Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Epidemiology of Human Norovirus in Korea in 2013

Norovirus is a major cause of acute gastroenteritis. The molecular epidemiology of norovirus exhibits temporal and geographical fluctuations, and new variants of the GII.4 genotype emerge every 2-3 years to cause global epidemics of acute gastroenteritis. We investigated GI and GII genotypes of human norovirus strains isolated from patients with acute gastroenteritis in Korea in 2013. Norovirus antigen test was performed on 2,980 fecal specimens from January to December 2013. RNA was extracted from norovirus antigen-positive fecal suspensions, and the norovirus capsid (VP1) and polymerase (RdRp) genes were characterized by RT-PCR and sequencing. Of the 230 genotyped strains, GII.4 (77.3%) was the most frequently observed capsid genotype, followed by GII.3 (6.1%) and GII.13 (3.9%). A norovirus GII.4 variant, GII.Pe/GII.4 Sydney 2012, was the most frequently found polymerase/capsid genotype (65.7%), followed by GII.P17/GII.17 (2.1%) and GII.P21/GII.3 (2.1%). Phylogenetic, similarity, and capsid epitope analyses of GII.Pe/GII.4 Sydney 2012 strains were performed. We concluded that the norovirus GII.4 variant, GII.Pe/GII.4 Sydney 2012, was the main cause of norovirus-related gastroenteritis in Korea in 2013.
Cough Aerosols of Mycobacterium tuberculosis in the Prediction of Incident Tuberculosis Disease in Household Contacts.

BACKGROUND Tuberculosis disease develops in only 5%-10% of humans infected with Mycobacterium tuberculosis The mechanisms underlying this variability remain poorly understood. We recently demonstrated that colony-forming units of M. tuberculosis in cough-generated aerosols are a better predictor of infection than the standard sputum acid-fast bacilli smear. We hypothesized that cough aerosol cultures may also predict progression to tuberculosis disease in contacts. METHODS We conducted a retrospective cohort study of 85 patients with smear-positive tuberculosis and their 369 household contacts in Kampala, Uganda. Index case patients underwent a standard evaluation, and we cultured M. tuberculosis from cough aerosols. Contacts underwent a standard evaluation at enrollment, and they were later traced to determine their tuberculosis status. RESULTS During a median follow-up of 3.9 years, 8 (2%) of the contacts developed tuberculosis disease. In unadjusted and adjusted analyses, incident tuberculosis disease in contacts was associated with sputum Mycobacterial Growth Indicator Tube culture (odds ratio, 8.2; 95% confidence interval, 1.1-59.2; P = .04), exposure to a high-aerosol tuberculosis case patient (6.0, 1.4-25.2; P = .01), and marginally, human immunodeficiency virus in the contact (6.11; 0.89-41.7; P = .07). We present data demonstrating that sputum and aerosol specimens measure 2 related but different phenomena. CONCLUSIONS We found an increased risk of tuberculosis progression among contacts of high-aerosol case patients. The hypothesis that a larger infectious inoculum, represented by high aerosol production, determines the risk of disease progression deserves evaluation in future prospective studies.
Associations between Disaster Exposures, Peritraumatic Distress, and Posttraumatic Stress Responses in Fukushima Nuclear Plant Workers following the 2011 Nuclear Accident: The Fukushima NEWS Project Study

