bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accuracy improvement of phase estimation in electron holography using noise reduction methods
Authors: Midoh Yoshihiro , Nakamae Koji 
Published: November 2019

Abstract
We try to improve the limit of the phase estimation of the interference fringe at low electron dose levels in electron holography by a noise reduction method. In this paper, we focus on unsupervised approaches to apply it to electron beam-sensitive and unknown samples and describe an overview of denoising methods used widely in image processing, such as wiener filter, total variation denoising, nonlocal mean filters and wavelet thresholding. We compare the wavelet hidden Markov model (WHMM) denoising that we have studied so far with the other conventional noise reduction methods. We evaluate the denoise performance of each method using the peak signal-to-noise ratio between noise-free and the target holograms (noisy or denoised holograms) and the root mean-square error (RMSE) between the true phase of the fringe and the measured phase by the discrete Fourier transform phase estimator. We show the denoised holograms for simulation and experimental data by using each noise reduction method and then discuss evaluation indexes obtained from these denoised holograms. From experimental results, it can be seen that the WHMM denoising can reduce the RMSE of fringe phase to about 1/4.5 for noisy simulation holograms and it has stable and good performance for noise reduction of observed holograms with various image qualities.
Kinematical investigation of possible fast collimated outflows in twelve planetary nebulae
Authors: Rechy-García J S , Guerrero M A , Duarte Puertas S , Chu Y-H , Toalá J A , Miranda L F 
Published: November 2019

ABSTRACT
A significant fraction of planetary nebulae (PNe) exhibit collimated outflows, distinct narrow kinematical components with notable velocity shifts with respect to the main nebular shells typically associated with low-ionization compact knots and linear or precessing jet-like features. We present here a spatio-kinematical investigation of a sample of 12 PNe with morphologies in emission lines of low-ionization species suggestive of collimated outflows. Using archival narrow-band images and our own high-dispersion long-slit echelle spectra, we confirm the presence of collimated outflows in Hen 2-429, J 320, M 1-66, M 2-40, M 3-1, and NGC 6210 and possibly in NGC 6741, for which the spatio-kinematical data can also be interpreted as a pair of bipolar lobes. The presence of collimated outflows is rejected in Hen 2-47, Hen 2-115, M 1-26, and M 1-37, but their morphology and kinematics are indicative of the action of supersonic outflows that have not been able to pierce through the nebular envelope. In this sense, M 1-66 appears to have experienced a similar interaction between the outflow and nebular envelope, but, as opposed to these four PNe, the outflow has been able to break through the nebular envelope. It is suggested that the PNe without collimated outflows in our sample are younger or descend from lower mass progenitors than those that exhibit unambiguous collimated outflows.
Freshwater Perkinsea: diversity, ecology and genomic information
Authors: Jobard M , Wawrzyniak I , Bronner G , Marie D , Vellet A , Sime-Ngando T , Debroas D , Lepère C 
Published: November 2019

AbstractStudies on freshwater Perkinsea are scarce compared to their marine counterparts; they are therefore not well ecologically characterized. In this study, we investigated the diversity, distribution and ecological role of Perkinsea in freshwater ecosystems. Our approach included (1) the phylogenetic analyses of near full-length SSU and LSU sequences of freshwater Perkinsea, (2) a meta-analysis of public Perkinsea 18S ribosomal RNA gene sequences available from the freshwater environments (25 lakes, 4 rivers), (3) microscopic observations of Perkinsea associated with planktonic communities and (4) single amplified genome analysis. Whereas Perkinsea appear to be rare in river ecosystems (85 reads), they are found in almost all of the lakes studied. However, their diversity does vary considerably between lakes (from 0 to 2 463 Operational Taxonomic Units (OTUs)). Phylogenetic analysis showed that the Parvilucifera/Dinovorax/Snorkelia and Perkinsus/Xcellia/Gadixcellia clades resulted from an initial speciation event. This second clade is further split into well-supported, monophyletic groups, including a clade dominated by freshwater representatives, which is further structured into three distinct subclades: freshwater clade 1, freshwater clade 2 and a freshwater and brackish clade. The Perkinsea Single Amplified Genome (SAG) as well as most of the abundant Operational Taxonomic Units (OTUs) fall into freshwater clade 2. The tyramide signal amplification-fluorescent in situ hybridization method showed an internal association between Perkinsea and the colonial phytoplankton Sphaerocystis. The Single Amplified Genome (SAG) annotation contained 698 genes and gene ontology terms could be assigned to 486 protein-coding genes. Although the number of genes appears to be low (10.6% of the entire gene set assessed by BUSCO), the analysis of the proteome revealed some putative secreted virulence factors. This study showed a large distribution of Perkinsea across lake ecosystems and potential parasitic association with phytoplankton. However, further investigations are needed for a better knowledge on the role of these microorganisms in freshwater ecosystems.
Use of effective training and quality assurance strategies is associated with high-fidelity EBI implementation in practice settings: a case analysis
Authors: Dolcini M Margaret , Davey-Rothwell Melissa A , Singh Ryan R , Catania Joseph A , Gandelman Alice A , Narayanan Vasudha , Harris Justin , McKay Virginia R 
Published: November 2019

