Miracle-dz/UniFAR-FTUs huggingface dataset:
Toward Exascale Computing Systems: An Energy Efficient Massive Parallel Computational Model

The emerging Exascale supercomputing system expected till 2020 will unravel many scientific mysteries. This extreme computing system will achieve a thousand-fold increase in computing power compared to the current petascale computing system. The forthcoming system will assist system designers and development communities in navigating from traditional homogeneous to the heterogeneous systems that will be incorporated into powerful accelerated GPU devices beside traditional CPUs. For achieving ExaFlops (10^18 calculations per second) performance through the ultrascale and energy-efficient system, the current technologies are facing several challenges. Massive parallelism is one of these challenges, which requires a novel energy-efficient parallel programming (PP) model for providing the massively parallel performance. In the current study, a new parallel programming model has been proposed, which is capable of achieving massively parallel performance through coarse-grained and fine-grained parallelism over inter-node and intra-node architectural-based processing. The suggested model is a tri-level hybrid of MPI, OpenMP and CUDA that is computable over a heterogeneous system with the collaboration of traditional CPUs and energy-efficient GPU devices. Furthermore, the developed model has been demonstrated by implementing dense matrix multiplication (DMM). The proposed model is considered an initial and leading model for obtaining massively parallel performance in an Exascale computing system.
Prevalence and Correlates of Prescription Drug Misuse Among a Racially Diverse Sample of Young Sexual Minority Men.

PURPOSE Sexual minority men (SMM) are at greater risk than heterosexual men for misusing prescription psychotropic medications. However, community prevalence estimates of prescription drug misuse among young SMM are lacking. The current study described lifetime and past-6-month stimulant, painkiller, and depressant/tranquilizer misuse in a large, racially diverse sample of 967 SMM aged 16-29 in Chicago, Illinois, and investigated demographic and other substance use associations. METHODS Data came from the baseline visit of the RADAR longitudinal cohort study. Associations were examined using bivariate and multivariable logistic regression. RESULTS A quarter of the sample reported ever misusing any prescription drug, and 14.2% reported recent misuse. Lifetime class-specific misuse was 16.9% for stimulants, 11.0% for painkillers, and 11.4% for depressants/tranquilizers; recent misuse was 8.0%, 5.7%, and 6.2%, respectively. In multivariable analysis, Non-Hispanic black participants had lower odds of lifetime stimulant and depressant/tranquilizer misuse and recent stimulant misuse than non-Hispanic white participants, and bisexual participants had greater odds of lifetime and recent painkiller and depressant/tranquilizer misuse than gay participants. Generally, using other substances was associated with greater odds of prescription drug misuse. Having ever been prescribed a psychotropic medication was associated with higher odds of lifetime painkiller misuse after controlling for covariates. CONCLUSION These results provide critical information on a growing public health problem among young SMM. Future research should explore why differential rates of misuse exist across subgroups. New interventions emphasizing the risk of prescription drugs, discouraging drug sharing, and bolstering refusal and coping skills should be developed and evaluated.
Multiple object tracking by incorporating a particle filter into the min-cost flow model

A novel network flow model is proposed for multiple object tracking. Based on tracklets, only a short and reliable detection sequence is needed for an effective tracking. Our model fuses the local and global data association strategies to compensate for their respective shortcomings, which can be divided into two stages: A local stage and a global stage. In the local stage, we follow the tracking-by-detection framework to generate confident tracklets by employing a boosted particle filter. In the global stage, the data association problem is formulated as a Maximum-a-Posteriori (MAP) problem and solved by a typical min-cost flow algorithm. A double-step optimization is designed to solve the long term occlusion. The experimental results show that our method outperforms several state-of-the-art methods for multiple object tracking.
Broad epitope coverage of a human in vitro antibody library

