Miracle-dz/UniFAR-FTUs huggingface dataset:
Mapping Late Leaf Spot Resistance in Peanut (Arachis hypogaea) Using QTL-seq Reveals Markers for Marker-Assisted Selection

Late leaf spot (LLS; Cercosporidium personatum) is a major fungal disease of cultivated peanut (Arachis hypogaea). A recombinant inbred line population segregating for quantitative field resistance was used to identify quantitative trait loci (QTL) using QTL-seq. High rates of false positive SNP calls using established methods in this allotetraploid crop obscured significant QTLs. To resolve this problem, robust parental SNPs were first identified using polyploid-specific SNP identification pipelines, leading to discovery of significant QTLs for LLS resistance. These QTLs were confirmed over 4 years of field data. Selection with markers linked to these QTLs resulted in a significant increase in resistance, showing that these markers can be immediately applied in breeding programs. This study demonstrates that QTL-seq can be used to rapidly identify QTLs controlling highly quantitative traits in polyploid crops with complex genomes. Markers identified can then be deployed in breeding programs, increasing the efficiency of selection using molecular tools. Key Message: Field resistance to late leaf spot is a quantitative trait controlled by many QTLs. Using polyploid-specific methods, QTL-seq is faster and more cost effective than QTL mapping.
What Makes a Strong Team?: Using Collective Intelligence to Predict Team Performance in League of Legends

Recent research has demonstrated that (a) groups can be characterized by a collective intelligence (CI) factor that measures their ability to perform together on a wide range of different tasks, and (b) this factor can predict groups' performance on other tasks in the future. The current study examines whether these results translate into the world of teams in competitive online video games where self-organized, time-pressured, and intense collaboration occurs purely online. In this study of teams playing the online game League of Legends, we find that CI does, indeed, predict the competitive performance of teams controlling for the amount of time played as a team. We also find that CI is positively correlated with the presence of a female team member and with the team members' average social perceptiveness. Finally, unlike in prior studies, tacit coordination in this setting plays a larger role than verbal communication.
Debt and Investment: A Firm Level Evidence

In this study, the panel smooth transition model will be used to analyze the nonlinear relationship between debt and investment. It can be inferred from the results that debt drives investment when the debt level is relatively low. However, a rise in debt reaching the “threshold” level diminishes the chances of an increase in investments. The results above indicate: the current economic downturn being experienced will not be resolved by further leverage.
Functional activation independently contributes to naming ability and relates to lesion site in post‐stroke aphasia

Language network reorganization in aphasia may depend on the degree of damage in critical language areas, making it difficult to determine how reorganization impacts performance. Prior studies on remapping of function in aphasia have not accounted for the location of the lesion relative to critical language areas. They rectified this problem by using a multimodal approach, combining multivariate lesion‐symptom mapping and fMRI in chronic aphasia to understand the independent contributions to naming performance of the lesion and the activity in both hemispheres. Activity was examined during two stages of naming: covert retrieval, and overt articulation. Regions of interest were drawn based on over‐ and under‐activation, and in areas where activity had a bivariate relationship with naming. Regressions then tested whether activation of these regions predicted naming ability, while controlling for lesion size and damage in critical left hemisphere naming areas, as determined by lesion‐symptom mapping. Engagement of the right superior temporal sulcus (STS) and disengagement of the left dorsal pars opercularis (dPOp) during overt naming was associated with better than predicted naming performance. Lesions in the left STS prevented right STS engagement and resulted in persistent left dPOp activation. In summary, changes in activity during overt articulation independently relate to naming outcomes, controlling for stroke severity. Successful remapping relates to network disruptions that depend on the location of the lesion in the left hemisphere. Hum Brain Mapp 38:2051–2066, 2017. © 2017 Wiley Periodicals, Inc.
PhaseLin: Linear phase retrieval

