bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parametric study of high-frequency characteristics of plasma synthetic jet actuator
Authors: SONG Guozheng , ZONG Haohua , LIANG Hua , SU Zhi , XIE Like , ZHENG Xing 
Published: October 2021

Abstract
A major issue of plasma synthetic jet actuator (PSJA) is the severe performance deterioration at high working frequency. In this study, experiments and numerical simulation are combined together to investigate the influence of thermal conductivity, throat length (L
th) and discharge duration (T
d) on the high-frequency characteristics of PSJA. Results show that the variation of the actuator thermal conductivity and discharge duration will not alter the saturation frequency of the actuator, whereas decreasing the throat length results in an increase of the saturation frequency. For a short-duration capacitive discharge of 1.7 μs, a clear shock wave is issued from the orifice, followed by a weak jet. As a comparison, when the discharge duration is increased up to 202.6 μs, a strong jet column is formed and no obvious shock wave can be visualized. Based on numerical simulation results, it becomes clear that the long-duration pulse-DC discharge is able to heat the cavity gas to a much higher temperature (3141 K) than capacitive discharge, greatly improving the conversion efficiency of the arc discharge energy to the internal energy of the cavity gas. In addition, high-speed Schlieren imaging is deployed to study the performance degradation mechanism of PSJA at high working frequency. Monitor of the exit jet grayscale indicates that as long as the saturation frequency is exceeded, the actuator becomes unstable due to insufficient refresh time. The higher the discharge frequency, the more frequently the phenomenon of ‘misfires’ will occur, which explains well the decaying jet total pressure at above saturation frequency.
Different transcriptional levels of Corazonin, Elevenin, and PDF according to the body color of the two-spotted cricket, Gryllus bimaculatus
Authors: Seike Hitomi , Nagata Shinji 
Published: October 2021

ABSTRACT
Body color in insects changes according to the living environment and physiological stresses possibly involved in endocrine factors. To date, 3 predominant bioactive peptides, Corazonin, Elevenin, and pigment-dispersing factor (PDF), have been illuminated to be involved in the body color in insects and crustaceans. Here, we examined the possibilities that these 3 factors would contribute to body color changes via melanization in the two-spotted cricket, Gryllus bimaculatus, whose body color changes according to population density drastically. Quantitative analyses revealed the higher transcriptional levels of Corazonin and Elevenin in the crowded-conditioned crickets, whereas the transcriptional level of PDF was higher in the isolated-conditioned crickets. However, the body color was not changed by knockdown of Corazonin, Elevenin, and PDF by RNA interference. The present data indicated that coloration mechanisms in G. bimaculatus is differently controlled from the previous observation in Locusta migratoria, a closely related orthopteran species.
Testing hormonal responses to real and simulated social challenges in a competitive female bird
Authors: George Elizabeth M , Wolf Sarah E , Bentz Alexandra B , Rosvall Kimberly A 
Published: October 2021

Abstract
Competitive interactions often occur in series; therefore animals may respond to social challenges in ways that prepare them for success in future conflict. Changes in the production of the steroid hormone testosterone (T) are thought to mediate phenotypic responses to competition, but research over the past few decades has yielded mixed results, leading to several potential explanations as to why T does not always elevate following a social challenge. Here, we measured T levels in tree swallows (Tachycineta bicolor), a system in which females compete for limited nesting cavities and female aggression is at least partially mediated by T. We experimentally induced social challenges in two ways: (1) using decoys to simulate territorial intrusions and (2) removing subsets of nesting cavities to increase competition among displaced and territory-holding females. Critically, these experiments occurred pre-laying, when females are physiologically capable of rapidly increasing circulating T levels. However, despite marked aggression in both experiments, T did not elevate following real or simulated social challenges, and in some cases, socially challenged females had lower T levels than controls. Likewise, the degree of aggression was negatively correlated with T levels following a simulated territorial intrusion. Though not in line with the idea that social challenges prompt T elevation in preparation for future challenges, these patterns nevertheless connect T to territorial aggression in females. Coupled with past work showing that T promotes aggression, these results suggest that T may act rapidly to allow animals to adaptively respond to the urgent demands of a competitive event.
Matrix factorization for biomedical link prediction and scRNA-seq data imputation: an empirical survey
Authors: Ou-Yang Le , Lu Fan , Zhang Zi-Chao , Wu Min 
Published: October 2021

