Miracle-dz/UniFAR-FTUs huggingface dataset:
An electrostatic selection mechanism controls sequential kinase signaling downstream of the T cell receptor

The sequence of events that initiates T cell signaling is dictated by the specificities and order of activation of the tyrosine kinases that signal downstream of the T cell receptor. Using a platform that combines exhaustive point-mutagenesis of peptide substrates, bacterial surface-display, cell sorting, and deep sequencing, we have defined the specificities of the first two kinases in this pathway, Lck and ZAP-70, for the T cell receptor ζ chain and the scaffold proteins LAT and SLP-76. We find that ZAP-70 selects its substrates by utilizing an electrostatic mechanism that excludes substrates with positively-charged residues and favors LAT and SLP-76 phosphosites that are surrounded by negatively-charged residues. This mechanism prevents ZAP-70 from phosphorylating its own activation loop, thereby enforcing its strict dependence on Lck for activation. The sequence features in ZAP-70, LAT, and SLP-76 that underlie electrostatic selectivity likely contribute to the specific response of T cells to foreign antigens. DOI: http://dx.doi. org/10.7554/eLife.20105. 001
At What Level of Heat Load Are Age-Related Impairments in the Ability to Dissipate Heat Evident in Females?

Studies have reported that older females have impaired heat loss responses during work in the heat compared to young females. However, it remains unclear at what level of heat stress these differences occur. Therefore, we examined whole-body heat loss [evaporative (HE) and dry heat loss, via direct calorimetry] and changes in body heat storage (∆Hb, via direct and indirect calorimetry) in 10 young (23±4 years) and 10 older (58±5 years) females matched for body surface area and aerobic fitness (VO2peak) during three 30-min exercise bouts performed at incremental rates of metabolic heat production of 250 (Ex1), 325 (Ex2) and 400 (Ex3) W in the heat (40°C, 15% relative humidity). Exercise bouts were separated by 15 min of recovery. Since dry heat gain was similar between young and older females during exercise (p=0.52) and recovery (p=0.42), differences in whole-body heat loss were solely due to HE. Our results show that older females had a significantly lower HE at the end of Ex2 (young: 383±34 W; older: 343±39 W, p=0.04) and Ex3 (young: 437±36 W; older: 389±29 W, p=0.008), however no difference was measured at the end of Ex1 (p=0.24). Also, the magnitude of difference in the maximal level of HE achieved between the young and older females became greater with increasing heat loads (Ex1=10.2%, Ex2=11.6% and Ex3=12.4%). Furthermore, a significantly greater ∆Hb was measured for all heat loads for the older females (Ex1: 178±44 kJ; Ex2: 151±38 kJ; Ex3: 216±25 kJ, p=0.002) relative to the younger females (Ex1: 127±35 kJ; Ex2: 96±45 kJ; Ex3: 146±46 kJ). In contrast, no differences in HE or ∆Hb were observed during recovery (p>0.05). We show that older habitually active females have an impaired capacity to dissipate heat compared to young females during exercise-induced heat loads of ≥325 W when performed in the heat.
Polyunsaturated fatty acid intake is adversely related to liver function in HIV-infected subjects : the THUSA study 1 – 3

