Miracle-dz/UniFAR-FTUs huggingface dataset:
Burden of HIV and Syphilis: A Comparative Evaluation between Male Sex Workers and Non-Sex-Worker Men Who Have Sex with Men in Urban China

Background The increasing burden of sexually transmitted infections (STIs) including HIV and syphilis among male sex workers (MSWs) is a major global concern. The aim of our study was to evaluate the difference between MSWs and non-commercial MSMs in China. Methods During 2008-09, in a cross-sectional study, 2618 adult MSM were recruited through respondent-driven and snowball sampling from seven cities of China. Information regarding socio-demographics, risk behaviors, HIV-related knowledge and STI-related symptoms were collected and participants were tested for HIV and syphilis. Results Among 2618 participating MSM, 9.97% sold sex to males. HIV prevalence was 7.45% (6.13% among MSWs and 7.59% among non-MSW MSM) and syphilis prevalence was 14.32% (10.73% for MSWs and 14.72% for non-MSW MSM). Compared to non-MSW MSM, MSWs were more likely to be younger (adjusted odds ratio: aOR = 0.91, 95% confidence interval: 95%CI=0.88-0.93), never married (aOR = 4.38, 95% CI = 2.38-6.80), less educated, heterosexual (aOR = 13.04, 95% CI = 6.08-27.95), less knowledgeable regarding HIV (aOR = 0.70, 95% CI=0.51-0.96), experiencing symptoms of STI (aOR = 2.16, 95% CI = 1.47-3.19), engaging in condomless vaginal intercourse (aOR = 2.16, 95% CI = 1.47-3.19) and less likely to engage in condomless anal intercourse (aOR = 0.62, 95% CI = 0.46-0.85). Conclusions High HIV and syphilis prevalence warranted urgent intervention targeting MSWs as a separate sentinel group for efficient surveillance owing to their different distribution from non-MSW MSM. Although male sex workers and non-commercial homosexuals have similar rates of HIV and syphilis, MSWs have different characteristics which should be considered in designing intervention programs targeting them.
Graph-based multiple-instance learning for object-based image retrieval

We study in this paper the problem of using multiple-instance semi-supervised learning to solve object-based image retrieval problem, in which the user is only interested in a portion of the image, and the rest of the image is considered as irrelevant. Although many multiple-instance learning (MIL) algorithms have been proposed to solve object-based image retrieval problem, most of them only have a supervised manner and do not fully utilize the information of the unlabeled data in the image collection. In this paper, to make use of the large amount of unlabeled data, we present a semi-supervised version of multiple-instance learning, i.e. multiple-instance semi-supervised learning (MISSL). By taking into account both the multiple-instance property and the semi-supervised property simultaneously, a novel regularization framework for MISSL is presented. Based on this framework, a graph-based multiple-instance learning (GMIL) algorithm is developed, in which three kinds of data, i.e. labeled data, semi-labeled data, and unlabeled data simultaneously propagate information on a graph. Moreover, under the same framework, GMIL can be reduced to a novel standard MIL algorithm (GMIL-M) by ignoring unlabeled data. We theoretically prove the convergence of the iterative solutions for GMIL and GMIL-M. We apply GMIL algorithm to solving object-based image retrieval problem, and experimental results show the superiority of the proposed method. Some experiments on standard MIL problems are also provided to show the competitiveness of the proposed algorithms compared with state-of-the-art MIL algorithms.
Limits to Adaptation in Partially Selfing Species

In outcrossing populations, “Haldane’s sieve” states that recessive beneficial alleles are less likely to fix than dominant ones, because they are less exposed to selection when rare. In contrast, selfing organisms are not subject to Haldane’s sieve and are more likely to fix recessive types than outcrossers, as selfing rapidly creates homozygotes, increasing overall selection acting on mutations. However, longer homozygous tracts in selfers also reduce the ability of recombination to create new genotypes. It is unclear how these two effects influence overall adaptation rates in partially selfing organisms. Here, we calculate the fixation probability of beneficial alleles if there is an existing selective sweep in the population. We consider both the potential loss of the second beneficial mutation if it has a weaker advantage than the first one, and the possible replacement of the initial allele if the second mutant is fitter. Overall, loss of weaker adaptive alleles during a first selective sweep has a larger impact on preventing fixation of both mutations in highly selfing organisms. Furthermore, the presence of linked mutations has two opposing effects on Haldane’s sieve. First, recessive mutants are disproportionally likely to be lost in outcrossers, so it is likelier that dominant mutations will fix. Second, with elevated rates of adaptive mutation, selective interference annuls the advantage in selfing organisms of not suffering from Haldane’s sieve; outcrossing organisms are more able to fix weak beneficial mutations of any dominance value. Overall, weakened recombination effects can greatly limit adaptation in selfing organisms.
Interactive and Independent Associations between the Socioeconomic and Objective Built Environment on the Neighbourhood Level and Individual Health: A Systematic Review of Multilevel Studies