AbstractAdvances in high-throughput experimental technologies promote the accumulation of vast number of biomedical data. Biomedical link prediction and single-cell RNA-sequencing (scRNA-seq) data imputation are two essential tasks in biomedical data analyses, which can facilitate various downstream studies and gain insights into the mechanisms of complex diseases. Both tasks can be transformed into matrix completion problems. For a variety of matrix completion tasks, matrix factorization has shown promising performance. However, the sparseness and high dimensionality of biomedical networks and scRNA-seq data have raised new challenges. To resolve these issues, various matrix factorization methods have emerged recently. In this paper, we present a comprehensive review on such matrix factorization methods and their usage in biomedical link prediction and scRNA-seq data imputation. Moreover, we select representative matrix factorization methods and conduct a systematic empirical comparison on 15 real data sets to evaluate their performance under different scenarios. By summarizing the experimental results, we provide general guidelines for selecting matrix factorization methods for different biomedical matrix completion tasks and point out some future directions to further improve the performance for biomedical link prediction and scRNA-seq data imputation.
TargetNet: functional microRNA target prediction with deep neural networks
Authors: Min Seonwoo , Lee Byunghan , Yoon Sungroh 
Published: October 2021

Abstract

Motivation
MicroRNAs (miRNAs) play pivotal roles in gene expression regulation by binding to target sites of messenger RNAs (mRNAs). While identifying functional targets of miRNAs is of utmost importance, their prediction remains a great challenge. Previous computational algorithms have major limitations. They use conservative candidate target site (CTS) selection criteria mainly focusing on canonical site types, rely on laborious and time-consuming manual feature extraction, and do not fully capitalize on the information underlying miRNA–CTS interactions.

Results
In this article, we introduce TargetNet, a novel deep learning-based algorithm for functional miRNA target prediction. To address the limitations of previous approaches, TargetNet has three key components: (i) relaxed CTS selection criteria accommodating irregularities in the seed region, (ii) a novel miRNA–CTS sequence encoding scheme incorporating extended seed region alignments and (iii) a deep residual network-based prediction model. The proposed model was trained with miRNA–CTS pair datasets and evaluated with miRNA–mRNA pair datasets. TargetNet advances the previous state-of-the-art algorithms used in functional miRNA target classification. Furthermore, it demonstrates great potential for distinguishing high-functional miRNA targets.

Availability and implementation
The codes and pre-trained models are available at https://github.com/mswzeus/TargetNet.
Phylotranscriptomic patterns of network stochasticity and pathway dynamics during embryogenesis
Authors: Ko Kuei-Yueh , Chen Cho-Yi , Juan Hsueh-Fen , Huang Hsuan-Cheng 
Published: October 2021

Abstract

Motivation
The hourglass model is a popular evo-devo model depicting that the developmental constraints in the middle of a developmental process are higher, and hence the phenotypes are evolutionarily more conserved, than those that occur in early and late ontogeny stages. Although this model has been supported by studies analyzing developmental gene expression data, the evolutionary explanation and molecular mechanism behind this phenomenon are not fully understood yet. To approach this problem, Raff proposed a hypothesis and claimed that higher interconnectivity among elements in an organism during organogenesis resulted in the larger constraints at the mid-developmental stage. By employing stochastic network analysis and gene-set pathway analysis, we aim to demonstrate such changes of interconnectivity claimed in Raff’s hypothesis.

Results
We first compared the changes of network randomness among developmental processes in different species by measuring the stochasticity within the biological network in each developmental stage. By tracking the network entropy along each developmental process, we found that the network stochasticity follows an anti-hourglass trajectory, and such a pattern supports Raff’s hypothesis in dynamic changes of interconnections among biological modules during development. To understand which biological functions change during the transition of network stochasticity, we sketched out the pathway dynamics along the developmental stages and found that species may activate similar groups of biological processes across different stages. Moreover, higher interspecies correlations are found at the mid-developmental stages.

