Miracle-dz/UniFAR-FTUs huggingface dataset:
Adaptive value of novel MHC immune gene variants

The major histocompatibility complex (MHC) is a core component of the vertebrate immune system and has puzzled immunologists, geneticists, and evolutionary biologists for more than half a century. The so-called classical MHC genes (in humans also called HLA) code for cell surface molecules that present antigens to immune effector cells and thus play a critical role in triggering a specific immune response. Their exceptional polymorphism had been discovered early on (1), but the exact mechanisms that maintain this polymorphism remain enigmatic up until today. Indeed, one of the first and maybe most intuitive mechanisms, proposed as early as 1972 by Walter Bodmer (2), has remained the hardest to prove: the idea that the fitness advantage associated with an MHC allele is negatively proportional to its frequency in the population, because parasites tend to adapt to the more common alleles in a given host population. This mechanism, called “negative frequency-dependent selection” (NFDS), has become part of the core terminology of any essay addressing the polymorphism in the MHC, despite the continuous lack of robust empirical evidence for this process in nature. Now, in PNAS, Phillips et al. (3) describe an elegant experiment that uses natural populations of freshwater fish (guppies) and one of their native parasites in controlled infections to test one of the core predictions of NFDS. They show that MHC alleles can confer increased parasite resistance when they are introduced into a host population where they were previously not present, supporting the idea that novel MHC alleles can be advantageous and thus confirming one of the pillars of NFDS. Sixty-five years ago, the brilliant immunologist Peter Medawar noted the following:Although there are no factual grounds for supposing that antigenic diversity is anything but an unfortunate consequence of constitutional differences between individuals of a species, yet one is under … [↵][1]1Email: lenz{at}post.harvard. edu. [1]: #xref-corresp-1-1
Microstructural and mechanical properties of injection moulded gas and water atomised 17-4 PH stainless steel powder

This paper describes the microstructural and mechanical properties of injection moulded 17-4 PH stainless steel gas and water atomised powder. Gas and water atomised stainless steel powders were injection moulded with wax based binder. The critical powder loading for injection moulding were 62·5 and 55 vol.-% for gas and water atomised powders respectively. Binder debinding was performed using solvent and thermal method. After dedinding the samples were sintered at different temperatures for 1 h in pure H2. Metallographic studies were conducted to determine to extend densification and the corresponding microstructural changes. The results show that gas atomised powder could be sintered to a maximum (98·7%) of theoretical density, and water atomised powder could be sintered to a maximum (97·08%) of theoretical density. Maximum tensile strength was obtained for gas atomised powder sintered at 1350°C. The tensile strength of the water atomised powder sintered at the same temperature was lower owing to higher porosity. Finally, mechanical tests show that the water atomised powder has lower mechanical properties than gas atomised powder.
How feedback, motor imagery, and reward influence brain self‐regulation using real‐time fMRI

The learning process involved in achieving brain self‐regulation is presumed to be related to several factors, such as type of feedback, reward, mental imagery, duration of training, among others. Explicitly instructing participants to use mental imagery and monetary reward are common practices in real‐time fMRI (rtfMRI) neurofeedback (NF), under the assumption that they will enhance and accelerate the learning process. However, it is still not clear what the optimal strategy is for improving volitional control. We investigated the differential effect of feedback, explicit instructions and monetary reward while training healthy individuals to up‐regulate the blood‐oxygen‐level dependent (BOLD) signal in the supplementary motor area (SMA). Four groups were trained in a two‐day rtfMRI‐NF protocol: GF with NF only, GF,I with NF + explicit instructions (motor imagery), GF,R with NF + monetary reward, and GF,I,R with NF + explicit instructions (motor imagery) + monetary reward. Our results showed that GF increased significantly their BOLD self‐regulation from day‐1 to day‐2 and GF,R showed the highest BOLD signal amplitude in SMA during the training. The two groups who were instructed to use motor imagery did not show a significant learning effect over the 2 days. The additional factors, namely motor imagery and reward, tended to increase the intersubject variability in the SMA during the course of training. Whole brain univariate and functional connectivity analyses showed common as well as distinct patterns in the four groups, representing the varied influences of feedback, reward, and instructions on the brain. Hum Brain Mapp 37:3153–3171, 2016. © 2016 Wiley Periodicals, Inc.
Ionic conductivity and dielectric studies of LiClO4 doped poly(vinylalcohol)(PVA)/chitosan(CS) composites

