Miracle-dz/UniFAR-FTUs huggingface dataset:
The K1K2 Region of Lys-Gingipain of Porphyromonas gingivalis Blocks Induction of HLA Expression by Gamma Interferon

ABSTRACT In the context of periodontal disease, cysteine proteinases or gingipains from Porphyromonas gingivalis have been implicated in the hydrolysis of cytokines, including gamma interferon (IFN-γ). This cytokine plays a crucial role in host defenses, in part, by regulating expression of major histocompatibility complex molecules. Our recent analysis has identified three structurally defined modules, K1, K2, and K3, of the hemagglutinin region of the lysine gingipain Kgp. These three structurally homologous domains have a common β-sandwich topology that is similar to that found in a superfamily of adhesins and carbohydrate binding domains. The three Kgp hemagglutinin modules are distinguished by variation in some of the loops projecting from the β-sandwich core. Recombinant products corresponding to both single and multidomain regions as well as native Kgp bound IFN-γ with similar affinities. Among the adhesin domain constructs, only the K1K2 polypeptide inhibited the upregulation of HLA-1 expression in a human erythroleukemia (K562) line induced by both recombinant and native IFN-γ. The K1K2 polypeptide also inhibited HLA-DR expression induced by IFN-γ in human umbilical vein endothelial cells. These effects were competitively inhibited by coincubation with sodium or potassium chloride solution. The N-terminal residues of IFN-γ were implicated in mediating the effect of K1K2, while antibody binding to loop 1 of K2 blocked the action of K1K2. The findings indicate the potential significance of structurally defined Kgp adhesin modules in the inactivation of IFN-γ but also the potential of K1K2 in locating the target for the catalytic domain of Kgp.
Language-Independent Clone Detection Applied to Plagiarism Detection

Clone detection is usually applied in the context of detecting small-to medium scale fragments of duplicated code in large software systems. In this paper, we address the problem of clone detection applied to plagiarism detection in the context of source code assignments done by computer science students. Plagiarism detection comes with a distinct set of constraints to usual clone detection approaches, which influenced the design of the approach we present in this paper. For instance, the source code can be heavily changed at a superficial level (in an attempt to look genuine), yet be functionally very similar. Since assignments turned in by computer science students can be in a variety of languages, we work at the syntactic level and do not consider the source-code semantics. Consequently, the approach we propose is endogenous and makes no assumption about the programming language being analysed. It is based on an alignment method using the parallel principle at local resolution (character level) to compute similarities between documents. We tested our framework on hundreds of real source files, involving a wide array of programming languages (Java, C, Python, PHP, Haskell, bash). Our approach allowed us to discover previously undetected frauds, and to empirically evaluate its accuracy and robustness.
Review of energy storage and transportation of energy

Energy storage and transportation are essential keys to make sure the continuity of energy to the customer. Electric power generation is changing dramatically across the world due to the environmental effects of Greenhouse gases (GHG) produced by fossil fuels. The unpredictable daily and seasonal variations in demand for electrical energy can be tackled by introducing the energy storage systems (ESSs) and hence mitigating the extra GHG emission in the atmosphere. Energy storage techniques can be mechanical, electro‐chemical, chemical, or thermal, and so on. The most popular form of energy storage is hydraulic power plants by using pumped storage and in the form of stored fuel for thermal power plants. The classification of ESSs, their current status, flaws and present trends, are presented in this article. The present state of fossil fuel reserves, their production, consumption, and as a consequence of these the CO2 emissions are also discussed. The primary energy carriers coal, oil and gas are not evenly distributed along the globe. Long distances are involved in transporting these energy carriers and transportation and delivery of these key resources to the prime customers is always necessary. The different methods to transport the energy from the source end to demand end is also discussed in this article. The assessment of various energy storage methods on the basis of several factors and present status and development of storage and transportation of energy in Pakistan is discussed.
Nutrients Content in Some Vegetables Grown in South-Central Coastal Regions of Bangladesh

