Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecule Targeting Glucosyltransferase Inhibits Streptococcus mutans Biofilm Formation and Virulence

ABSTRACT Dental plaque biofilms are responsible for numerous chronic oral infections and cause a severe health burden. Many of these infections cannot be eliminated, as the bacteria in the biofilms are resistant to the host's immune defenses and antibiotics. There is a critical need to develop new strategies to control biofilm-based infections. Biofilm formation in Streptococcus mutans is promoted by major virulence factors known as glucosyltransferases (Gtfs), which synthesize adhesive extracellular polysaccharides (EPS). The current study was designed to identify novel molecules that target Gtfs, thereby inhibiting S. mutans biofilm formation and having the potential to prevent dental caries. Structure-based virtual screening of approximately 150,000 commercially available compounds against the crystal structure of the glucosyltransferase domain of the GtfC protein from S. mutans resulted in the identification of a quinoxaline derivative, 2-(4-methoxyphenyl)-N-(3-{[2-(4-methoxyphenyl)ethyl]imino}-1,4-dihydro-2-quinoxalinylidene)ethanamine, as a potential Gtf inhibitor. In vitro assays showed that the compound was capable of inhibiting EPS synthesis and biofilm formation in S. mutans by selectively antagonizing Gtfs instead of by killing the bacteria directly. Moreover, the in vivo anti-caries efficacy of the compound was evaluated in a rat model. We found that the compound significantly reduced the incidence and severity of smooth and sulcal-surface caries in vivo with a concomitant reduction in the percentage of S. mutans in the animals' dental plaque (P < 0.05). Taken together, these results represent the first description of a compound that targets Gtfs and that has the capacity to inhibit biofilm formation and the cariogenicity of S. mutans.
Dempster-shafer based probabilistic fuzzy logic system for wind speed prediction

This paper proposes an improved probabilistic fuzzy logic system with Dempster-Shafer structure (DS-PFLS) for wind speed prediction. The Dempster-Shafer theory and 3-sigma results are integrated into probabilistic fuzzy logic system (PFLS) to address the complex derivation of the secondary probability density function and to eliminate the computational overload. The secondary probability density function based on the center of primary fuzzy membership in PFLS is proposed. Moreover, an improved Chicken Swarm Optimization (CSO) is developed for optimizing the related parameters of DS-PFLS. Simulations and comparisons based on the wind speed prediction demonstrate the effectivity and efficiency of the proposed method.
Role of GATA transcription factor ELT-2 and p38 MAPK PMK-1 in recovery from acute P. aeruginosa infection in C. elegans

ABSTRACT Infectious diseases caused by bacterial pathogens reduce the fitness of their associated host but are generally limited in duration. In order for the diseased host to regain any lost fitness upon recovery, a variety of molecular, cellular, and physiological processes must be employed. To better understand mechanisms underlying the recovery process, we have modeled an acute Pseudomonas aeruginosa infection in C. elegans using brief exposures to this pathogen and subsequent antibiotic treatment. To identify host genes altered during recovery from P. aeruginosa infection, we performed whole genome expression profiling. The analysis of this dataset indicated that the activity of the host immune system is down-regulated upon recovery and revealed shared and pathogen-specific host responses during recovery. We determined that the GATA transcription factor ELT-2 and the p38 MAP kinase PMK-1 are necessary for animals to successfully recover from an acute P. aeruginosa infection. In addition, we found that ELT-2 plays a more prominent and earlier role than PMK-1 during recovery. Our data sheds further light on the molecular mechanisms and transcriptional programs involved in recovery from an acute bacterial infection, which provides a better understanding of the entire infectious disease process.
Semi-supervised hierarchical semantic object parsing

