Miracle-dz/UniFAR-FTUs huggingface dataset:
Automatic parametrization of age/ sex Leslie matrices for human populations

In this paper, we present a technique for parameterizing Leslie transition matrices from simple age and sex population counts, using an implementation of "Wood's Method" [wood]; these matrices can forecast population by age and sex (the "cohort component" method) using simple matrix multiplication and a starting population. Our approach improves on previous methods for creating Leslie matrices in two respects: it eliminates the need to calculate input demographic rates from "raw" data, and our new format for the Leslie matrix more elegantly reveals the population's demographic components of change (fertility, mortality, and migration). The paper is organized around three main themes. First, we describe the underlying algorithm, "Wood's Method," which uses quadratic optimization to fit a transition matrix to age and sex population counts. Second, we use demographic theory to create constraint sets that make the algorithm useable for human populations. Finally, we use the method to forecast 3,120 US counties and show that it holds promise for automating cohort-component forecasts. This paper describes the first published successful application of Wood's method to human populations; it also points to more general promise of constrained optimization techniques in demographic modeling.
Absence of spontaneous disease and comparative prion susceptibility of transgenic mice expressing mutant human prion proteins

Approximately 15 % of human prion disease is associated with autosomal-dominant pathogenic mutations in the prion protein (PrP) gene. Previous attempts to model these diseases in mice have expressed human PrP mutations in murine PrP, but this may have different structural consequences. Here, we describe transgenic mice expressing human PrP with P102L or E200K mutations and methionine (M) at the polymorphic residue 129. Although no spontaneous disease developed in aged animals, these mice were readily susceptible to prion infection from patients with the homotypic pathogenic mutation. However, while variant Creutzfeldt–Jakob disease (CJD) prions transmitted infection efficiently to both lines of mice, markedly different susceptibilities to classical (sporadic and iatrogenic) CJD prions were observed. Prions from E200K and classical CJD M129 homozygous patients, transmitted disease with equivalent efficiencies and short incubation periods in human PrP 200K, 129M transgenic mice. However, mismatch at residue 129 between inoculum and host dramatically increased the incubation period. In human PrP 102L, 129M transgenic mice, short disease incubation periods were only observed with transmissions of prions from P102L patients, whereas classical CJD prions showed prolonged and variable incubation periods irrespective of the codon 129 genotype. Analysis of disease-related PrP (PrPSc) showed marked alteration in the PrPSc glycoform ratio propagated after transmission of classical CJD prions, consistent with the PrP point mutations directly influencing PrPSc assembly. These data indicate that P102L or E200K mutations of human PrP have differing effects on prion propagation that depend upon prion strain type and can be significantly influenced by mismatch at the polymorphic residue 129.
Misconceptions about oral contraception pills among adolescents and physicians.

BACKGROUND Limited access to contraception and poor compliance are the major reasons for unintended pregnancy in adolescence. This study was designed to compare knowledge of the combined oral contraceptive pill (COCP) in teenage users and non-users. We speculated that consultations between COCP users and their physicians would dispel misconceptions. METHODS A cross-sectional survey was undertaken in public clinics affiliated with an academic center. High school-educated female adolescents aged 14-20 years opting for contraception (n = 254) and Israeli physicians (n = 114) specializing in Obstetrics, Gynecology and Reproductive Endocrinology participated in the study. Information about past or present COCP use and views of the COCP were recorded by employing a ten-question YES/NO self-completion questionnaire, designed by the researchers. RESULTS The prevalence of incorrect beliefs was exceedingly high in the whole adolescent study group and relatively high among the physicians. The prevalence of incorrect beliefs was comparable between COCP users and non-users, regarding the 10 misconceptions investigated. The duration of COCP use did not influence the prevalence of misconceptions about the pill. Age did not serve as a confounding factor for all misconceptions. CONCLUSIONS Lack of informative communication between COCP-prescribing physicians and users and mistaken knowledge of the caring physicians may contribute to adolescent ignorance of the COCP. Focusing on adolescent-specific disbeliefs could lead to construction of better educational programs in schools and clinics.
A point mutation in the murine Hem1 gene reveals an essential role for Hematopoietic Protein 1 in lymphopoiesis and innate immunity

