Miracle-dz/UniFAR-FTUs huggingface dataset:
A conceptual model exploring the relationship between HIV stigma and implementing HIV clinical trials in rural communities of North Carolina.

BACKGROUND HIV/AIDS disproportionately affects minority groups in the United States, especially in the rural southeastern states. Poverty and lack of access to HIV care, including clinical trials, are prevalent in these areas and contribute to HIV stigma. This is the first study to develop a conceptual model exploring the relationship between HIV stigma and the implementation of HIV clinical trials in rural contexts to help improve participation in those trials. METHODS We conducted focus groups with HIV service providers and community leaders, and individual interviews with people living with HIV/AIDS in six counties in rural North Carolina. Themes related to stigma were elicited. We classified the themes into theoretical constructs and developed a conceptual model. RESULTS HIV stigma themes were classified under the existing theoretical constructs of perceived, experienced, vicarious, and felt normative stigma. Two additional constructs emerged: causes of HIV stigma (e.g., low HIV knowledge and denial in the community) and consequences of HIV stigma (e.g., confidentiality concerns in clinical trials). The conceptual model illustrates that the causes of HIV stigma can give rise to perceived, experienced, and vicarious HIV stigma, and these types of stigma could lead to the consequences of HIV stigma that include felt normative stigma. LIMITATIONS Understanding HIV stigma in rural counties of North Carolina may not be generalizeable to other rural US southeastern states. CONCLUSION The conceptual model emphasizes that HIV stigma--in its many forms--is a critical barrier to HIV clinical trial implementation in rural North Carolina.
The Neural Correlates of Hierarchical Predictions for Perceptual Decisions

Sensory information is inherently noisy, sparse, and ambiguous. In contrast, visual experience is usually clear, detailed, and stable. Bayesian theories of perception resolve this discrepancy by assuming that prior knowledge about the causes underlying sensory stimulation actively shapes perceptual decisions. The CNS is believed to entertain a generative model aligned to dynamic changes in the hierarchical states of our volatile sensory environment. Here, we used model-based fMRI to study the neural correlates of the dynamic updating of hierarchically structured predictions in male and female human observers. We devised a crossmodal associative learning task with covertly interspersed ambiguous trials in which participants engaged in hierarchical learning based on changing contingencies between auditory cues and visual targets. By inverting a Bayesian model of perceptual inference, we estimated individual hierarchical predictions, which significantly biased perceptual decisions under ambiguity. Although “high-level” predictions about the cue–target contingency correlated with activity in supramodal regions such as orbitofrontal cortex and hippocampus, dynamic “low-level” predictions about the conditional target probabilities were associated with activity in retinotopic visual cortex. Our results suggest that our CNS updates distinct representations of hierarchical predictions that continuously affect perceptual decisions in a dynamically changing environment. SIGNIFICANCE STATEMENT Bayesian theories posit that our brain entertains a generative model to provide hierarchical predictions regarding the causes of sensory information. Here, we use behavioral modeling and fMRI to study the neural underpinnings of such hierarchical predictions. We show that “high-level” predictions about the strength of dynamic cue–target contingencies during crossmodal associative learning correlate with activity in orbitofrontal cortex and the hippocampus, whereas “low-level” conditional target probabilities were reflected in retinotopic visual cortex. Our findings empirically corroborate theorizations on the role of hierarchical predictions in visual perception and contribute substantially to a longstanding debate on the link between sensory predictions and orbitofrontal or hippocampal activity. Our work fundamentally advances the mechanistic understanding of perceptual inference in the human brain.
Polyglutamine- and Temperature-Dependent Conformational Rigidity in Mutant Huntingtin Revealed by Immunoassays and Circular Dichroism Spectroscopy