Background The 2011 Fukushima Daiichi Nuclear Power Plant accident was the worst nuclear disaster since Chernobyl. The nearby Daini plant also experienced substantial damage but remained intact. Workers for the both plants experienced multiple stressors as disaster victims and workers, as well as the criticism from the public due to their company's post-disaster management. Little is known about the psychological pathway mechanism from nuclear disaster exposures, distress during and immediately after the event (peritraumatic distress; PD), to posttraumatic stress responses (PTSR). Methods A self-report questionnaire was administered to 1,411 plant employees (Daiichi, n = 831; Daini, n = 580) 2–3 months post-disaster (total response rate: 80.2%). The socio-demographic characteristics and disaster-related experiences were assessed as independent variables. PD and PTSR were measured by the Japanese versions of Peritraumatic Distress Inventory and the Impact of Event Scale-Revised, respectively. The analysis was conducted separately for the two groups. Bivariate regression analyses were performed to assess the relationships between independent variables, PD, and PTSR. Significant variables were subsequently entered in the multiple regression analyses to explore the pathway mechanism for development of PTSR. Results For both groups, PTSR highly associated with PD (Daiichi: adjusted β, 0.66; p<0.001; vs. Daini: adjusted β, 0.67; p<0.001). PTSR also associated with discrimination/slurs experience (Daiichi: 0.11; p<0.001; vs. Daini, 0.09; p = 0.005) and presence of preexisting illness(es) (Daiichi: 0.07; p = 0.005; vs. Daini: 0.15; p<.0001). Other disaster-related variables were likely to be associated with PD than PTSR. Conclusion Among the Fukushima nuclear plant workers, disaster exposures associated with PD. PTSR was highly affected by PD along with discrimination/slurs experience.
Formal aspects of model validity and validation in system dynamics

Model validation constitutes a very important step in system dynamics methodology. Yet, both published and informal evidence indicates that there has been little effort in system dynamics community explicitly devoted to model validity and validation. Validation is a prolonged and complicated process, involving both formal/quantitative tools and informal/qualitative ones. This paper focuses on the formal aspects of validation and presents a taxonomy of various aspects and steps of formal model validation. First, there is a very brief discussion of the philosophical issues involved in model validation, followed by a flowchart that describes the logical sequence in which various validation activities must be carried out. The crucial nature of structure validity in system dynamics (causal-descriptive) models is emphasized. Then examples are given of specific validity tests used in each of the three major stages of model validation: Structural tests, structure-oriented behavior tests and behavior pattern tests. Also discussed is if and to what extent statistical significance tests can be used in model validation. Among the three validation stages, the special importance of structure-oriented behavior tests is emphasized. These are strong behavior tests that can provide information on potential structure flaws. Since structure-oriented behavior tests combine the strength of structural orientation with the advantage of being quantifiable, they seem to be the most promising direction for research on model validation.
Porosity and grain size controls on compaction band formation in Jurassic Navajo Sandstone

Determining the rock properties that permit or impede the growth of compaction bands in sedimentary sequences is a critical problem of importance to studies of strain localization and characterization of subsurface geologic reservoirs. We determine the porosity and average grain size of a sequence of stratigraphic layers of Navajo Sandstone that are then used in a critical state model to infer plastic yield envelopes for the layers. Pure compaction bands are formed in layers having the largest average grain sizes (0.42–0.45 mm) and porosities (28%), and correspondingly the smallest values of critical pressure (∼22 MPa) in the sequence. The results suggest that compaction bands formed in these layers after burial to ∼1.5 km depth in association with thrust faulting beneath the nearby East Kaibab monocline, and that hardening of the yield caps accompanied compactional deformation of the layers.
The LX—M relation of clusters of galaxies

We present a new measurement of the scaling relation between X-ray luminosity and total mass for 17,000 galaxy clusters in the maxBCG cluster sample. Stacking sub-samples within fixed ranges of optical richness, N200, we measure the mean 0.1-2.4 keV X-ray luminosity, , from the ROSAT All-Sky Survey. The mean mass, , is measured from weak gravitational lensing of SDSS background galaxies (Johnston et al. 2007). For 9 {le} N{sub 200} /10{sup 42} h{sup -2} ergs{sup -1} = (12.6{sub -1.3}{sup +1.4}(stat) {+-} 1.6 (sys)) ( /10{sup 14} h{sup -1} M{sub {circle_dot}}){sup 1.65{+-}0.13}. The slope agrees to within 10% with previous estimates based on X-ray selected catalogs, implying that the covariance in L{sub X} and N{sub 200} at fixed halo mass is not large. The luminosity intercept is 30%, or 2{sigma}, lower than determined from the X-ray flux-limited sample of Reiprich & Boehringer (2002), assuming hydrostatic equilibrium. This slight difference could arise from a combination of Malmquist bias and/or systematic error in hydrostatic mass estimates, both of which are expected. The intercept agrees with that derived by Stanek et al. (2006) using a model for the statistical correspondence betweenmore » clusters and halos in a WMAP3 cosmology with power spectrum normalization {sigma}{sub 8} = 0.85. Similar exercises applied to future data sets will allow constraints on the covariance among optical and hot gas properties of clusters at fixed mass. « less
Thermoinactivation of Human Cytomegalovirus