Soil salinity is one of the most important abiotic stresses for crop production. A study was conducted to analyze the relationship between salinity level and nutrient contents in some popular vegetables grown in some selected tidal areas of Barguna and Patuakhali districts of Bangladesh. Samples of six different vegetables such as bottle gourd leaf (Lagenaria siceraria), sweet gourd leaf (Cucurbita maxima), radish leaf (Raphanus sativus), bean (Lablab niger), red amaranth (Amaranthus gangeticus) and spinach (Spinacia oleracea) were collected along with soils from different locations of the study areas and were analyzed for phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg), sulphur (S) contents. Soil pH and electrical conductivity (EC) were determined. In saline areas, comparatively lower amounts of P, K, Ca, Mg and S were detected in most of the collected vegetables than those of non-saline areas. Conversely, bottle gourd leaf, radish leaf and bean accumulated comparatively higher amount of Ca at higher salinity levels. The uptake of P by bottle gourd leaf and radish leaf, Mg by bottle gourd leaf and red amaranth was also higher in the saline soil. The inconsistent uptake of Ca, Mg and P were found in some vegetables due to the differences of fertilizer application and intercultural operation. The vegetables could tolerate moderate soil salinity (soil EC up to7.9 dSm-1) and might be recommended to grow in the tidal saline areas of Barguna and Patuakhali districts of Bangladesh. The Agriculturists 2018; 16(2) 43-57
Age‐related change in the association between a polymorphism in the PER3 gene and preferred timing of sleep and waking activities

The objective of this study was to investigate the effect of age on the association between preferred timing of sleep and waking activities and a coding‐region variable number tandem repeat (VNTR) polymorphism in the clock gene PER3. We have previously reported this polymorphism to associate with diurnal preference and delayed sleep phase syndrome (DSPS). Participants (n = 1590; 707 males and 883 females) completed the Horne–Östberg (HÖ) questionnaire for diurnal preference and provided a DNA sample. Overall HÖ scores were plotted against age. The 5% extremes and intermediates were selected for genotyping. Frequencies of the PER3 4‐ and 5‐repeat alleles were examined in separate age groups (18–29, 30–39, 40–49 and 50+ years of age). The 4‐repeat allele was significantly more frequent in evening types, and the 5‐repeat allele more frequent in morning types (Fisher's exact test, P = 0.016). Analysis in the four age groupings revealed that the strength of this association attenuated with age and was significant only in the youngest group (18–29 years). These results extend our previous finding of an association between the PER3 VNTR and diurnal preference. They also demonstrate that diurnal preference in young people is more closely associated with this polymorphism than it is in other age groups.
Eco-evolutionary buffering: rapid evolution facilitates regional species coexistence despite local priority effects

Inhibitory priority effects, in which early-arriving species exclude competing species from local communities, are thought to enhance regional species diversity via community divergence. Theory suggests, however, that these same priority effects make it difficult for species to coexist in the region unless individuals are continuously supplied from an external species pool, often an unrealistic assumption. Here we develop an eco-evolutionary hypothesis to solve this conundrum. We build a metacommunity model in which local priority effects occur between two species via interspecific interference. Within each species there are two genotypes: one is more resistant to interspecific interference than the other, but pays a fitness cost for its resistance. Because of this trade-off, species evolve to become less resistant as they become regionally more common. Rare species can then invade some local patches and consequently recover in regional frequency. This “eco-evolutionary buffering” enables the regional coexistence of species despite local priority effects, even in the absence of immigration from an external species pool. Our model predicts that eco-evolutionary buffering is particularly effective when local communities are small and connected by infrequent dispersal.
Grid cell hexagonal patterns formed by fast self‐organized learning within entorhinal cortex

Grid cells in the dorsal segment of the medial entorhinal cortex (dMEC) show remarkable hexagonal activity patterns, at multiple spatial scales, during spatial navigation. It has previously been shown how a self‐organizing map can convert firing patterns across entorhinal grid cells into hippocampal place cells that are capable of representing much larger spatial scales. Can grid cell firing fields also arise during navigation through learning within a self‐organizing map? This article describes a simple and general mathematical property of the trigonometry of spatial navigation which favors hexagonal patterns. The article also develops a neural model that can learn to exploit this trigonometric relationship. This GRIDSmap self‐organizing map model converts path integration signals into hexagonal grid cell patterns of multiple scales. GRIDSmap creates only grid cell firing patterns with the observed hexagonal structure, predicts how these hexagonal patterns can be learned from experience, and can process biologically plausible neural input and output signals during navigation. These results support an emerging unified computational framework based on a hierarchy of self‐organizing maps for explaining how entorhinal‐hippocampal interactions support spatial navigation. © 2010 Wiley Periodicals, Inc.
ETORPHINE–KETAMINE–MEDETOMIDINE TOTAL INTRAVENOUS ANESTHESIA IN WILD IMPALA (AEPYCEROS MELAMPUS) OF 120-MINUTE DURATION