Background In Huntington's disease, expansion of a CAG triplet repeat occurs in exon 1 of the huntingtin gene (HTT), resulting in a protein bearing>35 polyglutamine residues whose N-terminal fragments display a high propensity to misfold and aggregate. Recent data demonstrate that polyglutamine expansion results in conformational changes in the huntingtin protein (HTT), which likely influence its biological and biophysical properties. Developing assays to characterize and measure these conformational changes in isolated proteins and biological samples would advance the testing of novel therapeutic approaches aimed at correcting mutant HTT misfolding. Time-resolved Förster energy transfer (TR-FRET)-based assays represent high-throughput, homogeneous, sensitive immunoassays widely employed for the quantification of proteins of interest. TR-FRET is extremely sensitive to small distances and can therefore provide conformational information based on detection of exposure and relative position of epitopes present on the target protein as recognized by selective antibodies. We have previously reported TR-FRET assays to quantify HTT proteins based on the use of antibodies specific for different amino-terminal HTT epitopes. Here, we investigate the possibility of interrogating HTT protein conformation using these assays. Methodology/Principal Findings By performing TR-FRET measurements on the same samples (purified recombinant proteins or lysates from cells expressing HTT fragments or full length protein) at different temperatures, we have discovered a temperature-dependent, reversible, polyglutamine-dependent conformational change of wild type and expanded mutant HTT proteins. Circular dichroism spectroscopy confirms the temperature and polyglutamine-dependent change in HTT structure, revealing an effect of polyglutamine length and of temperature on the alpha-helical content of the protein. Conclusions/Significance The temperature- and polyglutamine-dependent effects observed with TR-FRET on HTT proteins represent a simple, scalable, quantitative and sensitive assay to identify genetic and pharmacological modulators of mutant HTT conformation, and potentially to assess the relevance of conformational changes during onset and progression of Huntington's disease.
Sociology Faculty Members Employed Part-time in Community Colleges

The large majority of faculty members teaching in community colleges are employed on a part-time basis, yet little is known about their working conditions and professional engagement. This article uses data from a recent national survey of faculty members teaching sociology in community colleges to provide this information, with particular attention to the different situations of those teaching full-time, part-time by choice, and part-time involuntarily. Contrary to previous analyses that assume homogeneous motivation and working conditions for part-time faculty members, our analysis finds differences between two categories in both structural aspects of their employment and perceptions of cultural devaluation expressed interpersonally. Both aspects serve as constraints on developing faculty-student relationships, a proven factor in student learning and success. We conclude that administrators and full-time colleagues must provide stronger support for the individuals introducing students to the discipline of sociology in the community college.
Using Health Surveillance Systems Data to Assess the Impact of AIDS and Antiretroviral Treatment on Adult Morbidity and Mortality in Botswana

Introduction Botswana's AIDS response included free antiretroviral treatment (ART) since 2002, achieving 80% coverage of persons with CD4<350 cells/µl by 2009–10. We explored impact on mortality and HIV prevalence, analyzing surveillance and civil registration data. Methods Hospital natural cause admissions and deaths from the Health Statistics Unit (HSU) over 1990–2009, all-cause deaths from Midnight Bed Census (MNC) over 1990–2011, institutional and non-institutional deaths recorded in the Registry of Birth and Deaths (RBD) over 2003–2010, and antenatal sentinel surveillance (ANC) over 1992–2011 were compared to numbers of persons receiving ART. Mortality was adjusted for differential coverage and completeness of institutional and non-institutional deaths, and compared to WHO and UNAIDS Spectrum projections. Results HSU deaths per 1000 admissions declined 49% in adults 15–64 years over 2003–2009. RBD mortality declined 44% (807 to 452/100,000 population in adults 15–64 years) over 2003–2010, similarly in males and females. Generally, death rates were higher in males; declines were greater and earlier in younger adults, and in females. In contrast, death rates in adults 65+, particularly females increased over 2003–2006. MNC all-age post-neonatal mortality declined 46% and 63% in primary and secondary level hospitals, over 2003–2011. We estimated RBD captured 80% of adult deaths over 2006–2011. Comparing empirical, completeness-adjusted deaths to Spectrum estimates, declines over 2003–2009 were similar overall (47% vs. 54%); however, Spectrum projected larger and earlier declines particularly in women. Following stabilization and modest decreases over 1998–2002, HIV prevalence in pregnant women 15–24 and 25–29-years declined by >50% and >30% through 2011, while continuing to increase in older women. Conclusions Adult mortality in Botswana fell markedly as ART coverage increased. HIV prevalence declines may reflect ART-associated reductions in sexual transmission. Triangulation of surveillance system data offers a reasonable approach to evaluate impact of HIV/AIDS interventions, complementing cohort approaches that monitor individual-level health outcomes.
Relating branes and matrices

