Miracle-dz/UniFAR-FTUs huggingface dataset:
BgTEP: An Antiprotease Involved in Innate Immune Sensing in Biomphalaria glabrata

Insect Thioester-containing protein (iTEP) is the most recently defined group among the TEP superfamily. TEPs are key components of the immune system, and iTEPs from flies and mosquitoes were shown to be major immune weapons. Initially characterised from insects, TEP genes homologous to iTEP were further described from several other invertebrates including arthropods, cniderians and mollusks albeit with few functional characterisations. In the freshwater snail Biomphalaria glabrata, a vector of the schistosomiasis disease, the presence of a TEP protein (BgTEP) was previously described in a well-defined immune complex involving snail lectins (FREP) and schistosome parasite mucins (SmPoMuc). To investigate the potential role of BgTEP in the immune response of the snail, we first characterised its genomic organisation and its predicted protein structure. A phylogenetic analysis clustered BgTEP in a well-conserved subgroup of mollusk TEP. We then investigated the BgTEP expression profile in different snail tissues, and followed immune challenges using different kinds of intruders during infection kinetics. Results revealed that BgTEP is particularly expressed in hemocytes, the immune-specialised cells in invertebrates, and is secreted into the hemolymph. Transcriptomic results further evidenced an intruder-dependent differential expression pattern of BgTEP whilst interactome experiments showed that BgTEP is capable of binding to the surface of different microbes and parasite either in its full length form or in processed forms. Through this work, we report the first characterisation of a snail TEP. Our study also reveals that BgTEP may display an unexpected functional dual-role. In addition to its previously characterised anti-protease activity, we demonstrate that BgTEP can bind to the intruder surface membrane, which supports a likely opsonin role.
A Summary Evaluation of the Top-Five Brazilian Psychology Journals by Native English-Language Scholars

In the current century, English is the language for the research and dissemination of scientific findings. But for many scholars, English is a foreign language. This is especially true among the emerging and developing nations (EDNs), such as the BRICS nations, encompassing Brazil, Russia, India, China, and South Africa. The present study conducted a survey examining the translational integrity and overall impression of translated summary materials (abstracts and titles) from the five highest ranking (SCImago Journal Rank) Brazilian journals in the field of psychology. Analysis proceeded with two models. In the first model, translated summary materials from 12 randomly-selected articles from four of the five journals were evaluated by a panel of three native English-language scholars. Findings indicated an inverse relationship between the overall impression of the materials and their: abstract errors, r(34) = -0.61, p < . 001; and total errors, r(34) = -0.62, p < . 001; suggesting a direct relationship between the translational integrity of these EDN materials and the overall impression they leave with native English-language scholars. A second model added 3 additional articles from the fifth journal (English-language only) to the materials described. The findings from this second model suggested that for EDN journals, an investment in language resources may substantially improve the impression they leave with native English-language scholars, and thus promote wider dissemination of their findings.
Distribution of ozone and its precursors over Bay of Bengal during winter 2009: role of meteorology

Abstract. Measurements of ozone and NO2 were carried out in the marine environment of the Bay of Bengal (BoB) during the winter months, December 2008–January 2009, as part of the second Integrated Campaign for Aerosols, gases and Radiation Budget conducted under the Geosphere Biosphere Programme of the Indian Space Research Organization. The ozone mixing ratio was found to be high in the head and the southeast BoB with a mean value of 61 ± 7 ppb and 53 ± 6 ppb, respectively. The mixing ratios of NO2 and CO were also relatively high in these regions. The spatial patterns were examined in the light of airflow patterns, air mass back trajectories and other meteorological conditions and satellite retrieved maps of tropospheric ozone, NO2, CO, and fire count in and around the region. The distribution of these gases was strongly associated with the transport from the adjoining land mass. The anthropogenic activities and forest fires/biomass burning over the Indo Gangetic Plains and other East Asian regions contribute to ozone and its precursors over the BoB. Similarity in the spatial pattern suggests that their source regions could be more or less the same. Most of the diurnal patterns showed decrease of the ozone mixing ratio during noon/afternoon followed by a nighttime increase and a morning high. Over this oceanic region, photochemical production of ozone involving NO2 was not very active. Water vapour played a major role in controlling the variation of ozone. An attempt is made to simulate ozone level over the north and south BoB using the photochemical box model (NCAR-MM). The present observed features were compared with those measured during the earlier cruises conducted in different seasons.
Ultrasound Strain Rate Imaging in Functional Dyspepsia : in-vitro and clinical evaluation

