Miracle-dz/UniFAR-FTUs huggingface dataset:
Soluble N-Ethylmaleimide-Sensitive Factor Attachment Protein Receptor-Derived Peptides for Regulation of Mast Cell Degranulation

Vesicle-associated V-soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins and target membrane-associated T-SNAREs (syntaxin 4 and SNAP-23) assemble into a core trans-SNARE complex that mediates membrane fusion during mast cell degranulation. This complex plays pivotal roles at various stages of exocytosis from the initial priming step to fusion pore opening and expansion, finally resulting in the release of the vesicle contents. In this study, peptides with the sequences of various SNARE motifs were investigated for their potential inhibitory effects against SNARE complex formation and mast cell degranulation. The peptides with the sequences of the N-terminal regions of vesicle-associated membrane protein 2 (VAMP2) and VAMP8 were found to reduce mast cell degranulation by inhibiting SNARE complex formation. The fusion of protein transduction domains to the N-terminal of each peptide enabled the internalization of the fusion peptides into the cells equally as efficiently as cell permeabilization by streptolysin-O without any loss of their inhibitory activities. Distinct subsets of mast cell granules could be selectively regulated by the N-terminal-mimicking peptides derived from VAMP2 and VAMP8, and they effectively decreased the symptoms of atopic dermatitis in mouse models. These results suggest that the cell membrane fusion machinery may represent a therapeutic target for atopic dermatitis.
Reclaiming Saline-Sodic Soils Using Electrochemical Processes: A Case Study From Sahl El-Tina Plain, Egypt

Abstract A leaching experiment was conducted using column techniques assessing efficiency of electrochemical process to reclaim saline-sodic soils. Soil material was collected from Sahl El-Tina plain, which located in North West coast of Sinai, Egypt. The experiment was designed as factorial randomized complete block and all treatments were replicated three times. Two 2.5 cm diameterx30 cm height mild stainless steel tubes were inserted into the soil matrix to serve as electrodes (i.e. cathode and anode). Distance between cathode and anode was 10 cm. Electrodes were supplied by a direct current (DC) power supply; Volt ages of 0.3 or 9 Volt. Leaching was done using the intermittent method so as to add portions to the already saturated soil columns, and obtain leachates equal to the added portions. Pore volume 0.1 PV was used in the leaching processes which are equal 498.4 cm3, i.e. PV being volume of pores per column, thus 1 PV equals volume of pores (cm3) expressed as water quantity. Electric remediation increased ionic mobility and separated salts from soil. All treatments decreased soil EC and soil sodicity expressed as SAR and ESP. Results showed that 9 Volt treatment was more effective in decreasing the soil EC and soil sodicity than the other treatments. Efficiency of treatments were 9-Volt > 3-Volt > leaching alone (non-DC treatment). This study suggests that leaching using direct current (DC) led to improvement of the chemical properties of saline sodic soils and required a short time to reclaim saline-sodic soils compared with leaching alone.
A novel single nucleotide polymorphism in exon 3 of MYOC enhances the risk of glaucoma

Genetic polymorphismsof MYOCalter the myocilin protein,which leads to disruption of thenormal regulation of intraocular pressure (IOP) that ultimately causes glaucoma.Theaim of the present study was to identify the polymorphism in exon 3 of the MYOC gene of theglaucoma patients in Lahore, Pakistan. We conducted a case-control study with 100 patients and 100 controls subjects. We extracted DNA from blood samples,amplified the target DNA fragmentby PCR, and identifiedpolymorphisms through sequencing. We observed that the allelic and genotypic frequencies of rs74315341 and rs879255525 were associated with glaucoma in our patient population. The polymorphism atrs74315341 led to the substitutionof serine for arginine,whereas the polymorphism at rs879255525 led to the substitution ofasparagine for lysine. The haplotype TGAAGCCATTTC was associated with disease onset, whereas the haplotype GGAAGCCATTTC was protective against disease development. In conclusion, weidentified MYOC gene polymorphisms in susceptible regions that were associated withglaucoma onset among the Lahore patient population.This is the first report to identify a novel mutation in rs879255525 in exon 3 of the MYOC genethat is associated withglaucoma.
12 Weeks of a Ribavirin‐Free Sofosbuvir and Nonstructural Protein 5A Inhibitor Regimen Is Enough to Treat Recurrence of Hepatitis C After Liver Transplantation

