Miracle-dz/UniFAR-FTUs huggingface dataset:
The Unfolded Protein Response Pathway in Saccharomyces cerevisiae

In eukaryotic cells, accumulation of unfolded proteins in the endoplasmic reticulum (ER) results in a transcriptional induction of a number of ER chaperone proteins. In Saccharomyces cerevisiae, the putative transmembrane receptor kinase, Ire1p (Ern1p), has been implicated as the sensor of unfolded proteins in the ER that initiates transmittance of the unfolded protein signal from the ER to the nucleus. We have shown that the cytoplasmic domain of Ire1p receptor indeed has intrinsic Ser/Thr kinase activity and contains Ser/Thr phosphorylation sites as well. The cytoplasmic domain is also shown to form oligomers in vivo and in vitro. The ability to form oligomers primarily resides within the last 130 amino acids of the cytoplasmic domain, a region that is dispensable for in vitro kinase activity of the receptor. Oligomerization of the cytoplasmic domains is required for receptor trans-phosphorylation and subsequent activation of the kinase function. The activated kinase may transmit the unfolded protein signal from the ER to the nucleus to activate the transcription of the chaperone genes in the nucleus.
A new approach of adaptive edge detection based on GAP predictor

Edge is one of the most fundamental features. Edge detection is an important method to extract the image's characteristics. Firstly gradient adjusted predictor was used to predict the image, and then aimed at the gained error image, a new adapted approach to selected threshold based on gradient mean-value histogram was proposed, and classified edge and non-edge by the gained threshold; to obtain single pixel edges, the gained edge image was far thinned by the thinning algorithm, and the last edge image was achieved. Simulation results show that have fine and continued edge characteristic, higher precision of localization by using the proposed method compared with other methods. The experimental results are more satisfactory.
Regionally specific increased volume of the amygdala in Williams syndrome: Evidence from surface‐based modeling

Williams syndrome (WS) is a condition caused by a contiguous deletion of approximately 26–28 genes from chromosome 7, and is characterized by abnormal social and emotional processing and abnormal structure and function of the amygdala. Prior studies show that the amygdala is relatively enlarged in WS, but very little is known regarding the regional specificity of increased amygdalar volume in this condition. Here we investigated the regional specificity of structural alterations of the amygdala in WS, compared to a typically developing (TD) control group. We acquired high resolution brain MRI data from 79 participants (39 WS, 40 TD) and used a surface‐based analytical modeling approach. The WS group exhibited several areas of increased radial expansion of the amygdalar surface and no areas of decreased radial expansion of the amygdalar surface compared to TD controls. The areas found to exhibit particularly increased radial expansion in WS included the bilateral posterior cortical nucleus, lateral nucleus, and the central nucleus. This greater regional and anatomical specificity of altered amygdala structure in WS contributes to a model relating genetic risk in WS to the development of key brain regions for social and emotional functioning. Hum Brain Mapp 35:866–874, 2014. © 2012 Wiley Periodicals, Inc.
Control of Mitochondrial pH by Uncoupling Protein 4 in Astrocytes Promotes Neuronal Survival*

Background: The role of uncoupling proteins (UCP) in the brain is unclear. Results: UCPs, present in astrocytes, mediate the intramitochondrial acidification leading to a decrease in mitochondrial ATP production. Conclusion: Astrocyte pH regulation promotes ATP synthesis by glycolysis whose final product, lactate, increases neuronal survival. Significance: We describe a new role for a brain uncoupling protein. Brain activity is energetically costly and requires a steady and highly regulated flow of energy equivalents between neural cells. It is believed that a substantial share of cerebral glucose, the major source of energy of the brain, will preferentially be metabolized in astrocytes via aerobic glycolysis. The aim of this study was to evaluate whether uncoupling proteins (UCPs), located in the inner membrane of mitochondria, play a role in setting up the metabolic response pattern of astrocytes. UCPs are believed to mediate the transmembrane transfer of protons, resulting in the uncoupling of oxidative phosphorylation from ATP production. UCPs are therefore potentially important regulators of energy fluxes. The main UCP isoforms expressed in the brain are UCP2, UCP4, and UCP5. We examined in particular the role of UCP4 in neuron-astrocyte metabolic coupling and measured a range of functional metabolic parameters including mitochondrial electrical potential and pH, reactive oxygen species production, NAD/NADH ratio, ATP/ADP ratio, CO2 and lactate production, and oxygen consumption rate. In brief, we found that UCP4 regulates the intramitochondrial pH of astrocytes, which acidifies as a consequence of glutamate uptake, with the main consequence of reducing efficiency of mitochondrial ATP production. The diminished ATP production is effectively compensated by enhancement of glycolysis. This nonoxidative production of energy is not associated with deleterious H2O2 production. We show that astrocytes expressing more UCP4 produced more lactate, which is used as an energy source by neurons, and had the ability to enhance neuronal survival.
TNF-α, IL-1β, and oxidative stress during fracture healing with or without ankaferd.