Functional dyspepsia (FD) is a chronic condition that is characterized by abdominal pain or discomfort, nausea, vomiting, early satiation and abdominal fullness. The Rome III classification of functional gastrointestinal disorders defines two distinct entities of functional dyspepsia (FD), namely “epigastric pain syndrome” (EPS) and “postprandial distress syndrome” (PDS). Strain rate imaging (SRI) is a new ultrasound modality that is used to give a quantitative measure of deformation. The method was developed to study the cardiac muscle during health and disease. In this doctoral thesis we used SRI to study antral contractions in healthy volunteers and in patients with FD. The original cardiac SRI method was first adjusted to be able to detect signals from slowly contracting tissues. The accuracy of the adjusted method was tested in a rubber phantom mimicking the antral muscular wall in thickness, homogeneity and contraction velocity (paper I). We found that SRI strains agreed well with calculated values for strain when SRI strain was measured as the average over several US beams and the strain sample size was 1.9 mm. The variance was substantial if single samples were used, especially for a small strain sample size (0.8 mm). The results showed low inter and intraobserver variation. With the new parameters acquired from that study, the method was then applied in an ex-vivo porcine antral wall (paper II). The agreement between radial strain values measured by SRI and B-mode, along and across several ultrasound beams, using US frequency 6.7 MHz and strain length (SL) = 1.9 mm was good and it was better than with SL 1.2 mm. The method was then applied on the stomachs of healthy individuals (paper III). 1
Fast Euclidean OPTICS with Bounded Precision in Low Dimensional Space

OPTICS is a popular method for visualizing multidimensional clusters. All the existing implementations of this method have a time complexity of $O(n^2)$ --- where n is the size of the input dataset --- and thus, may not be suitable for datasets of large volumes. This paper alleviates the problem by resorting to approximation with guarantees. The main result is a new algorithm that runs in $O(n łog n)$ time under any fixed dimensionality, and computes a visualization that has provably small discrepancies from that of OPTICS. As a side product, our algorithm gives an index structure that occupies linear space, and supports the cluster group-by query with near-optimal cost. The quality of the cluster visualizations produced by our techniques and the efficiency of the proposed algorithms are demonstrated with an empirical evaluation on real data.
Is Something Better than Nothing? Automatically Predicting Stance-based Arguments Using Deep Learning and Small Labelled Dataset

Online reviews have become a popular portal among customers making decisions about purchasing products. A number of corpora of reviews have been widely investigated in NLP in general, and, in particular, in argument mining. This is a subset of NLP that deals with extracting arguments and the relations among them from user-based content. A major problem faced by argument mining research is the lack of human-annotated data. In this paper, we investigate the use of weakly supervised and semi-supervised methods for automatically annotating data, and thus providing large annotated datasets. We do this by building on previous work that explores the classification of opinions present in reviews based whether the stance is expressed explicitly or implicitly. In the work described here, we automatically annotate stance as implicit or explicit and our results show that the datasets we generate, although noisy, can be used to learn better models for implicit/explicit opinion classification.
Classifying images by light aesthetics

With the growing availability of storage space for data, such as images, comes the need for research tools that reach beyond usual criteria. Such tools include, but are not limited to, the automatic prediction of aesthetic value for indexing purpose. For this reason, the field of supervised learning for aesthetic prediction has been widely active for more than a decade. We propose a new method aimed at classifying photos based on the aesthetic of their lightning. It comes as an introduction to providing more accurate specialized supervised learning solutions for inferring photo aesthetic. In the field of Aesthetic prediction classifier are broadly used, combining them with expert knowledge of the medium allow predictions with a score up to 70% matching the aesthetic judgement of humans. However, Supervised Learning solutions have a hard time dealing with the notion of different style in the datasets. While some aspects of photography, such a spatial composition, are considered as general and always applicable, the notion of style de fines specific aesthetics choice that change drastically the way the lightning (for example) is done. For this reason, the classifiers performances are limited. We choose to focus on the subject of light aesthetic in photography because we think it is relevant to be able to assess if a photo belongs to High-Key, Medium-Key or Low-key style prior to trying to infer it's aesthetic value. We show that it is possible to achieve such classification with over 80% success rate while only studying pixel populations of input images.
Internet Performance Analysis of South Asian Countries Using End-to-End Internet Performance Measurements

Internet performance is highly correlated with key economic development metrics of a region. According to World Bank, the economic growth of a country increases 1.3% with a 10% increase in the speed of the Internet. Therefore, it is necessary to monitor and understand the performance of the Internet links in the region. It helps to figure out the infrastructural inefficiencies, poor resource allocation, and routing issues in the region. Moreover, it provides healthy suggestions for future upgrades. Therefore, the objective of this paper is to understand the Internet performance and routing infrastructure of South Asian countries in comparison to the developed world and neighboring countries using end-to-end Internet performance measurements. The South Asian countries comprise nearly 32% of the Internet users in Asia and nearly 16% of the world. The Internet performance metrics in the region are collected through the PingER framework. The framework is developed by the SLAC National Accelerator Laboratory, USA and is running for the last 20 years. PingER has 16 monitoring nodes in the region, and in the last year PingER monitors about 40 sites in South Asia using the ubiquitous ping facility. The collected data is used to estimate the key Internet performance metrics of South Asian countries. The performance metrics are compared with the neighboring countries and the developed world. Particularly, the TCP throughput of the countries is also correlated with different development indices. Further, worldwide Internet connectivity and routing patterns of the countries are investigated to figure out the inconsistencies in the region. The performance analysis revealed that the South Asia region is 7-10 years behind the developed regions of North America (USA and Canada), Europe, and East Asia.
Trust and Signals in Workplace Organization: Evidence from Job Autonomy Differentials between Immigrant Groups

