bluuebunny/crossref_metadata_2025 huggingface dataset:
Using Galaxy to Perform Large‐Scale Interactive Data Analyses—An Update
Authors: Ostrovsky Alexander , Hillman‐Jackson Jennifer , Bouvier Dave , Clements Dave , Afgan Enis , Blankenberg Daniel , Schatz Michael C. , Nekrutenko Anton , Taylor James , Team the Galaxy , Lariviere Delphine
Published: February 2021

Modern biology continues to become increasingly computational. Datasets are becoming progressively larger, more complex, and more abundant. The computational savviness necessary to analyze these data creates an ongoing obstacle for experimental biologists. Galaxy (galaxyproject.org) provides access to computational biology tools in a web‐based interface. It also provides access to major public biological data repositories, allowing private data to be combined with public datasets. Galaxy is hosted on high‐capacity servers worldwide and is accessible for free, with an option to be installed locally. This article demonstrates how to employ Galaxy to perform biologically relevant analyses on publicly available datasets. These protocols use both standard and custom tools, serving as a tutorial and jumping‐off point for more intensive and/or more specific analyses using Galaxy. © 2021 Wiley Periodicals LLC.

This article was corrected on 19 July 2022. See the end of the full text for details.

Basic Protocol 1: Finding human coding exons with highest SNP density

Basic Protocol 2: Calling peaks for ChIP‐seq data

Basic Protocol 3: Compare datasets using genomic coordinates

Basic Protocol 4: Working with multiple alignments

Basic Protocol 5: Single cell RNA‐seq
Theoretical Study on the Effect of Solvent Behavior on Ammonium Dinitramide (ADN)/1,4,7,10,13,16‐Hexaoxacyclooctadecane (18‐Crown‐6) Cocrystal Growth Morphology at Different Temperatures
Authors: Xie Hong , Gou Rui‐jun , Zhang Shu‐hai
Published: February 2021

The cocrystal of ammonium dinitramide (ADN)/1,4,7,10,13,16‐hexaoxacyclooctadecane (18‐Crown‐6) has effectively reduced the hygroscopicity of ADN. In order to understand the effect of solvent on the crystal growth, the interfacial models of ADN/18‐Crown‐6–ethanol are built and simulated by the molecular dynamics (MD) method at different temperatures (293–323 K, 10 K intervals). The energy, mass density, radial distribution function, and diffusion capacity of solvent are analyzed. The modified attachment energy (MAE) model is employed to study the solvent effect on cocrystal morphology. Results of MD simulation show that ADN/18‐Crown‐6 cocrystal has four important growth surfaces in vacuum, i.e., (2 0 0), (0 0 2), (1 1 0), and (2 0 −2). The binding energy of cocrystal and the absorbed energy of cocrystal–solvent are larger at 293 K than other temperatures. Hydrogen bonding interactions are formed between ADN/18‐Crown‐6 and solvent. More ethanol molecules adsorb on the crystal surface at lower temperatures, and hence the interaction between cocrystal and solvent is stronger. The morphology of ADN/18‐Crown‐6 cocrystal is different at various temperatures. The predicted morphology at 303 K is consistent with experimental shape. Moreover, cocrystal morphology at 293 K is a sphere‐like shape, which may reduce the hygroscopicity of ADN/18‐Crown‐6 cocrystal.
Catalytic Conversion of Biomass to Furanic Derivatives with Deep Eutectic Solvents
Authors: Chen Binglin , Peng Zhiqing , Li Chuang , Feng Yunchao , Sun Yong , Tang Xing , Zeng Xianhai , Lin Lu
Published: February 2021

Biomass is the only renewable organic carbon resource in nature, and the transformation of abundant biomass into various chemicals has received immense spotlight. As a novel generation of designer solvents, deep eutectic solvents (DESs) have been widely used in biorefinery due to their excellent properties including low cost, easy preparation, and biodegradability. Although there have been some reports summarizing the performance of DESs for the transformation of biomass into various chemicals, few Reviews illuminate the relationship between the functional structure of DESs and catalytic conversion of biomass. Hence, this Minireview comprehensively summarizes the effects of the types of functional groups in DESs on catalytic conversion of biomass into furanic derivatives, such as carboxylic acid‐based hydrogen‐bond donors (HBDs), carbohydrate‐based HBDs, polyalcohol‐based HBDs, amine/amide‐based HBDs, spatial structure of HBDs, and various hydrogen‐bond acceptors (HBAs). It also further summarizes the effects of adding different additives into the DESs on the synthesis of high value‐added chemicals, including water, liquid inorganic acids, Lewis acids, heteropoly acids, and typical solid acids. Moreover, current challenges and prospects for the application of DESs in biomass conversion are provided.
Vitamin D3 ameliorates nitrogen mustard‐induced cutaneous inflammation by inactivating the NLRP3 inflammasome through the SIRT3–SOD2–mtROS signaling pathway
Authors: Dong Xunhu , He Ying , Ye Feng , Zhao Yuanpeng , Cheng Jin , Xiao Jingsong , Yu Wenpei , Zhao Jiqing , Sai Yan , Dan Guorong , Chen Mingliang , Zou Zhongmin
Published: February 2021

