Miracle-dz/UniFAR-FTUs huggingface dataset:
Physical Activity and Incident Hypertension in African Americans: The Jackson Heart Study

There is limited empirical evidence to support the protective effects of physical activity in the prevention of hypertension among African Americans. The purpose of this study was to examine the association of physical activity with incident hypertension among African Americans. We studied 1311 participants without hypertension at baseline enrolled in the Jackson Heart Study, a community-based study of African Americans residing in Jackson, Mississippi. Overall physical activity, moderate–vigorous physical activity, and domain-specific physical activity (work, active living, household, and sport/exercise) were assessed by self-report during the baseline examination (2000–2004). Incident hypertension, assessed at examination 2 (2005–2008) and examination 3 (2009–2013), was defined as the first visit with systolic/diastolic blood pressure ≥140/90 mm Hg or self-reported antihypertensive medication use. Over a median follow-up of 8.0 years, there were 650 (49.6%) incident hypertension cases. The multivariable-adjusted hazard ratios (95% confidence interval) for incident hypertension comparing participants with intermediate and ideal versus poor levels of moderate–vigorous physical activity were 0.84 (0.67–1.05) and 0.76 (0.58–0.99), respectively (P trend=0.038). A graded, dose–response association was also present for sport/exercise-related physical activity (Quartiles 2, 3, and 4 versus Quartile 1: 0.92 [0.68–1.25], 0.87 [0.67–1.13], 0.75 [0.58–0.97], respectively; P trend=0.032). There were no statistically significant associations observed for overall physical activity, or work, active living, and household-related physical activities. In conclusion, the results of the current study suggest that regular moderate–vigorous physical activity or sport/exercise-related physical activity may reduce the risk of developing hypertension in African Americans.
Improving the performance of minimizers and winnowing schemes

The minimizers scheme is a method for selecting k-mers from sequences. It is used in many bioinformatics software tools to bin comparable sequences or to sample a sequence in a deterministic fashion at approximately regular intervals, in order to reduce memory consumption and processing time. Although very useful, the minimizers selection procedure has undesirable behaviors (e.g., too many k-mers are selected when processing certain sequences). Some of these problems were already known to the authors of the minimizers technique, and the natural lexicographic ordering of k-mers used by minimizers was recognized as their origin. Many software tools using minimizers employ ad hoc variations of the lexicographic order to alleviate those issues. We provide an in-depth analysis of the effect of k-mer ordering on the performance of the minimizers technique. By using small universal hitting sets (a recently defined concept), we show how to significantly improve the performance of minimizers and avoid some of its worse behaviors. Based on these results, we encourage bioinformatics software developers to use an ordering based on a universal hitting set or, if not possible, a randomized ordering, rather than the lexicographic order. This analysis also settles negatively a conjecture (by Schleimer et al.) on the expected density of minimizers in a random sequence. The software used for this analysis is available on GitHub: https://github.com/gmarcais/minimizers.git. Contact: gmarcais@cs.cmu. edu
On the Throughput of MIMO-Empowered Multihop Cognitive Radio Networks

Cognitive radio (CR) and multiple-input multiple-output (MIMO) are two independent physical layer technologies that have made significant impact on wireless networking. CR operates on the channel/band level to exploit white space across spectrum dimension while MIMO operates within the same channel to improve spectral efficiency within the same band. In this paper, we explore MIMO-empowered CR network, which we call CRNMIMO, to achieve the ultimate flexibility and efficiency in dynamic spectrum access and spectrum utilization. Given that CR and MIMO handle interference at different levels (across channels vs. within a channel), we are interested in how to jointly optimize both so as to maximize user throughput in a multihop network. To answer this question, we develop a tractable mathematical model for CRNMIMO, which captures the essence of channel assignment (for CR) and degree-of-freedom (DoF) allocation (for MIMO) within a channel. Based on this mathematical model, we use numerical results to show how channel assignment in CRN and DoF allocation in MIMO can be jointly optimized to maximize throughput. More important, for a CRNMIMO with AMIMO antennas at each node, we show that joint optimization of CR and MIMO offers more than AMIMO-fold throughput increase than a CRN (without MIMO).
Screening for Helicobacter pylori and nonsteroidal anti-inflammatory drug use in medicare patients hospitalized with peptic ulcer disease.