Sofosbuvir (SOF) combined with nonstructural protein 5A (NS5A) inhibitors has demonstrated its efficacy in treating a recurrence of hepatitis C virus (HCV) after liver transplantation (LT). However, the duration of treatment and need for ribavirin (RBV) remain unclear in this population. Our aim was to determine whether LT recipients could be treated with an SOF + NS5A inhibitor‐based regimen without RBV for 12 weeks post‐LT. Between October 2013 and December 2015, 699 LT recipients experiencing an HCV recurrence were enrolled in the multicenter ANRS CO23 CUPILT cohort. We selected patients receiving SOF and NS5A inhibitor ± RBV and followed for at least 12 weeks after treatment discontinuation. The primary efficacy endpoint was a sustained virological response 12 weeks after the end of treatment (SVR12). Among these 699 patients, 512 fulfilled the inclusion criteria. Their main characteristics were: 70.1% genotype 1, 18.2% genotype 3, 21.1% cirrhosis, and 34.4% previously treated patients. We identified four groups of patients according to their treatment and duration: SOF + NS5A without RBV for 12 (156 patients) or 24 (239 patients) weeks; SOF + NS5A + RBV for 12 (47 patients) or 24 (70 patients) weeks. SVR12 values reached 94.9%, 97.9%, 95.7%, and 92.9%, respectively (P = 0.14). Only 20 patients experienced a treatment failure. Under multivariate analysis, factors such as fibrosis stage, previous treatment, HCV genotype, and baseline HCV viral load did not influence SVR12 rates in the four groups (P = 0.21). Hematological adverse events (AEs) were more common in the RBV group: anemia (P < 0.0001) and blood transfusion (P = 0.0001). Conclusion: SOF + NS5A inhibitors without RBV for 12 weeks constituted reliable therapy for recurrent HCV post‐LT with an excellent SVR12 whatever the fibrosis stage, HCV genotype, and previous HCV treatment. (Hepatology 2018; 00:000‐000).
Evidence for mtDNA Admixture between the Finns and the Saami

Objectives: The Finns, and to a more extreme extent the Saami, are genetic outliers in Europe. Despite the close geographical contact between these populations, no major contribution of Saami mtDNA haplotypes to the Finnish population has been detected. Methods: To examine the extent of maternal gene flow from the Saami into Finnish populations, we determined the mtDNA variation in 403 persons living in four provinces in central and northern Finland. For all of these samples, we assessed the frequencies of mtDNA haplogroups and examined sequence variation in the hypervariable segment I (HVS-I). The resulting data were compared with published information for Saami populations. Results: The frequencies of the mtDNA haplogroups differed between the populations of the four provinces, suggesting a distinction between northern and central Finland. Analysis of molecular variance suggested that the Saami deviated less from the population of northern Finland than from that of central Finland. Five HVS-I haplotypes, including that harboring the Saami motif and the Asian-specific haplogroup Z, were shared between the Finns and the Saami and allowed comparisons between the populations. Their frequency was highest in the Saami and decreased towards central Finland. Conclusions: The high frequency of certain mtDNA haplotypes considered to be Saami specific in the Finnish population suggests a genetic admixture, which appears to be more pronounced in northern Finland. Furthermore, the presence of haplogroup Z in the Finns and the Saami indicates that traces of Asian mtDNA genotypes have survived in the contemporary populations.
Materials for future quantum dot-based memories

The present paper investigates the current status of the storage times in self-organized QDs, surveying a variety of heterostructures advantageous for strong electron and/or hole confinement. Experimental data for the electronic properties, such as localization energies and capture cross-sections, are listed. Based on the theory of thermal emission of carriers from QDs, we extrapolate the values for materials that would increase the storage time at room temperature to more than millions of years. For electron storage, GaSb/AlSb, GaN/AlN, and InAs/AlSb are proposed. For hole storage, GaSb/Al0.9Ga0. 1As, GaSb/GaP, and GaSb/AlP are promising candidates.
Four distinct immune microenvironment subtypes in gastric adenocarcinoma with special reference to microsatellite instability