Models based on Convolutional Neural Networks (CNNs) have been proven very successful for semantic segmentation and object parsing that yield hierarchies of features. Our key insight is to build convolutional networks that take input of arbitrary size and produce object parsing output with efficient inference and learning. In this work, we focus on the task of instance segmentation and parsing which recognizes and localizes objects down to a pixel level base on deep CNN. Therefore, unlike some related work, a pixel cannot belong to multiple instances and parsing. Our model is based on a deep neural network trained for object masking that supervised with input image and follow incorporates a Conditional Random Field (CRF) with end-to-end trainable piecewise order potentials based on object parsing outputs. In each CRF unit we designed terms to capture the short range and long range dependencies from various neighbors. The accurate instance-level segmentation that our network produce is reflected by the considerable improvements obtained over previous work at high APr thresholds. We demonstrate the effectiveness of our model with extensive experiments on challenging dataset subset of PASCAL VOC 2012.
Impaired rich club and increased local connectivity in children with traumatic brain injury: Local support for the rich?

Recent evidence has shown the presence of a “rich club” in the brain, which constitutes a core network of highly interconnected and spatially distributed brain regions, important for high‐order cognitive processes. This study aimed to map the rich club organization in 17 young patients with moderate to severe TBI (15.71 ± 1.75 years) in the chronic stage of recovery and 17 age‐ and gender‐matched controls. Probabilistic tractography was performed on diffusion weighted imaging data to construct the edges of the structural connectomes using number of streamlines as edge weight. In addition, the whole‐brain network was divided into a rich club network, a local network and a feeder network connecting the latter two. Functional outcome was measured with a parent questionnaire for executive functioning. Our results revealed a significantly decreased rich club organization (p values < .05) and impaired executive functioning (p < .001) in young patients with TBI compared with controls. Specifically, we observed reduced density values in all three subnetworks (p values < .005) and a reduced mean strength in the rich club network (p = .013) together with an increased mean strength in the local network (p = .002) in patients with TBI. This study provides new insights into the nature of TBI‐induced brain network alterations and supports the hypothesis that the local subnetwork tries to compensate for the biologically costly subnetwork of rich club nodes after TBI.
Healthcare services utilization following admission for hip fracture in elderly patients

Objectives To assess the effect of hip fracture on healthcare utilization among elderly patients. Design Retrospective cohort study. Setting Eight general hospitals in Israel, owned by Clalit. Participants Enrollees >65 years, admitted with a hip fracture during 2009-2013. Main outcome measures Data collected included demographics, comorbidities, admission details related to the surgical and rehabilitation hospitalizations, mortality and costs. Mean monthly costs before and after the event were compared. Quantile regression was used to analyze associations between patient characteristics and healthcare expenditure in univariate and multivariate analysis. Results Of 9650 patients admitted with hip fracture during the study period, 6880 (71%) were Clalit enrollees and included in the present study (69% females, median age: 83 years). Total mean monthly costs increased by 96% during the follow-up year ($1470 vs. $749). Costs for rehabilitation accounted for 40% of costs during the first follow-up year. Mean monthly non-rehabilitation costs increased by 21% ($877 vs. $722). Several factors were found to be consistently associated with increased mean monthly costs during the follow-up year. These included Charlson's comorbidity index, hypertension, baseline expenditure in the base year, the location of the fracture, procedure performed, department on admission, admission to the intensive care unit, discharge to a rehabilitation facility and mortality during the follow-up year. Conclusions Hip fractures in adults in Israel are associated with a significant increase in healthcare utilization and costs. The largest increment was seen in costs for rehabilitation. However, increased costs were noted in all sub-categories of healthcare costs.
Metagenomic insights into zooplankton‐associated bacterial communities