This paper focuses on the dielectric constant (e′), dielectric loss factor (e″) and frequency dependent conductivity (σac) properties of newly prepared poly(vinylalcohol) (PVA) chitosan (CS) composite films incorporated with different concentrations of LiClO4. The composite films were prepared using solution casting technique. The complexation between salt and polymer host is confirmed by FT Raman and UV-Vis studies. The sample containing 20 wt. % LiClO4 exhibits a highest ionic conductivity of 3 × 10-6 S/cm at room temperature. The dielectric properties of the composites follow non-Debye behavior.
Subunit rotation in single FRET-labeled F1-ATPase hold in solution by an anti-Brownian electrokinetic trap

FoF1-ATP synthase catalyzes the synthesis of adenosine triphosphate (ATP). The F1 portion can be stripped from the membrane-embedded Fo portion of the enzyme. F1 acts as an ATP hydrolyzing enzyme, and ATP hydrolysis is associated with stepwise rotation of the γ and ε subunits of F1. This rotary motion was studied in great detail for the last 15 years using single F1 parts attached to surfaces. Subunit rotation of γ was monitored by videomicroscopy of bound fluorescent actin filaments, nanobeads or nanorods, or single fluorophores. Alternatively, we applied single-molecule Förster resonance energy transfer (FRET) to monitor subunit rotation in the holoenzyme FoF1-ATP synthase which was reconstituted in liposomes. Now we aim to extend the observation times of single FRET-labeled F1 in solution using a modified version of the anti-Brownian electrokinetic trap (ABELtrap) invented by A. E. Cohen and W. E. Moerner. We used Monte Carlo simulations to reveal that stepwise FRET efficiency changes can be analyzed by Hidden Markov Models even at the limit of a low signal-to-background ratio that was expected due to high background count rates caused by the microfluidics of the ABELtrap.
Local Feature-Based Attribute Profiles for Optical Remote Sensing Image Classification

This paper introduces an extension of morphological attribute profiles (APs) by extracting their local features. The so-called local feature-based APs (LFAPs) are expected to provide a better characterization of each APs’ filtered pixel (i.e., APs’ sample) within its neighborhood, and hence better deal with local texture information from the image content. In this paper, LFAPs are constructed by extracting some simple first-order statistical features of the local patch around each APs’ sample such as mean, standard deviation, and range. Then, the final feature vector characterizing each image pixel is formed by combining all local features extracted from APs of that pixel. In addition, since the self-dual APs (SDAPs) have been proved to outperform the APs in recent years, a similar process will be applied to form the local feature-based SDAPs (LFSDAPs). In order to evaluate the effectiveness of LFAPs and LFSDAPs, supervised classification using both the random forest and the support vector machine classifiers is performed on the very high resolution Reykjavik image as well as the hyperspectral Pavia University data. Experimental results show that LFAPs (respectively, LFSDAPs) can considerably improve the classification accuracy of the standard APs (respectively, SDAPs) and the recently proposed histogram-based APs.
Closing the Loop: User-Centered Design and Evaluation of a Human-in-the-Loop Topic Modeling System

Human-in-the-loop topic modeling allows users to guide the creation of topic models and to improve model quality without having to be experts in topic modeling algorithms. Prior work in this area has focused either on algorithmic implementation without understanding how users actually wish to improve the model or on user needs but without the context of a fully interactive system. To address this disconnect, we implemented a set of model refinements requested by users in prior work and conducted a study with twelve non-expert participants to examine how end users are affected by issues that arise with a fully interactive, user-centered system. As these issues mirror those identified in interactive machine learning more broadly, such as unpredictability, latency, and trust, we also examined interactive machine learning challenges with non-expert end users through the lens of human-in-the-loop topic modeling. We found that although users experience unpredictability, their reactions vary from positive to negative, and, surprisingly, we did not find any cases of distrust, but instead noted instances where users perhaps trusted the system too much or had too little confidence in themselves.
LMWH in the prevention of preeclampsia and fetal growth restriction in women without thrombophilia