Vonka, Vladimir (Baylor University College of Medicine, Houston, Tex.), and Matilda Benyesh-Melnick. Thermoinactivation of human cytomegalovirus. J. Bacteriol. 91:221–226. 1966. —The inactivation at 4 and 37 C of several strains of human cytomegalovirus was studied. The preliminary findings that freshly harvested cytomegalovirus was inactivated more rapidly at 4 C than at higher temperatures was confirmed. Intracellular virus still within infected cells was found to be more stable at 4 C than virus released by sonic treatment just before incubation at 4 C. The composition of the diluent played an important role. In tris(hydroxymethyl)-aminomethane buffer, virus was unstable at both 4 and 37 C, with the rate of inactivation faster at 4 than at 37 C. Similar results were obtained when bicarbonate-phosphate buffer or Eagle's medium when bicarbonate was used as virus diluent. Calf serum stabilized the virus at 37 C, but not at 4 C. The deletion of bicarbonate from Eagle's medium had a stabilizing effect at both temperatures. An even greater stabilizing effect at both 4 and 37 C was obtained when distilled water was used as virus diluent. Inactivation rates varied from one strain to the next at 4 C but not at 37 C. Differences were found also with virus progeny derived from a single strain, but harvested at different stages during virus multiplication. Virus harvested early was more labile at 4 than at 37 C, whereas the late virus was more labile at the higher temperature. Intracellular and extracellular virus preparations were inactivated at the same rates at either 4 or 37 C.
Repeated Occurrences of the Baldwin Effect Can Guide Evolution on Rugged Fitness Landscapes

The Baldwin effect is known as a possible scenario of interactions between evolution and learning caused by the balances between benefit and cost of learning. It is still controversial how learning can affect evolution on rugged fitness landscapes because previous studies merely focused on a process in which the population reaches a local optimum through a single occurrence of this effect, even though there exist a lot of local optimums on the landscape. Our purpose is to clarify whether and how learning can facilitate the adaptive evolution of population on rugged fitness landscapes in view of the repeated occurrences of the Baldwin effect. For this purpose, we constructed a simple fitness function that represents a multi-modal fitness landscape in which there is a trade-off between the adaptivity of individual and the strength of the epistatic interactions among its phenotypes. Phenotypic plasticity is introduced into our model, in which whether each phenotype is plastic or not is genetically defined and plastic phenotypes can be adjusted by learning. The evolutionary experiments clearly showed that the Baldwin effect repeatedly occurred through the evolutionary process of the population on this landscape, and facilitated its adaptive evolution as a whole
Habitat Heterogeneity Affects Plant and Arthropod Species Diversity and Turnover in Traditional Cornfields

The expansion of the agricultural frontier by the clearing of remnant forests has led to human-dominated landscape mosaics. Previous studies have evaluated the effect of these landscape mosaics on arthropod diversity at local spatial scales in temperate and tropical regions, but little is known about fragmentation effects in crop systems, such as the complex tropical traditional crop systems that maintain a high diversity of weeds and arthropods in low-Andean regions. To understand the factors that influence patterns of diversity in human-dominated landscapes, we investigate the effect of land use types on plant and arthropod diversity in traditionally managed cornfields, via surveys of plants and arthropods in twelve traditional cornfields in the Colombian Andes. We estimated alpha and beta diversity to analyze changes in diversity related to land uses within a radius of 100 m to 1 km around each cornfield. We observed that forests influenced alpha diversity of plants, but not of arthropods. Agricultural lands had a positive relationship with plants and herbivores, but a negative relationship with predators. Pastures positively influenced the diversity of plants and arthropods. In addition, forest cover seemed to influence changes in plant species composition and species turnover of herbivore communities among cornfields. The dominant plant species varied among fields, resulting in high differentiation of plant communities. Predator communities also exhibited high turnover among cornfields, but differences in composition arose mainly among rare species. The crop system evaluated in this study represents a widespread situation in the tropics, therefore, our results can be of broad significance. Our findings suggest that traditional agriculture may not homogenize biological communities, but instead could maintain the regional pool of species through high beta diversity.
Connect and Control Things: Integrating Lightweight IoT Framework into a Mobile Application