Hem1 (Hematopoietic protein 1) is a hematopoietic cell-specific member of the Hem family of cytoplasmic adaptor proteins. Orthologues of Hem1 in Dictyostelium discoideum, Drosophila melanogaster, and Caenorhabditis elegans are essential for cytoskeletal reorganization, embryonic cell migration, and morphogenesis. However, the in vivo functions of mammalian Hem1 are not known. Using a chemical mutagenesis strategy in mice to identify novel genes involved in immune cell functions, we positionally cloned a nonsense mutation in the Hem1 gene. Hem1 deficiency results in defective F-actin polymerization and actin capping in lymphocytes and neutrophils caused by loss of the Rac-controlled actin-regulatory WAVE protein complex. T cell development is disrupted in Hem1-deficient mice at the CD4−CD8− (double negative) to CD4+CD8+ (double positive) cell stages, whereas T cell activation and adhesion are impaired. Hem1-deficient neutrophils fail to migrate in response to chemotactic agents and are deficient in their ability to phagocytose bacteria. Remarkably, some Rac-dependent functions, such as Th1 differentiation and nuclear factor κB (NF-κB)–dependent transcription of proinflammatory cytokines proceed normally in Hem1-deficient mice, whereas the production of Th17 cells are enhanced. These results demonstrate that Hem1 is essential for hematopoietic cell development, function, and homeostasis by controlling a distinct pathway leading to cytoskeletal reorganization, whereas NF-κB–dependent transcription proceeds independently of Hem1 and F-actin polymerization.
Access Education: What Is Needed to Have Accessible Higher Education for Students with Disabilities in Jordan?.

The number of students with disabilities attending universities is increased, and several challenges face them in higher education institutions. This study aims to determine accessibility needs of computer laboratories, libraries and websites for students with disabilities at Jordanian universities and colleges. The sample consists of staff in computer laboratories and libraries, web developers and e-learning staff to identify environmental and technological barriers from their perspective, as well as, to check their knowledge about assistive technology (AT) and issues related to accessibility. Questionnaires and expert review methods are used to test accessibility of websites in the investigated universities and colleges. Results indicated that current status of accessibility does not meet the expectations of equal access nor the needs of students with disabilities where there is shortages of ATs in computer labs and libraries, lack of awareness and insufficient training for the universities’ staff and web developers related to accessibility issues, and all the evaluated universities web sites are inaccessible. Implications that should be contemplated by policy makers are highlighted and other recommendations are explored .
Artificial Muscles from Fishing Line and Sewing Thread

Toward an Artificial Muscle In designing materials for artificial muscles, the goals are to find those that will combine high strokes, high efficiency, long cycle life, low hysteresis, and low cost. Now, Haines et al. (p. 868; see the Perspective by Yuan and Poulin) show that this is possible. Twisting high-strength, readily available polymer fibers, such as those used for fishing lines or sewing thread, to the point where they coil up, allowed construction of highly efficient actuators that could be triggered by a number of stimuli. Polymer fibers can be transformed into highly efficient artificial muscles through the application of extreme twist. [Also see Perspective by Yuan and Poulin] The high cost of powerful, large-stroke, high-stress artificial muscles has combined with performance limitations such as low cycle life, hysteresis, and low efficiency to restrict applications. We demonstrated that inexpensive high-strength polymer fibers used for fishing line and sewing thread can be easily transformed by twist insertion to provide fast, scalable, nonhysteretic, long-life tensile and torsional muscles. Extreme twisting produces coiled muscles that can contract by 49%, lift loads over 100 times heavier than can human muscle of the same length and weight, and generate 5.3 kilowatts of mechanical work per kilogram of muscle weight, similar to that produced by a jet engine. Woven textiles that change porosity in response to temperature and actuating window shutters that could help conserve energy were also demonstrated. Large-stroke tensile actuation was theoretically and experimentally shown to result from torsional actuation.
Enhancing intentions to attend cervical cancer screening with a stage-matched intervention.