Supplementary information
Supplementary data are available at Bioinformatics online.
Advances and perspectives on the evolutionary history and diversification of Neotropical Myrteae (Myrtaceae)
Authors: De Souza Neto José Dias , Dos Santos Eliane Kaltchuk , Lucas Eve , Vetö Nicole Moreira , Barrientos-Diaz Ossman , Staggemeier Vanessa Graziele , Vasconcelos Thais , Turchetto-Zolet Andreia Carina 
Published: October 2021

AbstractMyrtaceae are one of the largest families of flowering plants and are widely distributed in the Neotropics, where they are mainly represented by the tribe Myrteae. Myrteae are the most species-rich tribe of Myrtaceae and include groups with significant ecological and economic importance. Myrteae are considered to be a model group for biodiversity studies in the Neotropics, and so understanding the history of their diversification in this area is extremely important. The last decade has witnessed an increase in macro- and microevolutionary studies of the group, and summarizing this knowledge is now crucial to plan future steps in research on Myrteae. Here we provide the first overview of evolution and diversification studies on Myrteae, highlighting recent advances in understanding their evolutionary history. We discuss biogeography, phylogeny, phylogeography, population genetics, genomics and cytology in light of current knowledge. Finally, we provide perspectives and open hypotheses to be tested in future studies to fill gaps in the evolutionary knowledge of specific groups/taxa in Myrteae.
The ABCD study: brain heterogeneity in intelligence during a neurodevelopmental transition stage
Authors: Zhao Qi , Voon Valerie , Zhang Lingli , Shen Chun , Zhang Jie , Feng Jianfeng 
Published: October 2021

AbstractA complex curvilinear relationship exists between intelligence and age during the neurodevelopment of cortical thickness. To parse out a more fine-grained relationship between intelligence and cortical thickness and surface area, we used a large-scale data set focusing on a critical transition juncture in neurodevelopment in preadolescence. Cortical thickness was derived from T1-weighted structural magnetic resonance images of a large sample of 9- and 11-year-old children from the Adolescent Brain Cognitive Development study. The NIH Toolbox Cognition Battery composite scores, which included fluid, crystallized, and total scores, were used to assess intelligence. Using a double generalized linear model, we assessed the independent association between the mean and dispersion of cortical thickness/surface area and intelligence. Higher intelligence in preadolescents was associated with higher mean cortical thickness in orbitofrontal and primary sensory cortices but with lower thickness in the dorsolateral and medial prefrontal cortex and particularly in the rostral anterior cingulate. The rostral anterior cingulate findings were particularly evident across all subscales of intelligence. Higher intelligence was also associated with greater interindividual similarity in the rostral cingulate. Intelligence during this key transition juncture in preadolescence appears to reflect a dissociation between the cortical development of basic cognitive processes and higher-order executive and motivational processes.
Therapeutic targeting of inflammation in hypertension: from novel mechanisms to translational perspective
Authors: Murray E C , Nosalski R , MacRitchie N , Tomaszewski M , Maffia P , Harrison D G , Guzik T J 
Published: October 2021

Abstract
Animal models, human observational and genetic studies have shown that immune and inflammatory mechanisms play a key role in hypertension and its complications. We review the effects of immunomodulatory interventions on blood pressure, target organ damage and cardiovascular risk in humans. In experimental and small clinical studies both non-specific immunomodulatory approaches, such as mycophenolate mofetil and methotrexate, and medications targeting T and B lymphocytes, such as tacrolimus, cyclosporine, everolimus, rituximab, lower blood pressure and reduce organ damage. Mechanistically targeted immune interventions include isolevuglandin (isoLG) scavengers to prevent neo-antigen formation, co-stimulation blockade (abatacept, belatacept), and anti-cytokine therapies (secukinumab, tocilizumab, canakinumab, TNF-α inhibitors). In many studies, trial designs have been complicated by a lack of blood pressure related endpoints, inclusion of largely normotensive study populations, polypharmacy, and established comorbidities. Among a wide range of interventions reviewed, TNF-α inhibitors have provided the most robust evidence of blood pressure lowering. Treatment of periodontitis also appears to deliver non-pharmacological antihypertensive effects. Evidence of immunomodulatory drugs influencing hypertension-mediated organ damage are discussed. Animal model, observational studies, and trial data in humans support the therapeutic potential of immune targeted therapies in blood pressure lowering and in hypertension-mediated organ damage. Targeted studies are now needed to address their effects on blood pressure in hypertensive individuals.
Genome sequencing of the NIES Cyanobacteria collection with a focus on the heterocyst-forming clade
Authors: Hirose Yuu , Ohtsubo Yoshiyuki , Misawa Naomi , Yonekawa Chinatsu , Nagao Nobuyoshi , Shimura Yohei , Fujisawa Takatomo , Kanesaki Yu , Katoh Hiroshi , Katayama Mitsunori , Yamaguchi Haruyo , Yoshikawa Hirofumi , Ikeuchi Masahiko , Eki Toshihiko , Nakamura Yasukazu , Kawachi Masanobu 
Published: October 2021