AIMS Whether ankaferd blood stopper (ABS) has a negative or positive effect on bone union during fracture healing is unknown. The purpose of this study was to evaluate the serum changes of oxidative stress markers, Tumor Necrosis Factor-α (TNF-α), Interleukin-1β (IL-1β), and Interleukin-10 (IL-10) during fracture healing process with or without ABS application to bone fracture. MATERIAL AND METHODS Eight rats were used as a control group (1) that was not subject to fracture. The remaining 48 rats were divided into six groups, 8 rats in each. The femoral shaft fracture was produced by cutting with bone-scissors. One ml of ABS was applied on the fracture region in groups 3 (7th day), 5 (21st day), and 7 (45th day) or saline instead of ABS on the fracture regions in groups 2 (7th day), 4 (21st day), and 6 (45th day). Radiographs and above parameters were examined on post-fracture days 7, 21, and 45. RESULTS Malondialdehyde and protein carbonyls were measured in high levels in the groups 2 and 4 with respect to control. Their levels did not change statistically in the experimental groups after ABS application. The values of TNF-α and IL-1β were elevated on 7th post-fracture day according to control, but were lower (by 11.86 % and 44.48 %) in the group 3 treated with ABS comparing to group 2. Radiographic examination indicated a low callus formation on fracture union in the femoral fractures of groups 3 and 5 treated with ABS. CONCLUSION The present findings may suggest that ABS application seems to be ineffective on fracture union in early fracture healing period, except for bleeding control (Tab. 2, Fig. 3, Ref. 26).
Two new large deletions of the AVPR2 gene causing nephrogenic diabetes insipidus and a review of previously published deletions.

BACKGROUND In this paper, we report two new original deletions and present an extended review of the previously characterized AVPR2 gene deletions to better understand the underlying deletion mechanisms. METHODS The two novel deletions were defined using polymerase chain reaction mapping and junction fragment sequencing. Bioinformatic analysis was performed on both the previously mapped deletions and the novel ones through several web tools. RESULTS In our two patients with nephrogenic diabetes insipidus, we found a 23 755 bp deletion and a 9264 bp deletion both comprising the entire AVPR2 gene and part of the ARHGAP4 gene. Through bioinformatic studies, the smallest overlapping region as well as several motifs and repeats that are known to promote rearrangements were confirmed. CONCLUSIONS Through this study, it was determined that the deletion mechanisms in the AVPR2 region do not follow the rules of non-allelic homologous recombination. Two of the 13 deletions can be attributed to the fork stalling and template switching (FoSTeS) mechanism, whereas the remaining 11 deletions could be caused either by non-homologous end joining or by the FoSTeS mechanism. Although no recurrence was found, several groupings of deletion breakpoints were identified.
Characterization of rat-liver microsomal glutathione S-transferase activity.