Introduction Programmed death-ligand 1 (PD-L1) can be overexpressed in tumours other than Epstein-Barr virus (EBV)-positive (EBV+) or microsatellite instability-high (MSI-H) gastric cancer (GC) subtypes. We aimed to determine the tumour immune microenvironment (TME) classification of GC to better understand tumour–immune interactions and help patient selection for future immunotherapy with special reference to MSI-H. Methods Immunohistochemistry (IHC) for PD-L1 and CD8+ T cells in three distinct subtypes of GC (43 EBV+, 79 MSI-H and 125 EBV−/MSS) were performed and analysed. In 66 MSI-H GC, mutation counts were compared with PD-L1 expression and survival of the patients. Results GC TME divided by PD-L1 IHC and tumour-infiltrating lymphocytes (TIL) measured by intratumoural CD8 density showed: (1) about 40% of GC are type I (PD-L1+/TIL+) consisting ~70% of MSI-H or EBV+ GC, and ~15% of EBV−/microsatellite stable (MSS) GC patients show the best survival in both disease-free (HR 2.044) and overall survival (HR 1.993); this type would respond to a checkpoint blockade therapy; (2) almost 30% of GC are type II (PD-L1−/TIL−) with the worst survival; (3) approximately 10% of GC are type III (PD-L1+/TIL−); and (4) up to 20% are type IV (PD-L1−/TIL+) and, unexpectedly, ~25% of EBV+ or MSI-H GC are within this subtype. In MSI-H GC, frequent frameshift mutations were observed in ARID1A, RNF43, NF1, MSH6, BRD3, NCOA3, BCORL1, TNKS2 and NPM1 and the numbers of frameshift mutation correlated significantly with PD-L1 expression (P<0.05). Discussion GC can be classified into four TME types based on PD-L1 and TIL, and numbers of frameshift mutation correlate well with PD-L1 expression in MSI-H GC.
Butterflies: a visual approach to characterize packages

Understanding sets of classes, or packages, is an important activity in the development and reengineering of large object-oriented systems. Packages represent the coarse grained structure of an application. They are artefacts to deploy and structure software, and therefore more than a simple generalization of classes. The relationships between packages and their contained classes are key in the decomposition of an application and its (re)-modularisation. However, it is difficult to quickly grasp the structure of a package and to understand how a package interacts with the rest of the system. We tackle this problem using butterfly visualizations, i.e., dedicated radar charts built from simple package metrics based on a language-independent meta-model. We illustrate our approach on two applications and show how we can retrieve the relevant characteristics of packages
Domain specific warnings: Are they any better?

Tools to detect coding standard violations in source code are commonly used to improve code quality. One of their original goals is to prevent bugs, yet, a high number of false positives is generated by the rules of these tools, i.e., most warnings do not indicate real bugs. There are empirical evidences supporting the intuition that the rules enforced by such tools do not prevent the introduction of bugs in software. This may occur because the rules are too generic and do not focus on domain specific problems of the software under analysis. We underwent an investigation of rules created for a specific domain based on expert opinion to understand if such rules are worthwhile enforcing in the context of defect prevention. In this paper, we performed a systematic study to investigate the relation between generic and domain specific warnings and observed defects. From our experiment on a real case, long term evolution, software, we have found that domain specific rules provide better defect prevention than generic ones.
Mitochondrial DNA and TLR9 drive muscle inflammation upon Opa1 deficiency

Opa1 participates in inner mitochondrial membrane fusion and cristae morphogenesis. Here, we show that muscle‐specific Opa1 ablation causes reduced muscle fiber size, dysfunctional mitochondria, enhanced Fgf21, and muscle inflammation characterized by NF‐κB activation, and enhanced expression of pro‐inflammatory genes. Chronic sodium salicylate treatment ameliorated muscle alterations and reduced the muscle expression of Fgf21. Muscle inflammation was an early event during the progression of the disease and occurred before macrophage infiltration, indicating that it is a primary response to Opa1 deficiency. Moreover, Opa1 repression in muscle cells also resulted in NF‐κB activation and inflammation in the absence of necrosis and/or apoptosis, thereby revealing that the activation is a cell‐autonomous process and independent of cell death. The effects of Opa1 deficiency on the expression NF‐κB target genes and inflammation were absent upon mitochondrial DNA depletion. Under Opa1 deficiency, blockage or repression of TLR9 prevented NF‐κB activation and inflammation. Taken together, our results reveal that Opa1 deficiency in muscle causes initial mitochondrial alterations that lead to TLR9 activation, and inflammation, which contributes to enhanced Fgf21 expression and to growth impairment.
The relationship between spiritual intelligence and aggression in medical science students in the southeast of Iran