Abstract
Cyanobacteria are a diverse group of Gram-negative prokaryotes that perform oxygenic photosynthesis. Cyanobacteria have been used for research on photosynthesis and have attracted attention as a platform for biomaterial/biofuel production. Cyanobacteria are also present in almost all habitats on Earth and have extensive impacts on global ecosystems. Given their biological, economical, and ecological importance, the number of high-quality genome sequences for Cyanobacteria strains is limited. Here, we performed genome sequencing of Cyanobacteria strains in the National Institute for Environmental Studies microbial culture collection in Japan. We sequenced 28 strains that can form a heterocyst, a morphologically distinct cell that is specialized for fixing nitrogen, and 3 non-heterocystous strains. Using Illumina sequencing of paired-end and mate-pair libraries with in silico finishing, we constructed highly contiguous assemblies. We determined the phylogenetic relationship of the sequenced genome assemblies and found potential difficulties in the classification of certain heterocystous clades based on morphological observation. We also revealed a bias on the sequenced strains by the phylogenetic analysis of the 16S rRNA gene including unsequenced strains. Genome sequencing of Cyanobacteria strains deposited in worldwide culture collections will contribute to understanding the enormous genetic and phenotypic diversity within the phylum Cyanobacteria.
Testing conditional moment restriction models using empirical likelihood
Authors: Berger Yves G 
Published: October 2021

Summary
An empirical likelihood test is proposed for parameters of models defined by conditional moment restrictions, such as models with nonlinear endogenous covariates, with and without heteroscedastic errors and non-separable transformation models. The number of empirical likelihood constraints is given by the size of the parameter, unlike alternative semi-parametric approaches. We show that the empirical likelihood ratio test is asymptotically pivotal, without explicit studentization. A simulation study shows that the observed size is close to the nominal level, unlike alternative empirical likelihood approaches. It also offers a major advantage over two-stage least-squares, because the relationship between endogenous and instrumental variables does not need to be known. An empirical likelihood model specification test is also proposed.
Emery-Dreifuss muscular dystrophy presenting as a heart rhythm disorders in children
Authors: Kovalchuk T S , Yakovleva E V , Fetisova S G , Vershinina T L , Pervunina T M , Kostareva A A , Vasichkina E S 
Published: October 2021

Abstract

Introduction
Emery-Dreifuss muscular dystrophy (EDMD) is an inherited muscle dystrophy often accompanied by cardiac abnormalities in the form of supraventricular arrhythmias, conduction defects, sinus node dysfunction. Cardiac phenotype typically arises years after skeletal muscle presentations, though, can be severe and life-threatening. The disease usually manifests during the third decade of life with elbow joint contractions and progressive muscle weakness and atrophy.

Objective
To present our clinical experience of diagnosis and treatment of arrhythmias in children with Emery-Dreifuss muscular dystrophy

Materials and methods
We enrolled 5 patients with different forms of EDMD (X-linked and autosomal dominant) linked to the mutations in EMD and LMNA genes, presented with early onset of cardiac abnormalities and no leading skeletal muscle phenotype. The predominant forms of cardiac pathology were atrial flutter, atrial fibrillation and conduction disturbances that progress over time.
Clinical examination included physical examination, 12-lead electrocardiography, Holter ECG monitoring (HM), transthoracic echocardiography, neurological examination and biochemical and hormone tests. Also we performed CMR, electrophysiological study (EPS), treadmill test of some patients. One patient underwent an endomyocardial biopsy to exclude inflammatory heart disease. Target sequencing was performed using a panel of 108 or 172 genes