Summary Zooplankton and microbes play a key role in the ocean's biological cycles by releasing and consuming copious amounts of particulate and dissolved organic matter. Additionally, zooplankton provide a complex microhabitat rich in organic and inorganic nutrients in which bacteria thrive. In this study, we assessed the phylogenetic composition and metabolic potential of microbial communities associated with crustacean zooplankton species collected in the North Atlantic. Using Illumina sequencing of the 16S rRNA gene, we found significant differences between the microbial communities associated with zooplankton and those inhabiting the surrounding seawater. Metagenomic analysis of the zooplankton‐associated microbial community revealed a highly specialized bacterial community able to exploit zooplankton as microhabitat and thus, mediating biogeochemical processes generally underrepresented in the open ocean. The zooplankton‐associated bacterial community is able to colonize the zooplankton's internal and external surfaces using a large set of adhesion mechanisms and to metabolize complex organic compounds released or exuded by the zooplankton such as chitin, taurine and other complex molecules. Moreover, the high number of genes involved in iron and phosphorus metabolisms in the zooplankton‐associated microbiome suggests that this zooplankton‐associated bacterial community mediates specific biogeochemical processes (through the proliferation of specific taxa) that are generally underrepresented in the ambient waters.
Performance of quadrature phase shift frequency selective receiver in presence of blockers

This paper evaluates the performance of a linear, low-power and blocker tolerant quadrature phase shift frequency selective (QPS-FS) receiver in the presence of blockers. The QPS-FS receiver has been tested to tolerate more than 0 dBm of continuous wave (CW) blocker power at a frequency offset of 40 MHz away from the RF signal carrier frequency with 6 dB degradation in the voltage conversion gain and without any significant loss in the receiver performance in terms of error vector magnitude (EVM) between the transmitted and the received constellation points. The QPS-FS receiver separates the undesired blockers and interferers from the desired band RF signal, which are collected for energy harvesting purposes.
Leaf Morphology, Taxonomy and Geometric Morphometrics: A Simplified Protocol for Beginners

Taxonomy relies greatly on morphology to discriminate groups. Computerized geometric morphometric methods for quantitative shape analysis measure, test and visualize differences in form in a highly effective, reproducible, accurate and statistically powerful way. Plant leaves are commonly used in taxonomic analyses and are particularly suitable to landmark based geometric morphometrics. However, botanists do not yet seem to have taken advantage of this set of methods in their studies as much as zoologists have done. Using free software and an example dataset from two geographical populations of sessile oak leaves, we describe in detailed but simple terms how to: a) compute size and shape variables using Procrustes methods; b) test measurement error and the main levels of variation (population and trees) using a hierachical design; c) estimate the accuracy of group discrimination; d) repeat this estimate after controlling for the effect of size differences on shape (i.e., allometry). Measurement error was completely negligible; individual variation in leaf morphology was large and differences between trees were generally bigger than within trees; differences between the two geographic populations were small in both size and shape; despite a weak allometric trend, controlling for the effect of size on shape slighly increased discrimination accuracy. Procrustes based methods for the analysis of landmarks were highly efficient in measuring the hierarchical structure of differences in leaves and in revealing very small-scale variation. In taxonomy and many other fields of botany and biology, the application of geometric morphometrics contributes to increase scientific rigour in the description of important aspects of the phenotypic dimension of biodiversity. Easy to follow but detailed step by step example studies can promote a more extensive use of these numerical methods, as they provide an introduction to the discipline which, for many biologists, is less intimidating than the often inaccessible specialistic literature.
The Primate Community of Cachoeira (Brazilian Amazonia): A Model to Decipher Ecological Partitioning among Extinct Species

Dental microwear analysis is conducted on a community of platyrrhine primates from South America. This analysis focuses on the primate community of Cachoeira Porteira (Para, Brazil), in which seven sympatric species occur: Alouatta seniculus, Ateles paniscus, Cebus apella, Chiropotes satanas, Pithecia Pithecia, Saguinus midas, and Saimiri sciureus. Shearing quotients are also calculated for each taxon of this primate community. Dental microwear results indicate significant differences between taxa, but are somewhat insufficient when it comes to discriminating between ecologically similar taxa. The primates of Cachoeira Porteira all incorporate a certain amount of fruit in their diet, entailing a definite amount of inter-specific competition as they must share food resources. Alouatta is the most folivorous taxon of this community, which is corroborated by dental microwear analysis. Ateles, although of a similar size to Alouatta, limits inter-specific competition by incorporating more fruit in its diet. Cebus has a very diverse omnivorous diet, which is highlighted in this study, as it compares to both fruit and leaf eating taxa. In some cases, microwear results need to be supplemented by other methods. For example, dental microwear seems insufficient to distinguish between Pithecia and Chiropotes, which eat foods with similar physical properties. However, other methods (i.e. shearing quotients and body mass) provide enough complimentary information to be able to highlight differences between the two taxa. On the other hand, dental microwear can highlight differences between primates which have similar diets, such as Saimiri and Saguinus. In this case, differences could be due to other exogenous factors.
Male Responses to Conspecific Advertisement Signals in the Field Cricket Gryllus rubens (Orthoptera: Gryllidae)