Summary Placental mediated pregnancy complications such as preeclampsia and fetal growth restriction (FGR) are common, serious, and associated with increased morbidity and mortality. We conducted a systematic review and meta-analysis to determine the effect of treatment with low-molecular-weight heparins (LMWHs) for secondary prevention of these complications in non thrombophilic women. We searched the electronic databases PubMed, Scopus, and Cochrane Library for randomised controlled trials addressing this question. Five studies including 403 patients met the inclusion criteria, 68 developed preeclampsia and 118 FGR. The studies were very heterogeneous in terms of inclusion criteria, LMWH preparation, and dosage. Meta-analyses were performed using random-effect models. The overall use of LMWHs was associated with a risk reduction for preeclampsia (Relative risk (RR) 0.366; 95 % confidence interval (CI), 0.219–0.614) and FGR (RR 0.409; 95 % CI, 0.195–0.932) vs. no treatment. From the data available for analysis it appears that the use of Dalteparin is associated with a risk reduction for preeclampsia (p=0.002) and FGR (p<0.001); while Enoxaparin is associated with risk reduction for preeclampsia (p=0.013) but not for FGR (p=0.3). In spite of the small number of studies addressing the research question, and the high variability among them, our meta-analysis found a modest beneficial effect of LMWH for secondary prevention of preeclampsia and FGR. Further studies are needed to address these questions before a definite conclusion can be reached. Supplementary Material to this article is available online at www.thrombosis-online.com.
Effect of Dietary Chlorella on the Growth Performance and Physiological Parameters of Gibel carp, Carassius auratus gibelio

In the present study, a chlorella-free control diet (C) and five experimental diets supplemented with 0.4~2.0% Chlorella were formulated. The gibel carp (Carassius auratus gibelio), one of the commercial fish in China, were fed with the designed diets for 60 days. At the end of trials, parameters of growth performance, blood and the digestive enzyme were analyzed. The results showed that the optimal dietary level of Chlorella as an additive in gibel carp diet was 0.8~1.2%. The growth performance including RGR, SGR, PER and PDR in 0.8 and 1.2% chlorella-adding group were significantly higher than that of control group (P<0.05). Meanwhile, some blood parameters including total protein, lysozyme in these two groups were also higher than in the control group. Furthermore, the chlorella could increase the digestive enzyme, e.g. amylase, lipase and protease in hepatopancreas and intestine. Our study confirmed that the Chlorella could be used as additive in gibel carp farming and the optimal adding level of Chlorella was 0.8%-1.2%, which could promote the growth performance, immune response and the activity of digestive enzyme.
The functional effects of physical interactions involving cytochromes P450: putative mechanisms of action and the extent of these effects in biological membranes

Abstract Cytochromes P450 represent a family of enzymes, which are responsible for the oxidative metabolism of a wide variety of xenobiotics. Although the mammalian P450s require interactions with their redox partners in order to function, more recently, P450 system proteins have been shown to exist as multi-protein complexes that include the formation of P450•P450 complexes. Evidence has shown that the metabolism of some substrates by a given P450 can be influenced by the specific interaction of the enzyme with other forms of P450. Detailed kinetic analysis of these reactions in vitro has shown that the P450–P450 interactions can alter metabolism by changing the ability of a P450 to bind to its cognate redox partner, NADPH-cytochrome P450 reductase; by altering substrate binding to the affected P450; and/or by changing the rate of a catalytic step of the reaction cycle. This review summarizes the known examples of P450–P450 interactions that have been shown in vitro to influence metabolism and categorizes them according to the mechanism(s) causing the effects. P450–P450 interactions have the potential to cause major changes in the metabolism and elimination of drugs in vivo. This review summarizes the evidence that the P450–P450 interactions influence metabolism in biological membranes and discusses the studies, which will provide further insight into the extent of these effects in the future.
New oral anticoagulants and prevention of thromboembolic events in patients with hypertension and atrial fibrillation: an appraisal