While much work has considered trust’s effect on workplace organization, particularly the granting of job autonomy, this relationship remains essentially a black box, lacking insight on the deeper process underlying employers’ ultimate trust or autonomy decision. I seek to unpack the trust-organization nexus, focusing on the role of employers’ inferences about employees’ trustworthiness. Integrating extant literatures, I posit that employers use group membership—and specific group-level traits—as an observable signal concerning individual employees’ trustworthiness and decide how much autonomy to grant to employees that have similar observable individual-level qualities but belong to different, easily recognizable social groups. Empirical analysis of job autonomy differentials between groups of migrants with different ethnonational identities reveals systematic patterns of variation that cannot be explained on the basis of observable employee traits alone. Hence, the evidence strongly supports the signalling value of group membership, demonstrating an important real-world feature of trust governing workplace organization.
Evaluating Nubian Population Structure from Cranial Nonmetric Traits: Gene Flow, Genetic Drift, and Population History of the Nubian Nile Valley

abstract Paleolithic archaeological and skeletal remains from the Nile Valley have yielded a complex picture of life along the river. Sociocultural and sociopolitical events during this time frame shaped population structure, while gene flow and genetic drift further developed it. In this study, we took a population genetics approach to modeling Nubian biological relationships in an effort to describe how an accumulation of events formed Nubian population structure. A variety of Nubian samples were utilized, spanning the Mesolithic-Christian time periods and geographically from just above the first through the third cataracts. Population genetics statistics were employed to estimate and depict biological affinities (Mahalanobis D2 with a tetrachoric matrix, principal coordinates analysis, FST, and Relethford-Blangero residuals), supplemented by spatial-temporal modeling (Mantel tests and PROTESTs). Variation was high among these groups, indicating an intricate pattern of relationships in their population history where similar levels of gene flow probably stemmed from extensive cultural contact with Egypt and other populations in a variety of contexts. Genetic drift was also apparent in some of these sites, which is consistent with social and political histories of these groups. Traditional modeling of spatial-temporal patterning was not successful, which may be attributed to the nonlinear, loose clustering of Nubian groups by site. Collectively, the archaeological, biological, and environmental evidence supports the ideas of multiple populations living in Lower Nubia during the Paleolithic and/or a new population entering the area and shaping Nubian population structure.
Supervoxels-Based Histon as a New Alzheimer’s Disease Imaging Biomarker

Alzheimer’s disease (AD) represents the prevalent type of dementia in the elderly, and is characterized by the presence of neurofibrillary tangles and amyloid plaques that eventually leads to the loss of neurons, resulting in atrophy in specific brain areas. Although the process of degeneration can be visualized through various modalities of medical imaging and has proved to be a valuable biomarker, the accurate diagnosis of Alzheimer’s disease remains a challenge, especially in its early stages. In this paper, we propose a novel classification method for Alzheimer’s disease/cognitive normal discrimination in structural magnetic resonance images (MRI), based on the extension of the concept of histons to volumetric images. The proposed method exploits the relationship between grey matter, white matter and cerebrospinal fluid degeneration by means of a segmentation using supervoxels. The calculated histons are then processed for a reduction in dimensionality using principal components analysis (PCA) and the resulting vector is used to train an support vector machine (SVM) classifier. Experimental results using the OASIS-1 database have proven to be a significant improvement compared to a baseline classification made using the pipeline provided by Clinica software.
Total energy intake according to the level of skeletal muscle mass in Korean adults aged 30 years and older: an analysis of the Korean National Health and Nutrition Examination Surveys (KNHANES) 2008–2011