OBJECTIVE The study evaluated the effects of a pros enhancing intervention on intention to uptake cervical cancer screening. It was hypothesized that the pros enhancement session (compared to an education session) would affect intentions of preintentional women, whereas it was expected to have negligible effects among women in intentional and actional stages of the health action process approach (HAPA). Thus, we tested the HAPA using stage-matched and stage-mismatched interventions. Further, a change in decisional balance was assumed to mediate the relationship between the group assignment and intention, with age acting as the moderator. DESIGN AND METHODS Respondents (1,436 women, aged 18-60) were randomly assigned to either the intervention or control condition and filled out questionnaires before and directly after the manipulation (in one web-based session). RESULTS Direct effects of the group assignment were observed only among preintentional women. Across the stages, however, change in decisional balance mediated the effects of the group assignment on the intention to uptake screening. Further, among participants in the preintentional stage, this mediation became significant only for women aged 35 or older. CONCLUSIONS Although direct effects are in line with stage assumptions of the HAPA, meditational analysis among pre- and post-intentional women indicated that similar processes accounted for post-manipulation intention. Future research testing stage models should account for the mediating processes, which explain the effects of the intervention.
Sexual dimorphism in the olfactory system of a solitary and a eusocial bee species

Sexually dimorphic sensory systems are common in Hymenoptera and are considered to result from sex‐specific selection pressures. An extreme example of sensory dimorphism is found in the solitary bee tribe Eucerini. Males of long‐horned bees bear antennae that exceed body length. This study investigated the pronounced sexual dimorphism of the peripheral olfactory system and its representation in higher brain centers of the species Eucera berlandi. Eucera males have elongated antennae, with 10 times more pore plates and three times more olfactory receptor neurons than females. The male antennal lobe (AL) comprises fewer glomeruli than the female AL (∼100 vs. ∼130), of which four are male‐specific macroglomeruli. No sex differences were found in the relative volume of the mushroom bodies, a higher order neuropil essential for learning and memory in Hymenoptera. Compared with the Western honeybee, the degree of sexual dimorphism in Eucera is more pronounced at the periphery. In contrast, sex differences in glomerular numbers are higher in the eusocial honeybee and a sexual dimorphism of the relative investment in mushroom body tissue is observed only in Apis. The observed differences between the eusocial and the solitary bee species may reflect differences in male‐specific behavioral traits and associated selection pressures, which are discussed in brief. J. Comp. Neurol. 521:2742–2755, 2013. © 2013 Wiley Periodicals, Inc.
Memory network plasticity after temporal lobe resection: a longitudinal functional imaging study

Memory decrements are the main neurocognitive complication of anterior temporal lobe resection for refractory temporal lobe epilepsy. Sidhu et al. report dynamic changes in memory-encoding networks three and twelve months post-surgery compared to preoperative measures and to healthy controls, and describe the neural correlates of successful post-operative memory reorganisation.
Analyses of Genotypic Diversity among North, South, and Central American Isolates of Sugarcane Yellow Leaf Virus: Evidence for Colombian Origins and for Intraspecific Spatial Phylogenetic Variation

