs represent interfaces. At the heart of our theory is a definition of what it means for a module to satisfy a set of interfaces as a service provider for some and as a service consumer for others. Our definition of interface satisfaction is designed to be separable; i.e., interfaces encode adequate information such that each module in a system can be designed and verified separately, and composable; i.e., we have proved a composition theorem for the system model in general. >
On Controllability of Neuronal Networks With Constraints on the Average of Control Gains

Control gains play an important role in the control of a natural or a technical system since they reflect how much resource is required to optimize a certain control objective. This paper is concerned with the controllability of neuronal networks with constraints on the average value of the control gains injected in driver nodes, which are in accordance with engineering and biological backgrounds. In order to deal with the constraints on control gains, the controllability problem is transformed into a constrained optimization problem (COP). The introduction of the constraints on the control gains unavoidably leads to substantial difficulty in finding feasible as well as refining solutions. As such, a modified dynamic hybrid framework (MDyHF) is developed to solve this COP, based on an adaptive differential evolution and the concept of Pareto dominance. By comparing with statistical methods and several recently reported constrained optimization evolutionary algorithms (COEAs), we show that our proposed MDyHF is competitive and promising in studying the controllability of neuronal networks. Based on the MDyHF, we proceed to show the controlling regions under different levels of constraints. It is revealed that we should allocate the control gains economically when strong constraints are considered. In addition, it is found that as the constraints become more restrictive, the driver nodes are more likely to be selected from the nodes with a large degree. The results and methods presented in this paper will provide useful insights into developing new techniques to control a realistic complex network efficiently.
Gender Differences in Sensation Seeking and Paranormal/Anomalous Experiences

Sensation seeking is the tendency to pursue sensory pleasure and excitement. A body of research indicates that sensation seeking may contribute to paranormal/anomalous experiences. Examination of relations between sensations seeking and paranormal beliefs has resulted in a limited body of research. This paper hypothesizes that both - sensation seeking and paranormal/anomalous experiences - will be significantly and positively correlated. Two samples of 446 fe- males and 162 males (MAge = 8.60, SD = 4.65) filled two questionnaires, Sensation Seeking Scale and a 10-item self-report inventory designed to collect information on spontaneous paranormal/anomalous experiences. An index of experiences (Index) was constructed to correlate with the sensations seeking. More than half have experienced different types of para- normal/anomalous experiences, mainly telepathy and deja-vu. The main hypothesis was supported for both, males (p = .002, one-tailed) and females (p < .001). Factor analysis showed that women tended to score higher than men, explaining the 6.5% of the variance. These findings also suggest that sensation seeking may have some utility in predicting subjects' psi performance.
A self-consistent model for high repetition rate copper vapor lasers

A computer model for a high repetition rate copper vapor laser is described. Equations for the discharge pulse, laser pulse, and interpulse afterglow period are simultaneously integrated over many discharge cycles until a consistent solution is obtained. In this way, consistent initial conditions are obtained and many scaling characteristics of the copper laser are successfully reproduced. This is a major improvement over models which consider only a single-laser pulse. By modeling both an ideal and real laser, and comparing the results to experimental data, we have determined that the peak-elctron temperature and the initial density of metastable copper are the factors which dominate the performance of the laser. Processes which effect these two quantities are therefore the most important in describing the laser.
MICHELL TRUSSES AND LINES OF PRINCIPAL ACTION

We study the problem of Michell trusses when the system of applied equilibrated forces is a vector measure with compact support. We introduce a class of stress tensors which can be written as a superposition of rank-one tensors carried by curves (lines of principal strains). Optimality conditions are given for such families showing in particular that optimal stress tensors are carried by mutually orthogonal families of curves. The method is illustrated on a specific example where uniqueness can be proved by studying an unusual system of hyperbolic PDEs. The questions we address here are of interest in elasticity theory, optimal designs, as well as in functional analysis.
Evaluating the Effectiveness of a Latrine Intervention on Childhood Diarrheal Health in Nyando District

A study to measure the effectiveness of the Community Led Total Sanitation latrine intervention in Nyando District, Kisumu County, Kenya was conducted using a condensed cohort study approach. Interviews were administered with 210 parents or caregivers in the 100% latrine using community and 216 parents or caregivers in the non-latrine using community at the household level. The survey ascertained information on childhood diarrhea illness, water safety, latrine behaviors, breastfeeding, demographics, hygiene, behaviors, and co-morbidities. Water testing was conducted to determine E. coli and turbidity levels for 55 water sources in the locations. Anthropometric data was obtained for each child subject. The non-ODF community had a non-significant slightly higher risk of diarrhea compared to the ODF community. Covariates including childhood HIV positivity, children stool disposal, and income were positively associated with diarrhea in the non-ODF community. The non-ODF location had safer water than the ODF, suggesting that the lack of association between ODF status and childhood diarrhea might due to unsafe water in the ODF community.
Extracting the temperature dependence of thermal resistance from temperature-controlled DC measurements of sige HBTs

In this paper we study and analyze the existing techniques in literature to extract the self-heating thermal resistance from the measured DC electrical behaviour of silicon-germanium heterojunction bipolar transistors (SiGe HBTs) focusing their dependence on device junction temperature and propose a simple extraction technique that shows superior accuracy than the existing extraction methodologies. Our approach is scalable and validated with model card simulations across different emitter geometries for a wide temperature range. We also present the applicability of our approach on measured data of a SiGe HBT fabricated in STMicroelectronics B55 process.