BACKGROUND Peptic ulcer disease has well-defined causes, with most cases related to Helicobacter pylori infection and nonsteroidal anti-inflammatory drug use. OBJECTIVES To report performance rates on measures of care related to peptic ulcer disease in hospitalized Medicare patients and to identify improvement opportunities. METHODS Retrospective study of 2267 Medicare beneficiaries hospitalized with peptic ulcer disease. Data were obtained from 2 sources: medical records (n = 1580) from 80 hospitals--16 hospitals in each of 5 states (Alabama, Florida, Louisiana, Tennessee, and Texas)-and a national random sample (n = 687). Three measures of care were evaluated: (1) rate of diagnostic screening or treatment for H. pylori infection, (2) rate of screening for nonsteroidal anti-inflammatory drug use on admission to the hospital, and (3) rate of assessment of risk factors for recurrence. RESULTS The rate of screening or treatment for H. pylori infection was 52.9% to 59.8% among the 5 states and 55.6% in the national random sample. The rate of screening for nonsteroidal anti-inflammatory drug use was 64.6% to 75.4% among the states and 73.4% in the national random sample. The rate of assessment at discharge from the hospital for additional risks for ulcer recurrence was 66.1% to 73.6% among the states and 70.9% in the national random sample. CONCLUSIONS Based on hospital records, slightly more than half of the Medicare patients admitted with diagnoses studied are being considered for H. pylori eradication. If recurrence of this disease is to be reduced, physicians must adopt current screening and treatment recommendations.
Cassandra smart-home system description

This paper presents the architecture and technologies used to develop a voice controlled system for home automation named Cassandra. We start with the goals of the project and a system description, then focusing on the main components and the way they interact with each other. We exemplify with a scenario where we ask the house to turn the lights off, going step-by-step over the communication sequence between the modules involved. The purpose of this paper is for the reader to get an overview of how the system works, without going deep into technical details.
The role of posttraumatic fear and social support in the relationship between trauma severity and posttraumatic growth among adolescent survivors of the Yaan earthquake

Middle school students in Lushan county (N = 315) were assessed 6 months after the Yaan earthquake using a trauma severity questionnaire, a posttraumatic fear questionnaire, a social support questionnaire and a posttraumatic growth inventory to examine the effects of posttraumatic fear and social support in the relationship between trauma severity and posttraumatic growth (PTG). The results showed that posttraumatic fear mediated the relationship between trauma severity and PTG, and social support moderated the relationship between posttraumatic fear and PTG. These findings suggested that trauma severity could be positively associated with PTG in a direct way or in an indirect way through posttraumatic fear. Moreover, posttraumatic fear had a positive relation to PTG under the condition of high social support level, whereas the relation was non-significant when the level of social support was low. These results were discussed in terms of their implications for adolescents after trauma.
Prevalence of Human Papillomavirus Type 58 in Women With or Without Cervical Lesions in Northeast Brazil