Phase retrieval deals with the recovery of complex-or real-valued signals from magnitude measurements. As shown recently, the method PhaseMax enables phase retrieval via convex optimization and without lifting the problem to a higher dimension. To succeed, PhaseMax requires an initial guess of the solution, which can be calculated via spectral initializers. In this paper, we show that with the availability of an initial guess, phase retrieval can be carried out with an ever simpler, linear procedure. Our algorithm, called PhaseLin, is the linear estimator that minimizes the mean squared error (MSE) when applied to the magnitude measurements. The linear nature of PhaseLin enables an exact and nonasymptotic MSE analysis for arbitrary measurement matrices. We furthermore demonstrate that by iteratively using PhaseLin, one arrives at an efficient phase retrieval algorithm that performs on par with existing convex and nonconvex methods on synthetic and real-world data.
Influences of Anlotinib on Cytochrome P450 Enzymes in Rats Using a Cocktail Method

The present study aimed to investigate the effect of anlotinib (AL3818) on pharmacokinetics of cytochrome P450 (CYP) enzymes (CYP1A2, CYP2C6, CYP2D1, CYP2D2, and CYP3A1/2) by using five cocktail probe drugs in vivo. After pretreatment for 7 days with anlotinib (treatment group) or saline (control group) by oral administration, probe drugs phenacetin, tolbutamide, omeprazole, metoprolol, and midazolam were administered to rats by oral administration. Blood samples were obtained at a series of time-points and the concentrations of five probe drugs in plasma were determined by a UHPLC-MS/MS method. The results showed that treatment with anlotinib had no significant effect on rat CYP1A2, CYP2D2, and CYP2C6. However, anlotinib had a significant inductive effect on CYP2D1 and CYP3A1/2. Therefore, caution is needed during the concomitant use of anlotinib with other drugs metabolized by CYP2D1 and CYP3A1/2 because of potential drug-anlotinib interactions.
A Finite Element Study of Friction Effect in Four-Point Bending Creep Test

Creep tests are often performed in four-point bending and the stress distribution in the bending specimen is nonlinear, so creep properties are estimated from bend creep test data. However, getting creep properties from bending creep tests is often doubted because of uncertainties from contact point shift and frictional effect between loading pin and specimen in four-point bending creep tests. Finite element simulations of the four-point bending creep tests were performed with geometric models which include contact conditions. It was found from simulation studies that friction in the bend tests can cause error in the estimation of creep properties, but when no friction was applied in simulations the creep properties were well predicted from bend test data.Copyright © 2003 by ASME
Extracorporeal bubbles: a word of caution.

OBJECTIVES Gaseous microemboli (GME) are a cause of neurocognitive deficit postcardiac surgery with cardiopulmonary bypass. However, the measurement of microbubbles during cardiopulmonary bypass is not easy, because blood is an opaque fluid and contains microparticles. Recently, two new microbubble counters, the Gampt BC200 and the emboli detection and classification (EDAC) quantifier, were developed for use during cardiac surgery. The accuracy of both devices was validated against industrial standards. METHODS A clear blood analogue (30%/70% glycerol-water) was pumped, by means of a rollerpump out of a partially filled arterial line screen filter with a nominal pore size of 20 microm. Downstream the pump, all test sensors and an optical cuvette, were inserted in a vertically mounted 3/8 inch tubing. Measurements were taken at flows of 405, 1080, 3000 and 6000 ml/min. Backlight shadowgraphy and optical counting were used as industrial reference techniques for measuring size and counts. RESULTS On average the EDAC quantifier underestimates average bubble diameter by 35+/-1%, 13+/-8%, 71+/-7% and 33+/-4% at 405, 1080, 3000 and 6000 ml/min, respectively. The Gampt BC200 has good sizing agreement at 1080 ml/min (+5+/-17%) and 3000 ml/min (+33+/-6%) but overestimates average diameter by 220+/-40% and 295+/-49% at 405 and 6000 ml/min, respectively. Both devices only partially count the number of microbubbles at higher flows. At 3 l/min the EDAC counts 38%, the Gampt 18% of total counts and at 6 l/min both the EDAC and Gampt only count 3% of total counts. CONCLUSIONS Both the EDAC and Gampt can be used in a clinical setting for monitoring basal GME production. However, both devices have some major limitations when used for studying 'worst case' scenarios. One should take great caution when correlating measured data with neurocognitive outcome. Finally, results obtained by one device in a first study cannot be compared nor exchanged with results from the other device in a second study.
Efficacy and Safety of L-Carnitine Treatment for Chronic Heart Failure: A Meta-Analysis of Randomized Controlled Trials