ABSTRACT Successful discovery of therapeutic antibodies hinges on the identification of appropriate affinity binders targeting a diversity of molecular epitopes presented by the antigen. Antibody campaigns that yield such broad “epitope coverage” increase the likelihood of identifying candidates with the desired biological functions. Accordingly, epitope binning assays are employed in the early discovery stages to partition antibodies into epitope families or “bins” and prioritize leads for further characterization and optimization. The collaborative program described here, which used hen egg white lysozyme (HEL) as a model antigen, combined 3 key capabilities: 1) access to a diverse panel of antibodies selected from a human in vitro antibody library; 2) application of state-of-the-art high-throughput epitope binning; and 3) analysis and interpretation of the epitope binning data with reference to an exhaustive set of published antibody:HEL co-crystal structures. Binning experiments on a large merged panel of antibodies containing clones from the library and the literature revealed that the inferred epitopes for the library clones overlapped with, and extended beyond, the known structural epitopes. Our analysis revealed that nearly the entire solvent-exposed surface of HEL is antigenic, as has been proposed for protein antigens in general. The data further demonstrated that synthetic antibody repertoires provide as wide epitope coverage as those obtained from animal immunizations. The work highlights molecular insights contributed by increasingly higher-throughput binning methods and their broad utility to guide the discovery of therapeutic antibodies representing a diverse set of functional epitopes.
Genomic Imprinting in the Endosperm Is Systematically Perturbed in Abortive Hybrid Tomato Seeds

Hybrid seed failure represents an important postzygotic barrier to interbreeding among species of wild tomatoes (Solanum section Lycopersicon) and other flowering plants. We studied genome-wide changes associated with hybrid seed abortion in the closely related Solanum peruvianum and S. chilense where hybrid crosses yield high proportions of inviable seeds due to endosperm failure and arrested embryo development. Based on differences of seed size in reciprocal hybrid crosses and developmental evidence implicating endosperm failure, we hypothesized that perturbed genomic imprinting is involved in this strong postzygotic barrier. Consequently, we surveyed the transcriptomes of developing endosperms from intra- and inter-specific crosses using tissues isolated by laser-assisted microdissection. We implemented a novel approach to estimate parent-of-origin–specific expression using both homozygous and heterozygous nucleotide differences between parental individuals and identified candidate imprinted genes. Importantly, we uncovered systematic shifts of “normal” (intraspecific) maternal:paternal transcript proportions in hybrid endosperms; the average maternal proportion of gene expression increased in both crossing directions but was stronger with S. peruvianum in the maternal role. These genome-wide shifts almost entirely eliminated paternally expressed imprinted genes in S. peruvianum hybrid endosperm but also affected maternally expressed imprinted genes and all other assessed genes. These profound, systematic changes in parental expression proportions suggest that core processes of transcriptional regulation are functionally compromised in hybrid endosperm and contribute to hybrid seed failure.
Analysis of Serum Cytokines and Single-Nucleotide Polymorphisms of SOD1, SOD2, and CAT in Erysipelas Patients

Increased free radical production had been documented in group A (β-hemolytic) streptococcus infection cases. Comparing 71 erysipelas patients to 55 age-matched healthy individuals, we sought for CAT, SOD1, and SOD2 single polymorphism mutation (SNPs) interactions with erysipelas' predisposition and serum cytokine levels in the acute and recovery phases of erysipelas infection. Whereas female patients had a higher predisposition to erysipelas, male patients were prone to having a facial localization of the infection. The presence of SOD1 G7958, SOD2 T2734, and CAT C262 alleles was linked to erysipelas' predisposition. T and C alleles of SOD2 T2734C individually were linked to patients with bullous and erythematous erysipelas, respectively. G and A alleles of SOD1 G7958A individually were associated with lower limbs and higher body part localizations of the infection, respectively. Serum levels of IL-1β, CCL11, IL-2Rα, CXCL9, TRAIL, PDGF-BB, and CCL4 were associated with symptoms accompanying the infection, while IL-6, IL-9, IL-10, IL-13, IL-15, IL-17, G-CSF, and VEGF were associated with predisposition and recurrence of erysipelas. While variations of IL-1β, IL-7, IL-8, IL-17, CCL5, and HGF were associated with the SOD2 T2734C SNP, variations of PDFG-BB and CCL2 were associated with the CAT C262T SNP.
Estimating Upper Bounds for Occupancy and Number of Manatees in Areas Potentially Affected by Oil from the Deepwater Horizon Oil Spill