Abstract
High-quality implementation of evidence-based interventions is important for program effectiveness and is influenced by training and quality assurance (QA). However, gaps in the literature contribute to a lack of guidance on training and supervision in practice settings, particularly when significant adaptations in programs occur. We examine training and QA in relationship to program fidelity among organizations delivering a widely disseminated HIV counseling and testing EBI in which significant adaptations occurred due to new testing technology. Using a maximum variation case study approach, we examined training and QA in organizations delivering the program with high- and low-fidelity (agencies: 3 = high; 3 = low). We identified themes that distinguished high- and low-fidelity agencies. For example, high-fidelity agencies more often employed a team approach to training; demonstrated use of effective QA strategies; leveraged training and QA to identify and adjust for fit problems, including challenges related to adaptations; and understood the distinctions between RESPECT and other testing programs. The associations between QA and fidelity were strong and straightforward, whereas the relationship between training and fidelity was more complex. Public health needs high-quality training and QA approaches that can address program fit and program adaptations. The study findings reinforced the value of using effective QA strategies. Future work should address methods of increasing program fit through training and QA, identify a set of QA strategies that maximize program fidelity and is feasible to implement, and identify low-cost supplemental training options.
Transcript degradation and codon usage regulate gene expression in a lytic phage†
Authors: Jack Benjamin R , Boutz Daniel R , Paff Matthew L , Smith Bartram L , Wilke Claus O 
Published: November 2019

AbstractMany viral genomes are small, containing only single- or double-digit numbers of genes and relatively few regulatory elements. Yet viruses successfully execute complex regulatory programs as they take over their host cells. Here, we propose that some viruses regulate gene expression via a carefully balanced interplay between transcription, translation, and transcript degradation. As our model system, we employ bacteriophage T7, whose genome of approximately sixty genes is well annotated and for which there is a long history of computational models of gene regulation. We expand upon prior modeling work by implementing a stochastic gene expression simulator that tracks individual transcripts, polymerases, ribosomes, and ribonucleases participating in the transcription, translation, and transcript-degradation processes occurring during a T7 infection. By combining this detailed mechanistic modeling of a phage infection with high-throughput gene expression measurements of several strains of bacteriophage T7, evolved and engineered, we can show that both the dynamic interplay between transcription and transcript degradation, and between these two processes and translation, appear to be critical components of T7 gene regulation. Our results point to targeted degradation as a generic gene regulation strategy that may have evolved in many other viruses. Further, our results suggest that detailed mechanistic modeling may uncover the biological mechanisms at work in both evolved and engineered virus variants.
ST3GAL3, ST3GAL4, and ST3GAL6 differ in their regulation of biological functions via the specificities for the α2,3‐sialylation of target proteins
Authors: Qi Feng , Isaji Tomoya , Duan Chengwei , Yang Jie , Wang Yuqin , Fukuda Tomohiko , Gu Jianguo 
Published: November 2019