Background. Whether additional benefit can be achieved with the use of L-carnitine (L-C) in patients with chronic heart failure (CHF) remains controversial. We therefore performed a meta-analysis of randomized controlled trials (RCTs) to evaluate the effects of L-C treatment in CHF patients. Methods. Pubmed, Ovid Embase, Web of Science, and Cochrane Library databases, Chinese National Knowledge Infrastructure (CNKI) database, Wanfang database, Chinese Biomedical (CBM) database, and Chinese Science and Technology Periodicals database (VIP) until September 30, 2016, were identified. Studies that met the inclusion criteria were systematically evaluated by two reviewers independently. Results. 17 RCTs with 1625 CHF patients were included in this analysis. L-C treatment in CHF was associated with considerable improvement in overall efficacy (OR = 3.47, P < 0.01), left ventricular ejection fraction (LVEF) (WMD: 4.14%, P = 0.01), strike volume (SV) (WMD: 8.21 ml, P = 0.01), cardiac output (CO) (WMD: 0.88 L/min, P < 0.01), and E/A (WMD: 0.23, P < 0.01). Moreover, treatment with L-C also resulted in significant decrease in serum levels of BNP (WMD: −124.60 pg/ml, P = 0.01), serum levels of NT-proBNP (WMD: −510.36 pg/ml, P < 0.01), LVESD (WMD: −4.06 mm, P < 0.01), LVEDD (WMD: −4.79 mm, P < 0.01), and LVESV (WMD: −20.16 ml, 95% CI: −35.65 to −4.67, P < 0.01). However, there were no significant differences in all-cause mortality, 6-minute walk, and adverse events between L-C and control groups. Conclusions. L-C treatment is effective for CHF patients in improving clinical symptoms and cardiac functions, decreasing serum levels of BNP and NT-proBNP. And it has a good tolerance.
Direct detection and characterization of foot‐and‐mouth disease virus in East Africa using a field‐ready real‐time PCR platform

Summary Effective control and monitoring of foot‐and‐mouth disease (FMD) relies upon rapid and accurate disease confirmation. Currently, clinical samples are usually tested in reference laboratories using standardized assays recommended by The World Organisation for Animal Health (OIE). However, the requirements for prompt and serotype‐specific diagnosis during FMD outbreaks, and the need to establish robust laboratory testing capacity in FMD‐endemic countries have motivated the development of simple diagnostic platforms to support local decision‐making. Using a portable thermocycler, the T‐COR™ 8, this study describes the laboratory and field evaluation of a commercially available, lyophilized pan‐serotype‐specific real‐time RT‐PCR (rRT‐PCR) assay and a newly available FMD virus (FMDV) typing assay (East Africa‐specific for serotypes: O, A, Southern African Territories [SAT] 1 and 2). Analytical sensitivity, diagnostic sensitivity and specificity of the pan‐serotype‐specific lyophilized assay were comparable to that of an OIE‐recommended laboratory‐based rRT‐PCR (determined using a panel of 57 FMDV‐positive samples and six non‐FMDV vesicular disease samples for differential diagnosis). The FMDV‐typing assay was able to correctly identify the serotype of 33/36 FMDV‐positive samples (no cross‐reactivity between serotypes was evident). Furthermore, the assays were able to accurately detect and type FMDV RNA in multiple sample types, including epithelial tissue suspensions, serum, oesophageal–pharyngeal (OP) fluid and oral swabs, both with and without the use of nucleic acid extraction. When deployed in laboratory and field settings in Tanzania, Kenya and Ethiopia, both assays reliably detected and serotyped FMDV RNA in samples (n = 144) collected from pre‐clinical, clinical and clinically recovered cattle. These data support the use of field‐ready rRT‐PCR platforms in endemic settings for simple, highly sensitive and rapid detection and/or characterization of FMDV.
Health Status, Health Shocks, and Asset Adequacy Over Retirement Years

