Citrus huanglongbing is the most destructive disease of citrus worldwide. It spread by psyllids and associated with a low-titer, phloem-limited infection any three uncultured species α-Proteobacteria, ‘Candidatus Liberibacter asiaticus’, ‘Ca. L. americanus’, africanus’. A complete circular asiaticus’ genome has been obtained metagenomics, using DNA extracted from single asiaticus’–infected psyllid. The 1.23-Mb an average 36.5% GC content. Annotation revealed high percentage genes involved in...

Intestinal luminal microbiota likely contribute to the etiology of necrotizing enterocolitis (NEC), a common disease in preterm infants. Microbiota development, cascade initial colonization events leading establishment diverse commensal microbiota, can now be studied infants using powerful molecular tools. Starting with first stool and continuing until discharge, weekly specimens were collected prospectively from gestational ages ≤32 completed weeks or birth weights≤1250 g. High throughput...

RELIEF is considered one of the most successful algorithms for assessing quality features. In this paper, we propose a set new feature weighting that perform significantly better than RELIEF, without introducing large increase in computational complexity. Our work starts from mathematical interpretation seemingly heuristic algorithm as an online method solving convex optimization problem with margin-based objective function. This explains success real application and enables us to identify...

The paper proposed a novel automatic target recognition (ATR) system for classification of three types ground vehicles in the moving and stationary acquisition (MSTAR) public release database. First MSTAR image chips are represented as fine raw feature vectors, where features compensate pose estimation error that corrupts features. Then, classified by using adaptive boosting (AdaBoost) algorithm with radial basis function (RBF) network base learner. Since RBF is binary classifier, multiclass...

Recent metagenomics studies of environmental samples suggested that microbial communities are much more diverse than previously reported, and deep sequencing will significantly increase the estimate total species diversity. Massively parallel pyrosequencing technology enables ultra-deep complex populations rapidly inexpensively. However, computational methods for analyzing large collections 16S ribosomal sequences limited. We proposed a new algorithm, referred to as ESPRIT, which addresses...

Late onset sepsis (LOS) is a major contributor to neonatal morbidity and mortality, especially in premature infants. Distortions the establishment of normal gut microbiota, commensal microbes that colonize digestive tract, might increase risk LOS via disruption mucosal barrier with resultant translocation luminal contents. Correlation distortions intestinal microbiota necessary first step design novel microbiota-based screening approaches lead early interventions prevent high Using...

<b>Objective: </b> To evaluate the efficacy and safety of donepezil for severe Alzheimer disease (AD). <b>Methods: Patients with AD (Mini-Mental State Examination [MMSE] scores 1 to 12 Functional Assessment Staging [FAST] ≥6) were enrolled in this multinational, double-blind, placebo-controlled trial at 98 sites. randomized 10 mg daily or placebo 24 weeks. Primary endpoints Severe Impairment Battery (SIB) Clinician9s Interview-Based Impression Change-Plus caregiver input (CIBIC-Plus)....

PURPOSE This phase III, placebo-controlled, randomized trial was designed to investigate efficacy and safety of two doses denileukin diftitox (DD; DAB(389)-interleukin-2 [IL-2]), a recombinant fusion protein targeting IL-2 receptor-expressing malignant T lymphocytes, in patients with stage IA CD25 assay-positive cutaneous T-cell lymphoma (CTCL), including the mycosis fungoides Sézary syndrome forms disease, who had received up three prior therapies. The primary end point overall response...

Accurate prognosis of breast cancer can spare a significant number patients from receiving unnecessary adjuvant systemic treatment and its related expensive medical costs. Recent studies have demonstrated the potential value gene expression signatures in assessing risk post-surgical disease recurrence. However, these all attempt to develop genetic marker-based prognostic systems replace existing clinical criteria, while ignoring rich information contained established markers. Given...

Recent advances in massively parallel sequencing technology have created new opportunities to probe the hidden world of microbes. Taxonomy-independent clustering 16S rRNA gene is usually first step analyzing microbial communities. Dozens algorithms been developed last decade, but a comprehensive benchmark study lacking. Here, we survey currently used by microbiologists, and compare seven representative methods large-scale that addresses several issues concern. A experimental protocol was...

Systemic acquired resistance (SAR) is a long-lasting plant immunity against broad spectrum of pathogens. Biological induction SAR requires the signal molecule salicylic acid (SA) and involves profound transcriptional changes that are largely controlled by transcription coactivator NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1 (NPR1). However, it unclear how signals transduced from NPR1 signaling node to general machinery. Here, we report Arabidopsis thaliana Mediator subunit16 (MED16) an...

Taxonomy-independent analysis plays an essential role in microbial community analysis. Hierarchical clustering is one of the most widely employed approaches to finding operational taxonomic units, basis for many downstream analyses. Most existing algorithms have quadratic space and computational complexities, thus can be used only small or medium-scale problems. We propose a new online learning-based algorithm that simultaneously addresses issues prior work. The basic idea partition sequence...