Nitrogen mustard (NM) causes severe skin injury with an obvious inflammatory response, which is lack of effective and targeted therapies. Vitamin D3 (VD3) has excellent anti‐inflammatory properties and is considered as a potential candidate for the treatment of NM‐induced dermal toxicity; however, the underlying mechanisms are currently unclear. Cyclooxygenase‐2 (COX2; a widely used marker of skin inflammation) plays a key role in NM‐induced cutaneous inflammation. Herein, we initially confirmed that NM markedly promoted COX2 expression in vitro and in vivo. NM also increased NOD‐like receptor family pyrin domain containing 3 (NLRP3) expression, caspase‐1 activity, and interleukin‐1β (IL‐1β) release. Notably, treatment with a caspase‐1 inhibitor (zYVAD‐fmk), NLRP3 inhibitor (MCC950), and NLRP3 or caspase‐1 siRNA attenuated NM‐induced NLRP3 inflammasome activation, with subsequent suppression of COX2 expression and IL‐1β release in keratinocytes. Meanwhile, NM increased mitochondrial reactive oxygen species (mtROS) and decreased manganese superoxide dismutase 2 (SOD2) and sirtuin 3 (SIRT3) activities. Mito‐TEMPO (a mtROS scavenger) ameliorated NM‐caused NLRP3 inflammasome activation in keratinocytes. Moreover, VD3 improved SIRT3 and SOD2 activities, decreased mtROS contents, inactivated the NLRP3 inflammasome, and attenuated cutaneous inflammation induced by NM in vitro and in vivo. The beneficial activity of VD3 against NM‐triggered cutaneous inflammation was enhanced by the inhibitors of IL‐1, mtROS, NLRP3, caspase‐1, and NLRP3 or caspase‐1 siRNAs, which was abolished in SIRT3 inhibitor or SIRT3 siRNA‐treated keratinocytes and skins from SIRT3−/− mice. In conclusion, VD3 ameliorated NM‐induced cutaneous inflammation by inactivating the NLRP3 inflammasome, which was partially mediated through the SIRT3–SOD2–mtROS signaling pathway.
Epigenome screening highlights that JMJD6 confers an epigenetic vulnerability and mediates sunitinib sensitivity in renal cell carcinoma
Authors: Zhang Chuanjie , Lu Xuan , Huang Jingyi , He Hongchao , Chen Li , Liu Yihan , Wang Haofei , Xu Yang , Xing Siwei , Ruan Xiaohao , Yang Xiaoqun , Chen Lu , Xu Danfeng
Published: February 2021

Aberrant epigenetic reprogramming represents a hallmark of renal cell carcinoma (RCC) tumorigenesis and progression. Whether there existed other epigenetic vulnerabilities that could serve as therapeutic targets remained unclear and promising. Here, we combined the clustered regularly interspaced short palindromic repeats functional screening results and multiple RCC datasets to identify JMJD6 as the potent target in RCC. JMJD6 expression correlated with poor survival outcomes of RCC patients and promoted RCC progression in vitro and in vivo. Mechanistically, aberrant p300 led to high JMJD6 expression, which activated a series of oncogenic crosstalk. Particularly, high‐throughput sequencing data revealed that JMJD6 could assemble super‐enhancers to drive a list of identity genes in kidney cancer, including VEGFA, β‐catenin, and SRC. Moreover, this JMJD6‐mediated oncogenic effect could be suppressed by a novel JMJD6 inhibitor (SKLB325), which was further demonstrated in RCC cells, patient‐derived organoid models, and in vivo. Given the probable overlapped crosstalk between JMJD6 signature and tyrosine kinase inhibitors downstream targets, targeting JMJD6 sensitized RCC to sunitinib and was synergistic when they were combined together. Collectively, this study indicated that targeting JMJD6 was an effective approach to treat RCC patients.
Cyclosporine modulates neutrophil functions via the SIRT6–HIF‐1α–glycolysis axis to alleviate severe ulcerative colitis
Authors: Lu Huiying , Lin Jian , Xu Chunjin , Sun Mingming , Zuo Keqiang , Zhang Xiaoping , Li Mingsong , Huang Hailiang , Li Zhong , Wu Wei , Feng Baisui , Liu Zhanju
Published: February 2021

Background

Cyclosporine A (CsA) is routinely used to treat patients with steroid‐refractory acute severe ulcerative colitis (ASUC). Here, we studied the underlying mechanisms of CsA‐mediated alleviation in ASUC patients.