This article uses data on a sample of retirees drawn from the Health and Retirement Study (HRS) to examine changes in health over the retirement years and to estimate the effects of health changes in retirement on wealth. Using the framework of item response theory, we develop a novel measure of health that makes use of multiple indicators of physical health that are available in the HRS. We find that large negative shocks to the health of male retirees and their spouses are frequent in retirement and that when such shocks do occur, recovery to the preshock level of health is rare. Using a dynamic panel data model, we then estimate short- and long-run effects of changes in health on wealth. While our estimated short-run effects are modest, long-run estimates of the impact of health shocks on wealth are large, ranging from a 12% to 20% reduction in wealth by the 10th year, following a permanent one standard deviation decrease in health.
NKILA inhibits NF-κB signaling and suppresses tumor metastasis

The long non-coding RNA (lncRNA) NKILA (nuclear transcription factor NF-κB interacting lncRNA) functions as a suppressor in human breast cancer and tongue cancer. However, the clinical significance and biological roles of NKILA in esophageal squamous cell carcinoma (ESCC) remain unknown. In this study, we showed that NKILA was downregulated in ESCC tissues and cancer cells compared with their normal counterparts. Low NKILA expression correlated with large tumor size and advanced TNM stage, and predicted poor overall and disease-free survival of ESCC patients. Further loss- and gain-of-function assays indicated that NKILA inhibited proliferation and migration of ESCC cells in vitro, suppressed tumor growth and lung metastasis in vivo. Mechanistically, NKILA could inhibit phosphorylation of IκBα, suppress p65 nuclear translocation and downregulate the expression of NF-κB target genes in ESCC cells. These results suggest NKILA could suppress malignant development of ESCC via abrogation of the NF-κB signaling and may potentially serve as a prognostic marker for ESCC.
Relationship of Genetic Variants With Procedural Pain, Anxiety, and Distress in Children

Objective: This study used a candidate gene approach to examine genomic variation associated with pain, anxiety, and distress in children undergoing a medical procedure. Study Design: Children aged 4–10 years having an IV catheter insertion were recruited from three Midwestern children’s hospitals. Self-report measures of pain, anxiety, and distress were obtained as well as an observed measure of distress. Samples were collected from children and biological parents for analysis of genomic variation. Genotyped variants had known or suspected association with phenotypes of interest. Analyses included child-only association and family-based transmission disequilibrium tests. Results: Genotype and phenotype data were available from 828 children and 376 family trios. Children were 50% male, had a mean age of 7.2 years, and were 84% White/non-Hispanic. In family-based analysis, one single-nucleotide polymorphism (SNP; rs1143629, interleukin (IL1B) 1β) was associated with observed child distress at Bonferroni-corrected levels of significance (p = .00013), while two approached significance for association with high state anxiety (rs6330 Nerve Growth Factor, Beta Subunit, [NGFB]) and high trait anxiety (rs6265 brain-derived neurotrophic factor [BDNF]). In the child-only analysis, multiple SNPs showed nominal evidence of relationships with phenotypes of interest. rs6265 BDNF and rs2941026 cholecystokinin B receptor had possible relationships with trait anxiety in child-only and family-based analyses. Conclusions: Exploring genomic variation furthers our understanding of pain, anxiety, and distress and facilitates genomic screening to identify children at high risk of procedural pain, anxiety, and distress. Combined with clinical observations and knowledge, such explorations could help guide tailoring of interventions to limit procedure-related distress and identify genes and pathways of interest for future genotype–phenotype studies.
ASCUS-LSIL Triage Study