Abstract: There is a growing necessity to perform long-term anesthesia in wildlife, especially antelope. The costs and logistics of transporting wildlife to veterinary practices make surgical intervention a high-stakes operation. Thus there is a need for a field-ready total intravenous anesthesia (TIVA) infusion to maintain anesthesia in antelope. This study explored the feasibility of an etorphine–ketamine–medetomidine TIVA for field anesthesia. Ten wild-caught, adult impala (Aepyceros melampus) were enrolled in the study. Impala were immobilized with a standardized combination of etorphine (2 mg) and medetomidine (2.2 mg), which equated to a median (interquartile range [IQR]) etorphine and medetomidine dose of 50.1 (46.2–50.3) and 55.1 (50.8–55.4) μg/kg, respectively. Recumbency was attained in a median (IQR) time of 13.9 (12.0–16.5) min. Respiratory gas tensions, spirometry, and arterial blood gas were analyzed over a 120-min infusion. Once instrumented, the TIVA was infused as follows: etorphine at a variable rate initiated at 40 μg/kg per hour (adjusted according to intermittent deep-pain testing); ketamine and medetomidine at a fixed rate of 1.5 mg/kg per hour and 5 μg/kg per hour, respectively. The etorphine had an erratic titration to clinical effect in four impala. Arterial blood pressure and respiratory and heart rates were all within normal physiological ranges. However, arterial blood gas analysis revealed severe hypoxemia, hypercapnia, and acidosis. Oxygenation and ventilation indices were calculated and highlighted possible co-etiologies to the suspected etorphine-induced respiratory depression as the cause of the blood gas derangements. Impala recovered in the boma post atipamezole (13 mg) and naltrexone (42 mg) antagonism of medetomidine and etorphine, respectively. The etorphine–ketamine–medetomidine TIVA protocol for impala may be sufficient for field procedures of up to 120-min duration. However, hypoxemia and hypercapnia are of paramount concern and thus oxygen supplementation should be considered mandatory. Other TIVA combinations may be superior and warrant further investigation.
Polar codes: Robustness of the successive cancellation decoder with respect to quantization

Polar codes provably achieve the capacity of a wide array of channels under successive decoding. This assumes infinite precision arithmetic. Given the successive nature of the decoding algorithm, one might worry about the sensitivity of the performance to the precision of the computation. We show that even very coarsely quantized decoding algorithms lead to excellent performance. More concretely, we show that under successive decoding with an alphabet of cardinality only three, the decoder still has a threshold and this threshold is a sizable fraction of capacity. More generally, we show that if we are willing to transmit at a rate δ below capacity, then we need only c log(1/δ) bits of precision, where c is a universal constant.
Coherent Radio-Over-Fiber and Millimeter-Wave Radio Seamless Transmission System for Resilient Access Networks

We propose a millimeter-wave (MMW) coherent radio-over-fiber (RoF) transmission system for application to an access network with a direct broadband last-mile wireless connection to an optical fiber network. The coherent RoF system comprises an optical two-tone RoF signal generator with an advanced modulation format for high-throughput transmission and employs a digital-signal-processing-aided coherent detection technique for MMW radio, which is a technique similar to that of optical digital coherent detection. As proof of concept, a 20-GBd quadrature phase-shift keying RoF transmission over 20 km of optical fiber before a radio transmission over 20 m of air is demonstrated. The results of the radio transmissions using Cassegrain-type antenna pairs with a gain of 50 dBi are consistent with theoretical estimations; this suggests the possibility of developing a midrange transmission system using a high-power MMW amplifier.
In Vitro and in Vivo Properties of 3-tert-Butyl-7-(5-methylisoxazol-3-yl)-2-(1-methyl-1H-1,2,4-triazol-5-ylmethoxy)-pyrazolo[1,5-d]-[1,2,4]triazine (MRK-016), a GABAA Receptor α5 Subtype-Selective Inverse Agonist

