Miracle-dz/UniFAR-FTUs huggingface dataset:
Recent HIV prevalence trends among pregnant women and all women in sub-Saharan Africa: implications for HIV estimates

Objectives:National population-wide HIV prevalence and incidence trends in sub-Saharan Africa (SSA) are indirectly estimated using HIV prevalence measured among pregnant women attending antenatal clinics (ANC), among other data. We evaluated whether recent HIV prevalence trends among pregnant women are representative of general population trends. Design:Serial population-based household surveys in 13 SSA countries. Methods:We calculated HIV prevalence trends among all women aged 15–49 years and currently pregnant women between surveys conducted from 2003 to 2008 (period 1) and 2009 to 2012 (period 2). Log-binomial regression was used to test for a difference in prevalence trend between the two groups. Prevalence among pregnant women was age-standardized to represent the age distribution of all women. Results:Pooling data for all countries, HIV prevalence declined among pregnant women from 6.5 [95% confidence interval (CI) 5.3–7.9%] to 5.3% (95% CI 4.2–6.6%) between periods 1 and 2, whereas it remained unchanged among all women at 8.4% (95% CI 8.0–8.9%) in period 1 and 8.3% (95% CI 7.9–8.8%) in period 2. Prevalence declined by 18% (95% CI −9–38%) more in pregnant women than nonpregnant women. Estimates were similar in Western, Eastern, and Southern regions of SSA; none were statistically significant (P > 0.05). HIV prevalence decreased significantly among women aged 15–24 years while increasing significantly among women 35–49 years, who represented 29% of women but only 15% of pregnant women. Age-standardization of prevalence in pregnant women did not reconcile the discrepant trends because at older ages prevalence was lower among pregnant women than nonpregnant women. Conclusion:As HIV prevalence in SSA has shifted toward older, less-fertile women, HIV prevalence among pregnant women has declined more rapidly than prevalence in women overall. Interpretation of ANC prevalence data to inform national HIV estimates should account for both age-specific fertility patterns and HIV-related sub-fertility.
Pricing Cloud Compute Commodities: A Novel Financial Economic Model

In this study, we design, develop, and simulate a cloud resources pricing model that satisfies two important constraints: the dynamic ability of the model to provide a high satisfaction guarantee measured as Quality of Service (QoS) - from users perspectives, profitability constraints - from the cloud service providers perspectives We employ financial option theory and treat the cloud resources as underlying assets to capture the realistic value of the cloud compute commodities (C3). We then price the cloud resources using our model. We discuss the results for four different metrics that we introduce to guarantee the quality of service and price as follows: (a) Moore's law based depreciation of asset values, (b) new technology based volatility measures in capturing price changes, (c) a new financial option pricing based model combining the above two concepts, and (d) the effect of age of resources and depreciation of cloud resource on QoS. We show that the cloud parameters can be mapped to financial economic model and we discuss the results of cloud compute commodity pricing for various parameters, such as the age of the resource, quality of service, and contract period.
A Comparison of Two Ambulatory Blood Pressure Monitors Worn at the Same Time

There are limited data in the literature comparing two simultaneously worn ambulatory blood pressure (BP) monitoring (ABPM) devices. The authors compared BPs from two monitors (Mobil‐O‐Graph [I.E.M., Stolberg, Germany] and Spacelabs 90207 [Spacelabs Medical, Issequah, WA]). In the nonrandomized component of the study, simultaneous 8‐hour BP and heart rate data were measured by Mobil‐O‐Graph, consistently applied to the nondominant arm, and Spacelabs to the dominant arm on 12 untreated adults. Simultaneous 8‐hour BP and heart data were obtained by the same monitors randomly assigned to a dominant or nondominant arm on 12 other untreated adults. Oscillometric BP profiles were obtained in the dominant and nondominant arms of the above 24 patients using an Accutorr (Datascope, Mahwah, NJ) device. The Spacelabs monitor recorded a 10.2‐mm Hg higher systolic pressure in the nonrandomized (P=.0016) and a 7.9‐mm Hg higher systolic pressure in the randomized studies (P=.00008) compared with the Mobil‐O‐Graph. The mean arterial pressures were 1 mm Hg to 2 mm Hg different between monitors in the two studies, and heart rates were nearly identical. Our observations, if confirmed in larger cohorts, support the concern that ABPM device manufacturers consider developing normative databases for their devices.
A peptide targeting an interaction interface disrupts the dopamine D1‐D2 receptor heteromer to block signaling and function in vitro and in vivo: effective selective antagonism