Arterial hypertension (HTN) and atrial fibrillation often coexist and the combination of these two conditions carries an increased risk of stroke. HTN is one of the most important risk factors included in the scores for stoke prediction in atrial fibrillation used to assess the need of anticoagulation, and HTN has also been strictly related to bleeding complications of antithrombotic therapy. Antithrombotic drugs options include vitamin K antagonists, or new oral anticoagulants, recently approved for stroke prevention in nonvalvular atrial fibrillation. More favorable new oral anticoagulant efficacy and safety, compared with warfarin, have been reported in hypertensive patients, making these drugs a first-line choice in this population to prevent cerebrovascular events and reduce the risk of major bleedings. The aim of this review is to explore the relationship among HTN, atrial fibrillation and the risk of stroke and to summarize the evidence on the impact of HTN on the choice of the most appropriate anticoagulation treatment.
Characteristics of complete mitogenome of the lesser short-nosed fruit bat Cynopterus brachyotis (Chiroptera: Pteropodidae) in Malaysia

Abstract We describe the characteristics of complete mitogenome of C. brachyotis in this article. The complete mitogenome of C. brachyotis is 16,701 bp long with a total base composition of 32.4% A, 25.7% T, 27.7% C and 14.2% G. The mitogenome consists of 13 protein-coding genes (11,408 bp), (KM659865) two rRNA (12S rRNA and 16S rRNA) genes (2,539 bp), 22 tRNA genes (1518 bp) and one control region (1239 bp).
Increased Cadmium Accumulation in the Ipsilateral Testis of Rats with Experimental Left Varicocele

OBJECTIVES: In 2004, Benoff et al. reported the increased accumulation of cadmium (Cd) in testes of infertile men with left varicocele. We used an animal model to determine whether the cadmium concentration changed in the ipsilateral testis of rats with an experimentally induced left varicocele. MATERIALS AND METHODS: An experimental left varicocele (ELV) was created by partial ligation of the left renal vein in 24 adult male Sprague-Dawley rats as the study group. An additional 16 rats that underwent a laparotomy and left renal vein handling without ligation served as the sham control group. Six rats of the study group (n=6) and 4 rats of control group (n=4) were sacrificed at 2, 4, 8, and 12 weeks following varicocele creation. The left testicular tissue of both groups was sampled. We used atomic absorption spectrophotometry with a graphite furnace for the Cd analysis. RESULTS: The numbers of rats in the varicocele group were 4, 5, 6, and 5 at 2, 4, 8, and 12 weeks, respectively, after varicocele creation. The Cd concentration in the left testis was lower than the detectable level to 2.4±0.9ng/g dry weight in the control group, but in the varicocele group, it was significantly higher than in the control group. However, there were no significant differences among the various treatment times. CONCLUSIONS: This is the first report to prove that the Cd concentration in the ipsilateral testis of rats with a left varicocele was higher than that in the control group. Further additional studies are needed to investigate the relationship of Cd and varicocele-induced male infertility.
Dimensional, Pilling, and Abrasion Properties of Weft Knits Made from Open-End and Ring Spun Yarns