We construct a general map between a Dp-brane with magnetic flux and a matrix configuration of D0-branes, by showing how one can rewrite the boundary state of the Dp-brane in terms of its D0-brane constituents. This map gives a simple prescription for constructing the matrices of fuzzy spaces corresponding to branes of arbitrary shape and topology. Since we explicitly identify the D0-brane degrees of freedom on the brane, we also derive the D0-brane charge of the brane in a very direct way including the ? -genus term. As a check on our formalism, we use our map to derive the abelian-Born-Infeld equations of motion from the action of the D0-brane matrices.
Depletion of the ER chaperone ENPL-1 sensitizes C. elegans to the anticancer drug cisplatin

Cisplatin is an essential chemotherapeutic drug in the treatment of many cancers. Its use, however, is limited by the development of resistance in many tumors. The ability to re-sensitize resistant tumors could significantly strengthen cisplatin therapy in patients. Caenorhabditis elegans is a suitable model for studying the cytoplasmic role of cisplatin in tumor cells. We have previously shown that the ATPase ASNA-1 has similar roles as a factor governing cisplatin sensitivity in mammalian tumor cells and C. elegans. Here we study the endoplasmic reticulum (ER) resident chaperone ENPL-1/GRP94 and find that its depletion makes worms sensitive to cisplatin. Elevated ER stress levels in enpl-1 mutants is the likely cause of this sensitivity because a correlation can be made between cisplatin sensitivity and the high ER stress levels. We also find that asna-1 mutants have elevated unfolded protein response (UPR) activity and that the intrinsically cisplatin resistant wild-type worms become sensitive when ER stress is high. We conclude that enpl-1 is a cisplatin sensitizing factor and suggest that manipulation of its levels or of UPR activity will enhance the effects of cisplatin based cancer therapy.
Application of sorting and next generation sequencing to study 5΄-UTR influence on translation efficiency in Escherichia coli

Abstract Yield of protein per translated mRNA may vary by four orders of magnitude. Many studies analyzed the influence of mRNA features on the translation yield. However, a detailed understanding of how mRNA sequence determines its propensity to be translated is still missing. Here, we constructed a set of reporter plasmid libraries encoding CER fluorescent protein preceded by randomized 5΄ untranslated regions (5΄-UTR) and Red fluorescent protein (RFP) used as an internal control. Each library was transformed into Escherchia coli cells, separated by efficiency of CER mRNA translation by a cell sorter and subjected to next generation sequencing. We tested efficiency of translation of the CER gene preceded by each of 48 natural 5΄-UTR sequences and introduced random and designed mutations into natural and artificially selected 5΄-UTRs. Several distinct properties could be ascribed to a group of 5΄-UTRs most efficient in translation. In addition to known ones, several previously unrecognized features that contribute to the translation enhancement were found, such as low proportion of cytidine residues, multiple SD sequences and AG repeats. The latter could be identified as translation enhancer, albeit less efficient than SD sequence in several natural 5΄-UTRs.
Regional, Household and Individual Factors that Influence Soil Transmitted Helminth Reinfection Dynamics in Preschool Children from Rural Indigenous Panamá