Although the dopamine D1‐D2 receptor heteromer has emerging physiological relevance and a postulated role in different neuropsychiatric disorders, such as drug addiction, depression, and schizophrenia, there is a need for pharmacological tools that selectively target such receptor complexes in order to analyze their biological and pathophysiological functions. Since no selective antagonists for the D1‐D2 heteromer are available, serial deletions and point mutations were used to precisely identify the amino acids involved in an interaction interface between the receptors, residing within the carboxyl tail of the D1 receptor that interacted with the D2 receptor to form the D1‐D2 receptor heteromer. It was determined that D1 receptor carboxyl tail residues 404Glu and 405Glu were critical in mediating the interaction with the D2 receptor. Isolated mutation of these residues in the D1 receptor resulted in the loss of agonist activation of the calcium signaling pathway mediated through the D1‐D2 receptor heteromer. The physical interaction between the D1 and D2 receptor could be disrupted, as shown by coimmunoprecipitation and BRET analysis, by a small peptide generated from the D1 receptor sequence that contained these amino acids, leading to a switch in G‐protein affinities and loss of calcium signaling, resulting in the inhibition of D1‐D2 heteromer function. The use of the D1‐D2 heteromer‐disrupting peptide in vivo revealed a pathophysiological role for the D1‐D2 heteromer in the modulation of behavioral despair. This peptide may represent a novel pharmacological tool with potential therapeutic benefits in depression treatment. —Hasbi, A. , Perreault, M. L. , Shen, M. Y. F. , Zhang, L. , To, R. , Fan, T. , Nguyen, T. , Ji, X. , O'Dowd, B. F. , George, S. R. , A peptide targeting an interaction interface disrupts the dopamine D1‐D2 receptor heteromer to block signaling and function in vitro and in vivo: effective selective antagonism
Detecting ecological impacts : concepts and applications in coastal habitats

An Introduction to Ecological Impact Assessment: Principles and Goals: C.W. Osenberg and R.J. Schmitt, Detecting Ecological Impacts Caused by Human Activities. A. Stewart-Oaten, Goals in Environmental Monitoring. G.P. Jones and U.L. Kaly, Criteria for Selecting Marine Organisms in Biomonitoring Studies. S.F. Thrush, R.D. Pridmore, and J.E. Hewitt, Impacts on Soft-Sediment Macrofauna: The Effects of Spatial Variation on Temporal Trends. B.D. Mapstone, Scalable Decision Criteria for Environmental Impact Assessment: Effect, Size, Type I, and Type II Errors. Improving Field Assessments of Local Impacts: Before-After-Control-Impact Designs: C.W. Osenberg, R.J. Schmitt, S.J.Holbrook, K.E. Abu-Saba, and A.R. Flegal, Detection of Environmental Impacts: Natural Variability, Effect Size and Power Analysis. A. Stewart-Oaten, Problems in the Analysis of Environmental Monitoring Data. J.R. Bence, A. Stewart-Oaten, and S.C. Schroeter, Estimating the Size of an Effect from Before-After-Control-Impact-Pairs Design: The Predictive Approach Applied to a Power Plant Study. A.J. Underwood, On Beyond BACI: Sampling Designs That Might Reliably DetectEnvironmental Disturbances. Extension of Local Impacts to Larger Scale Consequences: P.T. Raimondi and D.C. Reed, Determining the Spatial Extent of Ecological Impacts Caused by Local Anthropogenic Disturbances in Coastal Marine Habitats. M.J. Keough and K.P. Black, Predicting the Scale of Marine Impacts: Understanding Planktonic Links between Populations. M.J. Kingsford and C.A. Gray, Influence of Pollutants and Oceanography on Abundance and Deformities of Wild Fish Larvae. R.M. Nisbet, W.W. Murdoch, and A. Stewart-Oaten, Consequences for Adult Fish Stocks of Human-Induced Mortality on Immatures. The Link between Administrative Environmental Impact Studies and Well-Designed Field Assessments: R.J. Schmitt, C.W. Osenberg, W.J. Douros, and J. Chesson, The Art and Science of Administrative Environmental Impact Assessment. R.S. Carney, On the Adequacy and Improvement of Marine Benthic Pre-Impact Surveys: Examples from the Gulf of Mexico Outer Continental Shelf. F.M. Piltz, Organization Constraits on Environmental Impact Assessment Research. C. Lester, Administrative, Legal, and Public Policy Constraints on Environmental Impact Assessment. R.F. Ambrose, R.J. Schmitt, and C.W. Osenberg, Predicted and Observed Environmental Impacts: Can We Foretell Ecological Change? Glossary. Author Index. Subject Index.
Online learning over graphs