In many species males aggregate and produce long-range advertisement signals to attract conspecific females. The majority of the receivers of these signals are probably other males most of the time, and male responses to competitors' signals can structure the spatial and temporal organization of the breeding aggregation and affect male mating tactics. I quantified male responses to a conspecific advertisement stimulus repeatedly over three age classes in Gryllus rubens (Orthoptera: Gryllidae) in order to estimate the type and frequency of male responses to the broadcast stimulus and to determine the factors affecting them. Factors tested included body size, wing dimorphism, age, and intensity of the broadcast stimulus. Overall, males employed acoustic response more often than positive phonotactic response. As males aged, the frequency of positive phonotactic response decreased but that of the acoustic response increased. That is, males may use positive phonotaxis in the early stages of their adult lives, possibly to find suitable calling sites or parasitize calling males, and then later in life switch to acoustic responses in response to conspecific advertisement signals. Males with smaller body size more frequently exhibited acoustic responses. This study suggests that individual variation, more than any factors measured, is critical for age-dependent male responses to conspecific advertisement signals.
The association between different features of sleep‐disordered breathing and blood pressure: A cross‐sectional study

Sleep disordered breathing (SDB) is highly prevalent in patients with high blood pressure (BP). Severity of SDB can be evaluated by the number of apneas and hypopneas per hour (AHI) or by measures of hypoxia. The objective of this study was to assess the association between different measures of SDB and BP. In 134 consecutive patients, polygraphy was performed to determine the AHI. Pulse oximetry was used to determine hypoxemic burden (time below 90% oxygen saturation [T90] and hypoxia load [HL], representing the integrated area above the curve of desaturation). AHI did not correlate with systolic and diastolic BP or pulse pressure. In contrast, HL correlated with pulse pressure during the day (P = .01) and night (P = .0034) before and after adjustment for body mass index. The correlation between systolic BP and HL at night disappeared following adjustment for body mass index. This study generates the hypothesis that nocturnal hypoxemic burden may represent a suitable marker of BP pattern and a potential treatment target in hypertensive patients.
Including Pervasive Web Content in Evidence-Based Software Engineering: A Case Study

Context: Both scientific publications and grey literature have widely been employed as sources of empirical evidence in evidence-based software engineering (EBSE). However, there is still a fierce debate about whether or not the pervasive Web content can act as an alternative means to gather evidence for EBSE. Aim: To help ourselves enter this debate, this work aims to obtain some pre-evidence of reviewing Web documents for verifying the value and reliability of online materials. Method: Given the unique characteristics of Web content, we adapted the traditional Systematic Literature Review (SLR) methodology in EBSE, and conducted a review case study in the deep learning domain. Results: Our study selected four different search sources and captured 5082 "deep learning"-relevant Web documents. After a set of thematic synthesis steps ranging from keyword identification to brainstorming, the collected raw data were eventually evolved into a mind map of six semantic topics. Conclusions: We confirm that Web content can provide valuable information as supplementary evidence in EBSE. However, reviewing Web content introduces more search source bias rather than academic publications' location bias that is due to factors like ease of access or indexing levels in digital libraries.
Improving Classification of Cancer and Mining Biomarkers from Gene Expression Profiles Using Hybrid Optimization Algorithms and Fuzzy Support Vector Machine