Background Few studies have investigated the relative influence of individual susceptibility versus household exposure factors versus regional clustering of infection on soil transmitted helminth (STH) transmission. The present study examined reinfection dynamics and spatial clustering of Ascaris lumbricoides, Trichuris trichiura and hookworm in an extremely impoverished indigenous setting in rural Panamá over a 16 month period that included two treatment and reinfection cycles in preschool children. Methodology/Principle Findings Spatial cluster analyses were used to identify high prevalence clusters for each nematode. Multivariate models were then used (1) to identify factors that differentiated households within and outside the cluster, and (2) to examine the relative contribution of regional (presence in a high prevalence cluster), household (household density, asset-based household wealth, household crowding, maternal education) and individual (age, sex, pre-treatment eggs per gram (epg) feces, height-for-age, latrine use) factors on preschool child reinfection epgs for each STH. High prevalence spatial clusters were detected for Trichuris and hookworm but not for Ascaris. These clusters were characterized by low household density and low household wealth indices (HWI). Reinfection epg of both hookworm and Ascaris was positively associated with pre-treatment epg and was higher in stunted children. Additional individual (latrine use) as well as household variables (HWI, maternal education) entered the reinfection models for Ascaris but not for hookworm. Conclusions/Significance Even within the context of extreme poverty in this remote rural setting, the distinct transmission patterns for hookworm, Trichuris and Ascaris highlight the need for multi-pronged intervention strategies. In addition to poverty reduction, improved sanitation and attention to chronic malnutrition will be key to reducing Ascaris and hookworm transmission.
Spatial Speaker: 3D Java Text-to-Speech Converter

Text-to-speech (TTS) converters are the key components of various types of auditory displays. Such converters are extremely useful for visually impaired computer users who depend on synthesized speech read from the computer screen or directly from the web. In this paper we propose an enhancement of a Java FreeTTS speech synthesizer by adding the function of spatial positioning of both the speaker and the listener. With our module, an arbitrary text from a file or the web can be read to the user through the headphones from a fixed or changing position in space. In our solution, we combine the following modules: FreeTTS speech synthesizer, a custom made speech processing unit, MIT Media Lab HRTF library, JOAL positioning library and Creative X-Fi sound card. Although the main focus of the paper is on the design of the "Spatial Speaker", three different applications are proposed and some results of preliminary evaluation studies and user feedback are given. The entire system is developed as a single Java class which can be used in any auditory interface developed in Java.
Ho‘o Ponopono: A Traditional Hawaiian Practice for Setting Relationships Right:

The author presents the traditional Hawaiian practice of ho'o ponopono: “The act of bringing into being a mental cleansing of thoughts, feelings and actions in order to rectify problems in interpersonal relationships” (Pukui, Elbert, Mookini, & Nishizawa, 1986, p. 341). The five types of relationship interactions in which ho'o ponopono is used to intervene are: (1) to address problems between two unrelated persons, (2) to address problems between two family members, (3) to address conflict between different families, (4) to address specific problems with individuals that are affecting the community, and (5) to resolve relationship problems of any type on a spiritual level. The five-step process involved in ho'o ponopono—meditation, visualization, forgiveness, discussion, and mutual restitution—is presented. Each step in the process of ho'o ponopono is discussed with a relevant element of transactional analysis theory.
Zinc-Dependent Transcriptional Regulation in Paracoccus denitrificans

Zinc homeostasis is critical for bacterial survival and is mediated largely at the transcriptional level by the regulation of zinc uptake and efflux genes. Here we use RNA-seq to assess transcriptional changes as a result of zinc limitation in the denitrifying bacterium Paracoccus denitrificans. The results identify the differential expression of 147 genes, most of which were upregulated in zinc-depleted medium. Included in this set of genes are a large number of transition metal transporters, several transcription factors, and hypothetical proteins. Intriguingly, genes encoding nitric oxide reductase (norCB) and nitrite reductase (nirS) were also upregulated. A Zur consensus binding motif was identified in the promoters of the most highly upregulated genes. The zinc uptake regulator (Zur) from this organism was also characterized and shown to bind to the Zur motif in a zinc-dependent manner. This work expands our current understanding of the transcriptional response of gram-negative bacteria to zinc limitation and identifies genes involved in denitrification as part of the Zur regulon.
Curvibacter fontana sp. nov., a microaerobic bacteria isolated from well water.