Methods

Neutrophil functions including expression of cytokines, apoptosis, and migration were measured by qRT‐PCR, flow cytometry, and Transwell assay. Dynamic changes of glycolysis and tricarboxylic acid (TCA) cycle were measured by a Seahorse extracellular flux analyzer. Gene differences were determined and verified by RNA sequencing, qRT‐PCR, and Western blotting. Small interfering RNA and inhibitors were used to knock down Sirtuin 6 (SIRT6) in HL‐60 cells and block expression of SIRT6, hypoxia‐inducible factor‐1α (HIF‐1α), and pyruvate dehydrogenase lipoamide kinase isozyme 4 (PDK4) in neutrophils.

Results

We found that HIF‐1α expression and glycolysis significantly increased, while the release of IL‐8, myeloperoxidase (MPO) and reactive oxygen species (ROS), the apoptosis, and ability of migration markedly decreased in neutrophils of ASUC patients who responded to CsA (Response group) compared with those who did not respond to CsA (Nonresponse group). We also observed that CsA‐induced functional alternation of neutrophils was initiated through suppressing SIRT6 expression, which is responsible for expression of the downstream signaling molecules (e.g., HIF‐1α, PFKFB3) and PDK4 ubiquitination, leading to fueling neutrophil glycolysis and TCA cycle. Furthermore, blockage of SIRT6 signaling demonstrated to be the same functional changes as CsA to decrease the migration of neutrophils.

Conclusions

The data reveal a novel mechanism of CsA in alleviating ASUC by promoting neutrophil HIF‐1α expression and restricting excessive neutrophil activation in a SIRT6−HIF‐1α−glycolysis axis, suggesting SIRT6 as a candidate target for maintaining mucosal homeostasis and treating intestinal inflammation.
Hybrid anti‐jamming algorithm for Indian Regional Navigation Satellite System receivers using variational mode decomposition and wavelet packet transform
Authors: Silva Lorraine Kambham Jacob , Ramarakula Madhu
Published: February 2021

Continuous wave interference has found to be one of the major menaces that deter the performance of the Indian Regional Navigation Satellite System (IRNSS) receivers for seamless positioning and navigation. In this paper, a novel hybrid jamming mitigation method based on variational mode decomposition (VMD) and wavelet packet transform (WPT) has been proposed. VMD is used to decompose the received signal into various components referred to as intrinsic mode functions (IMFs). To have an optimum decomposition of the signal, the mode decomposition number of VMD is determined by employing the kurtosis principle. Then, a threshold based on the mutual information index is constructed to differentiate the information dominant and interference dominant modes. The information dominant modes are then processed by the wavelet packet filter to eliminate the remaining effects of jamming and noise present. Finally, the filtered modes and the retained modes are used to reconstruct the desired signal. The performance of the technique is analyzed in the presence of single‐tone, multitone, and chirp jamming scenarios with different levels of jamming power. The proposed method has been tested by simulations in comparison with the standard algorithms. Results show that the proposed hybrid algorithm outperforms the standard algorithms in reducing the jamming signal effectively.
Versuche am Bau mit Injektionsankern im Mauerwerk nach Technischer Regel des DIBt
Authors: Scheller Eckehard , Küenzlen Jürgen H. R. , Kuhn Thomas , Becker Rainer
Published: February 2021

Auf Baustellen trifft man auf eine Vielzahl an Mauersteinen, die sich durch den Baustoff (Ziegel, Porenbeton, Kalksandstein, Leichtbeton oder Normalbeton), die Struktur (Vollsteine, Lochsteine mit oder ohne Dämmstoff‐Füllung), die Geometrie, die Rohdichte und die Druckfestigkeit unterscheiden.

Im Rahmen von Zulassungsverfahren für Kunststoffdübel und Metall‐Injektionsanker wird es für Dübel‐Hersteller aber immer nur möglich sein, einen Teil dieser Vielfalt von Mauersteinen als zulässigen Verankerungsgrund abzubilden. (Dübel‐)Versuche am Bauwerk ermöglichen es dem Anwender dennoch unter bestimmten Bedingungen zulassungskonform zu bemessen und zu montieren, wenn der tatsächlich auf der Baustelle vorhandene Verankerungsgrund nicht in der Zulassung für das Dübelsystem abgebildet ist.

Der vorliegende Artikel ist ein Auszug aus dem Heft 4 der Schriftenreihe des Deutschen Ausschuss für Mauerwerk e.V. (DAfM) „(Dübel‐)Versuche am Bauwerk in Mauerwerk – Aktuelle Regelungen für Kunststoffdübel und Metall‐Injektionsanker zur Verankerung im Mauerwerk” und gibt einen Überblick zum dafür vorhandenen und zu beachtenden Regelwerk – insbesondere zu einer der beiden aktuellen Technischen Regeln des Deutschen Instituts für Bautechnik (DIBt) „Durchführung und Auswertung von Versuchen am Bau für Injektionsankersysteme im Mauerwerk”.
Eignungsprüfungen an Bauteilen und Bausystemen
Authors: Trümer André , Loderer Franz
Published: February 2021