Background: Gene expression data are characteristically high dimensional with a small sample size in contrast to the feature size and variability inherent in biological processes that contribute to difficulties in analysis. Selection of highly discriminative features decreases the computational cost and complexity of the classifier and improves its reliability for prediction of a new class of samples. Methods: The present study used hybrid particle swarm optimization and genetic algorithms for gene selection and a fuzzy support vector machine (SVM) as the classifier. Fuzzy logic is used to infer the importance of each sample in the training phase and decrease the outlier sensitivity of the system to increase the ability to generalize the classifier. A decision-tree algorithm was applied to the most frequent genes to develop a set of rules for each type of cancer. This improved the abilities of the algorithm by finding the best parameters for the classifier during the training phase without the need for trial-and-error by the user. The proposed approach was tested on four benchmark gene expression profiles. Results: Good results have been demonstrated for the proposed algorithm. The classification accuracy for leukemia data is 100%, for colon cancer is 96.67% and for breast cancer is 98%. The results show that the best kernel used in training the SVM classifier is the radial basis function. Conclusions: The experimental results show that the proposed algorithm can decrease the dimensionality of the dataset, determine the most informative gene subset, and improve classification accuracy using the optimal parameters of the classifier with no user interface.
Vitamin D and Diabetes

Diabetes is a leading cause of cardiovascular disease. Persons with diabetes are at greater risk for early cardiac mortality, and for repeat events if they survive their first cardiac event. Recently, low serum concentrations of vitamin D have been associated with increased risk for cardiac events. Evidence indicates that persons with diabetes have lower serum concentrations of vitamin D. In addition, persons at risk for diabetes or metabolic syndrome have inadequate serum concentrations of vitamin D. This review will assess the evidence relative to the impact of vitamin D in the development of diabetes, metabolic syndrome, and diabetes complications. Studies that address vitamin D and its impact on metabolic outcomes as well as possible mechanisms of action are provided. Finally, the assessment and suggested treatment for vitamin D deficiency is addressed. Effective detection and treatment of inadequate vitamin D concentrations in persons with diabetes or those at risk for diabetes may be an easy and cost-effective therapy which could improve their long-term health outcomes as well as their quality of life.
Phylodynamics of HIV-1 from a Phase III AIDS Vaccine Trial in Bangkok, Thailand

Background In 2003, a phase III placebo-controlled trial (VAX003) was completed in Bangkok, Thailand. Of the 2,546 individuals enrolled in the trial based on high risk for infection through injection drug use (IDU), we obtained clinical samples and HIV-1 sequence data (envelope glycoprotein gene gp120) from 215 individuals who became infected during the trial. Here, we used these data in combination with other publicly available gp120 sequences to perform a molecular surveillance and phylodynamic analysis of HIV-1 in Thailand. Methodology and Findings Phylogenetic and population genetic estimators were used to assess HIV-1 gp120 diversity as a function of vaccination treatment, viral load (VL) and CD4+ counts, to indentify transmission clusters and to investigate the timescale and demographics of HIV-1 in Thailand. Three HIV-1 subtypes were identified: CRF01_AE (85% of the infections), subtype B (13%) and CRF15_AE (2%). The Bangkok IDU cohort showed more gp120 diversity than other Asian IDU cohorts and similar diversity to that observed in sexually infected individuals. Moreover, significant differences (P<0.02) in genetic diversity were observed in CRF01_AE IDU with different VL and CD4+ counts. No phylogenetic structure was detected regarding any of the epidemiological and clinical factors tested, although high proportions (35% to 50%) of early infections fell into clusters, which suggests that transmission chains associated with acute infection play a key role on HIV-1 spread among IDU. CRF01_AE was estimated to have emerged in Thailand in 1984.5 (1983–1986), 3–6 years before the first recognition of symptomatic patients (1989). The relative genetic diversity of the HIV-1 population has remained high despite decreasing prevalence rates since the mid 1990s. Conclusions Our study and recent epidemiological reports indicate that HIV-1 is still a major threat in Thailand and suggest that HIV awareness and prevention needs to be strengthened to avoid AIDS resurgence.