Background: Human papillomavirus (HPV) has been recognized as a necessary, but not sufficient, cause of cervical cancer. Aim: In this study, we investigated the prevalence of HPV and the genotype distribution in women from Natal, North-East Brazil, with normal cytology and with cervical lesions of different degrees. Subjects and Methods: Included in this study were 110 women with a normal cytology and 315 with a previous history of cervical cytological abnormalities. The patients were enrolled between January 2005 and December 2008. The cytopathological analyzes were performed by the Pap smear exam, and the pre-malignant and maligant lesions were confirmed based on the histopathological analysis. The presence of HPV was detected by polymerase chain reaction with genotyping by dot blot hybridization. All the data were included in a database, using the software SPSS, Version 10.0 (Chicago Il, USA). Results: Overall HPV prevalence was 65.2% (277/425), with 85.9% (238/277) single and 14.1% (39/277) multiple infection. The most prevalent HPV types were HPVs 16, 58, 18, 31, and 45. HPV 16 was the most prevalent genotype, independently of the health status of patients. HPV 58 was the second most prevalent type in women with normal cytology and in those who had mild or moderate dysplasia. HPV 58 presented equal prevalence to HPV 18 in patients with severe dysplasia. However, it was less prevalent than HPV 18 in women with cervical cancer. Conclusions: The results show a high prevalence of HPV 58, especially in women with mild and moderate dysplasia, revealing the high-frequency circulation of this genotype of HPV in the local population. This finding suggests the need to include this genotype in future HPV vaccines targeting women in this region.
The Identification of the Closest Living Relative(s) of Tetrapods: Phylogenomic Lessons for Resolving Short Ancient Internodes.

Identifying the closest living relative(s) of tetrapods is an important, yet still contested question in vertebrate phylogenetics. Three hypotheses are possible and ruling out alternatives has proven difficult even with large molecular data sets due to weak phylogenetic signal coupled nonphylogenetic noise resulting from relatively rapid speciation events that occurred a long time ago ([Formula: see text]400 Ma). Here, we revisit the identity of the closest living relative of land vertebrates from a phylogenomic perspective and include new genomic data for all extant lungfish genera. RNA-seq proves to be a great alternative to genomic sequencing, which currently is technically not feasible in lungfishes due to their huge (50-130 Gb) and repetitive genomes. We examined the most important sources of systematic error, namely long-branch attraction (LBA), compositional heterogeneity and distribution of missing data and applied different correction techniques. A multispecies coalescent approach is used to account for deep coalescence that might come from the short and deep internodes separating early sarcopterygian splits. Concatenation methods favored lungfishes as the closest living relatives of tetrapods with strong statistical support. Amino acid profile mixture models can unambiguously resolve this difficult internode thanks to their ability to avoid systematic error. We assessed the performance of different site-heterogeneous models and data partitioning and compared the ability of different strategies designed to overcome LBA, including taxon manipulation, reduction of among-lineage rate heterogeneity and removal of fast-evolving or compositionally heterogeneous positions. The identification of lungfish as sister group of tetrapods is robust regarding the effects of nonstationary composition and distribution of missing data. The multispecies coalescent method reconstructed strongly supported topologies that were congruent with concatenation, despite pervasive gene tree heterogeneity. We reject alternative topologies for early sarcopterygian relationships by increasing the signal-to-noise ratio in our alignments. The analytical pipeline outlined here combines probabilistic phylogenomic inference with methods for evaluating data quality, model adequacy, and assessing systematic error, and thus is likely to help resolve similarly difficult internodes in the tree of life. [Coalescence; coelacanth; compositional heterogeneity; gene tree; long-branch attraction; lungfish; missing data; model misspecification; phylogenomic; species tree; systematic error. ].
Distributed One-Class Learning

We propose a cloud-based filter trained to block third parties from uploading privacy-sensitive images of others to online social media. The proposed filter uses Distributed One-Class Learning, which decomposes the cloud-based filter into multiple one-class classifiers. Each one-class classifier captures the properties of a class of privacy-sensitive images with an autoencoder. The multi-class filter is then reconstructed by combining the parameters of the one-class autoen-coders. The training takes place on edge devices (e.g. smartphones) and therefore users do not need to upload their private and/or sensitive images to the cloud. A major advantage of the proposed filter over existing distributed learning approaches is that users cannot access, even indirectly, the parameters of other users. Moreover, the filter can cope with the imbalanced and complex distribution of the image content and the independent probability of addition of new users. We evaluate the performance of the proposed distributed filter using the exemplar task of blocking a user from sharing privacy-sensitive images of other users. In particular, we validate the behavior of the proposed multi-class filter with non-privacy-sensitive images, the accuracy when the number of classes increases, and the robustness to attacks when an adversary user has access to privacy-sensitive images of other users.
Association of the Jumping to Conclusions and Evidence Integration Biases With Delusions in Psychosis: A Detailed Meta-analysis