ABSTRACT We have analyzed the genotypic diversity of Sugarcane yellow leaf virus (SCYLV) collected from North, South, and Central America by fingerprinting assays and selective cDNA cloning and sequencing. One group of isolates from Colombia, designated the C-population, has been identified as residing at the root node between a separable superpopulation structure of SCYLV and other members of the family Luteoviridae, indicating that the progenitor viruses of the North, South, and Central American isolates of the SCYLV superpopulation most likely arose from a C-population structure. From a model of intrafamilial evolution (F. Moonan et al., Virology 269:156–171, 2000), a prediction could be made that within the SCYLV species, the capacity of genomic sequence divergence would range from lowest in the capsid protein open reading frame 3 (ORF 3) to highest in a region spanning across the carboxy-terminal end of the RNA-dependent RNA polymerase ORF. We have demonstrated the validity and applicability of this intrafamilial model for the prediction of intraspecies SCYLV diversity. Analysis of spatial phylogenetic variation (SPV) within the SCYLV isolates could not be assessed by application of a “partial likelihoods assessed through optimization” (PLATO)-derived intraspecies model alone. However, application of a PLATO-derived intrafamilial model with the intraspecies-derived model allowed distinction of three forms of SPV. Two of the SPV forms identified correspond to the extremes in a continuum of sequence evolution displayed in a SCYLV superpopulation structure, and the third form was diagnostic of a C-population structure. The application of these types of models has value in terms of predicting the types of SCYLV intraspecies diversity that may exist worldwide, and in general, may be useful in application for more informed design of transgenes for use in the elicitation of homology-dependent virus resistance mechanisms in transgenic plants.
Regulation of Huntingtin Gene Expression by miRNA-137, -214, -148a, and Their Respective isomiRs

With the advent of deep sequencing technology, a variety of miRNA length and sequence variants, termed isomiRNAs (isomiRs), have been discovered. However, the functional roles of these commonly detected isomiRs remain unknown. In this paper, we demonstrated that miRNAs regulate the expression of the HTT gene, whose mutation leads to Huntington’s disease (HD), a hereditary degenerative disorder. Specifically, we validated the interactions of canonical miRNAs, miR-137, miR-214, and miR-148a, with the HTT 3′UTR using a luciferase assay. Moreover, we applied synthetic miRNA mimics to examine whether a slight shifting of miRNA seed regions might alter the regulation of the HTT transcript. We also examined miR-137, miR-214, and miR-148a isomiRs and showed the activity of these isoforms on reporter constructs bearing appropriate sequences from the HTT 3′UTR. Hence, we demonstrated that certain 5′-end variants of miRNAs might be functional for the regulation of the same targets as canonical miRNAs.
Cross-frequency interaction of the eye-movement related LFP signals in V1 of freely viewing monkeys

Recent studies have emphasized the functional role of neuronal activity underlying oscillatory local field potential (LFP) signals during visual processing in natural conditions. While functionally relevant components in multiple frequency bands have been reported, little is known about whether and how these components interact with each other across the dominant frequency bands. We examined this phenomenon in LFP signals obtained from the primary visual cortex of monkeys performing voluntary saccadic eye movements (EMs) on still images of natural-scenes. We identified saccade-related changes in respect to power and phase in four dominant frequency bands: delta-theta (2–4 Hz), alpha-beta (10–13 Hz), low-gamma (20–40 Hz), and high-gamma (>100 Hz). The phase of the delta-theta band component is found to be entrained to the rhythm of the repetitive saccades, while an increment in the power of the alpha-beta and low-gamma bands were locked to the onset of saccades. The degree of the power modulation in these frequency bands is positively correlated with the degree of the phase-locking of the delta-theta oscillations to EMs. These results suggest the presence of cross-frequency interactions in the form of phase-amplitude coupling (PAC) between slow (delta-theta) and faster (alpha-beta and low gamma) oscillations. As shown previously, spikes evoked by visual fixations during free viewing are phase-locked to the fast oscillations. Thus, signals of different types and at different temporal scales are nested to each other during natural viewing. Such cross-frequency interaction may provide a general mechanism to coordinate sensory processing on a fast time scale and motor behavior on a slower time scale during active sensing.
DIETARY SURVEYS AND NUTRITIONAL EPIDEMIOLOGY Eating patterns are associated with biomarkers in a selected population of university students and employees