The genus Curvibacter was created by Ding and Yokota (2004), within the family Comamonadaceae (Willems et al., 1991), to accommodate Gram-negative, heterotrophic, aerobic, curved rod-formed bacteria. At present, genus Curvibacter comprises three recognized species, the type species Curvibacter gracilis, Curvibacter delicatus (formerly [Aquaspirillum] delicatum), and Curvibacter lanceolatus (formerly [Pseudomonas] lanceolata) (Ding and Yokota, 2004). The major characteristics of the genus Curvibacter are the cell shape is slightly curved rods, the fl agella arrangement is polar or none, they are aerobic or microaerobic, the colony pigmentation is yellow-brown, and the ubiquinone is Q-8. During the survey of microbial diversity of aqueous environments, three novel bacterial strains, designated AQ9T, AQ10 and AQ12, were isolated from well water in Osaka, Japan, and studied using a polyphasic taxonomic approach. On the basis of the results of this study, a novel species Curvibacter fontana sp. nov. is proposed. The three strains were grown in PYMB medium (Polypepton 1 g, yeast extract 0.2 g, MgSO4・7H2O 1 g, brain heart infusion 2 g, agar 15 g, distilled water 1,000 ml, pH 7.0). Because of the poor growth of these strains, we added 10% sterile supernatant of late logarithmic growth phase culture broth of Micrococcus luteus IAM 14879T, which was obtained by incubating at 25‒30°C for 7‒10 days followed by centrifugation. The composition of the medium used for cultivating Micrococcus luteus IAM 14879T was NH4Cl 4 g, KH2PO4 1.4 g, biotin 5 mg, L-methionine 20 mg, thiamine 40 mg, inosine 1 g, MgSO4 70 mg, CuSO4 24 μg, MnCl2 0.5 mg, FeSO4 1 mg, Na2MoO4 25 μg, ZnSO4 50 μg, lithium Llactate 10 g, pH 7.5, autoclaving 121°C 25 min (Kaprelyants and Kell, 1992). These strains all slowly grew on the agar plate under aerobic condition, but were better on the slant under microaerobic conditions. The polymerase chain reaction (PCR) of 16S rRNA gene sequences amplifi cation was performed, and sequencing of the PCR products was carried out as described previously (Ding and Yokota, 2004). The 16S rRNA gene sequences obtained from the DNA database were aligned using CLUSTAL_X, version 1.83 (Thompson et al., 1994). Alignment gaps and ambiguous bases were not taken into consideration. The evolutionary distances [distance options according to the Kimura’s two-parameter model (Kimura, 1980)] and clustering with the neighbor-joining algorithm (Saitou and Nei, 1987) were determined by using bootstrap values for 1,000 replications (Felsenstein, 1985). The similarity J. Gen. Appl. Microbiol. , 56, 267‒271 (2010)
Risk factors and types of cerebral palsy.

OBJECTIVE To determine the risk factors and associated types of cerebral palsy in a squatter settlement of Karachi. METHODS The pilot cross-sectional study was conducted in Karachi during 2010 and 2011. Data was collected through an interviewed questionnaire from the mothers of cerebral palsy victims children from a population of 6000. Sample sizes of 20 pre-diagnosed victims were selected through snowball sampling. SPSS 20 was used for statistical significance. RESULTS The mean age of the 20 children was 8.7 +/- 6.4 years. Of them, 16 (80%) were males and 4 (20%) were females. Major risk factors identified were; home and assisted delivery 5 (75%), consanguinity 10 (50%), infections 8 (40%) and lack of antenatal care 6 (30%). Out of 20 cases, 15 (75%) had spastic type of cerebral palsy, which was further classified as diplegia 7 (35%), quadriplegia 6 (30%) and hemiplegia 2 (10%). Mixed and dystonic types were found in 3 (15%) and 2 (10%) children respectively. CONCLUSION Important risk factors identified were home delivery, consanguinity and infections during pregnancy. Spastic type of cerebral palsy was the most common type in the study population.
A socio-internactive framework for the fuzzy front end

This paper aims to illustrate that the dominating rational-analytic perspective on the Fuzzy Front End (FFE) of innovation could benefit by a complementary sociointeractive perspective that addresses the social processes during the FFE. We have developed a still fledgling socio-interactive framework blending existing knowledge of the FFE with theories from design methodology and the psycho-social sciences. For the framework constructs like the interplay of design problem and design solution, mental models and social processes are used and applied to the results of an empirical study for illustration. The paper ends by discussing the results and presenting a future research agenda including implications for management.