We completed a meta-analysis to investigate the relationship between delusions in psychosis and 4 cognitive biases: "jumping to conclusions" (JTC), the "bias against disconfirmatory evidence" (BADE), the "bias against confirmatory evidence" (BACE), and "liberal acceptance" (LA). Building on recent meta-analyses we compared more narrowly defined groups. We identified 35 JTC, 8 BADE, 7 BACE, and 6 LA studies for inclusion. Groups with schizophrenia who were currently experiencing delusions demonstrated greater JTC, BADE, BACE, and LA than groups with schizophrenia who were not currently experiencing delusions, who in turn demonstrated no more JTC than healthy control groups. Hence JTC, BADE, BACE, and LA co-vary with delusions in cross-sectional samples of people with schizophrenia. Groups who were experiencing delusions due to other psychiatric illnesses also demonstrated greater JTC than healthy controls, and equivalent JTC to groups with schizophrenia currently experiencing delusions. Hence JTC is associated with delusions across a range of diagnoses. Groups with other, non-delusional psychiatric illnesses demonstrated less JTC, BADE, BACE, and LA than groups with schizophrenia currently experiencing delusions, less JTC than groups experiencing delusions due to other diagnoses, and no more JTC, BADE, BACE, or LA than healthy control groups. Hence JTC, BADE, BACE, and LA were not associated with psychiatric illnesses in general. Our results indicate all 4 biases are associated with delusions specifically rather than merely with a diagnosis of schizophrenia or with being psychiatrically ill, consistent with the possibility that they contribute to delusional severity.
Early stages of Alzheimer's disease are alarming signs in injury deaths caused by traffic accidents in elderly people (≥60 years of age): A neuropathological study

Background: There is little information available in the literature concerning the contribution of dementia in injury deaths in elderly people (≥60 years). Aim: This study was intended to investigate the extent of dementia-related pathologies in the brains of elderly people who died in traffic accidents or by suicide and to compare our findings with age- and sex-matched natural deaths in an elderly population. Materials and Methods: Autopsy-derived human brain samples from nine injury death victims (5 suicide and 4 traffic accidents) and nine age- and sex-matched natural death victims were screened for neurodegenerative and cerebrovascular pathologies using histopathological and immunohistochemical techniques. For the analysis, Statistical Package for the Social Sciences (SPSS) version 16.0 was used. Results: There was a greater likelihood for Alzheimer's disease (AD)-related changes in the elders who succumbed to traffic accidents (1 out of 4) compared to age- and sex-matched suicides (0 out of 5) or natural deaths (0 out of 9) as assessed by the National Institute on Aging – Alzheimer's Association guidelines. Actual burden of both neurofibrillary tangles (NFTs) and (SPs) was comparatively higher in the brains of traffic accidents, and the mean NFT counts were significantly higher in the region of entorhinal cortex (P < 0.05). However, associations obtained for other dementia-related pathologies were not statistically important. Conclusion: Our findings suggest that early Alzheimer stages may be a contributing factor to injury deaths caused by traffic accidents in elderly people whereas suicidal brain neuropathologies resembled natural deaths.
Analysis of Differential Efficacy and Affinity of GABAA (α1/α2) Selective Modulators.

