Next generation sequencing (NGS) technologies provide a high-throughput means to generate large amount of sequence data. However, quality control (QC) of sequence data generated from these ...technologies is extremely important for meaningful downstream analysis. Further, highly efficient and fast processing tools are required to handle the large volume of datasets. Here, we have developed an application, NGS QC Toolkit, for quality check and filtering of high-quality data. This toolkit is a standalone and open source application freely available at http://www.nipgr.res.in/ngsqctoolkit.html. All the tools in the application have been implemented in Perl programming language. The toolkit is comprised of user-friendly tools for QC of sequencing data generated using Roche 454 and Illumina platforms, and additional tools to aid QC (sequence format converter and trimming tools) and analysis (statistics tools). A variety of options have been provided to facilitate the QC at user-defined parameters. The toolkit is expected to be very useful for the QC of NGS data to facilitate better downstream analysis.
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Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Prematurity is the leading cause of infant mortality worldwide. In developed countries, extremely preterm infants contribute disproportionately to both neonatal and infant mortality. Survival of this ...high-risk population has incrementally improved in recent years. Despite these improvements, approximately one in four extremely preterm infants dies during the birth hospitalization. Among those who survive, respiratory and other morbidities are common, although their effect on quality of life is variable. In addition, long-term neurodevelopmental impairment is a large concern for patients, clinicians, and families. However, the interplay of multiple factors contributes to neurodevelopmental impairment, with measures that change over time and outcomes that can be difficult to define and predict. Understanding outcomes of extremely preterm infants can help better counsel families regarding antenatal and postnatal care and guide strategies to improve survival without morbidity. This review summarizes recent evidence to provide an overview into the short- and long-term outcomes for extremely preterm infants.
Microbial fuel cell (MFC) is a promising renewable energy technology wherein electrical power is obtained from the metabolism of microorganisms and simultaneous wastewater treatment. For efficient ...operation, MFCs need a control system for balance across fuel supply, mass, charge, and electrical load. Control-oriented models help in developing model based control strategies. Control-oriented parametrized model of single chamber single microorganism is presented in this paper. A backstepping and an adaptive backstepping control of a single chamber microbial fuel cell (MFC) with single microorganism kinetics, is presented. The key advantage of the backstepping scheme is its ability to handle systems with different relative degrees (difference between number of poles and zeros). In order to control the substrate concentration, the dilution rate of the MFC is used as a manipulated input variable. An adaptive action is provided for robustness to model uncertainties and online parameter estimation is performed. Lyapunov stability analysis ensures a convergent control scheme, and the control performances are illustrated using MATLAB/Simulink.
•Control-Oriented Parametrized model for Microbial Fuel Cell is proposed.•A novel adaptive backstepping control strategy is developed.•Adaptive control strategy applied to single chamber single population MFC.•Using dilution rate as input variable, substrate concentration is controlled.
Abstract Little is known about specific modes of death in patients with heart failure with preserved ejection fraction (HFpEF). Herein, the authors critically appraise the current state of data and ...offer potential future directions. They conducted a systematic review of 1,608 published HFpEF papers from January 1, 1985, to December 31, 2015, which yielded 8 randomized clinical trials and 24 epidemiological studies with mode-of-death data. Noncardiovascular modes of death represent an important competing risk in HFpEF. Although sudden death accounted for ∼25% to 30% of deaths in trials, its definition is nonspecific; it is unclear what proportion represents arrhythmic deaths. Moving forward, reporting and definitions of modes of death must be standardized and tailored to the HFpEF population. Broad-scale systematic autopsies and long-term rhythm monitoring may clarify the underlying pathology and mechanisms driving mortal events. There is an unmet need for a longitudinal multicenter, global registry of patients with HFpEF to map its natural history.
IMPORTANCE: The Eunice Kennedy Shriver National Institute of Child Health and Human Development Neonatal Research Network (NRN) extremely preterm birth outcome model is widely used for ...prognostication by practitioners caring for families expecting extremely preterm birth. The model provides information on mean outcomes from 1998 to 2003 and does not account for substantial variation in outcomes among US hospitals. OBJECTIVE: To update and validate the NRN extremely preterm birth outcome model for most extremely preterm infants in the United States. DESIGN, SETTING, AND PARTICIPANTS: This prognostic study included 3 observational cohorts from January 1, 2006, to December 31, 2016, at 19 US centers in the NRN (derivation cohort) and 637 US centers in Vermont Oxford Network (VON) (validation cohorts). Actively treated infants born at 22 weeks’ 0 days’ to 25 weeks’ 6 days’ gestation and weighing 401 to 1000 g, including 4176 in the NRN for 2006 to 2012, 45 179 in VON for 2006 to 2012, and 25 969 in VON for 2013 to 2016, were studied. VON cohorts comprised more than 85% of eligible US births. Data analysis was performed from May 1, 2017, to March 31, 2019. EXPOSURES: Predictive variables used in the original model, including infant sex, birth weight, plurality, gestational age at birth, and exposure to antenatal corticosteroids. MAIN OUTCOMES AND MEASURES: The main outcome was death before discharge. Secondary outcomes included neurodevelopmental impairment at 18 to 26 months’ corrected age and measures of hospital resource use (days of hospitalization and ventilator use). RESULTS: Among 4176 actively treated infants in the NRN cohort (48% female; mean SD gestational age, 24.2 0.8 weeks), survival was 63% vs 62% among 3702 infants in the era of the original model (47% female; mean SD gestational age, 24.2 0.8 weeks). In the concurrent (2006-2012) VON cohort, survival was 66% among 45 179 actively treated infants (47% female; mean SD gestational age, 24.1 0.8 weeks) and 70% among 25 969 infants from 2013 to 2016 (48% female; mean SD gestational age, 24.1 0.8 weeks). Model C statistics were 0.74 in the 2006-2012 validation cohort and 0.73 in the 2013-2016 validation cohort. With the use of decision curve analysis to compare the model with a gestational age–only approach to prognostication, the updated model showed a predictive advantage. The birth hospital contributed equally as much to prediction of survival as gestational age (20%) but less than the other factors combined (60%). CONCLUSIONS AND RELEVANCE: An updated model using well-known factors to predict survival for extremely preterm infants performed moderately well when applied to large US cohorts. Because survival rates change over time, the model requires periodic updating. The hospital of birth contributed substantially to outcome prediction.