Rat liver microsomes were shown to catalyze the conjugation of 1-chloro-2,4-dinitrobenzene with glutathione and this activity has been characterized. It cannot be removed from the microsomes by washing or other procedures which release loosely bound material from membranes. The microsomal glutathione S-transferase can be activated up to eight fold by treatment with N-ethylmaleimide. This activation also affects the apparent Km of the enzyme(s) for both glutathione and 1-chloro-2,4-dinitrobenzene. Upon subcellular fractionation of the liver the N-ethylmaleimide-activateable glutathione S-transferase distributes in the same manner as a marker for the endoplasmic reticulum and unlike markers for the other organelles and for the cytoplasm. Treatment of microsomes with proteases revealed that the enzyme is at least partially exposed on the cytoplasmic surface of the endoplasmic reticulum. Finally, three inducers of drug-metabolizing systems-i.e. phenobarbital, methylcholanthrene, and trans-stilbene oxide-all increase the activity of the cytoplasmic glutathione S-transferases, but they do not affect the microsomal activity. These and other considerations indicate that the microsomal glutathione S-transferase(s) is distinct from the cytoplasmic enzymes catalyzing similar reactions. The microsomal enzyme is likely to be involved in drug metabolism and the possibility of activating it through attack on a sulfhydryl group may represent an important physiological response to certain xenobiotics.
Body size and breast cancer risk: Findings from the European prospective investigation into cancer and nutrition (EPIC)

The evidence for anthropometric factors influencing breast cancer risk is accumulating, but uncertainties remain concerning the role of fat distribution and potential effect modifiers. We used data from 73,542 premenopausal and 103,344 postmenopausal women from 9 European countries, taking part in the EPIC study. RRs from Cox regression models were calculated, using measured height, weight, BMI and waist and hip circumferences; categorized by cohort‐wide quintiles; and expressed as continuous variables, adjusted for study center, age and other risk factors. During 4.7 years of follow‐up, 1,879 incident invasive breast cancers were identified. In postmenopausal women, current HRT modified the body size–breast cancer association. Among nonusers, weight, BMI and hip circumference were positively associated with breast cancer risk (all ptrend ≤ 0.002); obese women (BMI > 30) had a 31% excess risk compared to women with BMI < 25. Among HRT users, body measures were inversely but nonsignificantly associated with breast cancer. Excess breast cancer risk with HRT was particularly evident among lean women. Pooled RRs per height increment of 5 cm were 1.05 (95% CI 1.00–1.16) in premenopausal and 1.10 (95% CI 1.05–1.16) in postmenopausal women. Among premenopausal women, hip circumference was the only other measure significantly related to breast cancer (ptrend = 0.03), after accounting for BMI. In postmenopausal women not taking exogenous hormones, general obesity is a significant predictor of breast cancer, while abdominal fat assessed as waist–hip ratio or waist circumference was not related to excess risk when adjusted for BMI. Among premenopausal women, weight and BMI showed nonsignificant inverse associations with breast cancer. © 2004 Wiley‐Liss, Inc.
Transient early post‐inoculation anti‐retroviral treatment facilitates controlled infection with sparing of CD4+ T cells in gut‐associated lymphoid tissues in SIVmac239‐infected rhesus macaques, but not resistance to rechallenge

Abstract: Like human immunodeficiency virus infection of humans, infection of rhesus macaques with pathogenic simian immunodeficiency virus (SIV) strains typically results in persistent progressive infection, leading to clinically significant immunosuppression. In previous studies, we administered short term anti‐retroviral treatment, shortly after intravenous inoculation with SIVsmE660, in an effort to allow immunologic sensitization under conditions not characterized by overwhelming cytopathic infection compromising the developing immune response. We showed that such treatment allowed control of off treatment viremia and was associated with resistance to rechallenge. Control of off treatment viremia was associated, at least in part, with CD8+ lymphocytes, based on in vivo CD8 depletion studies. In the present study, six rhesus macaques were infected intravenously with 100 MID(50) of SIVmac239; four then received 30 days of treatment with tenofovir 9‐[2‐(R)‐(phosphonomethoxy)propyl]adenine (PMPA); 20–30 mg/kg, subcutaneously) starting 24 hours post‐inoculation. Tenofovir‐treated animals showed low (<500 copy Eq/ml) or undetectable (<100 copy Eq/ml) plasma SIV RNA levels during treatment, with undetectable plasma viremia following discontinuation of treatment. Plasma SIV RNA remained <100 copy Eq/ml, even after depletion of CD8+ lymphocytes, 6 weeks after discontinuation of tenofovir treatment. In contrast to untreated infected control animals that showed substantial depletion of CD4+ T cells from gut‐associated lymphoid tissues (GALT), tenofovir‐treated animals showed sparing of GALT CD4+ T cells both during the treatment period and in the off treatment follow‐up period. However, in contrast to earlier results with animals infected with SIVsmE660, in the present study, the animals did not develop readily measurable cellular anti‐SIV immune responses, and did not resist homologous rechallenge with SIVmac239, administered 44 weeks after the initial infection. Differences in the animals and virus strains employed may in part account for the differences in results observed. Comparative analysis of virologic and immunologic parameters in this model system may provide important insights for understanding the basis of effective immunologic control of SIV infection.
Does pay raise decrease temporary agency workers’ voluntary turnover over time in China? Understanding the moderating role of demographics