Selective modulators of the γ-amino butyric acid (GABAA) family of receptors have the potential to treat a range of disease states related to cognition, pain, and anxiety. While the development of various α subunit-selective modulators is currently underway for the treatment of anxiety disorders, a mechanistic understanding of the correlation between their bioactivity and efficacy, based on ligand-target interactions, is currently still lacking. In order to alleviate this situation, in the current study we have analyzed, using ligand- and structure-based methods, a data set of 5440 GABAA modulators. The Spearman correlation (ρ) between binding activity and efficacy of compounds was calculated to be 0.008 and 0.31 against the α1 and α2 subunits of GABA receptor, respectively; in other words, the compounds had little diversity in structure and bioactivity, but they differed significantly in efficacy. Two compounds were selected as a case study for detailed interaction analysis due to the small difference in their structures and affinities (ΔpKi(comp1_α1 - comp2_α1) = 0.45 log units, ΔpKi(comp1_α2 - comp2_α2) = 0 log units) as compared to larger relative efficacies (ΔRE(comp1_α1 - comp2_α1) = 1.03, ΔRE(comp1_α2 - comp2_α2) = 0.21). Docking analysis suggested that His-101 is involved in a characteristic interaction of the α1 receptor with both compounds 1 and 2. Residues such as Phe-77, Thr-142, Asn-60, and Arg-144 of the γ chain of the α1γ2 complex also showed interactions with heterocyclic rings of both compounds 1 and 2, but these interactions were disturbed in the case of α2γ2 complex docking results. Binding pocket stability analysis based on molecular dynamics identified three substitutions in the loop C region of the α2 subunit, namely, G200E, I201T, and V202I, causing a reduction in the flexibility of α2 compared to α1. These amino acids in α2, as compared to α1, were also observed to decrease the vibrational and dihedral entropy and to increase the hydrogen bond content in α2 in the apo state. However, freezing of both α1 and α2 was observed in the ligand-bound state, with an increased number of internal hydrogen bonds and increased entropy. Therefore, we hypothesize that the amino acid differences in the loop C region of α2 are responsible for conformational changes in the protein structure compared to α1, as well as for the binding modes of compounds and hence their functional signaling.
Engineered cell migration to lesions linked to autoimmune disease

The damaging and degenerative effects in autoimmune diseases such as rheumatoid arthritis, multiple sclerosis and Crohn's disease often manifests as the formation of lesions that feature a high local concentration of granulocyte–macrophage colony‐stimulating factor (GM‐CSF). GM‐CSF along with other pro‐inflammatory factors form a positive feedback loop that ultimately perpetuate the lesions. Hence, to engineer chemotaxis to GM‐CSF, we created a new chimeric GM‐CSF receptor alpha subunit (GMRchi) that was coupled with a previously engineered Ca2+‐activated RhoA. When these proteins were expressed in mammalian cells, it allowed migration to chemical and cellular sources of GM‐CSF. As a possible therapeutic intervention, we further implemented the mechanism of cell–cell membrane fusion and subsequent death. Since the microenvironment of lesions is more than just GM‐CSF secretion, the further ability to recognize a combination of other features such as tissue markers will be needed for greater specificity. Nonetheless, this work represents a first step to enable cell‐based therapy of autoimmune lesions.
Genome analysis PRIMEGENS-v 2 : genome-wide primer design for analyzing DNA methylation patterns of CpG islands

Motivation: DNA methylation plays important roles in biological processes and human diseases, especially cancers. High-throughput bisulfite genomic sequencing based on new generation of sequencers, such as the 454-sequencing system provides an efficient method for analyzing DNA methylation patterns. The successful implementation of this approach depends on the use of primer design software capable of performing genome-wide scan for optimal primers from in silico bisulfite-treated genome sequences. We have developed a method, which fulfills this requirement and conduct primer design for sequences including regions of given promoter CpG islands. Results: The developed method has been implemented using the C and JAVA programming languages. The primer design results were tested in the PCR experiments of 96 selected human DNA sequences containing CpG islands in the promoter regions. The results indicate that this method is efficient and reliable for designing sequence-specific primers. Availability: The sequence-specific primer design for DNA methylated sequences including CpG islands has been integrated into the second version of PRIMEGENS as one of the primer design features. The software is freely available for academic use at http://digbio.missouri.edu/primegens/. Contact: xudong@missouri.edu