Results
We observed five patients with EDMD and cardiac debut during first-second decades of life: 3 with 1st subtype (variants in EMD gene) and 2 with 2nd subtype (variants in LMNA gene). All patients were males. The mean age of cardiac manifestation was 13,2±3,11 (from 9 to 16 y.o.). The mean follow-up period was 7,4±2,6 years.
All patients presented with sinus node dysfunction and four out of five with AV conduction abnormalities. The leading arrhythmic phenotypes included various types of supraventricular arrhythmias: multifocal atrial tachycardia (AT) (n=4), premature atrial captures (PACs) (n=4), atrial flutter, (AF) (n=3), atrial fibrillation (AFib) (n=3) and AV nodal recurrent tachycardia (AVRNT). Heart rhythm disorders were the first manifestation in all three patients with 1st EDMD subtype. Radiofrequency ablation was performed in 2 patients, one of them received permanent pacemaker implantation.

Conclusions
In conclusion, while being the rare cases, heart rhythm disorders can represent the first and for a long time, the only clinical symptom of EDMD even in the pediatric group of patients. Therefore, thorough laboratory and neurological screening along with genetic studies, are of importance in each pediatric patient presenting with complex heart rhythm disorders of primary supraventricular origin to exclude EDMD or other neuromuscular disorders.

Funding Acknowledgement
Type of funding sources: None.
Predictors of cardiac implantable electronic device infection in the United States
Authors: Shah K , Modi V , Gandhi H , Thyagaturu H , Walker A , Shirani J 
Published: October 2021

Abstract

Background
Cardiac implantable electronic devices (CIED) are important tools for managing arrhythmias, improving hemodynamics, and preventing sudden cardiac death. Device infection (DI) remains a significant complication of CIED and is associated with high morbidity, mortality, and healthcare cost.

Purpose
To analyze predictors of DI and its in-hospital outcomes.

Methods
National Inpatient Sample 2011–2018 database was analyzed for admissions for CIED implantation or DI. Baseline and hospital level characteristics were derived. The Chi-square test and student t-test were used for comparison of categorical and continuous variables respectively. Variables with p&lt;0.20 from univariate analysis were included in the multivariate logistic regression to identify independent predictors of DI.

Results
A total of 1,604,173 admissions for CIED implantations and 71,007 (4.4%) admissions for DI were reported during 2011–2018. There was no significant change in annual admissions for DI (range 8550 to 9307, p for trend=0.98). Those with DI were more likely to be male (69.3 vs 57%, p&lt;0.001) and had higher Charlson comorbidity index score ≥3 (46.6%-vs-36.8%, p&lt;0.001). Multivariate analysis identified post-procedural hematoma (odds ratio (OR)=3.96; 95% Confidence Interval (CI)=3.46–4.54), congestive heart failure (CHF; OR=2.80, 95% CI=2.66–2.96), age group 45–60 years (OR=2.46, 95% CI=2.30–2.63), malnutrition (OR=1.99, 95% CI=1.85–2.15), coagulopathy (OR=1.75, 95% CI=1.64–1.86), end-stage renal disease (OR=1.65, 95% CI=1.53–1.78), atrial fibrillation (OR=1.42; 95% CI=1.35–1.49), non-Hispanic race (OR=1.25; 95% CI=1.16–1.36), coronary artery disease (OR=1.21; 95% CI=1.15–1.26), and thyroid disease (OR=1.15; 95% CI=1.09–1.12) [all p&lt;0.001] as independent predictors of DI. Prevalence of CHF, malnutrition, and atrial fibrillation increased in those admitted with DI over the observation period as shown in Figure 1 (p for trend &lt;0.001). Prevalence of diabetes mellitus also increased during the observation period although it was not an independent predictor of DI (p for trend &lt;0.001). Pulmonary embolism and deep vein thrombosis were most common complications in those with DI (4.1 and 3.6% respectively). Annual in-hospital mortality ranged from 3.9 to 5.7% (mean 4.4%, p for trend=0.07).

Conclusion
DI is relatively common and continues to be associated with high morbidity and mortality. Prevalence of DI has not changed significantly despite technical and technological advances in device implantation. Evaluation of risk factors for DI and management of modifiable comorbidities may be needed to reduce the incidence of this important complication of CIED implantation.

Funding Acknowledgement
Type of funding sources: None.