2,703 research outputs found
Characterization of a novel reassortant H5N6 highly pathogenic avian influenza virus clade 2.3.4.4 in Korea, 2017
The C-Fern (Ceratopteris richardii) Genome: Insights Into Plant Genome Evolution With the First Partial Homosporous Fern Genome Assembly
Ferns are notorious for possessing large genomes and numerous chromosomes. Despite decades of speculation, the processes underlying the expansive genomes of ferns are unclear, largely due to the absence of a sequenced homosporous fern genome. The lack of this crucial resource has not only hindered investigations of evolutionary processes responsible for the unusual genome characteristics of homosporous ferns, but also impeded synthesis of genome evolution across land plants. Here, we used the model fern species Ceratopteris richardii to address the processes (e.g., polyploidy, spread of repeat elements) by which the large genomes and high chromosome numbers typical of homosporous ferns may have evolved and have been maintained. We directly compared repeat compositions in species spanning the green plant tree of life and a diversity of genome sizes, as well as both short- and long-read-based assemblies of Ceratopteris. We found evidence consistent with a single ancient polyploidy event in the evolutionary history of Ceratopteris based on both genomic and cytogenetic data, and on repeat proportions similar to those found in large flowering plant genomes. This study provides a major stepping-stone in the understanding of land plant evolutionary genomics by providing the first homosporous fern reference genome, as well as insights into the processes underlying the formation of these massive genomes
Development, Calibration, and Validation of a U.S. White Male Population-Based Simulation Model of Esophageal Adenocarcinoma
The incidence of esophageal adenocarcinoma (EAC) has risen rapidly in the U.S. and western world. The aim of the study was to begin the investigation of this rapid rise by developing, calibrating, and validating a mathematical disease simulation model of EAC using available epidemiologic data.The model represents the natural history of EAC, including the essential biologic health states from normal mucosa to detected cancer. Progression rates between health states were estimated via calibration, which identified distinct parameter sets producing model outputs that fit epidemiologic data; specifically, the prevalence of pre-cancerous lesions and EAC cancer incidence from the published literature and Surveillance, Epidemiology, and End Results (SEER) data. As an illustrative example of a clinical and policy application, the calibrated and validated model retrospectively analyzed the potential benefit of an aspirin chemoprevention program.Model outcomes approximated calibration targets; results of the model's fit and validation are presented. Approximately 7,000 cases of EAC could have been prevented over a 30-year period if all white males started aspirin chemoprevention at age 40 in 1965.The model serves as the foundation for future analyses to determine a cost-effective screening and management strategy to prevent EAC morbidity and mortality
Prognostic relevance of a T-type calcium channels gene signature in solid tumours: A correlation ready for clinical validation
BackgroundT-type calcium channels (TTCCs) mediate calcium influx across the cell membrane. TTCCs regulate numerous physiological processes including cardiac pacemaking and neuronal activity. In addition, they have been implicated in the proliferation, migration and differentiation of tumour tissues. Although the signalling events downstream of TTCC-mediated calcium influx are not fully elucidated, it is clear that variations in the expression of TTCCs promote tumour formation and hinder response to treatment.MethodsWe examined the expression of TTCC genes (all three subtypes; CACNA-1G, CACNA-1H and CACNA-1I) and their prognostic value in three major solid tumours (i.e. gastric, lung and ovarian cancers) via a publicly accessible database.ResultsIn gastric cancer, expression of all the CACNA genes was associated with overall survival (OS) among stage I-IV patients (all pConclusionsAlterations in CACNA gene expression are linked to tumour prognosis. Gastric cancer represents the most promising setting for further evaluation
Visual Depth Mapping from Monocular Images using Recurrent Convolutional Neural Networks
A reliable sense-and-avoid system is critical to enabling safe autonomous
operation of unmanned aircraft. Existing sense-and-avoid methods often require
specialized sensors that are too large or power intensive for use on small
unmanned vehicles. This paper presents a method to estimate object distances
based on visual image sequences, allowing for the use of low-cost, on-board
monocular cameras as simple collision avoidance sensors. We present a deep
recurrent convolutional neural network and training method to generate depth
maps from video sequences. Our network is trained using simulated camera and
depth data generated with Microsoft's AirSim simulator. Empirically, we show
that our model achieves superior performance compared to models generated using
prior methods.We further demonstrate that the method can be used for
sense-and-avoid of obstacles in simulation
Spectrum of confining strings in SU(N) gauge theories
We study the spectrum of the confining strings in four-dimensional SU(N)
gauge theories. We compute, for the SU(4) and SU(6) gauge theories formulated
on a lattice, the string tensions sigma_k related to sources with Z_N charge k,
using Monte Carlo simulations. Our results are consistent with the sine formula
sigma_k/sigma = sin k pi/N / sin pi/N for the ratio between sigma_k and the
standard string tension sigma.
For the SU(4) and SU(6) cases the accuracy is approximately 1% and 2%,
respectively. The sine formula is known to emerge in various realizations of
supersymmetric SU(N) gauge theories. On the other hand, our results show
deviations from Casimir scaling. We also discuss an analogous behavior
exhibited by two-dimensional SU(N) x SU(N) chiral models.Comment: Latex, 34 pages, 10 figures. Results of new SU(4) simulations added.
