Miracle-dz/UniFAR-FTUs huggingface dataset:
Best Linear Unbiased Prediction of Genomic Breeding Values Using a Trait-Specific Marker-Derived Relationship Matrix

Background With the availability of high density whole-genome single nucleotide polymorphism chips, genomic selection has become a promising method to estimate genetic merit with potentially high accuracy for animal, plant and aquaculture species of economic importance. With markers covering the entire genome, genetic merit of genotyped individuals can be predicted directly within the framework of mixed model equations, by using a matrix of relationships among individuals that is derived from the markers. Here we extend that approach by deriving a marker-based relationship matrix specifically for the trait of interest. Methodology/Principal Findings In the framework of mixed model equations, a new best linear unbiased prediction (BLUP) method including a trait-specific relationship matrix (TA) was presented and termed TABLUP. The TA matrix was constructed on the basis of marker genotypes and their weights in relation to the trait of interest. A simulation study with 1,000 individuals as the training population and five successive generations as candidate population was carried out to validate the proposed method. The proposed TABLUP method outperformed the ridge regression BLUP (RRBLUP) and BLUP with realized relationship matrix (GBLUP). It performed slightly worse than BayesB with an accuracy of 0.79 in the standard scenario. Conclusions/Significance The proposed TABLUP method is an improvement of the RRBLUP and GBLUP method. It might be equivalent to the BayesB method but it has additional benefits like the calculation of accuracies for individual breeding values. The results also showed that the TA-matrix performs better in predicting ability than the classical numerator relationship matrix and the realized relationship matrix which are derived solely from pedigree or markers without regard to the trait. This is because the TA-matrix not only accounts for the Mendelian sampling term, but also puts the greater emphasis on those markers that explain more of the genetic variance in the trait.
Review of Medically Indicated Preterm Births Due to Hypertensive Disorders in Pregnancy at a Tertiary Hospital in Abuja: Maternal Characteristics and Neonatal Outcome.

Background Preterm birth is the delivery of a baby before 37 weeks of gestation. Hypertension in pregnancy has been found to be the most common cause of medically indicated preterm birth leading to significant neonatal mortality and morbidity. Objective To evaluate the prevalence of medically indicated preterm births due to hypertension in pregnancy, the pattern of maternal characteristics and the immediate neonatal outcome. Study Design: A descriptive cross-sectional study of all medically indicated preterm births due to hypertensive disorders in pregnancy at National Hospital Abuja from 1st January 2008 to 31st December 2012. Results The total number of births over the five-year period was 9055 with preterm births contributing 1075(11.9%), 523(48.7%) were spontaneous while 552(51.3%) were medically indicated. Hypertension in pregnancy was the indication for 254(23.6%) of the overall preterm births and 46% of medically indicated preterm births. Preeclampsia was the diagnosis in 77.1% of the cases of hypertensive disorders, 33.5% deliveries were between 34-36 weeks gestational age and the mean birth weight was 1.82kg. Conclusion Hypertensive disorder was a major contributor to medically indicated preterm birth in this study with Preeclampsia as the predominant form. Proper preconception and antenatal care with institution of preventive measures for preeclampsia will help prolong gestation in at risk mothers to ensure better survival for neonates.
Chinese Term Extraction from Web Pages Based on Compound Term Productivity

In this paper, we propose an automatic term recognition system for Chinese. Our idea is based on the relation between a compound word and its constituents that are simple words or individual Chinese character. More precisely, we basically focus on how many words/characters adjoin the word/character in question to form compound words. We also take into account the frequency of term. We evaluated word based method and character based method with several Chinese Web pages, resulting in precision of 75% for top ten candidate terms.
Cigarette Smoking and Indicators of Psychosocial Distress in Southeast Asian and Central-Eastern European Adolescents