Xella produziert Baustoffe nach europäischen Produktnormen bzw. auf Basis europäischer technischer Bewertungen. Neue Produkttypen wie auch Produkte, die mit einem neuen Rohstoff hergestellt werden, durchlaufen ein internes Freigabeverfahren, in dem die Anforderungen der Normen sowie ergänzender nationaler Anwendungsdokumente, Zulassungen und Bauartgenehmigungen nachgewiesen werden. Zusätzlich werden Prüfungen durchgeführt, in denen das Zusammenwirken der Xella Baustoffe im System mit weiteren am Bau eingesetzten Produkten bewertet wird. Zu diesen mehrkomponentigen Bauteilen zählen Mauerwerk, Wärmedämm‐Verbundsysteme (WDVS), Putzsysteme, großformatige bewehrte Bauteile, zugehörige Befestigungsmittel und vieles mehr. Der Umfang der Systemprüfungen richtet sich nach dem jeweiligen Anwendungsfall und nach dem in vielen Punkten über die Regelwerke hinausgehenden Xella‐internen Anforderungsprofil. Der vorliegende Beitrag stellt das Spektrum dieser Prüfungen vor und erläutert am Beispiel der Putz‐ und Mörtelprüfungen das Wesen der internen Prüfrichtlinien.
Standsicherheitsberechnungen an bestehenden Gewichtsstützwänden
Authors: Fleischer Helmut , Schlegel Roger , Eckardt Stefan
Published: February 2021

Große Teile älterer Wasserbauwerke bestehen aus massigen Gewichtsstützwänden. Die Bauweise ist durch teilweise mehrere Meter mächtige Querschnitte aus unbewehrtem Beton oder Mauerwerk gekennzeichnet. Neben Erddruck und Einwirkungen aus dem Anlagenbetrieb sind oft hohe Wasserlasten aufzunehmen. Statische Nachrechnungen nach geltendem Regelwerk mit den üblichen vereinfachten Ansätzen führen fast immer zu rechnerischen Standsicherheitsdefiziten, aus denen wiederum aufwendige statische Verstärkungsmaßnahmen oder gar Ersatzneubauten resultieren. Defizite ergeben sich vor allem aus der Vernachlässigung des mehrdimensionalen Spannungs‐ bzw. Dehnungszustands und dem sehr konservativen Ansatz für den im Bauteilinneren wirkenden Riss‐ und Porenwasserdruck nach geltender Norm. Im folgenden Beitrag wird anhand erster numerischer Analysen an einem zweidimensionalen FE‐Stützwandmodell unter Berücksichtigung der Wechselwirkung zwischen Rissbildung und Verteilung des inneren Wasserdrucks gezeigt, dass mit einer genaueren Erfassung der statischen Verhältnisse rechnerische Sicherheitsreserven klar nachweisbar sind. Es ist empfehlenswert, diese Untersuchungen fortzuführen und auf eine größere Modellpalette auszudehnen, um zu verallgemeinerungsfähigen Aussagen zu kommen und damit die Basis zur Aufwertung des in der Praxis gängigen Ingenieurmodells zu schaffen.
Insights into antimicrobial peptides in fighting anthrax: A review
Authors: Leonard Theodore Ebenezer , Siratan Elsabda , Hartiadi Leonny Yulita , Crystalia Audrey Amira
Published: February 2021

Anthrax is an infectious disease occurring worldwide and is a threat to global society due to its possible misuse as a biological weapon. Bacillus anthracis is the etiologic agent of this disease which can be transmitted via inhalation, ingestion, and skin contact. Globally, it is estimated around 2000 anthrax cases occur per year. Upon infection, the organism can cause cytolysis of macrophage and produce exotoxin capable of inducing edema and lymphatic blockage. Another challenge posed by the organism is the ability to form spores in harsh conditions. Various antibiotics have been used to fight the disease. However, like many other microbes, B. anthracis may develop resistance, thus the discovery of new therapeutics is urgently required. Antimicrobial peptides (AMPs) have been discovered since 1980s and attracted researchers in the antimicrobial field. In this review, the work and studies on the attempts to discover potent AMPs to treat anthrax together with the brief overview of the synthesis and modification pathways of several AMPs have been presented.
Prenatal maternal distress and immune cell epigenetic profiles at 3‐months of age
Authors: Letourneau Nicole , Ntanda Henry , Jong Victor L. , Mahinpey Newsha , Giesbrecht Gerald , Ross Kharah M. ,   the APrON Team
Published: February 2021

Background

Prenatal maternal distress predicts altered offspring immune outcomes, potentially via altered epigenetics. The role of different kinds of prenatal maternal distress on DNA methylation profiles is not understood.