The new data are included in the analysis, leading to improved final
estimates for SU(4). Conclusions unchange
Results of soy-based meal replacement formula on weight, anthropometry, serum lipids & blood pressure during a 40-week clinical weight loss trial
BACKGROUND: To evaluate the intermediate-term health outcomes associated with a soy-based meal replacement, and to compare the weight loss efficacy of two distinct patterns of caloric restriction. METHODS: Ninety overweight/obese (28 < BMI ≤ 41 kg/m(2)) adults received a single session of dietary counseling and were randomized to either 12 weeks at 1200 kcal/day, 16 weeks at 1500 kcal/d and 12 weeks at 1800 kcal/d (i.e., the 12/15/18 diet group), or 28 weeks at 1500 kcal/d and 12 weeks at 1800 kcal/d (i.e., the 15/18 diet group). Weight, body fat, waist circumference, blood pressure and serum lipid concentrations were measured at 4-week intervals throughout the 40-week trial. RESULTS: Subjects in both treatments showed statistically significant improvements in outcomes. A regression model for weight change suggests that subjects with larger baseline weights tended to lose more weight and subjects in the 12/15/18 group tended to experience, on average, an additional 0.9 kg of weight loss compared with subjects in the 15/18 group. CONCLUSION: Both treatments using the soy-based meal replacement program were associated with significant and comparable weight loss and improvements on selected health variables
Interplay between pleiotropy and secondary selection determines rise and fall of mutators in stress response
Dramatic rise of mutators has been found to accompany adaptation of bacteria
in response to many kinds of stress. Two views on the evolutionary origin of
this phenomenon emerged: the pleiotropic hypothesis positing that it is a
byproduct of environmental stress or other specific stress response mechanisms
and the second order selection which states that mutators hitchhike to fixation
with unrelated beneficial alleles. Conventional population genetics models
could not fully resolve this controversy because they are based on certain
assumptions about fitness landscape. Here we address this problem using a
microscopic multiscale model, which couples physically realistic molecular
descriptions of proteins and their interactions with population genetics of
carrier organisms without assuming any a priori fitness landscape. We found
that both pleiotropy and second order selection play a crucial role at
different stages of adaptation: the supply of mutators is provided through
destabilization of error correction complexes or fluctuations of production
levels of prototypic mismatch repair proteins (pleiotropic effects), while rise
and fixation of mutators occur when there is a sufficient supply of beneficial
mutations in replication-controlling genes. This general mechanism assures a
robust and reliable adaptation of organisms to unforeseen challenges. This
study highlights physical principles underlying physical biological mechanisms
of stress response and adaptation
Atomistic origins of high-performance in hybrid halide perovskite solar cells
The performance of organometallic perovskite solar cells has rapidly
surpassed that of both conventional dye-sensitised and organic photovoltaics.
High power conversion efficiency can be realised in both mesoporous and
thin-film device architectures. We address the origin of this success in the
context of the materials chemistry and physics of the bulk perovskite as
described by electronic structure calculations. In addition to the basic
optoelectronic properties essential for an efficient photovoltaic device
(spectrally suitable band gap, high optical absorption, low carrier effective
masses), the materials are structurally and compositionally flexible. As we
show, hybrid perovskites exhibit spontaneous electric polarisation; we also
suggest ways in which this can be tuned through judicious choice of the organic
cation. The presence of ferroelectric domains will result in internal junctions
that may aid separation of photoexcited electron and hole pairs, and reduction
of recombination through segregation of charge carriers. The combination of
high dielectric constant and low effective mass promotes both Wannier-Mott
exciton separation and effective ionisation of donor and acceptor defects. The
photoferroic effect could be exploited in nanostructured films to generate a
higher open circuit voltage and may contribute to the current-voltage
hysteresis observed in perovskite solar cells.Comment: 6 pages, 5 figure
Anaerobic Carbon Monoxide Dehydrogenase Diversity in the Homoacetogenic Hindgut Microbial Communities of Lower Termites and the Wood Roach
Anaerobic carbon monoxide dehydrogenase (CODH) is a key enzyme in the Wood-Ljungdahl (acetyl-CoA) pathway for acetogenesis performed by homoacetogenic bacteria. Acetate generated by gut bacteria via the acetyl-CoA pathway provides considerable nutrition to wood-feeding dictyopteran insects making CODH important to the obligate mutualism occurring between termites and their hindgut microbiota. To investigate CODH diversity in insect gut communities, we developed the first degenerate primers designed to amplify cooS genes, which encode the catalytic (β) subunit of anaerobic CODH enzyme complexes. These primers target over 68 million combinations of potential forward and reverse cooS primer-binding sequences. We used the primers to identify cooS genes in bacterial isolates from the hindgut of a phylogenetically lower termite and to sample cooS diversity present in a variety of insect hindgut microbial communities including those of three phylogenetically-lower termites, Zootermopsis nevadensis, Reticulitermes hesperus, and Incisitermes minor, a wood-feeding cockroach, Cryptocercus punctulatus, and an omnivorous cockroach, Periplaneta americana. In total, we sequenced and analyzed 151 different cooS genes. These genes encode proteins that group within one of three highly divergent CODH phylogenetic clades. Each insect gut community contained CODH variants from all three of these clades. The patterns of CODH diversity in these communities likely reflect differences in enzyme or physiological function, and suggest that a diversity of microbial species participate in homoacetogenesis in these communities
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