The spaceflight environment presents unique challenges to terrestrial biology, including but not limited the direct effects of gravity. As we near end Space Shuttle era, there remain fundamental questions about response and adaptation plants orbital conditions. We address a key baseline question whether gene expression changes are induced by environment, then ask undifferentiated cells, cells presumably lacking typical gravity mechanisms, perceive spaceflight. Arabidopsis seedlings cultured...

The modern Western diet is rich in advanced glycation end products (AGEs). We have previously shown an association between dietary AGEs and markers of inflammation oxidative stress a population stage renal disease (ESRD) patients undergoing peritoneal dialysis (PD). In the current pilot study we explored effects on gut bacterial microbiota composition similar patients. play important role development progression cardiovascular (CVD) disease. Plasma concentrations different been to predict...

Abstract Motivation Cancer subtype classification has the potential to significantly improve disease prognosis and develop individualized patient management. Existing methods are limited by their ability handle extremely high-dimensional data influence of misleading, irrelevant factors, resulting in ambiguous overlapping subtypes. Results To address above issues, we proposed a novel approach disentangling eliminating factors leveraging power deep learning. Specifically, designed...

Reticulitermes flavipes (Isoptera: Rhinotermitidae) is a highly eusocial insect that thrives on recalcitrant lignocellulosic diets through nutritional symbioses with gut-dwelling prokaryotes and eukaryotes. In the R. hindgut, there are up to 12 eukaryotic protozoan symbionts; number of prokaryotic symbionts has been estimated in hundreds. Despite its biological relevance, this diverse community, date, investigated only by culture- cloning-dependent methods. Moreover, it unclear how termite...

Currently, taxonomic interrogation of microbiota is based on amplification 16S rRNA gene sequences in clinical and scientific settings. Accurate evaluation the depends heavily primers used, genus/species resolution bias can arise with non-representative genomic regions. The latest Illumina MiSeq sequencing chemistry has extended read length to 300 bp, enabling deep profiling large number samples a single paired-end reaction at fraction cost. An increasingly researchers have adopted this...

We present a new dimensionality reduction setting for large family of real-world problems. Unlike traditional methods, the aims to explicitly represent and learn an intrinsic structure from data in high-dimensional space, which can greatly facilitate visualization scientific discovery downstream analysis. propose dimensionality-reduction framework that involves learning mapping function projects points original space latent low-dimensional are then used directly construct graph. Local...

Intestinal colonization of the oral bacterium Haemophilus parainfluenzae has been associated with Crohn's disease (CD) severity and progression. This study examines role periodontal (PD) as a modifier for H. in patients CD explores mechanisms behind parainfluenzae-mediated intestinal inflammation. Fifty subjects without were evaluated presence PD, their fecal microbiomes characterized. PD is increased levels strains CD. Oral inoculation elicits strain-dependent inflammation murine models...

Abstract Background Obesity is an important risk factor for heart failure (HF). Hypothesis Visceral adiposity index (VAI) a simple metric assessing obesity; however, the association between VAI and HF has not been studied. Methods A cross‐sectional study involving 28 764 participants ≥18 years of age from National Health Nutrition Examination Survey (NHANES), 2009–2018, in United States was performed. calculated using body mass (BMI), waist circumference (WC), triglycerides (TG),...

We propose a series of new feature weighting algorithms, all stemming from interpretation RELIEF as an online algorithm that solves convex optimization problem with margin-based objective function. The explains the simplicity and effectiveness RELIEF, enables us to identify some its weaknesses. offer analytic solution mitigate these problems. extend newly proposed handle multiclass problems by using margin definition. To reduce computational costs, learning is also developed. Convergence...

The Arabidopsis thaliana Elongator complex subunit2 (ELP2) genetically interacts with NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1 (NPR1), a key transcription coactivator of plant immunity, and regulates the induction kinetics defense genes. However, mechanistic relationship between ELP2 NPR1 how gene are unclear. Here, we demonstrate that is an epigenetic regulator required for pathogen-induced rapid transcriptome reprogramming. We show functions in transcriptional feed-forward loop...

Bladder cancer is among the five most common malignancies worldwide, and due to high rates of recurrence, one prevalent. Improvements in noninvasive urine-based assays detect bladder would benefit both patients health care systems. In this study, goal was identify urothelial cell transcriptomic signatures associated with cancer.Gene expression profiling (Affymetrix U133 Plus 2.0 arrays) applied exfoliated urothelia obtained from a cohort 92 subjects known disease status. Computational...

Summary Pathogen infection in plants triggers large‐scale transcriptional changes, both locally and systemically. Emerging evidence suggests that the A rabidopsis M ediator complex plays a crucial role these changes. Mediator is highly conserved eukaryotes, its core comprises more than 20 subunits organized into three modules named head, middle tail. The head interact with general transcription factors RNA polymerase II , whereas tail module associates activators, signals through to basal...