BACKGROUND/OBJECTIVES Since gain or loss of skeletal muscle mass is a gradual event and occurs due to a combination of lifestyle factors, assessment of dietary factors related to skeletal muscle is complicated. The aim of this study was to investigate the changes in total energy intake according to the level of skeletal muscle mass. SUBJECTS/METHODS A total of 8,165 subjects ≥ 30 years of age from the Korean National Health and Nutrition Examination Surveys (KNHANES) 2008–2011 were included in the analysis, and multivariate-adjusted regression analyses were performed to analyze the association of the quartiles of sarcopenia index (SI) with energy intake of the study population after adjusting for age and metabolic parameters. RESULTS The increase in SI quartile was in proportion to the gradual decrease in systemic lipids and the anthropometric measurement of fat accumulation (P < 0.001). Subjects in higher SI quartiles tended to consume more total energy and energy-producing nutrients than those in lower quartiles (P < 0.001). After age, body weight, alcohol consumption, and metabolic parameters were adjusted in the analysis, total energy intake gradually increased according to the increase in SI quartile, and the association between total energy intake and SI was more pronounced in men. However, the risk (odd ratio) of having a low SI was not affected by any single macronutrient intake. CONCLUSIONS In this study, total energy intake was positively associated with SI and relative skeletal mass in both men and women. However, no significant association or a weak association was observed between any single macronutrient intake and skeletal muscle mass. The data indicated that acquiring more energy intake within the normal range of energy consumption may help to maintain skeletal muscle mass.
Immunotherapy with CAR-Modified T Cells: Toxicities and Overcoming Strategies

T cells modified via chimeric antigen receptors (CARs) have emerged as a promising treatment modality. Unparalleled clinical efficacy recently demonstrated in refractory B-cell malignancy has brought this new form of adoptive immunotherapy to the center stage. Nonetheless, its current success has also highlighted its potential treatment-related toxicities. The adverse events observed in the clinical trials are described in this review, after which, some innovative strategies developed to overcome these unwanted toxicities are outlined, including suicide genes, targeted activation, and other novel strategies.
Therapeutic Potential of a Scorpion Venom-Derived Antimicrobial Peptide and Its Homologs Against Antibiotic-Resistant Gram-Positive Bacteria

The alarming rise in the prevalence of antibiotic resistance among pathogenic bacteria poses a unique challenge for the development of effective therapeutic agents. Antimicrobial peptides (AMPs) have attracted a great deal of attention as a possible solution to the increasing problem of antibiotic-resistant bacteria. Marcin-18 was identified from the scorpion Mesobuthus martensii at both DNA and protein levels. The genomic sequence revealed that the marcin-18 coding gene contains a phase-I intron with a GT-AG splice junction located in the DNA region encoding the N-terminal part of signal peptide. The peptide marcin-18 was also isolated from scorpion venom. A protein sequence homology search revealed that marcin-18 shares extremely high sequence identity to the AMPs meucin-18 and megicin-18. In vitro, chemically synthetic marcin-18 and its homologs (meucin-18 and megicin-18) showed highly potent inhibitory activity against Gram-positive bacteria, including some clinical antibiotic-resistant strains. Importantly, in a mouse acute peritonitis model, these peptides significantly decreased the bacterial load in ascites and rescued nearly all mice heavily infected with clinical methicillin-resistant Staphylococcus aureus from lethal bacteremia. Peptides exerted antimicrobial activity via a bactericidal mechanism and killed bacteria through membrane disruption. Taken together, marcin-18 and its homologs have potential for development as therapeutic agents for treating antibiotic-resistant, Gram-positive bacterial infections.
Three-Dimensional Modeling of Hydrodynamics and Salinity in the San Francisco Estuary: An Evaluation of Model Accuracy, X2, and the Low–Salinity Zone

doi: http://dx.doi. org/10.15447/sfews.2015v13iss1art2 The three-dimensional UnTRIM San Francisco Bay–Delta model was applied to simulate tidal hydrodynamics and salinity in the San Francisco Estuary (estuary) using an unstructured grid. We compared model predictions to observations of water level, tidal flow, current speed, and salinity collected at 137 locations throughout the estuary. A quantitative approach based on multiple model assessment metrics was used to evaluate the model's accuracy for each comparison. These comparisons demonstrate that the model accurately predicted water level, tidal flow, and salinity during a 3-year simulation period that spanned a large range of flow and salinity conditions. The model is therefore suitable for detailed investigation of circulation patterns and salinity distributions in the estuary. The model was used to investigate the location, and spatial and temporal extent of the low-salinity zone (LSZ), defined by salinity between 0.5 and 6 psu. We calculated X2, the distance up the axis of the estuary to the daily-averaged 2-psu near-bed salinity, and the spatial extent of the LSZ for each day during the 3-year simulation. The location, area, volume, and average depth of the low-salinity zone varied with X2; however this variation was not monotonic and was largely controlled by the geometry of the estuary. We used predicted daily X2 values and the corresponding daily Delta outflow for each day during the 3-year simulation to develop a new equation to relate X2 to Delta outflow. This equation provides a conceptual improvement over previous equations by allowing the time constant for daily changes in X2 to vary with flow conditions. This improvement resulted in a smaller average error in X2 prediction than previous equations. These analyses demonstrate that a well-calibrated three-dimensional (3-D) hydrodynamic model is a valuable tool for investigating the salinity distributions in the estuary, and their influence on the distribution and abundance of physical habitat.