Abstract Background Due to their presence in clinical educational settings when dealing with patients, medical science students are more affected by mental disorders than other students. Some experts believe that spiritual intelligence enhances people adaptability and compatibility and creates calm in humans, especially in stressful situations. Objective The objective of this study was to investigate the relationship between spiritual intelligence and aggression among students of medical sciences in the southeast of Iran. Methods This analytical-descriptive study was conducted among bachelor students of Medical Sciences in the Southeast of Iran and examples of the research were selected from the Schools of Nursing and Midwifery, Public Health, Paramedical and Management by a stratified random sampling method. To examine samples questionnaires were used which examined students’ demographic information, and included King’s 24-item Questionnaire of Spiritual Intelligence and the Buss-Perry Aggression Questionnaire (AQ). After completing the questionnaires, data were analyzed using statistical analysis software (SPSS version18) with a significance level (p < 0.05). Results The results showed that there is a significant negative correlation between spiritual intelligence and aggression of students (r = −0/19, p = 0/001). Results also showed that Students of Medical Sciences in the Southeast of Iran with a spiritual intelligence average score of 52.28 have an average spiritual intelligence and those with an aggression average score of 78.57 have higher aggression than average. Conclusion The results showed that with increasing spiritual intelligence, aggression decreases. The results can be used by policymakers and managers to take steps to reduce aggressive behaviors and mental disorders and for the promotion of spiritual intelligence of students of medical sciences.
ParaXpress: an experimental extension of the FICO Xpress-Optimizer to solve hard MIPs on supercomputers

The Ubiquity Generator (UG) is a general framework for the external parallelization of mixed integer programming (MIP) solvers. In this paper, we present ParaXpress, a distributed memory parallelization of the powerful commercial MIP solver FICO Xpress. Besides sheer performance, an important feature of Xpress is that it provides an internal parallelization for shared memory systems. When aiming for a best possible performance of ParaXpress on a supercomputer, the question arises how to balance the internal Xpress parallelization and the external parallelization by UG against each other. We provide computational experiments to address this question and we show computational results for running ParaXpress on a Top500 supercomputer, using up to 43,344 cores in parallel.
Classification of loaded/unloaded micro-drones using multistatic radar

Preliminary results on the use of multistatic radar and micro-Doppler analysis to detect and discriminate between micro-drones hovering carrying different payloads are presented. Two suitable features related to the centroid of the micro-Doppler signature have been identified and used to perform classification, investigating also the added benefit of using information from a multistatic radar as opposed to a conventional monostatic system. Very good performance with accuracy above 90% has been demonstrated for the classification of hovering micro-drones.
Consumption of Sugar-Sweetened Beverages Among US Adults in 6 States: Behavioral Risk Factor Surveillance System, 2011

Introduction Sugar-sweetened beverage (SSB) intake is linked to weight gain. Our objective was to examine state-specific SSB intake and behavioral characteristics associated with SSB intake. Methods We used data from the 2011 Behavioral Risk Factor Surveillance System for 38,978 adults aged 18 years or older from 6 states: Delaware, Hawaii, Iowa, Minnesota, New Jersey, and Wisconsin. Multivariate logistic regression was used to estimate adjusted odds ratios for characteristics associated with SSB intake from regular soda and fruit drinks. Results Overall, 23.9% of adults drank SSBs at least once a day. Odds of drinking SSBs 1 or more times per day were significantly greater among younger adults; males; non-Hispanic blacks; adults with lower education; low-income adults or adults with missing income data; adults living in Delaware, Iowa, and Wisconsin versus those living in Minnesota; adults with fruit intake of less than 1 time a day versus 1 or more times a day; adults who were physically inactive versus highly active adults; and current smokers versus nonsmokers. Odds for drinking SSBs 1 or more times per day were significantly lower among adults with 100% fruit juice intake of less than 1 time per day versus 1 or more times per day and among adults who drank alcohol versus those who did not drink alcohol. Conclusion SSB intake varied by states and certain sociodemographic and behavioral characteristics. States can use findings from this study to tailor efforts to decrease SSB intake and to encourage consumption of more healthful beverages (eg, water) among their high-risk populations.
Exciton Dynamics in White Organic Light-Emitting Diodes comprising Triplet Harvesting