Background The research question how contextual factors of neighbourhood environments influence individual health has gained increasing attention in public health research. Both socioeconomic neighbourhood characteristics and factors of the built environment play an important role for health and health-related behaviours. However, their reciprocal relationships have not been systematically reviewed so far. This systematic review aims to identify studies applying a multilevel modelling approach which consider both neighbourhood socioeconomic position (SEP) and factors of the objective built environment simultaneously in order to disentangle their independent and interactive effects on individual health. Methods The three databases PubMed, PsycINFO, and Web of Science were systematically searched with terms for title and abstract screening. Grey literature was not included. Observational studies from USA, Canada, Australia, New Zealand, and Western European countries were considered which analysed simultaneously factors of neighbourhood SEP and the objective built environment with a multilevel modelling approach. Adjustment for individual SEP was a further inclusion criterion. Results Thirty-three studies were included in qualitative synthesis. Twenty-two studies showed an independent association between characteristics of neighbourhood SEP or the built environment and individual health outcomes or health-related behaviours. Twenty-one studies found cross-level or within-level interactions either between neighbourhood SEP and the built environment, or between neighbourhood SEP or the built environment and individual characteristics, such as sex, individual SEP or ethnicity. Due to the large variation of study design and heterogeneous reporting of results the identification of consistent findings was problematic and made quantitative analysis not possible. Conclusions There is a need for studies considering multiple neighbourhood dimensions and applying multilevel modelling in order to clarify their causal relationship towards individual health. Especially, more studies using comparable characteristics of neighbourhood SEP and the objective built environment and analysing interactive effects are necessary to disentangle health impacts and identify vulnerable neighbourhoods and population groups.
Spontaneous scalarization and boson stars

We study spontaneous scalarization in scalar-tensor boson stars. We find that scalarization does not occur in stars whose bosons have no self-interaction. We introduce a quartic self-interaction term into the boson Lagrangian and show that when this term is large, scalarization does occur. Strong self-interaction leads to a large value of the compactness (or sensitivity) of the boson star, a necessary condition for scalarization to occur, and we derive an analytical expression for computing the sensitivity of a boson star in Brans-Dicke theory from its mass and particle number. Next we comment on how one can use the sensitivity of a star in any scalar-tensor theory to determine how its mass changes when it undergoes gravitational evolution. Finally, in the Appendix, we derive the most general form of the boson wave function that minimizes the energy of the star when the bosons carry a $U(1)$ charge.
Identification of a Regulatory T Cell Specific Cell Surface Molecule that Mediates Suppressive Signals and Induces Foxp3 Expression

Regulatory T (Treg) cells control immune activation and maintain tolerance. How Tregs mediate their suppressive function is unclear. Here we identified a cell surface molecule, called GARP, (or LRRC32), which within T cells is specifically expressed in Tregs activated through the T cell receptor (TCR). Ectopic expression of GARP in human naïve T (TN) cells inhibited their proliferation and cytokine secretion upon TCR activation. Remarkably, GARP over-expression in TN cells induced expression of Treg master transcription factor Foxp3 and endowed them with a partial suppressive function. The extracellular but not the cytoplasmic region of GARP, was necessary for these functions. Silencing Foxp3 in human Treg cells reduced expression of GARP and attenuated their suppressive function. However, GARP function was not affected when Foxp3 was downregulated in GARP-overexpressing cells, while silencing GARP in Foxp3-overexpressing cells reduced their suppressive activity. These findings reveal a novel cell surface molecule-mediated regulatory mechanism, with implications for modulating aberrant immune responses.
Invited address at the occasion of the Bertelson Award 2011 Organisation of executive functions : Hemispheric asymmetries

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Ball control in high-speed batting motion using hybrid trajectory generator

Speeding up robot motion provides not only improvement in operating efficiency but also improves dexterous manipulation by taking advantage of an unstable state or noncontact state. In this paper we describe a hybrid trajectory generator that produces high-speed manipulation. This algorithm produces both mechanical high-speed motion and sensor-based reactive motion. As an example of high-speed manipulation, a robotic ball control in a batting task has been achieved. Performance evaluation is also analyzed
Is Double Reionization Physically Plausible?