Methods

A sample of 117 women (APrON cohort) were followed from pregnancy to the postpartum period. Maternal distress (depressive symptoms, pregnancy‐specific anxiety, stressful life events) were assessed mid‐pregnancy, late‐pregnancy, and 3‐months postpartum. DNA methylation profiles were obtained from 3‐month‐old blood samples. Principal component analysis identified two epigenetic components, characterized as Immune Signaling and DNA Transcription through gene network analysis. Covariates were maternal demographics, pre‐pregnancy body mass index, child sex, birth gestational age, and postpartum maternal distress. Penalized regression (LASSO) models were used.

Results

Late‐pregnancy stressful life events, b = 0.006, early‐pregnancy depressive symptoms, b = 0.027, late‐pregnancy depressive symptoms, b = 0.014, and pregnancy‐specific anxiety during late pregnancy, b = −0.631, were predictive of the Immune Signaling component, suggesting that these aspects of maternal distress could affect methylation in offspring immune signaling pathways. Only early‐pregnancy depressive symptoms was predictive of the DNA Transcription component, b = −0.0004, suggesting that this aspect of maternal distress is implicated in methylation of offspring DNA transcription pathways.

Conclusions

Exposure timing and kind of prenatal maternal distress could matter in the prediction of infant immune epigenetic profiles.
Range expansion, habitat use, and choosiness in a butterfly under climate change: Marginality and tolerance of oviposition site selection
Authors: Martin Youri , Titeux Nicolas , Van Dyck Hans
Published: February 2021

Poleward range shifts under climate change involve the colonization of new sites and hence the foundation of new populations at the expanding edge. We studied oviposition site selection in a butterfly under range expansion (Lycaena dispar), a key process for the establishment of new populations. We described and compared the microhabitats used by the species for egg laying with those available across the study sites both in edge and in core populations. We carried out an ecological niche factor analysis (ENFA) to estimate (1) the variety of microhabitats used by the butterfly for egg laying (tolerance) and (2) the extent to which these selected microhabitats deviated from those available (marginality). Microhabitat availability was similar in edge and core populations. Ambient temperature recorded at the site level above the vegetation was on average lower at core populations. In contrast with what is often assumed, edge populations did not have narrower microhabitat use compared to core populations. Females in edge populations even showed a higher degree of generalism: They laid eggs under a wider range of microhabitats. We suggest that this pattern could be related to an overrepresentation of fast deciding personalities in edge populations. We also showed that the thermal time window for active female behavior was reduced in edge populations, which could significantly decrease the time budget for oviposition and decrease the threshold of acceptance during microhabitat selection for oviposition in recently established populations.
Larger workers outperform smaller workers across resource environments: An evaluation of demographic data using functional linear models
Authors: Kerr Natalie Z. , Malfi Rosemary L. , Williams Neal M. , Crone Elizabeth E.
Published: February 2021

Behavior and organization of social groups is thought to be vital to the functioning of societies, yet the contributions of various roles within social groups toward population growth and dynamics have been difficult to quantify. A common approach to quantifying these role‐based contributions is evaluating the number of individuals conducting certain roles, which ignores how behavior might scale up to effects at the population‐level. Manipulative experiments are another common approach to determine population‐level effects, but they often ignore potential feedbacks associated with these various roles.

Here, we evaluate the effects of worker size distribution in bumblebee colonies on worker production in 24 observational colonies across three environments, using functional linear models. Functional linear models are an underused correlative technique that has been used to assess lag effects of environmental drivers on plant performance. We demonstrate potential applications of this technique for exploring high‐dimensional ecological systems, such as the contributions of individuals with different traits to colony dynamics.

We found that more larger workers had mostly positive effects and more smaller workers had negative effects on worker production. Most of these effects were only detected under low or fluctuating resource environments suggesting that the advantage of colonies with larger‐bodied workers becomes more apparent under stressful conditions.

We also demonstrate the wider ecological application of functional linear models. We highlight the advantages and limitations when considering these models, and how they are a valuable complement to many of these performance‐based and manipulative experiments.
Enhancing an unsupervised clustering algorithm with a spatial contiguity constraint for river habitat analysis
Authors: van Rooijen Erik , Vanzo Davide , Vetsch David F. , Boes Robert M. , Siviglia Annunziato
Published: February 2021

The spread of two‐dimensional numerical hydrodynamic tools for ecohydraulic applications allowed for the development of automatic habitat detection methods, adopted as predicting tools for river habitat analysis. These automatic approaches differ for the employed identification rules, such as preference curves, fuzzy rules and clustering methods. Previous research has shown promising results in the automatic identification of mesoscale habitat patches by using clustering algorithms together with numerical hydrodynamic model results. These algorithms attempt to implement and simulate some of the expert‐based requirements adopted in the field to delineate habitat patches. Spatial contiguity is one of such expert‐based requirements that has not been enforced and exploited in automatic mesohabitat identification so far. In this work, we propose a novel tool (BASEmeso) based on an agglomerative hierarchical clustering algorithm where we enforced a spatial contiguity criteria. We compare our approach with a more established method without spatial constraints, considering a synthetic river reach where the composition of mesohabitat patches is known a priori, and on three experimental river reaches, to investigate the effects of different river morphologies. Our results show that when employing a contiguity constraint, a patch's extent is better captured, different patches can be distinguished better and the distribution of patch characteristics is smoother. This holds for all investigated morphologies. Together, it suggests that including a spatial contiguity constraint can improve the automatic delineation of river mesohabitat patches. The proposed methodology could positively contribute in the development of automatic, objective and predictive meso‐scale habitat assessment workflows.
Using terrestrial leeches to assess the genetic diversity of an elusive species: The Annamite striped rabbit Nesolagus timminsi
Authors: Nguyen Thanh V. , Tilker Andrew , Nguyen An , Hörig Lisa , Axtner Jan , Schmidt Anke , Le Minh , Nguyen Anh H. Q. , Rawson Benjamin M. , Wilting Andreas , Fickel Joerns
Published: February 2021