3-tert-Butyl-7-(5-methylisoxazol-3-yl)-2-(1-methyl-1H-1,2,4-triazol-5-ylmethoxy)-pyrazolo[1,5-d][1,2,4]triazine (MRK-016) is a pyrazolotriazine with an affinity of between 0.8 and 1.5 nM for the benzodiazepine binding site of native rat brain and recombinant human α1-, α2-, α3-, and α5-containing GABAA receptors. It has inverse agonist efficacy selective for the α5 subtype, and this α5 inverse agonism is greater than that of the prototypic α5-selective compound 3-(5-methylisoxazol-3-yl)-6-[(1-methyl-1,2,3-triazol-4-hdyl)methyloxy]-1,2,4-triazolo[3,4-a]phthalazine (α5IA). Consistent with its greater α5 inverse agonism, MRK-016 increased long-term potentiation in mouse hippocampal slices to a greater extent than α5IA. MRK-016 gave good receptor occupancy after oral dosing in rats, with the dose required to produce 50% occupancy being 0.39 mg/kg and a corresponding rat plasma EC50 value of 15 ng/ml that was similar to the rhesus monkey plasma EC50 value of 21 ng/ml obtained using [11C]flumazenil positron emission tomography. In normal rats, MRK-016 enhanced cognitive performance in the delayed matching-to-position version of the Morris water maze but was not anxiogenic, and in mice it was not proconvulsant and did not produce kindling. MRK-016 had a short half-life in rat, dog, and rhesus monkey (0.3–0.5 h) but had a much lower rate of turnover in human compared with rat, dog, or rhesus monkey hepatocytes. Accordingly, in human, MRK-016 had a longer half-life than in preclinical species (∼3.5 h). Although it was well tolerated in young males, with a maximal tolerated single dose of 5 mg corresponding to an estimated occupancy in the region of 75%, MRK-016 was poorly tolerated in elderly subjects, even at a dose of 0.5 mg, which, along with its variable human pharmacokinetics, precluded its further development.
No Association Between Return to Play After Injury and Increased Rate of Anterior Cruciate Ligament Injury in Men’s Professional Soccer

Background: Studies have shown that previous injury, not necessarily anatomically related, is an important injury risk factor. However, it is not known whether a player runs an increased risk of anterior cruciate ligament (ACL) injury after returning to play from other injury types. Purpose: To analyze whether professional soccer players are more susceptible to ACL injury after returning to play from any previous injury. Study Design: Case-control study; Level of evidence, 3. Methods: A total of 101 elite male soccer players suffering a first-time complete ACL injury between 2001 and 2014 were included and matched according to team, age, and playing position with control players who did not have a current injury (1:1 match). For each injured player, the 90-day period prior to the ACL injury was analyzed for injuries and compared with that of control players by using odds ratios (ORs) and 95% CIs. Results: The odds of a player with an ACL injury sustaining a previous injury in the 90-day period did not differ significantly from that of controls (OR, 1.20; 95% CI, 0.66-2.17; P = .65). Testing the frequency of absence periods due to injury between the groups revealed that the odds of a player with an ACL injury having a previous period of absence due to injury did not differ compared with controls (OR, 1.14; 95% CI, 0.64-2.01; P = .77). Conclusion: Players with ACL injury did not have a greater occurrence of absence due to injury in the 3 months preceding their ACL injury compared with matched controls. This indicates that previous injury of any type does not increase the risk of suffering an ACL injury.
T Cell Receptor-dependent Tyrosine Phosphorylation of β2-Chimaerin Modulates Its Rac-GAP Function in T Cells*