Recent observations of z ~ 6 quasars and the cosmic microwave background imply a complex history of cosmic reionization. Such a history requires some form of feedback to extend reionization over a long time interval, but the nature of the feedback and how rapidly it operates remain highly uncertain. Here we focus on one aspect of this complexity: which physical processes can cause the global ionized fraction to evolve nonmonotonically with cosmic time? We consider a range of mechanisms and conclude that double reionization is much less likely than a long, but still monotonic, ionization history. We first examine how galactic winds affect the transition from metal-free to normal star formation. Because the transition is actually spatially inhomogeneous and temporally extended, this mechanism cannot be responsible for double reionization, given plausible parameters for the winds. We next consider photoheating, which causes the cosmological Jeans mass to increase in ionized regions and hence suppresses galaxy formation there. In this case, double reionization requires that small halos form stars efficiently, that the suppression from photoheating is strong relative to current expectations, and that ionizing photons are preferentially produced outside previously ionized regions. Finally, we consider H2 photodissociation, in which the buildup of a soft ultraviolet background suppresses star formation in small halos. This can in principle cause the ionized fraction to temporarily decrease, but only during the earliest stages of reionization. Finally, we briefly consider the effects of some of these feedback mechanisms on the topology of reionization.
ON THE COLOR–MAGNITUDE RELATION OF EARLY-TYPE GALAXIES

In this Letter, we present a study of the color–magnitude relation (CMR) of 468 early-type galaxies in the Virgo Cluster with Sloan Digital Sky Survey imaging data. The analysis of our homogeneous, model-independent data set reveals that, in all colors (u − g, g − r, g − i, i − z) similarly, giant and dwarf early-type galaxies follow a continuous CMR that is best described by an S shape. The magnitude range and quality of our data allows us to clearly confirm that the CMR in Virgo is not linear. Additionally, we analyze the scatter about the CMR and find that it increases in the intermediate-luminosity regime. Nevertheless, despite this observational distinction, we conclude from the similarly shaped CMR of semianalytic model predictions that dwarfs and giants could be of the same origin.
Human induced pluripotent stem cell‐derived versus adult cardiomyocytes: an in silico electrophysiological study on effects of ionic current block

Two new technologies are likely to revolutionize cardiac safety and drug development: in vitro experiments on human‐induced pluripotent stem cell‐derived cardiomyocytes (hiPSC‐CMs) and in silico human adult ventricular cardiomyocyte (hAdultV‐CM) models. Their combination was recently proposed as a potential replacement for the present hERG‐based QT study for pharmacological safety assessments. Here, we systematically compared in silico the effects of selective ionic current block on hiPSC‐CM and hAdultV‐CM action potentials (APs), to identify similarities/differences and to illustrate the potential of computational models as supportive tools for evaluating new in vitro technologies.
Analysis of X chromosome genomic DNA sequence copy number variation associated with premature ovarian failure (POF).

BACKGROUND Premature ovarian failure (POF) is a heterogeneous disease defined as amenorrhoea for >6 months before age 40, with an FSH serum level >40 mIU/ml (menopausal levels). While there is a strong genetic association with POF, familial studies have also indicated that idiopathic POF may also be genetically linked. Conventional cytogenetic analyses have identified regions of the X chromosome that are strongly associated with ovarian function, as well as several POF candidate genes. Cryptic chromosome abnormalities that have been missed might be detected by array comparative genomic hybridization. METHODS In this study, samples from 42 idiopathic POF patients were subjected to a complete end-to-end X/Y chromosome tiling path array to achieve a detailed copy number variation (CNV) analysis of X chromosome involvement in POF. The arrays also contained a 1 Mb autosomal tiling path as a reference control. Quantitative PCR for selected genes contained within the CNVs was used to confirm the majority of the changes detected. The expression pattern of some of these genes in human tissue RNA was examined by reverse transcription (RT)-PCR. RESULTS A number of CNVs were identified on both Xp and Xq, with several being shared among the POF cases. Some CNVs fall within known polymorphic CNV regions, and others span previously identified POF candidate regions and genes. CONCLUSIONS The new data reported in this study reveal further discrete X chromosome intervals not previously associated with the disease and therefore implicate new clusters of candidate genes. Further studies will be required to elucidate their involvement in POF.
A differential developmental pattern of spinal interneuron apoptosis during synaptogenesis: insights from genetic analyses of the protocadherin-γ gene cluster