OBJECTIVE To describe the design and methods of the ASCUS-LSIL Triage Study (ALTS), a multicenter, randomized clinical trial designed to evaluate three alternative methods of managing low grade (LSIL) and equivocal (ASCUS) cervical cytologic diagnoses. STUDY DESIGN Nonpregnant women, 18+ years old, with ASCUS or LSIL, no prior hysterectomy or ablative therapy to the cervix, were referred to one of four clinical centers around the United States. Eligible and consenting participants were administered a risk-factor questionnaire and underwent a pelvic examination, collection of cervical specimens for liquid-based cytology and human papillomavirus (HPV) testing and Cervicography (National Testing Laboratories, Fenton, Missouri, U.S.A.). Patients were randomized to one of three arms: (1) immediate referral for colposcopy at enrollment, (2) follow-up with cytology only, and (3) use of HPV DNA testing to triage to colposcopy. All women are followed every six months for two years with pelvic examinations, cytologic and masked HPV testing, and masked Cervicography. Digital cervical images and cytology and histology slides are externally reviewed to maximize patient safety. RESULTS We enrolled and randomized 3,488 eligible women with ASCUS and 1,572 women with LSIL. CONCLUSION The successful enrollment, randomization and high rates of follow-up are encouraging. The study will help clarify the optimal strategies for managing low grade cervical abnormalities.
Guidelines for snowballing in systematic literature studies and a replication in software engineering

Background: Systematic literature studies have become common in software engineering, and hence it is important to understand how to conduct them efficiently and reliably. Objective: This paper presents guidelines for conducting literature reviews using a snowballing approach, and they are illustrated and evaluated by replicating a published systematic literature review. Method: The guidelines are based on the experience from conducting several systematic literature reviews and experimenting with different approaches. Results: The guidelines for using snowballing as a way to search for relevant literature was successfully applied to a systematic literature review. Conclusions: It is concluded that using snowballing, as a first search strategy, may very well be a good alternative to the use of database searches.
CONCENTRATIONS OF DIMETHYLSULFONIOPROPIONATE AND DIMETHYL SULFIDE ARE STRAIN‐SPECIFIC IN SYMBIOTIC DINOFLAGELLATES (SYMBIODINIUM SP., DINOPHYCEAE) 1

Dimethyl sulfide (DMS) and dimethylsulfoniopropionate (DMSP) are sulfur compounds that may function as antioxidants in algae. Symbiotic dinoflagellates of the genus Symbiodinium show strain‐specific differences in their susceptibility to temperature‐induced oxidative stress and have been shown to contain high concentrations of DMSP. We investigated continuous cultures of four strains from distinct phylotypes (A1, A13, A2, and B1) that can be characterized by differential thermal tolerances. We hypothesized that strains with high thermal tolerance have higher concentrations of DMSP and DMS in comparison to strains with low thermal tolerance. DMSP concentrations were strain‐specific with highest concentrations occurring in A1 (225 ± 3.5 mmol · L−1 cell volume [CV]) and lowest in A2 (158 ± 3.8 mmol · L−1 CV). Both strains have high thermal tolerance. Strains with low thermal tolerance (A13 and B1) showed DMSP concentrations in between these extremes (194 ± 19.0 and 160 ± 6.1 mmol · L−1 CV, respectively). DMS data further confirmed this general pattern with high DMS concentrations in A1 and A13 (4.1 ± 1.22 and 2.1 ± 0.37 mmol · L−1 CV, respectively) and low DMS concentrations in A2 and B1 (0.3 ± 0.06 and 0.5 ± 0.22 mmol · L−1 CV, respectively). Hence, the strain‐specific differences in DMSP and DMS concentrations did not match the different abilities of the four phylotypes to withstand thermal stress. Future work should quantify the possible dynamics in DMSP and DMS concentrations during periods of high oxidative stress in Symbiodinium sp. and address the role of these antioxidants in zooxanthellate cnidarians.
Split-Second Trustworthiness Detection From Faces in an Economic Game

Economic interactions often imply to gauge the trustworthiness of others. Recent studies showed that when making trust decisions in economic games, people have some accuracy in detecting trustworthiness from the facial features of unknown partners. Here we provide evidence that this face-based trustworthiness detection is a fast and intuitive process by testing its performance at split-second levels of exposure. Participants played a Trust game, in which they made decisions whether to trust another player based on their picture. In two studies, we manipulated the exposure time of the picture. We observed that trustworthiness detection remained better than chance for exposure times as short as 100 ms, although it disappeared with an exposure time of 33 ms. We discuss implications for ongoing debates on the use of facial inferences for social and economic decisions.