We apply classic online learning techniques similar to the perceptron algorithm to the problem of learning a function defined on a graph. The benefit of our approach includes simple algorithms and performance guarantees that we naturally interpret in terms of structural properties of the graph, such as the algebraic connectivity or the diameter of the graph. We also discuss how these methods can be modified to allow active learning on a graph. We present preliminary experiments with encouraging results.
Collagen Remodeling of the Pressure‐Overloaded, Hypertrophied Nonhuman Primate Myocardium

Cardiac muscle is tethered within a fibrillar collagen matrix that serves to maximize force generation. In the human pressure-overloaded, hypertrophied left ventricle, collagen concentration is known to be increased; however, the structural and biochemical remodeling of collagen and its relation to cell necrosis and myocardial mechanics is less clear. Accordingly, this study was undertaken in a nonhuman primate model of left ventricular hypertrophy caused by gradual onset experimental hypertension. The amount of collagen, its light microscopic features, and proportions of collagen types I, III, and V were determined together with diastolic and systolic mechanics of the intact ventricle during the evolutionary, early, and late phases of established left ventricular hypertrophy (4, 35, and 88 weeks, respectively). In comparison to controls, we found 1) increased collagen at 4 weeks, as well as a greater proportion of type III, in the absence of myocyte necrosis; 2) collagen septae were thick and dense at 35 weeks, while the proportion of types I and III had converted to control; 3) necrosis was evident at 88 weeks, and the structural remodeling and proportion of collagen types I and III reflected the extent of scar formation; and 4) unlike diastolic myocardial stiffness, which was unchanged at 4, 35, or 88 weeks, the systolic stress-strain relation of the myocardium was altered in either a beneficial or detrimental manner in accordance with structural remodeling of collagen and scar formation. Thus, early in left ventricular hypertrophy, reactive fibrosis and collagen remodeling occur in the absence of necrosis while, later on, reparative fibrosis is present. In this study, the remodeled collagen matrix appeared responsible for variations in force generation observed during various phases of left ventricular hypertrophy.
Treatment after failure: the problem of “non-responders”

Although the currently most effective treatment regimens cure about 90% of infections, 10% of patients remain Helicobacter pylori positive. Several factors contribute to treatment failure. These include patient compliance, bacterial resistance to antibiotics, and treatment related issues. Treatment failure leads to the development of bacterial resistance to metronidazole and clarithromycin. Retreatment can be undertaken after considering several different strategies: to repeat the same regimen with full doses of medications and a longer treatment duration, or to choose different regimens to avoid the antibiotic previously used, or to switch to proton pump inhibitor (PPI) based quadruple therapy or ranitidine bismuth citrate (RBC) based triple therapy. In principle, full doses and longer treatment durations are advisable. As retreatment is always difficult, choosing the best available first line treatment regimen is still the best "rescue" treatment.
Brain and the music: A window to the comprehension of the interactive brain functioning