AbstractThe α2,3‐sialylation of N‐glycans is considered important but complicated because the functions of the three β‐galactoside α2,3‐sialyltransferases, ST3GAL3, ST3GAL4, and ST3GAL6, could be compensating for one another. To distinguish their specific functions, we established each individual knockout (KO) cell line. Loss of either the ST3GAL3 or ST3GAL6 genes decreased cell proliferation and colony formation, as opposed to the effect in the ST3GAL4 KO cells. The phosphorylation levels of ERK and AKT were significantly suppressed in the ST3GAL6 KO and ST3GAL3 KO cells, respectively. The cell aggregations were clearly observed in the KO cells, particularly the ST3GAL3 KO and ST3GAL6 KO cells, and the expression levels of E‐cadherin and claudin‐1 were enhanced in both those cell lines, but were suppressed in the ST3GAL4 KO cells. Those alterations were reversed with an overexpression of each corresponding gene in rescued cells. Of particular interest, the α2,3‐sialylation levels of β1 integrin were clearly suppressed in the ST3GAL4 KO cells, but these were increased in the ST3GAL3 KO and ST3GAL6 KO cells, whereas the α2,3‐sialylation levels of EGFR were significantly decreased in the ST3GAL6 KO cells. The decrease in α2,3‐sialylation increased the α2,6‐sialylation on β1, but not EGFR. Furthermore, a cross‐restoration of each of the three genes in ST3GAL6 KO cells showed that overexpression of ST3GAL6 sufficiently rescued the total α2,3‐sialylation levels, cell morphology, and α2,3‐sialylation of EGFR, whereas the α2,3‐sialylation levels of β1 were greatly enhanced by an overexpression of ST3GAL4. These results clearly demonstrate that the three α2,3‐sialyltransferases modify characteristic target proteins and regulate cell biological functions in different ways.
Lineage specification and pluripotency revealed by transcriptome analysis from oocyte to blastocyst in pig
Authors: Kong Qingran , Yang Xu , Zhang Heng , Liu Shichao , Zhao Jianchao , Zhang Jiaming , Weng Xiaogang , Jin Junxue , Liu Zhonghua 
Published: November 2019

AbstractThe inner cell mass (ICM) in blastocyst is the origin of all somatic and germ cells in mammals and pluripotent stem cells (PSCs) in vitro. As the conserved principles between pig and human, here we performed comprehensive single‐cell RNA‐seq for porcine early embryos from oocyte to early blastocyst (EB). We show the specification of the ICM and trophectoderm in morula and the molecular signature of the precursors. We demonstrate the existence of naïve pluripotency signature in morula and ICM of EB, and the specific pluripotent genes and the activity of signalling pathways highlight the characteristics of the naïve pluripotency. We observe the absence of dosage compensation with respect to X‐chromosome (XC) in morula, and incomplete dosage compensation in the EB. However, the dynamics of dosage compensation may be independent of the expression of XIST induced XC inactivation. Our study describes molecular landmarks of embryogenesis in pig that will provide a better strategy for derivation of porcine PSCs and improve research in regenerative medicine.
Auxiliary subunits control biophysical properties and response to compound NS5806 of the Kv4 potassium channel complex
Authors: Zhang Hongxue , Zhang Hua , Wang Chanjuan , Wang Yuhong , Zou Ruya , Shi Chenxia , Guan Bingcai , Gamper Nikita , Xu Yanfang 
Published: November 2019

AbstractKv4 pore‐forming subunits co‐assemble with β‐subunits including KChIP2 and DPP6 and the resultant complexes conduct cardiac transient outward K+ current (Ito). Compound NS5806 has been shown to potentate Ito in canine cardiomyocytes; however, its effects on Ito in other species yet to be determined. We found that NS5806 inhibited native Ito in a concentration‐dependent manner (0.1~30 μM) in both mouse ventricular cardiomyocytes and human‐induced pluripotent stem cell‐derived cardiomyocytes (hiPSC‐CMs), but potentiated Ito in the canine cardiomyocytes. In HEK293 cells co‐transfected with cloned Kv4.3 (or Kv4.2) and β‐subunit KChIP2, NS5806 significantly increased the peak current amplitude and slowed the inactivation. In contrast, NS5806 suppressed the current and accelerated inactivation of the channels when cells were co‐transfected with Kv4.3 (or Kv4.2), KChIP2 and another β‐subunit, DPP6‐L (long isoform). Western blot analysis showed that DPP6‐L was dominantly expressed in both mouse ventricular myocardium and hiPSC‐CMs, while it was almost undetectable in canine ventricular myocardium. In addition, low level of DPP6‐S expression was found in canine heart, whereas levels of KChIP2 expression were comparable among all three species. siRNA knockdown of DPP6 antagonized the Ito inhibition by NS5806 in hiPSC‐CMs. Molecular docking simulation suggested that DPP6‐L may associate with KChIP2 subunits. Mutations of putative KChIP2‐interacting residues of DPP6‐L reversed the inhibitory effect of NS5806 into potentiation of the current. We conclude that a pharmacological modulator can elicit opposite regulatory effects on Kv4 channel complex among different species, depending on the presence of distinct β‐subunits. These findings provide novel insight into the molecular design and regulation of cardiac Ito. Since Ito is a potential therapeutic target for treatment of multiple cardiovascular diseases, our data will facilitate the development of new therapeutic Ito modulators.
Patterns of self-medication among university students in San Jose, Costa Rica
Authors: Norori Maria Natalia 
Published: November 2019