The purpose of this study was to examine the association of cigarette smoking and 2 indicators of psychosocial distress (hopelessness and loneliness) among adolescents from 2 distinctly different regions of the world: Central-Eastern Europe (Hungary, Ukraine, Slovakia, Czech Republic, Romania, Poland) and Southeast Asia (Thailand, Taiwan, and the Philippines). Among Southeast Asian boys and girls, smokers had elevated hopelessness in comparison to nonsmokers but among Central-Eastern European students, this relationship was true only for girls and there was no relationship for boys. Across the country samples, there was only association of smoking with loneliness among Southeast Asian girls and Central-Eastern European girls. While Southeast Asian girls who smoked scored higher on loneliness than nonsmokers, the opposite was true among Central-Eastern European girls, with smokers scoring lower on loneliness.
Needle Fracture during Endoscopic Ultrasound-Guided Fine-Needle Aspiration of Suspicious Thoracic Lymph Nodes

Endoscopic ultrasound fine-needle aspiration (EUS-FNA) is used to make a cytopathologic diagnosis of suspicious lesions located around the gastrointestinal tract. It is a safe technique with few complications. The most common complications of EUS-FNA are related to pancreatic lesions (pancreatitis, bleeding, and abdominal pain). Rare complications have been noted such as stent malfunction, air embolism, infection, neural and vascular injuries, and tumor cell seeding. There are very few studies examining equipment malfunctions. We report a case of needle fracture during the EUS-FNA of suspicious thoracic lymph nodes in a 79-year-old man investigated for unexplained weight loss.
The Arabidopsis MYB5 Transcription Factor Regulates Mucilage Synthesis, Seed Coat Development, and Trichome Morphogenesis[W][OA]

The Arabidopsis thaliana MYB5 gene is expressed in trichomes and seeds, including the seed coat. Constitutive expression of MYB5 resulted in the formation of more small trichomes and ectopic trichomes and a reduction in total leaf trichome numbers and branching. A myb5 mutant displayed minimal changes in trichome morphology, while a myb23 mutant produced increased numbers of small trichomes and two-branched trichomes. A myb5 myb23 double mutant developed more small rosette trichomes and two-branched trichomes than the single mutants. These results indicate that MYB5 and MYB23 regulate trichome extension and branching. The seed coat epidermal cells of myb5 and myb5 myb23 were irregular in shape, developed flattened columellae, and produced less mucilage than those of the wild type. Among the downregulated genes identified in the myb5 seeds using microarray analysis were ABE1 and ABE4 (α/β fold hydrolase/esterase genes), MYBL2, and GLABRA2. The same genes were also downregulated in transparent testa glabra1 (ttg1) seeds, suggesting that MYB5 collaborates with TTG1 in seed coat development. These genes were upregulated in leaves and roots by ectopically expressed MYB5. The MYBL2, ABE1, and ABE4 promoters were active in seeds, including seed coats, and the latter two also in trichomes. Models of the MYB5 regulatory networks involved in seed coat and trichome development are presented.
Effect of Seasonal and Monthly Variation in Weather and Air Pollution Factors on Stroke Incidence in Seoul, Korea

Background and Purpose— The purpose of the present study was to determine whether seasonal and monthly variations in stroke incidence exist and whether they are related to meteorologic and air pollution parameters under similar weather and environmental conditions in selected areas of Seongdong district, Seoul, South Korea. Methods— From January 1, 2004, to December 31, 2013, 3001 consecutive stroke events were registered in residents of selected areas of Seongdong district, Seoul, South Korea. The authors calculated the stroke attack rate per 100 000 people per month and the relative risk of stroke incidence associated with meteorologic and air pollution parameters. We also analyzed odds ratios with a 95% confidence interval for seasonal and monthly stroke incidence. Results— The incidence of stroke in September was significantly higher (odds ratio, 1.233; 95% confidence interval, 1.042–1.468) compared with January. The seasonal ischemic stroke incidence in summer (odds ratio, 1.183; 95% confidence interval, 1.056–1.345) was significantly higher than in winter, whereas the seasonal incidence of intracerebral hemorrhage relative to winter was not significant. The mean temperature was positively correlated with ischemic stroke (relative risk, 1.006; P=0.003), and nitrogen dioxide (relative risk, 1.262; P=0.001) showed a strong positive correlation with intracerebral hemorrhage incidence among the older age group. Conclusions— We demonstrated distinct patterns of seasonal and monthly variation in the incidence of stroke and its subtypes through consideration of the meteorologic and air pollution parameters. We therefore expect that these findings may enhance our understanding of the relationships between stroke and weather and pollutants.
Causal effects from nonalcoholic fatty liver disease on cholelithiasis: A mendelian randomization study