Information on geographic patterns of species genetic diversity is often needed to inform conservation strategies. Obtaining data over large geographic areas can be difficult, especially for rare or elusive species. Here, we explore the use of invertebrate‐derived DNA (iDNA) obtained from terrestrial leeches to assess genetic diversity of the Annamite striped rabbit Nesolagus timminsi, a little‐known and highly threatened lagomorph endemic to the Annamites ecoregion of Vietnam and Laos. We collected 4,877 leeches pooled into 651 leech bulk samples from eight study areas across the northern and central Annamites. Using metabarcoding, we detected Annamite striped rabbit DNA in 11 leech bulk samples from five of the study areas. We amplified up to 3,000 bp of six mitochondrial DNA loci of Annamite striped rabbit from nine of the 11 bulk samples. Haplotype network analyses showed five shared haplotypes among these samples. Phylogenetic trees constructed using maximum likelihood and Bayesian inference showed little geographic structuring among the Annamite striped rabbit populations across the five study areas. Our results provide information that can be directly used to inform planned ex situ conservation measures for the Annamite striped rabbit. We discuss our results within the context of using iDNA to noninvasively obtain data to assess species genetic diversity, and the potential of this approach to be applied to other species and systems.
Mitohelper: A mitochondrial reference sequence analysis tool for fish eDNA studies
Authors: Lim Shen Jean , Thompson Luke R.
Published: February 2021

Fish eDNA metabarcoding is a nonintrusive, time‐ and cost‐effective way to detect biodiversity, with potential applications in ecosystem‐based management and fisheries assessment. Nevertheless, fish‐specific eDNA resources are currently not well‐developed, and many fish species are not yet sequenced in reference databases. We developed Mitohelper, a Python‐based command line tool to annotate and align fish mitochondrial sequences available in the existing MitoFish database. Mitohelper improves MitoFish annotations by adding gene names and additional taxonomic classifications. Using these improved reference datasets, Mitohelper's getrecord function searches MitoFish for available mitochondrial (cytochrome c oxidase, 12S rRNA, and others) gene sequences against a user‐provided list of fish taxonomic names. Mitohelper's getalignment function aligns (often partial) mitochondrial gene sequences to a user‐specified full‐length reference sequence for the assessment and visualization of overlapping sequencing regions. To facilitate the development of taxonomic classifiers, we combined Mitohelper's 12S rRNA dataset with SILVA’s 16S rRNA and 18S rRNA datasets in a QIIME 2‐compatible format. By providing valuable information on taxonomic and gene region coverage of currently available fish mitochondrial data, Mitohelper's functions promote informed experimental design that can guide sequencing and analysis strategies. In summary, Mitohelper improves the breadth and functionality of eDNA data resources, as well as the accuracy of taxonomic classification. Mitohelper and its reference datasets are updated approximately monthly and available at https://github.com/aomlomics/mitohelper.
Effects of preservation strategies on environmental DNA detection and quantification using ddPCR
Authors: Mauvisseau Quentin , Halfmaerten David , Neyrinck Sabrina , Burian Alfred , Brys Rein
Published: February 2021

Molecular‐based monitoring relying on environmental DNA (eDNA) detection became routinely used around the world in the last few years, especially in aquatic environments. The large potential and increasing applications of this technique calls for technical improvements to optimize the reliability of these surveys. An important technical aspect in the eDNA workflow is the appropriate preservation of samples taken in the field, as it can significantly affect eDNA recovery and ultimately false negative rates. In this study, we explored the efficiency of five different preservation strategies by using a controlled mesocosm experiment in which we included three fish communities of different composition. Specifically, we compared eDNA recovery in DNA extractions (a) performed immediately following collection, or after eight months storage from (b) frozen filters, (c) unfiltered water samples stored at −20°C, and filters preserved at room temperature with (d) Longmire and (e) Sarkosyl buffer. Effects of different preservation strategies were quantified using ddPCR measurements of three fish species (Neogobius melanostomus, Rutilus rutilus, and Lota lota) and total fish DNA content using group‐specific primers for Teleostei. Samples extracted immediately following collection without any further preservation yielded significantly less DNA compared to the other approaches. Overall, Longmire's buffer facilitated the best eDNA recovery across all fish species although approaches such as filter freezing or the use of Sarkosyl buffer yielded similar recovery results. Relative measurement variability, an important indicator for reliable eDNA quantification, was lowest when using Longmire's and Sarkosyl buffers and generally decreased when increasing eDNA quantity. Overall, our results clearly highlight the significant impact of sample preservation and how this can substantially affect the performance and reliability of eDNA‐based approaches.
Predicting the clinical course in hypertrophic cardiomyopathy using thallium‐201 myocardial scintigraphy
Authors: Hamada Mareomi , Shigematsu Yuji , Nakata Shigeru , Kuwahara Taishi , Ikeda Shuntaro , Ohshima Kiyotaka , Ogimoto Akiyoshi
Published: February 2021