Background: Dietary fat intake in the South African population is increasing. This population also has a high prevalence of HIV infection. However, information about metabolic effects of dietary fatty acids on HIV-infected subjects is lacking. Objective: Our objective was to investigate the relation between dietary fatty acid intake and liver function in HIV-infected compared with HIV-uninfected subjects. Design: This cross-sectional epidemiologic survey included a representative sample of 1854 apparently healthy black volunteers aged 15 y, who were recruited from 37 randomly selected sites throughout the North West province of South Africa. Data from 216 asymptomatic HIV-infected and 1604 HIV-uninfected subjects were used. Results: Intakes of polyunsaturated fatty acids (PUFAs), linoleic acid (n 6), and the ratio of PUFAs to saturated fatty acids (SFAs) were positively associated with all the liver enzymes measured in HIV-infected subjects (R 0.16–0.65). Most of these R values differed significantly from the R values for HIV-uninfected subjects. No associations were seen between liver enzymes and intakes of SFAs and monounsaturated fatty acids. Vitamin E intake was positively associated with serum -glutamyl transpeptidase (R 0.23), alanine aminotransferase (R 0.37), and aspartate aminotransferase (R 0.58) in HIV-infected subjects; these correlations differed significantly from those of the HIV-uninfected subjects because PUFA sources are the main carriers of vitamin E. Conclusions: The results suggest that n 6 PUFA intakes may be related to liver damage in these HIV-infected asymptomatic subjects. The reasons or mechanisms responsible are not clear, and further research is necessary to determine the optimal safe amounts for intake of n 6 PUFAs by HIV-infected subjects, especially in countries with traditionally high intakes of n 6 PUFA–rich vegetable oils. Am J Clin Nutr 2006;83:1193–8.
The practical implications of using standardized estimation equations in calculating the prevalence of chronic kidney disease.

BACKGROUND Kidney Disease Outcomes Quality Initiative (KDOQI) chronic kidney disease (CKD) guidelines have focused on the utility of using the modified four-variable MDRD equation (now traceable by isotope dilution mass spectrometry IDMS) in calculating estimated glomerular filtration rates (eGFRs). This study assesses the practical implications of eGFR correction equations on the range of creatinine assays currently used in the UK and further investigates the effect of these equations on the calculated prevalence of CKD in one UK region METHODS Using simulation, a range of creatinine data (30-300 micromol/l) was generated for male and female patients aged 20-100 years. The maximum differences between the IDMS and MDRD equations for all 14 UK laboratory techniques for serum creatinine measurement were explored with an average of individual eGFRs calculated according to MDRD and IDMS < 60 ml/min/1.73 m(2) and 30 ml/min/1.73 m(2). Similar procedures were applied to 712,540 samples from patients > or = 18 years (reflecting the five methods for serum creatinine measurement utilized in Northern Ireland) to explore, graphically, maximum differences in assays. CKD prevalence using both estimation equations was compared using an existing cohort of observed data. RESULTS Simulated data indicates that the majority of laboratories in the UK have small differences between the IDMS and MDRD methods of eGFR measurement for stages 4 and 5 CKD (where the averaged maximum difference for all laboratory methods was 1.27 ml/min/1.73 m(2) for females and 1.59 ml/min/1.73 m(2) for males). MDRD deviated furthest from the IDMS results for the Endpoint Jaffe method: the maximum difference of 9.93 ml/min/1.73 m(2) for females and 5.42 ml/min/1.73 m(2) for males occurred at extreme ages and in those with eGFR > 30 ml/min/1.73 m(2). Observed data for 93,870 patients yielded a first MDRD eGFR < 60 ml/min/1.73 m(2) in 2001. 66,429 (71%) had a second test > 3 months later of which 47,093 (71%) continued to have an eGFR < 60 ml/min/1.73 m(2). Estimated crude prevalence was 3.97% for laboratory detected CKD in adults using the MDRD equation which fell to 3.69% when applying the IDMS equation. Over 95% of this difference in prevalence was explained by older females with stage 3 CKD (eGFR 30-59 ml/min/1.73 m(2)) close to the stage 2 CKD (eGFR 60-90 ml/min/1.73 m(2)) interface. CONCLUSIONS Improved accuracy of eGFR is obtainable by using IDMS correction especially in the earlier stages of CKD 1-3. Our data indicates that this improved accuracy could lead to reduced prevalence estimates and potentially a decreased likelihood of onward referral to nephrology services particularly in older females.
Country, Cover or Protection: What Shapes the Distribution of Red Deer and Roe Deer in the Bohemian Forest Ecosystem?