The explosion of the Deepwater Horizon drilling platform created the largest marine oil spill in U.S. history. As part of the Natural Resource Damage Assessment process, we applied an innovative modeling approach to obtain upper estimates for occupancy and for number of manatees in areas potentially affected by the oil spill. Our data consisted of aerial survey counts in waters of the Florida Panhandle, Alabama and Mississippi. Our method, which uses a Bayesian approach, allows for the propagation of uncertainty associated with estimates from empirical data and from the published literature. We illustrate that it is possible to derive estimates of occupancy rate and upper estimates of the number of manatees present at the time of sampling, even when no manatees were observed in our sampled plots during surveys. We estimated that fewer than 2.4% of potentially affected manatee habitat in our Florida study area may have been occupied by manatees. The upper estimate for the number of manatees present in potentially impacted areas (within our study area) was estimated with our model to be 74 (95%CI 46 to 107). This upper estimate for the number of manatees was conditioned on the upper 95%CI value of the occupancy rate. In other words, based on our estimates, it is highly probable that there were 107 or fewer manatees in our study area during the time of our surveys. Because our analyses apply to habitats considered likely manatee habitats, our inference is restricted to these sites and to the time frame of our surveys. Given that manatees may be hard to see during aerial surveys, it was important to account for imperfect detection. The approach that we described can be useful for determining the best allocation of resources for monitoring and conservation.
Frailty Syndrome in Association with Depressive Symptoms and Functional Disability among Hospitalized Elderly

ABSTRACT We sought to examine the frailty association with depression and functional disability in hospitalized older adults. In particular, we compared non-frail, pre-frail, and frail elderly hospitalized individuals. We performed a cross-sectional study with 255 hospitalized Brazilian elderly patients. We used a structured instrument to assess socio-economic data, the Fried frailty phenotype and used morbidity scales (Geriatric Depression; Katz; Lawton and Brody). The adjusted analysis revealed that frail elderly exhibit increased odds ratios (OR) for depressive symptoms (OR = 2.72, 95% CI: 1.12–6.62), disability related to basic activities (OR = 3.50, 95% CI: 1.26–9.60), and instrumental daily living (OR = 2.70, 95% CI: 1.12–6.44). Frailty in hospitalized older adults is associated with depressive symptomatology and functional disability.
Boats and Tides and “Trickle Down” Theories: What Economists Presume about Wellbeing When They Employ Stochastic Process Theory in Modeling Behavior

Abstract Aphorisms that “rising tides raise all boats” or that material advances of the rich eventually “trickle down” to the poor are really maxims regarding the nature of stochastic processes that underlay the income/wellbeing paths of groups of individuals. This paper looks at the implications for the empirical analysis of wellbeing of conventional assumptions regarding such processes which are employed by both micro and macro economists in modeling economic behavior. The implications of attributing different processes to different groups in society following the club convergence literature are also discussed. Various forms of poverty, inequality, polarization and income mobility structures are considered and much of the conventional wisdom afforded us by such aphorisms is questioned. To exemplify these ideas the results are applied to the distribution of GDP per capita in the continent of Africa.
Childhood exposure to constricted living space: a possible environmental threat for myopia development

People in Hong Kong generally live in a densely populated area and their homes are smaller compared with most other cities worldwide. Interestingly, East Asian cities with high population densities seem to have higher myopia prevalence, but the association between them has not been established. This study investigated whether the crowded habitat in Hong Kong is associated with refractive error among children.
Eigenmode analysis of fishnet metamaterials

Eigenmodes in a typical fishnet metamaterial have been clarified based on precise numerical analysis. The lowest mode in energy splits into two branches at in-plane wave vector of k 6= 0. The lower branch is found to be the mode of in-plane negative group velocity, responsible for negative refraction in fishnet metamaterials.
A novel incentive negotiation mechanism for participatory sensing under budget constraints