The actin cytoskeleton has an important role in the organization and function of the immune synapse during antigen recognition. Dynamic rearrangement of the actin cytoskeleton in response to T cell receptor (TCR) triggering requires the coordinated activation of Rho family GTPases that cycle between active and inactive conformations. This is controlled by GTPase-activating proteins (GAP), which regulate inactivation of Rho GTPases, and guanine exchange factors, which mediate their activation. Whereas much attention has centered on guanine exchange factors for Rho GTPases in T cell activation, the identity and functional roles of the GAP in this process are largely unknown. We previously reported β2-chimaerin as a diacylglycerol-regulated Rac-GAP that is expressed in T cells. We now demonstrate Lck-dependent phosphorylation of β2-chimaerin in response to TCR triggering. We identify Tyr-153 as the Lck-dependent phosphorylation residue and show that its phosphorylation negatively regulates membrane stabilization of β2-chimaerin, decreasing its GAP activity to Rac. This study establishes the existence of TCR-dependent regulation of β2-chimaerin and identifies a novel mechanism for its inactivation.
Calbindin-D32k Is Localized to a Subpopulation of Neurons in the Nervous System of the Sea Cucumber Holothuria glaberrima (Echinodermata)

Members of the calbindin subfamily serve as markers of subpopulations of neurons within the vertebrate nervous system. Although markers of these proteins are widely available and used, their application to invertebrate nervous systems has been very limited. In this study we investigated the presence and distribution of members of the calbindin subfamily in the sea cucumber Holothuria glaberrima (Selenka, 1867). Immunohistological experiments with antibodies made against rat calbindin 1, parvalbumin, and calbindin 2, showed that these antibodies labeled cells and fibers within the nervous system of H. glaberrima. Most of the cells and fibers were co-labeled with the neural-specific marker RN1, showing their neural specificity. These were distributed throughout all of the nervous structures, including the connective tissue plexi of the body wall and podia. Bioinformatics analyses of the possible antigen recognized by these markers showed that a calbindin 2-like protein present in the sea urchin Strongylocentrotus purpuratus, corresponded to the calbindin-D32k previously identified in other invertebrates. Western blots with anti-calbindin 1 and anti-parvalbumin showed that these markers recognized an antigen of approximately 32 kDa in homogenates of radial nerve cords of H. glaberrima and Lytechinus variegatus. Furthermore, immunoreactivity with anti-calbindin 1 and anti-parvalbumin was obtained to a fragment of calbindin-D32k of H. glaberrima. Our findings suggest that calbindin-D32k is present in invertebrates and its sequence is more similar to the vertebrate calbindin 2 than to calbindin 1. Thus, characterization of calbindin-D32k in echinoderms provides an important view of the evolution of this protein family and represents a valuable marker to study the nervous system of invertebrates.
The Prevalence of Sexually Transmitted Infections in Papua New Guinea: A Systematic Review and Meta-Analysis

Background The potential for an expanded HIV epidemic in Papua New Guinea (PNG) demands an effective, evidence-based and locally-appropriate national response. As sexually transmitted infections (STIs) may be important co-factors in HIV transmission nationally, it is timely to conduct a systematic review of STI prevalences to inform national policy on sexual health and HIV/STI prevention. Methodology/Principal Findings We undertook a systematic review and meta-analysis of HIV and STI prevalences in PNG, reported in peer-reviewed and non-peer-reviewed publications for the period 1950–2010. Prevalence estimates were stratified by study site (community or clinic-based), geographic area and socio-demographic characteristics. The search strategy identified 105 reports, of which 25 studies (10 community-based; 10 clinic-based; and 5 among self-identified female sex workers) reported STI prevalences and were included in the systematic review. High prevalences of chlamydia, gonorrhoea, syphilis and trichomonas were reported in all settings, particularly among female sex workers, where pooled estimates of 26.1%, 33.6%, 33.1% and 39.3% respectively were observed. Pooled HIV prevalence in community-based studies was 1.8% (95% CI:1.2–2.4) in men; 2.6% (95% CI:1.7–3.5) in women; and 11.8% (95% CI:5.8–17.7) among female sex workers. Conclusions/Significance The epidemiology of STIs and HIV in PNG shows considerable heterogeneity by geographical setting and sexual risk group. Prevalences from community-based studies in PNG were higher than in many other countries in the Asia-Pacific. A renewed focus on national STI/HIV surveillance priorities and systems for routine and periodic data collection will be essential to building effective culturally-relevant behavioural and biomedical STI/HIV prevention programs in PNG.