The Bohemian Forest Ecosystem encompasses various wildlife management systems. Two large, contiguous national parks (one in Germany and one in the Czech Republic) form the centre of the area, are surrounded by private hunting grounds, and hunting regulations in each country differ. Here we aimed at unravelling the influence of management-related and environmental factors on the distribution of red deer (Cervus elaphus) and roe deer (Capreolus capreolus) in this ecosystem. We used the standing crop method based on counts of pellet groups, with point counts every 100 m along 218 randomly distributed transects. Our analysis, which accounted for overdispersion as well as zero inflation and spatial autocorrelation, corroborated the view that both human management and the physical and biological environment drive ungulate distribution in mountainous areas in Central Europe. In contrast to our expectations, protection by national parks was the least important variable for red deer and the third important out of four variables for roe deer; protection negatively influenced roe deer distribution in both parks and positively influenced red deer distribution in Germany. Country was the most influential variable for both red and roe deer, with higher counts of pellet groups in the Czech Republic than in Germany. Elevation, which indicates increasing environmental harshness, was the second most important variable for both species. Forest cover was the least important variable for roe deer and the third important variable for red deer; the relationship for roe deer was positive and linear, and optimal forest cover for red deer was about 70% within a 500 m radius. Our results have direct implications for the future conservation management of deer in protected areas in Central Europe and show in particular that large non-intervention zones may not cause agglomerations of deer that could lead to conflicts along the border of protected, mountainous areas.
Reflection on Mobile Applications for Blood Pressure Management: A Systematic Review on Potential Effects and Initiatives

INTRODUCTION Ischemic heart disease and stroke have been considered as the first global leading cause of death in last decades [1]. Blood pressure (BP) management is one of the easiest ways suggested for preventing and controlling cardiovascular diseases before the patient develops complications and death-following outcomes. Appearance of technology advancements in the health system has motivated researchers and health providers to study its different aspects and applications in order to improve disease prevention and management. Following these efforts, mobile health (mHealth) technologies were presented to provide people with fast and easier-to-use services. Although there are some unsolved challenges, these technologies have become popular among many people. As an important part of mHealth, mobile applications (apps) have been the focused subject of many studies in the last decade. The objective of this systematic review is to assess the potential effects of mobile apps designed for BP management by scrutinizing the related studies. MATERIALS AND METHODS Search methods: We searched the following electronic databases in December 2016: Medline (PubMed), National Center for Biotechnology Information (NCBI), Cochrane Central Register of Controlled Trials (CENTRAL), PsycINFO, Cumulative Index to Nursing and Allied Health Literature (CINAHL), Education Resources Information Center(ERIC), Web of Science, ProQuest, and Google Scholar. No language restriction and start point limitation were imposed. SELECTION CRITERIA We included studies that evaluated and assessed mobile apps for BP management and related clinical trials that considered mobile app as the only difference between intervention and control groups. DATA COLLECTION AND ANALYSIS Two review authors applied the eligibility criteria, extracted data and assessed the quality of included studies. RESULTS Literature search resulted in 13 included studies and 27 reviews. 12 records of 13 included studies identified as interventional studies. The review showed that the mobile apps may improve individual's BP condition and medication adherence. CONCLUSION Most of the studies had emphasized positive effects of mobile apps in BP management. However, there is a necessity for performing further investigations due to the identified issues in this study such as low number of participants and limited intervention period in randomized controlled trials, and interventions limited to only hypertensive or high-risked individual.
Evaluation of the rhodopsin knockout mouse as a model of pure cone function.