AbstractBackgroundSelf-medication is defined as the use of drugs to treat self-diagnosed symptoms without the supervision of healthcare physicians. Self-medication is a growing public health phenomenon and is associated with risks such as misdiagnosis and drug toxicity. This study aimed to identify the patterns associated with the practice of self- medication among university students in San José, Costa Rica.MethodsA descriptive cross-sectional study was designed and conducted to identify variables associated. Information was collected on the conditions treated, medications used and their sources.ResultsThe study found that self-medication is highly prevalent among Costa Rican university students. 91.4% of the sample reported self-medicating, with each student consuming an average of 2.15, ± 1,08 drugs. The most Frequently used active ingredients were paracetamol and Ibuprofen. Results also show a relation between the most consumed types of drugs and the principal causes of drug intoxication reported by Costa Rica’s National Poison Center. 77.8% of the participants considered self-medication a risky practice.ConclusionsSelf-medication is common among Costa Rican university students. The prevalence found is higher than that reported in previous studies conducted in the country. These findings suggest the need to implement prevention campaigns and regulatory policies to ensure the safe consumption of medical drugs.
Algorithmic discovery of dynamic models from infectious disease data
Authors: Horrocks Jonathan , Bauch Chris T. 
Published: November 2019

ABSTRACTTheoretical models are typically developed through a deductive process where a researcher formulates a system of dynamic equations from hypothesized mechanisms. Recent advances in algorithmic methods can discover dynamic models inductively– directly from data. Most previous research has tested these methods by rediscovering models from synthetic data generated by the already known model. Here we apply Sparse Identification of Nonlinear Dynamics (SINDy) to discover mechanistic equations for disease dynamics from case notification data for measles, chickenpox, and rubella. The discovered models provide a good qualitative fit to the observed dynamics for all three diseases, However, the SINDy chickenpox model appears to overfit the empirical data, and recovering qualitatively correct rubella dynamics requires using power spectral density in the goodness-of-fit criterion. When SINDy uses a library of second-order functions, the discovered models tend to include mass action incidence and a seasonally varying transmission rate–a common feature of existing epidemiological models for childhood infectious diseases. We also find that the SINDy measles model is capable of out-of-sample prediction of a dynamical regime shift in measles case notification data. These results demonstrate the potential for algorithmic model discovery to enrich scientific understanding by providing a complementary approach to developing theoretical models.
Estimating the Per-Application Effectiveness of Chlorhexidine Gluconate and Mupirocin in Methicillin-resistant Staphylococcus aureus Decolonization in Intensive Care Units
Authors: Lofgren Eric T. , Mietchen Matthew , Short Christopher , Dicks Kristen V. , Moehring Rebekah , Anderson Deverick ,   for the CDC MIND-Healthcare Program
Published: November 2019