The association between diet and CVD cannot be assigned to a single nutrient, but rather to a set of nutrients and non-nutrients, and eating pattern analyses have become an important tool in investigation of this relationship. Our objective was to investigate eating patterns in relation to nutrient intake and serum concentration of folate, vitamin B12 and TAG in ninety-five healthy adult participants. Dietary information was collected by an FFQ, and eating patterns were obtained by principal components analyses of thirty-three food groups. Three eating patterns were extracted, a sweet eating pattern identified by intakes of cakes, snacks, sugar-sweetened drinks and chocolates; a prudent eating pattern identified by vegetables, fruits and olive oil; and a traditional food pattern identified by red meat, lean fish and cheese. Blood samples were collected in the morning after an overnight fast. Linear regression analyses adjusted for age, BMI and smoking showed a negative association between the sweet eating pattern scores and the serum concentration of folate (β = −2·31 (95 % CI −4·14, −0·45)) and a positive association with serum concentration of TAG (β = 0·35 (95 % CI 0·12, 0·57)). The prudent eating pattern scores were positively associated with the serum concentration of folate (β = 1·69 (95 % CI 0·44, 2·92)). In conclusion, a sweet eating pattern was associated with risk factors for CVD, whereas a prudent eating pattern was associated with protective factors.
Rates and Factors Associated with Major Modifications to First-Line Combination Antiretroviral Therapy: Results from the Asia-Pacific Region

Background In the Asia-Pacific region many countries have adopted the WHO’s public health approach to HIV care and treatment. We performed exploratory analyses of the factors associated with first major modification to first-line combination antiretroviral therapy (ART) in resource-rich and resource-limited countries in the region. Methods We selected treatment naive HIV-positive adults from the Australian HIV Observational Database (AHOD) and the TREAT Asia HIV Observational Database (TAHOD). We dichotomised each country’s per capita income into high/upper-middle (T-H) and lower-middle/low (T-L). Survival methods stratified by income were used to explore time to first major modification of first-line ART and associated factors. We defined a treatment modification as either initiation of a new class of antiretroviral (ARV) or a substitution of two or more ARV agents from within the same ARV class. Results A total of 4250 patients had 961 major modifications to first-line ART in the first five years of therapy. The cumulative incidence (95% CI) of treatment modification was 0.48 (0.44–0.52), 0.33 (0.30–0.36) and 0.21 (0.18–0.23) for AHOD, T-H and T-L respectively. We found no strong associations between typical patient characteristic factors and rates of treatment modification. In AHOD, relative to sites that monitor twice-yearly (both CD4 and HIV RNA-VL), quarterly monitoring corresponded with a doubling of the rate of treatment modifications. In T-H, relative to sites that monitor once-yearly (both CD4 and HIV RNA-VL), monitoring twice-yearly corresponded to a 1.8 factor increase in treatment modifications. In T-L, no sites on average monitored both CD4 & HIV RNA-VL concurrently once-yearly. We found no differences in rates of modifications for once- or twice-yearly CD4 count monitoring. Conclusions Low-income countries tended to have lower rates of major modifications made to first-line ART compared to higher-income countries. In higher-income countries, an increased rate of RNA-VL monitoring was associated with increased modifications to first-line ART.
Hierarchical neural model for workflow scheduling in Utility Management Systems

The emerging computational grid infrastructure consists of heterogeneous resources in widely distributed autonomous domains, which makes job scheduling very challenging. Although there is much work on static scheduling approaches for workflow applications in parallel environments, little work has been done on a real-world Grid environment for industrial systems. Utility Management Systems (UMS) are executing very large numbers of workflows with very high resource requirements. Unlike the grid approach for standard scientific workflows, UMS workflows have different set of computation requirements and thereby optimization of resource usage has to be made in a different way. This paper proposes architecture for a new scheduling mechanism that dynamically executes a scheduling algorithm using near real-time feedback about current status Grid nodes. Two Artificial Neural Networks (ANN) were created in order to solve scheduling problem. First ANN predicts future state of Grid based on current state and types of workflows that are currently executing. Second ANN output is optimal workflow type that should be executed. Inputs for second ANN are current state of the Grid and predicted future state (output of first ANN). Performance tests show that significant improvement of overall execution time can be achieved by this Hierarchical Artificial Neural Networks.