This work comprises different approaches for the efficiency enhancement of white organic light-emitting diodes (OLEDs). In particular, diffusion and transfer processes of excited singlet and triplet states are investigated. Generation of white light is realized by using the so-called triplet harvesting method where the otherwise nonradiatively decaying triplets of a blue fluorescent emitter are transferred to a highly efficient phosphorescent emitter and result in additional emission at lower energies. Triplet harvesting significantly increases the internal quantum efficiency in OLEDs. First, the well-known blue emitter 4P-NPD is investigated as model case. Using time-resolved spectroscopy, triplet harvesting by a yellow and red phosphorescent emitter, respectively is directly proven. However, triplet harvesting by a green emitter is not possible due to the low triplet energy of 4P-NPD. Using quantum chemical calculations, two new emitter molecules, 8M-4P-NPD and 8M-4P-FPD, are synthesized with the aim to rise the triplet energy. Their properties and their ability to facilitate triplet harvesting by a green emitter are studied. For the first time, a white triplet harvesting OLED is demonstrated where triplet harvesting occurs directly from a blue emitter to a green and a red emitter. Furthermore, an additional singlet transfer is observed in the triplet harvesting OLEDs under investigation. Using the phosphorescent emitter as singlet sensor, this effect allows the determination of the singlet diffusion length in 4P-NPD. By varying the distance between singlet generation zone and singlet sensor, a singlet diffusion length of 4.6 nm is found. One further approach to increase the efficiency is the optimization of a tandem OLED which comprises two single OLED units stacked on top of each other. At a luminance of 1,000 cd/m2, the white tandem OLED shows an external quantum efficiency of 25%, a luminous efficacy of 33 lm/W, a color rendering index (CRI) of 62, and Commission Internationale de l’Eclairage (CIE) color coordinates of (0.53/0.43). These efficiencies are comparable to state-of-the-art efficiencies of white OLEDs. Finally, the highly efficient white tandem structure is applied on an alternative electrode consisting of flattened silver nanowires. In comparison to the conventional OLED with indium-tin oxide (ITO) electrode, this OLED shows similarly high efficiencies as well as a superior color stability in terms of viewing angles. The color stability can be assigned to the light scattering properties of the nanowires. The OLED with silver nanowire electrode shows efficiencies of 24% and 30 lm/W at 1,000 cd/m2 with a CRI of 69 and CIE coordinates of (0.49/0.47).
An Empirical Model for Continuous and Weighted Metric Aggregation

It is now understood that software metrics alone are not enough to characterize software quality. To cope with this problem, most of advanced and/or industrially validated quality models aggregate software metrics: for example, cyclomatic complexity is combined with test coverage to stress the fact that it is more important to cover complex methods than accessors. Yet, aggregating and weighting metrics to produce quality indexes is a difficult task. Indeed, certain weighting approaches may lead to abnormal situations where a developer increasing the quality of a software component seeing the overall quality degrade. Finally, mapping combinations of metric values to quality indexes may be a problem when using thresholds. In this paper, we present the problems we faced when designing the Squale quality model, then we present an empirical solution based on weighted aggregations and on continuous functions. The solution has been termed the Squale quality model and validated over 4 years with two large multinational companies: Air France-KLM and PSA Peugeot-Citroen.
A survey of 
χ ‐boundedness

If a graph has bounded clique number and sufficiently large chromatic number, what can we say about its induced subgraphs? András Gyárfás made a number of challenging conjectures about this in the early 1980s, which have remained open until recently; but in the last few years there has been substantial progress. This is a survey of where we are now.