The application of deep learning toward discovery of data-driven models requires careful application of inductive biases to obtain a description of physics which is both accurate and robust. We ...present here a framework for discovering continuum models from high fidelity molecular simulation data. Our approach applies a neural network parameterization of governing physics in modal space, allowing a characterization of differential operators while providing structure which may be used to impose biases related to symmetry, isotropy, and conservation form. We demonstrate the effectiveness of our framework for a variety of physics, including local and nonlocal diffusion processes and single and multiphase flows. For the flow physics we demonstrate this approach leads to a learned operator that generalizes to system characteristics not included in the training sets, such as variable particle sizes, densities, and concentration.
•A regression method for discovering operators from molecular simulations is developed.•The enforcement of physical constraints using inductive biases is explored.•The method is demonstrated using local and nonlocal diffusion processes.•The method’s generalizability is shown using a parameterized flow physics example.
COVID‐19 and Older Adults: What We Know Shahid, Zainab; Kalayanamitra, Ricci; McClafferty, Brendan ...
Journal of the American Geriatrics Society,
20/May , Letnik:
68, Številka:
5
Journal Article
Recenzirano
Odprti dostop
Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), a novel virus that causes COVID‐19 infection, has recently emerged and caused a deadly pandemic. Studies have shown that this virus ...causes worse outcomes and a higher mortality rate in older adults and those with comorbidities such as hypertension, cardiovascular disease, diabetes, chronic respiratory disease, and chronic kidney disease (CKD). A significant percentage of older American adults have these diseases, putting them at a higher risk of infection. Additionally, many adults with hypertension, diabetes, and CKD are placed on angiotensin‐converting enzyme (ACE) inhibitors and angiotensin II receptor blockers. Studies have shown that these medications upregulate the ACE‐2 receptor, the very receptor that the SARS‐CoV‐2 virus uses to enter host cells. Although it has been hypothesized that this may cause a further increased risk of infection, more studies on the role of these medications in COVID‐19 infections are necessary. In this review, we discuss the transmission, symptomatology, and mortality of COVID‐19 as they relate to older adults, and possible treatments that are currently under investigation. J Am Geriatr Soc 68:926–929, 2020
We provide a protocol for precision nuclear run-on sequencing (PRO-seq) and its variant, PRO-cap, which map the location of active RNA polymerases (PRO-seq) or transcription start sites (TSSs) ...(PRO-cap) genome-wide at high resolution. The density of RNA polymerases at a particular genomic locus directly reflects the level of nascent transcription at that region. Nuclei are isolated from cells and, under nuclear run-on conditions, transcriptionally engaged RNA polymerases incorporate one or, at most, a few biotin-labeled nucleotide triphosphates (biotin-NTPs) into the 3' end of nascent RNA. The biotin-labeled nascent RNA is used to prepare sequencing libraries, which are sequenced from the 3' end to provide high-resolution positional information for the RNA polymerases. PRO-seq provides much higher sensitivity than ChIP-seq, and it generates a much larger fraction of usable sequence reads than ChIP-seq or NET-seq (native elongating transcript sequencing). Similarly to NET-seq, PRO-seq maps the RNA polymerase at up to base-pair resolution with strand specificity, but unlike NET-seq it does not require immunoprecipitation. With the protocol provided here, PRO-seq (or PRO-cap) libraries for high-throughput sequencing can be generated in 4-5 working days. The method has been applied to human, mouse, Drosophila melanogaster and Caenorhabditis elegans cells and, with slight modifications, to yeast.
Coalescence-induced jumping of condensate droplets from a superhydrophobic surface with hierarchical micro/nanoscale roughness is quantitatively characterized. Experimental observations show that the ...condensate droplet jumping is induced by coalescence of multiple droplets of different sizes, and that the coalesced droplet trajectories typically deviate from the surface normal. A depth-from-defocus image processing technique is developed to track the out-of-plane displacement of the jumping droplets, so as to accurately measure the droplet size and velocity. The results demonstrate that the highest jumping velocity is achieved when two droplets coalesce. The jumping velocity decreases gradually with an increase in the number of coalescing droplets, despite the greater potential surface energy released upon coalescence. A general theoretical model that accounts for viscous dissipation, surface adhesion, line tension, the initial droplet wetting states, and the number and sizes of the coalescing droplets is developed to explain the trends of droplet jumping velocity observed in the experiments.
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