Although the role of developmental apoptosis in shaping the complement and connectivity of sensory and motoneurons is well documented, the extent to which cell death affects the 13 cardinal classes of spinal interneurons is unclear. Using a series of genetic manipulations in vivo, we demonstrate for the first time a differential pattern of developmental apoptosis in molecularly identified spinal interneuron populations, and implicate the adhesion molecule family encoded by the 22-member protocadherin-γ (Pcdh-γ) gene cluster in its control. In constitutive Pcdh-γ null mouse embryos, many interneuron populations undergo increased apoptosis, but to differing extents: for example, over 80% of En1-positive V1 neurons are lost, whereas only 30% of Chx10-positive V2a neurons are lost and there is no reduction in the number of V1-derived Renshaw cells. We show that this represents an exacerbation of a normal, underlying developmental pattern: the extent of each population's decrease in Pcdh-γ mutants is precisely commensurate both with the extent of its loss during normal embryogenesis and with the extent of its increase in Bax-/- mice, in which apoptosis is genetically blocked. Interneuron apoptosis begins during the first wave of synaptogenesisis in the spinal cord, occurring first among ventral populations (primarily between E14 and E17), and only later among dorsal populations (primarily after P0). Utilizing a new, conditional Pcdh-γ mutant allele, we show that the γ-Pcdhs can promote survival non-cell-autonomously: mutant neurons can survive if they are surrounded by normal neurons, and normal neurons can undergo apoptosis if they are surrounded by mutant neurons.
Protein Trafficking through the Endosomal System Prepares Intracellular Parasites for a Home Invasion

Toxoplasma (toxoplasmosis) and Plasmodium (malaria) use unique secretory organelles for migration, cell invasion, manipulation of host cell functions, and cell egress. In particular, the apical secretory micronemes and rhoptries of apicomplexan parasites are essential for successful host infection. New findings reveal that the contents of these organelles, which are transported through the endoplasmic reticulum (ER) and Golgi, also require the parasite endosome-like system to access their respective organelles. In this review, we discuss recent findings that demonstrate that these parasites reduced their endosomal system and modified classical regulators of this pathway for the biogenesis of apical organelles.
Worst-case and average-case analysis of n-detection test sets

Test sets that detect each target fault n times (n-detection test sets) are typically generated for restricted values of n due to the increase in test set size with n. We perform both a worst-case analysis and an average-case analysis to check the effect of restricting n on the unmodeled fault coverage of an (arbitrary) n-detection test set. Our analysis is independent of any particular test set or test generation approach. It is based on a specific set of target faults and a specific set of untargeted faults. It shows that, depending on the circuit, very large values of n may be needed to guarantee the detection of all the untargeted faults. We discuss the implications of these results.
Therapeutics , Targets , and Chemical Biology Development of a Hypoxia Gene Expression Classifier with Predictive Impact for Hypoxic Modification of Radiotherapy in Head and Neck Cancer

Hypoxia, a common feature of the microenvironment in solid tumors, is associated with resistance to radiotherapy, reduced therapeutic response, and a poorer clinical outcome. In head and neck squamous cell carcinomas (HNSCC), the negative effect of hypoxia on radiotherapy can be counteracted via addition of hypoxic modification to the radiotherapy. To predict which patients harbor hypoxic tumors and would therefore benefit from hypoxic modification, clinically applicable methods for pretherapeutic hypoxic evaluation and categorization are needed. In this study, we developed a hypoxia classifier based on gene expression. Through study of xenograft tumors from human squamous cell carcinoma cell lines, we verified the in vivo relevance of previously identified in vitro derived hypoxia-induced genes. We then evaluated a training set of 58 hypoxia-evaluated HNSCCs to generate a gene expression classifier containing 15 genes. This 15-gene hypoxia classifier was validated in 323 patients with HNSCC randomized for hypoxic modification or placebo in combination with radiotherapy. Tumors categorized as hypoxic on the basis of the classifier were associated with a significantly poorer clinical outcome than nonhypoxic tumors. This outcome was improved and equalized to the nonhypoxic tumors by addition of hypoxic modification. Thus, findings show that the classifier attained both prognostic and predictive impact, and its pretherapeutic use may provide a method to identify those patients who will benefit from hypoxic modification of radiotherapy. Cancer Res; 71(17); 5923–31. 2011 AACR.
Context, Culture and Green Consumption: A New Framework

ABSTRACT Green consumption is context-dependent, complex, and multifaceted. Research from environmental psychology, environmental sociology, cross-cultural communication, and consumer behavior is integrated to develop a set of six hypotheses and a new model for green consumption. The model proposes a composite cultural profile (including individual, social/relational, temporal, and biospheric factors) as a mediating variable between individual factors, behavioral intention, and green consumption. The model further proposes contextual factors (economic, social, political, and technological) as a moderating variable on individual attitudes, values and perceived control, individual cultural profile, behavioral intention, and green consumption. A systems approach addresses weaknesses in previous a-contextual models that do not take into account emotional, symbolic, and cultural factors embedded in consumer consumption decisions. The model may offer superior explanations for green consumption behaviors in non-Western socio-technical contexts than that offered by existing theory, supporting more effective decision-making for managers and policymakers.