Aims

This study aimed to evaluate the changes in left ventricular remodelling with time in patients with hypertrophic cardiomyopathy (HCM) using thallium‐201 myocardial scintigraphy.

Methods and results

Forty‐eight patients with HCM participated in the study. The extent score (ES) and a newly devised index termed the ‘mean count change’ (MCC) were used to evaluate the myocardial perfusion defects. Using the amount of thallium‐201 uptake (TU), MCC (%) was calculated using the following formula: (last TU − initial TU)∕initial TU × 100. To confirm the site of the lesion, the left ventricle was divided into five segments: anterior, septal, inferior, lateral, and apex. Cardiovascular complications and deaths were recorded. The mean follow‐up period was 8.6 ± 2.0 years. ES increased from 17.4 ± 13.7% to 44.0 ± 22.3% (P < 0.0001). MCC increased from 0% to 12.0 ± 9.0% (P < 0.0001). The apex was the most frequent site of lesion. Twenty‐seven patients (56.3%) had experienced left ventricular heart failure (LVHF). Both ES and MCC were greater in patients with LVHF than in those without LVHF. An overlap between the two groups was greater in ES than in MCC. Patients with LVHF had a higher incidence of atrial fibrillation and apoplexy. Nineteen patients (39.6%) died during the study period; 14 died from LVHF, 3 from sudden cardiac death, and 2 from cancer.

Conclusions

Thallium‐201 myocardial scintigraphy is useful for detecting the severity of myocardial damage and for confirming the lesion site in patients with HCM. MCC may be superior to ES in the evaluation of these changes with time.
Type 2 diabetes and heart failure: insights from the global DISCOVER study
Authors: Arnold Suzanne V. , Khunti Kamlesh , Bonnet Fabrice , Charbonnel Bernard , Chen Hungta , Cid‐Ruzafa Javier , Cooper Andrew , Fenici Peter , Gomes Marilia B. , Hammar Niklas , Ji Linong , Luporini‐Saraiva Gabriela , Medina Jesús , Nicolucci Antonio , Ramirez Larisa , Shestakova Marina V. , Shimomura Iichiro , Surmont Filip , Tang Fengming , Vora Jiten , Watada Hirotaka , Kosiborod Mikhail ,   the DISCOVER investigators
Published: February 2021

Aims

Heart failure (HF) is increasingly recognized as a major cause of morbidity and mortality in patients with type 2 diabetes (T2D), but the global epidemiology and treatment of HF in T2D are not well defined. This study aimed to examine the global prevalence of HF and the incidence of HF over 3 years of follow‐up in patients with T2D [by presence and absence of co‐existing coronary artery disease (CAD)].

Methods and results

DISCOVER was a 3 year, prospective, observational study of T2D patients enrolled at initiation of second‐line glucose‐lowering therapy. Among 14 057 patients with T2D from 36 countries, 289 (2.1%) had a diagnosis of HF at enrolment; median prevalence across countries was 2.0% (inter‐quartile range 1.0–3.1%). Patients with HF at baseline were more likely to be older [HF vs. no HF: 67 ± 12 vs. 57 ± 12 years, standardized difference (StDiff) = 84%] and have longer duration of T2D (8.1 ± 7.2 vs. 5.6 ± 5.2 years, StDiff = 40%), CAD (44% vs. 6%, StDiff = 97%), atrial fibrillation (21% vs. 1%, StDiff = 66%), and kidney disease (23% vs. 4%, StDiff = 55%). Patients with HF were less likely to be on metformin (66% vs. 79%, StDiff = 28%) and thiazolidinediones (5.5% vs. 10.6%, StDiff = 19%) but had similar use of other glucose‐lowering medications. Among 9313 patients with follow‐up data, there were 70 incident cases of HF, which translates to an incidence of 2.6 cases per 1000 person years. Of these incident HF cases, 60% occurred in the absence of pre‐existing or concomitant CAD, and 73% were diagnosed in the outpatient setting.