This paper focuses on the dimensional, pilling, and abrasion properties of a series of plain jersey, lacoste, and two-thread fleece fabrics made from cotton ring and open-end spun yams as well as from blend yams (50/50 cotton/polyester, dyed). The results show that both structural differences and fiber type play a large part in determining the dimensions of these fabrics. It is apparent that the knits from blend yams have a lower dimensional stability when compared to fabrics from 100% cotton ring and open-end spun yams. Findings for the two-thread fleece fabrics suggest that the inlay yam mainly governs their dimensional behavior in the widthwise direction. The pilling tendency of the test samples and their resistance to abrasion are evaluated with the ICI pilling box (at three different test revolutions) and the Martindale abrasion tester, respectively. In addition, an extensive SEM examination is used to study the effect of fiber type and repeated launder ings on both pilling development and the degree of fiber damage within fuzz assemblies. The results show that unlike plain jersey fabrics, lacoste fabrics perform very well, and that in general fabrics knitted from open-end spun yams have a lower propensity to pilling. In the case of the two-thread fleece structure, the samples from 100% cotton (i.e., both face and fleece yam) open-end yams have higher pilling rates compared to FBOE (face yam is cotton, fleece yam is 50/50 PET/cotton) and FBB (both face and fleece yam are 50/50 PET/cotton) fabrics. The SEM study reveals that for the same number of test revolutions, the degree of damage to fibers within the fuzz entanglements tends to increase with an increased number of launderings, and that the kind of damage varies from small cracks and fractures to slight flaking, depending on the fabric and yam type. Note, however, that any damage occurring as a result of repeated launderings and pilling tests is not as severe as that reported in the literature. The lacoste fabrics have the least resistance to abrasion.
Hybrid Algorithm of Particle Swarm Optimization and Grey Wolf Optimizer for Improving Convergence Performance

A newly hybrid nature inspired algorithm called HPSOGWO is presented with the combination of Particle Swarm Optimization (PSO) and Grey Wolf Optimizer (GWO). The main idea is to improve the ability of exploitation in Particle Swarm Optimization with the ability of exploration in Grey Wolf Optimizer to produce both variants’ strength. Some unimodal, multimodal, and fixed-dimension multimodal test functions are used to check the solution quality and performance of HPSOGWO variant. The numerical and statistical solutions show that the hybrid variant outperforms significantly the PSO and GWO variants in terms of solution quality, solution stability, convergence speed, and ability to find the global optimum.
DynOmics: dynamics of structural proteome and beyond

Abstract DynOmics (dynomics.pitt.edu) is a portal developed to leverage rapidly growing structural proteomics data by efficiently and accurately evaluating the dynamics of structurally resolved systems, from individual molecules to large complexes and assemblies, in the context of their physiological environment. At the core of the portal is a newly developed server, ENM 1.0, which permits users to efficiently generate information on the collective dynamics of any structure in PDB format, user-uploaded or database-retrieved. ENM 1.0 integrates two widely used elastic network models (ENMs)—the Gaussian Network Model (GNM) and the Anisotropic Network Model (ANM), extended to take account of molecular environment. It enables users to assess potentially functional sites, signal transduction or allosteric communication mechanisms, and protein–protein and protein–DNA interaction poses, in addition to delivering ensembles of accessible conformers reconstructed at atomic details based on the global modes of motions predicted by the ANM. The ‘environment’ is defined in a flexible manner, from lipid bilayer and crystal contacts, to substrate or ligands bound to a protein, or surrounding subunits in a multimeric structure or assembly. User-friendly interactive features permit users to easily visualize how the environment alter the intrinsic dynamics of the query systems. ENM 1.0 can be accessed at http://enm.pitt. edu/ or http://dyn.life. nthu.edu. tw/oENM/.
A Viscoelastic Model for the Long‐Term Deflection of Segmental Prestressed Box Girders

Most of segmental prestressed concrete box girders exhibit excessive multidecade deflections unforeseeable by past and current design codes. To investigate such a behavior, mainly caused by creep and shrinkage phenomena, an effective finite element (FE) formulation is presented in this article. This formulation is developed by invoking the stationarity of an energetic principle for linear viscoelastic problems and relies on the Bazant creep constitutive law. A case study representative of segmental prestressed concrete box girders susceptible to creep is also analyzed in the article, that is, the Colle Isarco viaduct. Its FE model, based on the aforementioned energetic formulation, was successfully validated through the comparison with monitoring field data. As a result, the proposed 1D FE model can effectively reproduce the past behavior of the viaduct and predict its future behavior with a reasonable run time, which represents a decisive factor for the model implementation in a decision support system.