Incentive allocation is an important research issue in participatory sensing as it determines the willingness of participants in joining the sensing campaign. Existing incentive approaches either decide the payments without consulting the participants, or require burdensome negotiation procedures like bid-price auction. In this paper, we propose a novel incentive allocation mechanism, which encourages participation and allocates incentives dynamically to achieve accurate sensing results. The proposed mechanism consists of two major elements. The first is a lightweight incentive negotiation procedure, which dynamically offers incentives to participants in spatio-temporal subregions and collects their responses. The second is the optimization problem for incentive allocation as well as it's solution, which aims at maximizing data quality by capturing the amount and the distribution of data samples. Simulations with real datasets confirmed that the proposed solution can provide dynamic incentive offers according to the estimated value of participants' data contribution to the overall quality of sensing result.
Use of allogeneic apheresis stem cell products as an interlaboratory proficiency challenge

AABB Standards requires that laboratories participate in a proficiency test (PT) program for critical analytes. Institutions can purchase commercial PT materials; however, PT can also be performed through interlaboratory exchange. We investigated the utility of allogeneic hematopoietic progenitor cell apheresis (HPC‐A) products as an interlaboratory PT challenge for total nucleated cell count (TNC) and CD34 assessment.
Seeded Amplification of Chronic Wasting Disease Prions in Nasal Brushings and Recto-anal Mucosa-Associated Lymphoid Tissues from Elk by Real-Time Quaking-Induced Conversion

ABSTRACT Chronic wasting disease (CWD), a transmissible spongiform encephalopathy of cervids, was first documented nearly 50 years ago in Colorado and Wyoming and has since been detected across North America and the Republic of Korea. The expansion of this disease makes the development of sensitive diagnostic assays and antemortem sampling techniques crucial for the mitigation of its spread; this is especially true in cases of relocation/reintroduction or prevalence studies of large or protected herds, where depopulation may be contraindicated. This study evaluated the sensitivity of the real-time quaking-induced conversion (RT-QuIC) assay of recto-anal mucosa-associated lymphoid tissue (RAMALT) biopsy specimens and nasal brushings collected antemortem. These findings were compared to results of immunohistochemistry (IHC) analysis of ante- and postmortem samples. RAMALT samples were collected from populations of farmed and free-ranging Rocky Mountain elk (Cervus elaphus nelsoni; n = 323), and nasal brush samples were collected from a subpopulation of these animals (n = 205). We hypothesized that the sensitivity of RT-QuIC would be comparable to that of IHC analysis of RAMALT and would correspond to that of IHC analysis of postmortem tissues. We found RAMALT sensitivity (77.3%) to be highly correlative between RT-QuIC and IHC analysis. Sensitivity was lower when testing nasal brushings (34%), though both RAMALT and nasal brush test sensitivities were dependent on both the PRNP genotype and disease progression determined by the obex score. These data suggest that RT-QuIC, like IHC analysis, is a relatively sensitive assay for detection of CWD prions in RAMALT biopsy specimens and, with further investigation, has potential for large-scale and rapid automated testing of antemortem samples for CWD.
Appetite testing in HIV-infected African adults recovering from malnutrition and given antiretroviral therapy

Abstract Objective The Nutritional Support for Africans Starting Antiretroviral Therapy (NUSTART) trial was designed to determine whether nutritional support for malnourished HIV-infected adults starting antiretroviral therapy (ART) can improve early survival. Appetite is related to health outcomes in this population, but the optimal appetite metric for field use is uncertain. We evaluated two measures of appetite with the goal of improving understanding and treatment of malnutrition in HIV-infected adults. Design Longitudinal cohort study embedded in a clinical trial of vitamin and mineral-fortified, v. unfortified, lipid-based nutritional supplements. Setting HIV clinics in Mwanza, Tanzania and Lusaka, Zambia. Subjects Malnourished (BMI<18·5 kg/m2) HIV-infected adults starting ART. Results Appetite measurements, by short questionnaire and by weight of maize porridge consumed in a standardized test, were compared across time and correlated with changes in weight. Appetite questionnaire scores, from polychoric correlation, and porridge test results were normally distributed for Tanzanians (n 187) but clustered and unreliable for Zambians (n 297). Among Tanzanian patients, the appetite score increased rapidly from referral for ART, plateaued at the start of ART and then increased slowly during the 12-week follow-up. Change in appetite questionnaire score, but not porridge test, correlated with weight change in the corresponding two-week intervals (P=0·002) or over the whole study (P=0·05) but a point estimate of hunger did not predict weight change (P=0·4). Conclusions In Tanzania change in appetite score correlated with weight change, but single point measurements did not. Appetite increases several weeks after the start of ART, which may be an appropriate time for nutritional interventions for malnourished HIV-infected adults.
Accurate lattice energies of organic molecular crystals from periodic turbomole calculations