PURPOSE To determine a time window in the rhodopsin knockout (Rho(-/-)) mouse during which retinal function is already sufficiently developed but cone degeneration is not yet substantial, thus representing an all-cone retina. METHODS Electroretinograms (ERGs) were obtained from 14 homozygous Rho(-/-) mice and eight C57Bl/6 control mice. The same individuals were tested every 7 days, beginning as early as postnatal day (P)14. The ERG protocols included flash and flicker stimuli, both under photopic and scotopic conditions. Retinal and choroidal morphology was observed in animals of comparable age. RESULTS Functionally, the developmental phase lasted until postnatal week (PW)3 in both the Rho(-/-) mice and the control animals. During PW4 to 6, the Rho(-/-) mice showed a plateau in ERG parameters with normal or even supernormal cone responses and complete absence of rod contributions. At PW7, there was a marked onset of degeneration, which progressed so that no ERG signals were left at PW13, when the control eyes still had normal ERG responses. Microscopically, cone degeneration paralleled the functional changes, beginning at approximately PW6 and almost complete at PW13, whereas retinal pigment epithelium (RPE) and choroid did not show any abnormalities. CONCLUSIONS From PW4 to 6, Rho(-/-) mice appear to have normal cone and no rod function. Despite the missing rod outer segment (OS), the structure of retina, RPE, and choroid remained unchanged. Therefore, the Rho(-/-) mice can serve during this age period as a model for pure cone function. Such a model is particularly useful to evaluate rod-cone interaction and to dissect rod- from cone-mediated signaling pathways in vivo.
Evaluation of stage support for musicians ’ performance in a concert hall

Stage support for both vocal and instrumental performers was evaluated for ensemble performance in concert halls. Halls with different seating capacities were selected for measurements of stage acoustics: STEarly was measured at eight positions where musicians played for evaluation of ease in hearing oneself. In addition, mutual hearing on stage was evaluated by exchanging sources and receivers at the positions between soloist and orchestra. Stage acoustical parameters for stage support and mutual hearing are discussed with regard to the subjective tests results.
Investigating the Role of Free-Ranging Wild Boar (Sus scrofa) in the Re-Emergence of Enzootic Pneumonia in Domestic Pig Herds: A Pathological, Prevalence and Risk-Factor Study

Enzootic pneumonia (EP) caused by Mycoplasma hyopneumoniae has a significant economic impact on domestic pig production. A control program carried out from 1999 to 2003 successfully reduced disease occurrence in domestic pigs in Switzerland, but recurrent outbreaks suggested a potential role of free-ranging wild boar (Sus scrofa) as a source of re-infection. Since little is known on the epidemiology of EP in wild boar populations, our aims were: (1) to estimate the prevalence of M. hyopneumoniae infections in wild boar in Switzerland; (2) to identify risk factors for infection in wild boar; and (3) to assess whether infection in wild boar is associated with the same gross and microscopic lesions typical of EP in domestic pigs. Nasal swabs, bronchial swabs and lung samples were collected from 978 wild boar from five study areas in Switzerland between October 2011 and May 2013. Swabs were analyzed by qualitative real time PCR and a histopathological study was conducted on lung tissues. Risk factor analysis was performed using multivariable logistic regression modeling. Overall prevalence in nasal swabs was 26.2% (95% CI 23.3–29.3%) but significant geographical differences were observed. Wild boar density, occurrence of EP outbreaks in domestic pigs and young age were identified as risk factors for infection. There was a significant association between infection and lesions consistent with EP in domestic pigs. We have concluded that M. hyopneumoniae is widespread in the Swiss wild boar population, that the same risk factors for infection of domestic pigs also act as risk factors for infection of wild boar, and that infected wild boar develop lesions similar to those found in domestic pigs. However, based on our data and the outbreak pattern in domestic pigs, we propose that spillover from domestic pigs to wild boar is more likely than transmission from wild boar to pigs.
Modeling climate change effects on runoff and soil erosion in southeastern Arizona rangelands and implications for mitigation with conservation practices

Climate change is expected to impact runoff and soil erosion on rangelands in the western United States. This study evaluated the potential impacts of precipitation changes on soil erosion and surface runoff in southeastern Arizona using seven General Circulation Model (GCM) models with three emission scenarios for the 2050s and 2090s. A spatial-temporal downscaling process was used to generate daily precipitation series from GCM outputs for runoff and erosion modeling with the Rangeland Hydrology and Erosion Model (RHEM). Results were compared to 1970 through 1999 conditions. Our results suggested no significant changes in annual precipitation across the region under the three emission scenarios, while projected mean annual runoff and soil loss increased significantly, ranging from 79% to 92% and from 127% to 157%, respectively, relative to 1970 to 1999. At the seasonal scale, though an increase of summer precipitation and a reduction of winter precipitation were projected, both runoff and soil loss increased significantly for both periods. The dramatic increases in runoff and soil loss were attributed to the increase in the frequency and intensity of extreme events in the study area. Predicted soil loss from shrub communities increased more than that predicted for other plant communities under the three emission scenarios. Future increases in runoff and soil erosion may accelerate the transitions of grassland to shrublands or to more eroded states due to the positive vegetation-erosion feedback. Rangeland management policies and practices should consider these changes and adapt to the increased risk of runoff and soil erosion.
Nocturnal soil CO2 uptake and its relationship to subsurface soil and ecosystem carbon fluxes in a Chihuahuan Desert shrubland