Abstract Background and Aims Both nonalcoholic fatty liver disease (NAFLD) and cholelithiasis are highly prevalent hepatobiliary diseases with risk of progression into severe outcomes. Considering the close relationship between liver and gallbladder in anatomy and physiology, a potential causal relationship between NAFLD and cholelithiasis has been speculated. Methods Mendelian randomization (MR) was employed using genome‐wide association study (GWAS) summary statistics in Million Veteran Program (MVP) for NAFLD, and statistics in UK biobank for cholelithiasis. Results Our results demonstrate that NAFLD has a causal effect on cholelithiasis risk (OR, 1.003; 95%CI, 1.000–1.006; p = 0.03). We also performed the sensitivity analysis and heterogeneity test to ensure the accuracy of outcome and avoid the reverse causality. Conclusion NAFLD should be regarded as a potential pathogenic factor in pathogenesis study of cholelithiasis, and be considered in assessment and treatment of cholelithiasis.
Novel pyrazolopyrimidine derivatives as tyrosine kinase inhibitors with antitumoral activity in vitro and in vivo in papillary dedifferentiated thyroid cancer.

AIM We have studied the antitumoral activity of two new pyrazolo[3,4-d]pyrimidine compounds (CLM3 and CLM29) in primary papillary dedifferentiated thyroid cancer (DePTC) cells. METHODS The antiproliferative effect was tested in DePTC cells obtained at reoperation from patients with recurrence of the tumor. The concentrations of CLM3 and CLM29 used in the in vitro experiments were 1, 10, 30, and 50 μm. RESULTS Proliferation assays in DePTC cells showed a significant reduction of proliferation by CLM3 and CLM29, which was by 12% with CLM3 (the most potent compound) 10 μm, 43% with CLM3 30 μm, and 60% with CLM3 50 μm. CLM3 and CLM29 increased the percentage of apoptotic cells in DePTC cells dose dependently (P < 0.001) and inhibited migration (P < 0.001). A DePTC cell line (AL) was injected sc in CD nu/nu mice, and tumor masses became detectable 10 d after xenotransplantation. CLM3 (40 mg/kg · die) significantly inhibited tumor growth and weight, and the therapeutic effect was significant starting on the 19th day after cell implantation (4 d after the beginning of treatment). The CLM3-treated group of animals did not show any appreciable toxicity. CLM3 and CLM29 increased thrombospondin-1 expression in the AL cell line. A significant reduction of microvessels and in the percentage of antivascular endothelial growth factor antibody immunoreactivity was observed in the CLM3 treated tumors, with a simultaneous increase of the percentage of necrosis. CONCLUSION The antitumoral activity of two new pyrazolo[3,4-d]pyrimidine compounds (CLM3, CLM29) in vitro and CLM3 in vivo in DePTC has been shown, opening the way to a future clinical evaluation.
A Comparative Analysis of Perceptions of Pharmacy Students’ Stress and Stressors across Two Multicampus Universities

Objective. To compare perceived levels of stress, stressors, and academic self-efficacy among students at two multicampus colleges of pharmacy. Methods. A survey instrument using previously validated items was developed and administered to first-year, second-year, and third-year pharmacy students at two universities with multiple campuses in spring 2013. Results. Eight hundred twenty students out of 1115 responded (73.5% response rate). Institutional differences were found in perceived student stress levels, self-efficacy, and stress-related causes. An interaction effect was demonstrated between institution and campus type (main or branch) for perceived stress and self-efficacy although campus type alone did not demonstrate a direct effect. Institutional and campus differences existed in awareness of campus counseling services, as did a few differences in coping methods. Conclusion. Stress measures were similar for pharmacy students at main or branch campuses. Institutional differences in student stress might be explained by instructional methods, campus support services, institutional climate, and nonuniversity factors.
Model-assisted measurements of suspension-feeding flow velocities