Accurate lattice energies of organic crystals are important i.e. for the pharmaceutical industry. Periodic DFT calculations with atom‐centered Gaussian basis functions with the Turbomole program are used to calculate lattice energies for several non‐covalently bound organic molecular crystals. The accuracy and convergence of results with basis set size and k‐space sampling from periodic calculations is evaluated for the two reference molecules benzoic acid and naphthalene. For the X23 benchmark set of small molecular crystals accurate lattice energies are obtained using the PBE‐D3 functional. In particular for hydrogen‐bonded systems, a sufficiently large basis set is required. The calculated lattice energy differences between enantiopure and racemic crystal forms for a prototype set of chiral molecules are in good agreement with experimental results and allow the rationalization and computer‐aided design of chiral separation processes. © 2018 Wiley Periodicals, Inc.
Computationally efficient linear predictor for communication over doubly selective fast-fading channel

This paper proposes multidimensional diversity for the high-velocity channel while enabling pertinent tradeoffs among error performance and complexity. It also analyzes and compares the impact of transmit diversity of information transmission over wireless communication system. The paper considers a high-velocity outdoor system like a vehicular user for which the channel varies too rapidly to be tracked. A blind channel-estimation approach that incorporates a linear prediction and MMSE is proposed, which reduces the effect of any perturbation introduced by linear prediction, noise, and multipath. The comparison results reveal that the proposed method using recursive modified Cholesky (RChol) algorithm is computationally efficient when compared with the existing linear prediction based methods. This algorithm scales down the correlation matrix time averaging and hence unveils a significantly computationally efficient algorithm for the time-domain equalizer.
Increased Prevalence of the IL-6-174C Genetic Polymorphism in Long Distance Swimmers

Abstract The IL-6 -174G/C single nucleotide polymorphism (SNP) functionally affects IL-6 activity, with the G-allele associated with increased IL-6 levels. The C-allele was found to be associated with exercise-induced skeletal muscle damage. The aim of the present study was to examine the association between the IL-6 -174G/C polymorphism and athletic performance among elite swimmers and runners. The study sample included 180 track and field athletes and 80 swimmers. Track and field athletes were assigned to three sub-groups: long-distance runners, middle-distance runners and short-distance runners. Swimmers were assigned to two subgroups: long-distance swimmers and short-distance swimmers. The control group consisted of 123 non-athletic healthy individuals. Genomic DNA was extracted from peripheral blood following a standard protocol. Genotyping was performed using polymerase chain reaction (PCR). The CC genotype and C-allele frequency were significantly higher in the long-distance swimmers (18 and 43%, respectively) compared to the long-distance runners (3 and 14%, respectively, p < 0.001); middle-distance runners (4 and 22%, respectively, p < 0.001); and controls (5 and 19%, respectively, p < 0.001). In addition, the CC genotype and C-allele frequency were significantly higher (p < 0.001) in long-distance swimmers compared to short-distance swimmers (18 versus 5% and 43 versus 29% for the CC genotype and C-allele frequency, respectively). The higher frequency of the C-allele and CC genotype among long-distance swimmers suggests that the rarity of exercise-associated rhabdomyolysis among swimmers is probably related to other sports-specific or water-related protective mechanisms. It is possible that swimming selection in talented endurance athletes who are C-allele carriers represents an example of genetically-dependent sports selection.