Abstract Here we review the most important psychological aspects of music, its neural substrates, its universality and likely biological origins and, finally, how the study of neurocognition and emotions of music can provide one of the most important windows to the comprehension of the higher brain functioning and human mind. We begin with the main aspects of the theory of modularity, its behavioral and neuropsychological evidences. Then, we discuss basic psychology and neuropsychology of music and show how music and language are cognitively and neurofunctionally related. Subsequently we briefly present the evidences against the view of a high degree of specification and encapsulation of the putative language module, and how the ethnomusicological, pscychological and neurocognitive studies on music help to shed light on the issues of modularity and evolution, and appear to give further support for a cross-modal, interactive view of neurocognitive processes. Finally, we will argue that the notion of large modules do not adequately describe the organization of complex brain functions such as language, math or music, and propose a less radical view of modularity, in which the modular systems are specified not at the level of culturally determined cognitive domains but more at the level of perceptual and sensorimotor representations. © Cien. Cogn. 2011; Vol. 16 (1): 137-164. Keywords: music; language; modularity; brain; evolution; cognition. Resumo Aqui revisamos os aspectos psicologicos mais importantes da musica, seus substratos neurais, sua universalidade e provaveis origens biologicas e, finalmente, como o estudo da neurocognicao e das emocoes associadas a musica pode fornecer uma das mais importantes janelas para a compreensao das funcoes cerebrais superiores e da mente humana. Iniciamos com os principais aspectos da teoria da modularidade, suas evidencias comportamentais e neuropsicologicas. Entao discutimos a psicologia e a neuropsicologia basicas da musica e mostramos como a musica e a linguagem estao cognitiva e neurofuncionalmente interrelacionadas. Em seguida, apresentamos brevemente as evidencias contrarias a visao de um alto grau de especificacao e encapsulamento do modulo putativo da linguagem e como os estudos etnomusicologicos, psicologicos e neurocognitivos sobre musica auxiliam na elucidacao dos temas modularidade e evolucao e parecem fornecer subsidios adicionais para uma visao interativa e intermodal dos processos neurocognitivos. Finalmente iremos argumentar que a nocao de amplos modulos nao descreve adequadamente a organizacao de funcoes cerebrais complexas, como a linguagem, a matematica, ou a musica. Propomos uma visao menos radical de modularidade, na qual os sistemas modulares sao especificados nao ao nivel de dominios cognitivos culturalmente determinados, e sim mais ao nivel de representacoes perceptuais e sensoriomotoras. © Cien. Cogn. 2011; Vol. 16 (1): 137-164. Palavras-chave: musica; linguagem; modularidade; cerebro; evolucao; cognicao.
Palagonitic (Not Andesitic) Mars: Evidence from Thermal Emission and VNIR Spectra of Palgonitic Alteration Rinds on Basaltic Rock

Visible and near-IR (VNIR) spectra of both Martian bright and dark regions are characterized by a ferric absorption edge extending from approx. 400 to 750 nm, with bright regions having about twice the reflectivity at 750 nm as dark regions. Between 750 nm to beyond 2000 nm, bright and dark regions have nearly constant and slightly negative spectral slopes, respectively. Depending on location, bright regions have shallow reflectivity minima in the range 850-910 nm that are attributed to ferric oxides. Similarly, dark regions have shallow reflectivity minima near approx. 950 and 1700-2000 nm that are attributed to ferrous silicate minerals (pyroxene). Among terrestrial geologic materials, the best spectral analogues for Martian bright regions are certain palagonitic tephras from Mauna Kea Volcano (Hawaii). By definition, palagonite is a "yellow or orange isotropic mineraloid formed by hydration and devitrification of basaltic glass". The ferric pigment in palagonite is nanometer-sized ferric oxide particles (np-Ox) dispersed throughout the hydrated basaltic glass matrix. The hydration state of the np-Ox particles is not known, but the best Martian spectral analogues contain allophane-like materials and not crystalline phyllosilicates.
The provenance of sediments in the Barrême thrust-top basin, Haute-Provence, France