ABSTRACT Benthic marine suspension feeders provide an important link between benthic and pelagic ecosystems. The strength of this link is determined by suspension-feeding rates. Many studies have measured suspension-feeding rates using indirect clearance-rate methods, which are based on the depletion of suspended particles. Direct methods that measure the flow of water itself are less common, but they can be more broadly applied because, unlike indirect methods, direct methods are not affected by properties of the cleared particles. We present pumping rates for three species of suspension feeders, the clams Mya arenaria and Mercenaria mercenaria and the tunicate Ciona intestinalis, measured using a direct method based on particle image velocimetry (PIV). Past uses of PIV in suspension-feeding studies have been limited by strong laser reflections that interfere with velocity measurements proximate to the siphon. We used a new approach based on fitting PIV-based velocity profile measurements to theoretical profiles from computational fluid dynamic (CFD) models, which allowed us to calculate inhalant siphon Reynolds numbers (Re). We used these inhalant Re and measurements of siphon diameters to calculate exhalant Re, pumping rates, and mean inlet and outlet velocities. For the three species studied, inhalant Re ranged from 8 to 520, and exhalant Re ranged from 15 to 1073. Volumetric pumping rates ranged from 1.7 to 7.4 l h−1 for M. arenaria, 0.3 to 3.6 l h−1 for M. mercenaria and 0.07 to 0.97 l h−1 for C. intestinalis. We also used CFD models based on measured pumping rates to calculate capture regions, which reveal the spatial extent of pumped water. Combining PIV data with CFD models may be a valuable approach for future suspension-feeding studies. Summary: Mya arenaria, Mercenaria mercenaria and Ciona intestinalis exhibit a wide range of suspension feeding rates as demonstrated by a combined experimental and numerical approach to quantifying fluid flows.
A comparison of enumerative and adaptive codes

The problem of noiselessly encoding a message when prior statistics are known is considered. The close relationship of arithmetic and enumerative coding for this problem is shown by computing explicit arithmetic coding probabilities for various enumerative coding examples. This enables a comparison to be made of the coding efficiency of Markov models and enumerative codes as well as a new coding scheme intermediate between the two. These codes are then extended to messages whose statistics are not known {\em a priori} Two adaptive codes are described for this problem whose coding efficiency is upper-bounded by the extended enumerative codes. On some practical examples the adaptive codes perform significantly better than the nonadaptive ones.
The crystal structures of two cuticle–degrading proteases from nematophagous fungi and their contribution to infection against nematodes

Cuticle‐degrading proteases are involved in the breakdown of cuticle/eggshells of nematodes or insects, a hard physical barrier against fungal infections. Understanding the 3‐dimensional structures of these proteins can provide crucial information for improving the effectiveness of these fungi in biocontrol applications, e.g., by targeted protein engineering. However, the structures of these proteases remain unknown. Here, we report the structures of two cuticledegrading proteases from two species of nematophagous fungi. The two structures were solved with X‐ray crystallography to resolutions of 1.65 Å (Ver112) and 2.1 Å (PL646), respectively. Crystal structures of PL646 and Ver112 were found to be very similar to each other, and similar to that of proteinase K from another fungus Tritirachium album. Differences between the structures were found among residues of the substrate binding sites (S1 and S4). Experimental studies showed that the enzymes differed in hydrolytic activity to synthetic peptide substrates. Our analyses of the hydrophobic/ hydrophilic and electrostatic features of these two proteins suggest that their surfaces likely play important roles during fungal infection against nematodes. The two crystal structures provide a solid basis for investigating the relationship between structure and function of cuticle‐degrading proteases. —Liang, L. , Lou, Z. , Ye, F. , Yang, J., Liu, S. , Sun, Y. , Guo, Y. , Mi, Q. , Huang, X. , Zou, C, Meng, Z. , Rao, Z. , Zhang, K. ‐Q. The crystal structures of two cuticle‐degrading proteases from nematophagous fungi and their contribution to infection against nematodes. FASEB J. 24, 1391–1400 (2010). www.fasebj. org
Looking back and looking forward