Abstract China’s continued economic development relies heavily on its vibrant human resources, a large portion of which is accounted for by temporary agency workers (TAWs). However, researchers have yet to investigate the factors that are related to TAWs’ retention in China. To address this research void, we take a contingency perspective on the relationship between TAW pay raise and voluntary turnover by examining the moderation effects of demographics on the relationship. Drawing on economic exchange theory and human capital theory, we reason that six identity-related demographic factors (namely hukou status, gender, age, education, tenure and occupation type) may alter the negative relationship between pay raise and voluntary turnover (hereafter referred to as turnover). Probit regression analyses of unbalanced panel data from 1184 TAWs over four years support the moderating effects of five of the six demographics (hukou, gender, age, education and tenure) on the negative pay raise − turnover link. The findings of this study provide important theoretical and practical insights for understanding TAWs’ retention in China.
Estimating Burned Area in Mato Grosso, Brazil, Using an Object-Based Classification Method on a Systematic Sample of Medium Resolution Satellite Images

This paper presents a new approach for estimating burned areas at a regional scale, using a systematic sample of medium spatial resolution satellite images. This approach is based on a pan-tropical deforestation survey developed by the Joint Research Centre. We developed and tested our approach over Mato Grosso State, located in the Brazilian Legal Amazon region, with a total area of 903 366 km2. We analyze Landsat-5 TM imagery over 77 sample sites (20 km × 20 km in size) located at each full degree confluence of latitude and longitude. Our new approach leads to an estimate of burned area for year 2010 at 66 368 km2, representing approximately 7.3% of the Mato Grosso area. This estimate is compared to estimates from two different approaches: 1) from a method developed by the Brazilian Institute for Space Research, applied to a wall-to-wall coverage of Landsat-5 TM imagery and 2) from a method using MODIS MCD64A1 products of the University of Maryland, resulting in 70 232 and 55 157 km2 of burned area, respectively (representing 7.8% or 6.1% of Mato Grosso area). Our method produces statistically valid estimates of burned areas for the Brazilian State of Mato Grosso in a more efficient manner than previous methods and enables the inclusion of small burn scars typically missed by coarse resolution satellites. This approach can be applied for regional and global assessments as well as for refining and evaluating burned area products based on coarse spatial resolution imagery like MODIS or SPOT-VEGETATION.
Saturation anisotropy in V:YAG passive Q-switch at 1338 nm

Yttrium aluminum garnet YAG doped by Vanadium ions V3+ is a saturable absorber useful for passive Q-switching of lasers operating at wavelengths around 1.3 µm [1]. The topic of our present work was investigation of nonlinear transmission polarization anisotropy. The goal was to estimate V:YAG saturable absorber orientation in respect to cavity mode polarization to improve Q-switched laser output. The saturable absorber transmission in dependence on incident energy/power density was measured using the z-scan method. A diode pumped Nd:YAG/V:YAG microchip laser [2], operating at wavelength 1338 nm, was used as a polarized radiation source (pulse length 6.2 ns, energy 0.08 mJ). Measured data were fitted using a numerical model of a “thick“ saturable absorber transmission for Q-switched Gaussian laser beam [3]. Following parameters were estimated: saturable absorber initial transmission T0, saturation energy density ws, ground-state absorption cross-section σGSA, saturated absorber transmission Ts, excited-state absorption cross-section σESA, ratio γ = σGSA/σESA, and absorbing ions density. The saturable absorber nonlinear transmission curve was measured repetitively for absorber turning around longitudinal crystal axis. For each angle, measured data were processed and absorber parameters were obtained. This measurement was done for two various cuts of V:YAG crystal - [111] and [100].
Weighing asset pricing factors: a least squares model averaging approach