Mobile applications running on smart devices are important enablers for Internet of Things (IoT). This paper presents a novel mobile application called "Connect and Control Things" (CCT) which integrates a lightweight IoT framework into smartphones and tablets. The framework is designed to discover & interact with things, reason with M2M data, provide configuration management facilities along with subscription and notification functionalities. The novel capabilities of CCT are: (i) lightweight search engine based dynamic discovery of physical things, (ii) interaction with both sensors and actuators using Sensor Markup Language (SenML) and its extensions, (iii) integrating a lightweight reasoning engine to infer high level abstraction, (iv) CoRE Link Format based configuration management and (v) support for both smart and legacy things regardless of communication technologies. An IoT architecture is presented along with a prototype implementation details for Android powered devices. Uses of the prototype mobile application in home automation scenarios are outlined. The performance of CCT is evaluated in terms of memory requirement, CPU usage and power consumption. Experimental results establish that the overall design and implementation of CCT are lightweight which encourages the adoption of CCT. It enables offering consumer centric services for home automation domain. Finally the paper concludes with future research directions.
Optimistic planning for Markov decision processes

The reinforcement learning community has recently intensified its interest in online planning methods, due to their relative independence on the state space size. However, tight near-optimality guarantees are not yet available for the general case of stochastic Markov decision processes and closed-loop, state-dependent planning policies. We therefore consider an algorithm related to AO* that optimistically explores a tree representation of the space of closed-loop policies, and we analyze the near-optimality of the action it returns after n tree node expansions. While this optimistic planning requires a finite number of actions and possible next states for each transition, its asymptotic performance does not depend directly on these numbers, but only on the subset of nodes that significantly impact near-optimal policies. We characterize this set by introducing a novel measure of problem complexity, called the near-optimality exponent. Specializing the exponent and performance bound for some interesting classes of MDPs illustrates the algorithm works better when there are fewer near-optimal policies and less uniform transition probabilities.
Comparative analysis of OpenCL vs. HDL with image-processing kernels on Stratix-V FPGA

Application development with hardware description languages (HDLs) such as VHDL or Verilog involves numerous productivity challenges, limiting the potential impact of reconfigurable computing (RC) with FPGAs in high-performance computing. Major challenges with HDL design include steep learning curves, large and complex codes, long compilation times, and lack of development standards across platforms. A relative newcomer to RC, the Open Computing Language (OpenCL) reduces productivity hurdles by providing a platform-independent, C-based programming language. In this study, we conduct a performance and productivity comparison between three image-processing kernels (Canny edge detector, Sobel filter, and SURF feature-extractor) developed using Altera's SDK for OpenCL and traditional VHDL. Our results show that VHDL designs achieved a more efficient use of resources (59% to 70% less logic), however, both OpenCL and VHDL designs resulted in similar timing constraints (255MHz <; fmax <; 325MHz). Furthermore, we observed a 6× increase in productivity when using OpenCL development tools, as well as the ability to efficiently port the same OpenCL designs without change to three different RC platforms, with similar performance in terms of frequency and resource utilization.
PinX1 suppresses tumorigenesis by negatively regulating telomerase/telomeres in colorectal carcinoma cells and is a promising molecular marker for patient prognosis