AbstractIntroductionChlorhexidine gluconate and mupirocin are widely used to decolonize patients with methicillin-resistant Staphylococcus aureus (MRSA) and reduce risks of infection in hospitalized populations. The probability that a treated patient would be decolonized, which we term per-application effectiveness, is difficult to directly measure. Quantifying the efficacy of per-application effectiveness of CHG and mupirocin is important for studies evaluating alternative decolonization strategies or schedules as well as identifying whether there is room for improved decolonizing agents.MethodsUsing a stochastic compartmental model of an intensive care unit (ICU), the per-application effectiveness of chlorhexidine and mupirocin were estimated using approximate Bayesian computation. Extended sensitivity analysis examined the potential impact of a latent period between MRSA colonization and detection, the timing of decolonization administration, and parameter uncertainty.ResultsThe estimated per-application effectiveness of chlorhexidine was 0.15 (95% Credible Interval: 0.01, 0.42), while the estimated effectiveness of mupirocin was is 0.15 (95% CI: 0.01, 0.54). A lag in colonization detection markedly reduced both estimates, which were particularly sensitive to the value to the modeled contact rate between nurses and patients. Gaps longer than 24-hours in the administration of decolonizing agents still resulted in substantial reduction of within-ICU MRSA transmission.DiscussionThe per-application effectiveness estimates for chlorhexidine and mupirocin suggest there is room for substantial improvement in anti-MRSA disinfectants, either in the compounds themselves, or in their delivery mechanism. Despite these estimates, these agents are robust to delays in administration, which may help in alleviating concerns over patient comfort or toxicity.
A Cognitive Development Chart for School-age Children and Adolescents
Authors: Simioni André R. , Pine Daniel S. , Sato João R. , Pan Pedro M. , Fonseca Rochele Paz , Schafer Julia , Miguel Euripedes C. , Mari Jair J. , Gadelha Ary , Bressan Rodrigo A. , Rohde Luis A. , Salum Giovanni A. 
Published: November 2019

ABSTRACTObjectiveTo evaluate the reliability and predictive utility of a time-efficient cognitive development chart that seeks to identify children and adolescents with high-risk for multiple outcomes such as mental health problems, substance use, and educational difficulties.MethodWe analyzed data from the Brazilian High-Risk Cohort for Psychiatric Disorders (HRC), a longitudinal school-based study conducted from 2010-2011 to 2013-2014. Participants were 2,239 children and adolescents, 6 to 17 years of age, who completed the cognitive assessment at baseline. The task used to track cognitive development was the Two Choice Reaction Time task (<3 minutes of duration, computer-based), which assesses the accuracy and speed of perceptual decision-making. Mental health, substance use, and educational outcomes were assessed by validated standardized methods. Key variables were measured at baseline and 3-year follow-up. The predictive utility was assessed using static (deviations from the age-expected performance at baseline) and dynamic (deviations from the age-expected change in performance over time) indicators.ResultsThe reliability of the task parameter was high (intra-class correlation coefficient = 0.8). Static indicators of cognitive development significantly predicted concurrent mental, intellectual and educational difficulties, as well as incident and persistent educational difficulties and substance use in the 3-year follow-up. Dynamic indicators predicted persistent mental health problems.ConclusionPrimary-care and mental health professionals need a time-efficient tool for tracking deviations from age-expected cognitive development, which predicts multiple unwanted outcomes at the same time. If replicated, future results could support the generation of tools for tracking risk for mental health, substance use, and educational difficulties.
Electrophysiological Studies of Reception of Facial Communication in Autism Spectrum Disorder and Schizophrenia
Authors: Levy Emily J. , Foss-Feig Jennifer , Isenstein Emily L. , Srihari Vinod , Anticevic Alan , Naples Adam J. , McPartland James C. 
Published: November 2019

ABSTRACTAutism spectrum disorder (ASD) and schizophrenia spectrum disorders (SZ) are both characterized by difficulty with social cognition. Likewise, social brain activity is atypical in both disorders and indicates atypical reception of facial communication – a key area in the Research Domain Criteria framework for identifying common biological underpinnings of psychiatric disorders. To identify areas of overlap and dissociation between ASD and SZ, this paper reviews studies of electrophysiological (EEG) response to facial stimuli across ASD and SZ populations. We focus on findings regarding amplitude and latency of four brain responses implicated in social perception: P100, N170, N250, and P300. There were many inconsistent findings in both the ASD and SZ literatures; however, replication across studies was strongest for delayed N170 latency in ASD and attenuated N170 amplitude in SZ. EEG responses corresponded with clinical symptoms in multiple samples. These results highlight the challenges associated with replicating research findings in heterogeneous clinical populations, as well as the need for transdiagnostic research and for designing studies to examine relationships among continuous quantifications of behavior and neural activity across neurodevelopmental disorders.