Empirical evidence has demonstrated that certain factors in asset pricing models are more important than others for explaining specific portfolio returns. We propose a technique that evaluates the factors included in popular linear asset pricing models. Our method has the advantage of simultaneously ranking the relative importance of those pricing factors through comparing their model weights. As an empirical verification, we apply our method to portfolios formed following Fama and French [A five-factor asset pricing model. J. Financ. Econ., 2015, 116, 1–22] and demonstrate that models accommodated to our factor rankings do improve their explanatory power in both in-sample and out-of-sample analyses.
Affinity of TatCd for TatAd Elucidates Its Receptor Function in the Bacillus subtilis Twin Arginine Translocation (Tat) Translocase System*

Twin arginine translocation (Tat) systems catalyze the transport of folded proteins across the bacterial cytosolic membrane or the chloroplast thylakoid membrane. In the Tat systems of Escherichia coli and many other species TatA-, TatB-, and TatC-like proteins have been identified as essential translocase components. In contrast, the Bacillus subtilis phosphodiesterase PhoD-specific system consists only of a pair of TatAd/TatCd proteins and involves a TatAd protein engaged in a cytosolic and a membrane-embedded localization. Because soluble TatAd was able to bind the twin arginine signal peptide of prePhoD prior to membrane integration it could serve to recruit its substrate to the membrane via the interaction with TatCd. By analyzing the distribution of TatAd and studying the mutual affinity with TatCd we have shown here that TatCd assists the membrane localization of TatAd. Besides detergent-solubilized TatCd, membrane-integrated TatCd showed affinity for soluble TatAd. By using a peptide library-specific binding of TatAd to cytosolic loops of membrane protein TatCd was demonstrated. Depletion of TatCd in B. subtilis resulted in a drastic reduction of TatAd, indicating a stabilizing effect of TatCd for TatAd. In addition, the presence of the substrate prePhoD was the prerequisite for appropriate localization in the cytosolic membrane of B. subtilis as demonstrated by freeze-fracture experiments.
Haplotypes of surfactant protein C are associated with common paediatric lung diseases

Surfactant protein C is part of the surfactant complex lining up the alveoles and thereby inhibiting collapse of the airways. In addition it is involved in innate immune responses. Rare polymorphisms within surfactant protein C have been linked to sporadic paediatric lung diseases, like proteinosis or interstitial lung diseases. One study in the Finnish population described association of common polymorphisms with neonatal respiratory syndrome. Other common lung diseases have not yet been investigated for association with this gene. The aim of this study was to test surfactant protein C for association with bronchial asthma and with severe respiratory syncytial virus associated diseases in infancy. The two common amino acid variants Asn138Thr and Asn186Ser were genotyped on 322 children with asthma, 131 children with severe respiratory syncytial virus associated diseases and 270 controls. Statistical analyses of single polymorphisms made use of the Armitage's trend test; haplotypes were calculated with FAMHAP and FASTEHPLUS. Polymorphisms were in Hardy–Weinberg equilibrium and in tight linkage equilibrium in all populations. Single polymorphisms showed no association with the diseases, however, surfactant protein C haplotypes were associated with severe respiratory syncytial virus associated diseases (p = 0.013). Furthermore, an inverse haplotype distribution was found between children with asthma and respiratory syncytial virus infection (p = 0.00025). The results of our study might suggest opposing roles of surfactant Protein C in the genetic predisposition for respiratory syncytial virus associated diseases vs. asthma. The causal mechanism for this observation has still to be shown.
The Effects of IMF Loan Condition Compliance on GDP Growth

Since beginning operations in 1947, the International Monetary Fund (IMF) has evolved from its original purpose of overseeing the world’s monetary system to becoming a loan administrator for member nations facing extreme economic crises. Today, the IMF provides conditional lending programs to catalyze economic recovery and growth in recipient countries. Critics of these programs cite various reasons for conditional loan program failures, naming the borrowing countries, creditor countries, and/or the IMF itself as responsible. Using data from 8,377 loan conditions associated with 93 countries’ IMF loan arrangements from 2000 to 2014, this article studies the effects of complying with individual conditions on the borrowing countries’ real gross domestic product (GDP) growth rate. Our results suggest that real GDP growth rates are directly affected by meeting the compliance standards of select loan conditions. JEL Classifications : 019, F35