PinX1 plays positive and negative roles in the maintenance of telomerase and telomeres, as well as in tumorigenesis. The aim of the present study was to investigate the expression and clinical significance of PinX1 in colorectal carcinoma (CRC) and to determine the effect of PinX1 on CRC cell proliferation and apoptosis. A total of 86 CRC patients treated with radical resection and 5-fluorouracil-based adjuvant chemotherapy were enrolled in this study. The expression dynamics of PinX1 was detected by immunohistochemistry in the CRC patients and 25 normal colonic mucosa controls. PinX1 expression was significantly reduced in tumor tissues as compared to normal tissues, and the rate of PinX1 protein low/negative expression in CRC and normal tissues was 60% (52/86) and 24% (6/25), respectively (P=0.037). In addition, PinX1 downregulation was significantly associated with short overall survival (P=0.016) and disease-free survival (P=0.042) in CRC patients. Cox proportional hazards model further revealed that PinX1 expression was an independent factor in predicting overall survival and disease-free survival for CRC patients. Furthermore, we demonstrated that ectopic overexpression of PinX1 in CRC cells inhibited their proliferation, promoted apoptosis, repressed telomerase activity, and induced telomere shortening. These findings suggest that PinX1 may be a prognostic biomarker for CRC patients’ survival and that it inhibits cell proliferation and promotes apoptosis by repressing telomerase activity and inducing telomere shortening. Targeting PinX1 may therefore provide a novel therapeutic strategy for CRC patients.
The prevalence and clinical correlates of apathy and irritability in Alzheimer's disease

We examined the prevalence and correlates of apathy and irritability in a consecutive series of 101 patients with probable Alzheimer's disease (AD). Based on clinical criteria, 46 (46%) patients had apathy, and 13 (13%) patients had irritability. Apathy was significantly associated with more severe impairments in activities of daily living, significantly more severe extrapyramidal signs, and a significantly higher frequency of both major depression and dysthymia. Patients with irritability had significantly more severe impairments in activities of daily living and significantly higher depression and anosognosia scores. On the other hand, neither apathy nor irritability were significantly associated with deficits in specific cognitive domains.
Effect of folic acid supplementation on risk of cardiovascular diseases: a meta-analysis of randomized controlled trials.

CONTEXT Epidemiologic studies have suggested that folate intake decreases risk of cardiovascular diseases. However, the results of randomized controlled trials on dietary supplementation with folic acid to date have been inconsistent. OBJECTIVE To evaluate the effects of folic acid supplementation on risk of cardiovascular diseases and all-cause mortality in randomized controlled trials among persons with preexisting cardiovascular or renal disease. DATA SOURCES Studies were retrieved by searching MEDLINE (January 1966-July 2006) using the Medical Subject Headings cardiovascular disease, coronary disease, coronary thrombosis, myocardial ischemia, coronary stenosis, coronary restenosis, cerebrovascular accident, randomized controlled trial, clinical trials, homofolic acid, and folic acid, and the text words folic acid and folate. Bibliographies of all retrieved articles were also searched, and experts in the field were contacted. STUDY SELECTION From 165 relevant retrieved reports, 12 randomized controlled trials compared folic acid supplementation with either placebo or usual care for a minimum duration of 6 months and with clinical cardiovascular disease events reported as an end point. DATA EXTRACTION Data on study design, characteristics of participants, changes in homocysteine levels, and cardiovascular disease outcomes were independently abstracted by 2 investigators using a standardized protocol. DATA SYNTHESIS Studies including data from 16 958 participants with preexisting vascular disease were analyzed using a random-effects model. The overall relative risks (95% confidence intervals) of outcomes for patients treated with folic acid supplementation compared with controls were 0.95 (0.88-1.03) for cardiovascular diseases, 1.04 (0.92-1.17) for coronary heart disease, 0.86 (0.71-1.04) for stroke, and 0.96 (0.88-1.04) for all-cause mortality. The relative risk was consistent among participants with preexisting cardiovascular or renal disease. CONCLUSIONS Folic acid supplementation has not been shown to reduce risk of cardiovascular diseases or all-cause mortality among participants with prior history of vascular disease. Several ongoing trials with large sample sizes might provide a definitive answer to this important clinical and public health question.