Abstract This paper records the results of an integrated analysis of heavy minerals, sedimentary facies, palaeocurrents and structural data. The objective of the study was to evaluate the provenance of the sediments of the Barrême thrust-top basin. This basin contains a Late Eocene to Late Oligocene succession of shallow marine, alluvial and lacustrine sediments. Late Eocene marine transgression resulted in starvation of clastic supply to the basin hence the Calcaires Nummulitiques received only a limited influx of heavy minerals derived from local sedimentary sources, augmented by the first appearance of assemblages with andesitic affinities at c. 42–41 Ma. Clastic members associated with the overlying Marnes Bleues record a significant diversification of provenance and sediment transport paths. Clastic detritus supplied to the shallow marine Grès de Ville were derived from Permo-Triassic sediments to the south. Conglomeratic submarine channels of the La Poste member mark the introduction of Alpine ophiolite-blueschist-derived minerals at c. 37–35 Ma, eroded from the Embrun-Ubaya thrust complex to the NE. The deltaic St Lions member is dominated by volcaniclastic assemblages. Completing the marine fill, the shoreface Grès de Senez received detritus from the southerly Maures-Esterel crystalline massif. The succeeding Oligocene continental sediments record an increasing supply of minerals from Alpine lithologies. The alluvial Molasse Rouge contains reworked sedimentary detritus, including material cannibalized from the underlying marine Tertiary, and first-cycle Alpine minerals. The succeeding lacustrine Série Saumon-Série Grise show the increasing diversity of Alpine suites. The youngest sediments, the fluvial Grès Verts, signal a major influx of Alpine-derived assemblages related to reactivation of the Embrun-Ubaye thrusts between c. 28–27 and 25–24 Ma.
SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

MOTIVATION The application of next-generation sequencing (NGS) technologies to RNAs directly extracted from a community of organisms yields a mixture of fragments characterizing both coding and non-coding types of RNAs. The task to distinguish among these and to further categorize the families of messenger RNAs and ribosomal RNAs (rRNAs) is an important step for examining gene expression patterns of an interactive environment and the phylogenetic classification of the constituting species. RESULTS We present SortMeRNA, a new software designed to rapidly filter rRNA fragments from metatranscriptomic data. It is capable of handling large sets of reads and sorting out all fragments matching to the rRNA database with high sensitivity and low running time.
On the Development and Cause of the Weddell Polynya in a Sea Ice Simulation

Abstract Occurrence of the Weddell polynya, a large open-water area in the midst of the wintertime pack ice of the southern ocean, is examined through a sequence of numerical simulations of the sea ice cover. Using mean climatological input data, the numerical model realistically simulates the emergence of the polynya through the encircling of an open water region by ice. In addition, with only the wind fields altered, the model successfully simulates winter seasons totally lacking a Weddell polynya. Since the vertical ocean heat flux inserted into the model is spatially-invariant, these results call into question—without actually refuting—those explanations of the polynya based exclusively on oceanographic factors. On the other hand, the failure of the modeled polynya to survive the winter season without significant weakening, as the observed polynya did in each of the years 1974–76, suggests that the oceanography and/or the ocean/atmosphere feedbacks are essential to the polynya maintenance, even if not.
Spatially resolved fluorescence lifetime mapping of enzyme kinetics in living cells

Traditional cuvette‐based enzyme studies lack spatial information and do not allow real‐time monitoring of the effects of modulating enzyme functions in vivo. In order to probe the realistic timescales of steric modifications in enzyme–substrate complexes and functional binding–unbinding kinetics in living cells without losing spatial information, it is imperative to develop sensitive imaging strategies that can report enzyme kinetics in real time over a wide dynamic range of timescales. Here we present a multi‐photon excitation‐based, ultra‐fast photon detection using a streak camera and Laguerre expansion‐based fast deconvolution approach for achieving high spatio‐temporal resolution in monitoring real‐time enzyme kinetics in single cells. In particular, we report spatially resolved, nanosecond‐scale fluorescence dynamics associated with binding–unbinding kinetics of endogenous metabolic co‐factor nicotinamide adenine dinucleotide with enzymes in intact living cells. By monitoring real‐time kinetics of NAD(P)H–enzyme kinetics in primary hepatocytes isolated from young and aged mouse models, we observed that the mechanism of inhibition of mitochondrial respiration at complex I site is mediated by redistribution of free and protein‐bound nicotinamide adenine dinucleotide pools and that this equilibrium redistribution is affected by age‐related modifications in mitochondrial function. We describe unique advantages of Laguerre deconvolution algorithm in comparison with conventional lifetime analysis approaches. Non‐invasive monitoring of metabolic dysfunctions in intact animal models is an attractive strategy for gaining insight into the dynamics of tissue metabolism in health and in various metabolic syndromes such as cancer, diabetes and aging‐induced metabolic dysfunctions. Besides the example demonstrated above, we envisage that the proposed method can find applications in a variety of other situations where intensity‐based approaches fall short owing to spectroscopic artefacts.