Despite their prevalence, little attention has been given to quantifying arid land soil and ecosystem carbon fluxes over prolonged, annually occurring dry periods. We measured soil [CO2] profiles and fluxes (Fs) along with volumetric soil moisture and temperature in bare interplant canopy soils and in soils under plant canopies over a three‐month hot and dry period in a Chihuahuan Desert shrubland. Nocturnal Fs was frequently negative (from the atmosphere into the soil), a form of inorganic carbon exchange infrequently observed in other deserts. Negative Fs depended on air‐soil temperature gradients and were more frequent and stronger in intercanopy soils. Daily integrated ecosystem‐level Fs was always positive despite lower daily Fs in intercanopy soils due to nocturnal uptake and more limited positive response to isolated rains. Subsurface [CO2] profiles associated with negative Fs indicated that sustained carbonate dissolution lowered shallow‐soil [CO2] below atmospheric levels. In the morning, positive surface Fs started earlier and increased faster than shallow‐soil Fs, which was bidirectional, with upward flux toward the surface and downward flux into deeper soils. These dynamics are consistent with carbonate precipitation in conjunction with convection‐assisted CO2 outgassing from warming air and soil temperatures and produced a pronounced diurnal Fs temperature hysteresis. We concluded that abiotic nocturnal soil CO2 uptake, through a small carbon sink, modulates dry season ecosystem‐level carbon dynamics. Moreover, these abiotic carbon dynamics may be affected by future higher atmospheric carbon dioxide levels and predictions of more prolonged and regular hot and dry periods.
Water use efficiency of annual‐dominated and bunchgrass‐dominated savanna intercanopy space

In semi‐arid savannas, dominance of intercanopy space by annual or perennial grasses may alter partitioning of ecosystem water and carbon fluxes and affect ecosystem water use efficiency (WUEe), the ratio of net ecosystem carbon dioxide exchange (NEE) to evapotranspiration (ET). To establish if these contrasting growth habits changed controls to WUEe, we tracked volumetric soil moisture (θ25cm), ET and transpiration (T), NEE and its constituent ecosystem respiration (Reco) and gross ecosystem photosynthesis (GEP) fluxes, and community water use efficiency (WUEc = GEP : T) in annual‐dominated and bunchgrass‐dominated plots in a southern Arizona, United States, savanna. Annual and bunchgrass plots had similar θ25cm, ET, and T, suggesting the similarity in ET was due to higher soil evaporation in annual plots. Seasonal NEE was delayed and lower in annual plots compared with that in bunchgrass plots, owing to higher Reco in annual plots. Transpiration, GEP, and Reco in both vegetation types increased following late‐season rain, indicating similar late‐season phenological constraint. WUEe was lower in annual plots, but with similar WUEc between plot types. These results suggest that differences in annual plant biomass allocation and plot‐level leaf area distribution increased proportional soil evaporation and aboveground Reco contributions, reducing plot‐level WUEe, not lowering plant WUE typical of arid‐land annuals. Lower plot‐level WUEe suggests that any increase in annual plant dominance would increase interannual variation of productivity in savanna intercanopy spaces, which could enhance the negative effects of predicted higher temperatures, greater aridity, and larger and more widely spaced storms on arid‐land watershed processes. Published 2013. This article is a U.S. Government work and is in the public domain in the USA.