The past 10 years have delivered two significant revolutions. (1) Microprocessor design has been transformed by the limits of chip power, wire latency, and Dennard scaling---leading to multicore processors and heterogeneity. (2) Managed languages and an entirely new software landscape emerged---revolutionizing how software is deployed, is sold, and interacts with hardware. Researchers most often examine these changes in isolation. Architects mostly grapple with microarchitecture design through the narrow software context of native sequential SPEC CPU benchmarks, while language researchers mostly consider microarchitecture in terms of performance alone. This work explores the clash of these two revolutions over the past decade by measuring power, performance, energy, and scaling, and considers what the results may mean for the future. Our diverse findings include the following: (a) native sequential workloads do not approximate managed workloads or even native parallel workloads; (b) diverse application power profiles suggest that future applications and system software will need to participate in power optimization and management; and (c) software and hardware researchers need access to real measurements to optimize for power and energy.
Human disturbance in riparian areas disrupts predator–prey interactions between grizzly bears and salmon

Abstract Wildlife must increasingly balance trade‐offs between the need to access important foods and the mortality risks associated with human‐dominated landscapes. Human disturbance can profoundly influence wildlife behavior, but managers know little about the relationship between disturbance–behavior dynamics and associated consequences for foraging. We address this gap by empirically investigating the consequences of human activity on a keystone predator–prey interaction in a region with limited but varied industrial disturbance. Using stable isotope data from 226 hair samples of grizzly bears (Ursus arctos horribilis) collected from 1995 to 2014 across 22 salmon‐bearing watersheds (88,000 km2) in British Columbia, Canada, we examined how human activity influenced their consumption of spawning salmon (Oncorhynchus spp.), a fitness‐related food. Accounting for the abundance of salmon and other foods, salmon consumption strongly decreased (up to 59% for females) with increasing human disturbance (as measured by the human footprint index) in riparian zones of salmon‐bearing rivers. Declines in salmon consumption occurred with disturbance even in watersheds with low footprints. In a region currently among the least influenced by industrial activity, intensification of disturbance in river valleys is predicted to increasingly decouple bears from salmon, possibly driving associated reductions in population productivity and provisioning of salmon nutrients to terrestrial ecosystems. Accordingly, we draw on our results to make landscape‐scale and access‐related management recommendations beyond current streamside protection buffers. This work illustrates the interaction between habitat modification and food security for wildlife, highlighting the potential for unacknowledged interactions and cumulative effects in increasingly modified landscapes.
Turbulence causes kinematic and behavioural adjustments in a flapping flier

Turbulence is a widespread phenomenon in the natural world, but its influence on flapping fliers remains little studied. We assessed how freestream turbulence affected the kinematics, flight effort and track properties of homing pigeons (Columba livia), using the fine-scale variations in flight height as a proxy for turbulence levels. Birds showed a small increase in their wingbeat amplitude with increasing turbulence (similar to laboratory studies), but this was accompanied by a reduction in mean wingbeat frequency, such that their flapping wing speed remained the same. Mean kinematic responses to turbulence may therefore enable birds to increase their stability without a reduction in propulsive efficiency. Nonetheless, the most marked response to turbulence was an increase in the variability of wingbeat frequency and amplitude. These stroke-to-stroke changes in kinematics provide instantaneous compensation for turbulence. They will also increase flight costs. Yet pigeons only made small adjustments to their flight altitude, likely resulting in little change in exposure to strong convective turbulence. Responses to turbulence were therefore distinct from responses to wind, with the costs of high turbulence being levied through an increase in the variability of their kinematics and airspeed. This highlights the value of investigating the variability in flight parameters in free-living animals.