Conclusions

In a large, global cohort of patients with T2D, the majority of incident cases of HF occurred in outpatients and in the absence of known CAD. These findings highlight the need for greater awareness of HF risk in patients with T2D.
Sarcopenia in heart failure: a systematic review and meta‐analysis
Authors: Zhang Yan , Zhang Jia , Ni Wenqing , Yuan Xueli , Zhang Hongmin , Li Ping , Xu Jian , Zhao Zhiguang
Published: February 2021

Aims

Sarcopenia has been found to be frequently associated with co‐morbidity among patients with heart failure (HF). However, there remain insufficient data to accurately estimate the global prevalence of sarcopenia in HF. Therefore, the purpose of this research was to conduct a systematic review and meta‐analysis to estimate the current overall prevalence of sarcopenia in patients with HF.

Methods and results

We searched relevant databases for studies published up to 13 July 2020, assessing sarcopenia in vpatients with HF. After careful screening, data of included articles were extracted with a predesigned Excel form. Then the pooled prevalence of sarcopenia in patients with HF was calculated using the random‐effects model. The Q test was used to assess the heterogeneity, and I2 statistic was calculated to quantify and evaluate the heterogeneity. Subgroup analyses were conducted to determine potential sources of heterogeneity. A total of 2852 articles were initially identified, and after removing duplicate publications and applying the selection criteria, we reviewed 79 full‐text articles. Finally, 11 articles (n = 1742 patients with HF) were included in this systematic review and meta‐analysis. The pooled prevalence of sarcopenia in patients with HF was 34% [95% confidence interval (CI): 22–47%, I2 = 96.59%] and ranged from 10% to 69%. However, substantial heterogeneity between studies (I2 = 96.59%, P < 0.001) was observed. There was no significant heterogeneity between subgroups by sex (P = 0.803) or the method used to define sarcopenia (P = 0.307). While the heterogeneity between subgroups by population setting was statistically significant (P < 0.001), the pooled prevalence of sarcopenia was 55% (95% CI: 43–66%) for hospitalized patients with HF and 26% (95% CI: 16–37%) for ambulatory patients.

Conclusions

Sarcopenia was a common condition in patients with HF, and the prevalence of hospitalized patients was higher than for ambulatory patients. Early detection of sarcopenia was therefore important in patients with HF, and it was important to implement interventions so that physical therapists or managerial dieticians can easily be introduced into clinical practice.
Polydentate Phosphane Ligands Featuring N,N,N’‐Trialkylformamidines
Authors: Marchenko Anatoliy , Koidan Georgyi , Hurieva Anastasiya , Dyakonenko Viktoriya V. , Shishkina Svitlana V. , Rusanov Eduard B. , Kyrylchuk Andrii A. , Kostyuk Aleksandr
Published: February 2021

A set of novel polydentate phosphanes featuring one, two and three formamidine substituents was prepared by the reaction of C‐trimethylsilyl N,N,N’‐trialkylformamidines with P(III) chlorides. Chloro‐ and dichlorophosphanes gave tertiary phosphanes. More sterically congested adamantyldichlorophosphane reacted only with the least sterically congested silylformamidine. With phosphorus trichloride, five‐membered heterocycles, namely 1,4,2‐diazaphosphol‐4‐ium chlorides were formed in most cases. A mechanism for the formation of diazaphospholes was proposed and corroborated by DFT calculations. A key chlorophosphane underwent 1,2‐phosphorus shift giving the corresponding carbene that readily cyclized into diazaphospholium salts. The key compounds were studied by X‐ray diffractometry. Analysis of molecular structures of 1,4,2‐diazaphosphol‐4‐ium chloride 13 c and 1H‐1,4,2‐diazaphosphole 14 c revealed that the N‐Cring bonds for the orthogonally oriented i‐propylamino groups are unusually short. Only in the case of N,N‐dimethyl‐N’‐isopropyltrimethylsilylformamidine, we managed to isolate trisphosphane, albeit in a low yield.
An epidemiological survey of epilepsy in tropical rural areas of China
Authors: Zheng Guoxian , Li Futao , Chen Yongmin , Liu Huijuan , Wang Shurong , Lao Jitong , Chen Shuang , Zhang Yimin , Lu Rui , Liao Xiaoping , Ma Lin , Li Qifu
Published: February 2021

Objective

Epilepsy is a chronic neurological disease that is characterized by seizures. Seizure episodes, stigma, and high medical costs associated with this condition caused significant psychological distress. This study aimed to evaluate epidemiological characteristics and treatment status of epilepsy in individuals existing in the tropical rural areas of Hainan Province of China.

Methods

A household survey on epilepsy was conducted among the rural population of Chengmai County, Danzhou City, Baoting Autonomous County (Li and Miao nationalities), and Dingan County in Hainan Province, China. A screening questionnaire based on the standard screening questionnaires of the World Health Organization (WHO) was designed and a screening instrument of International Community‐based Epilepsy Research Group was used. Individuals suspected or previously diagnosed with epilepsy were reexamined by an experienced neurologist. Further clinical data were collected from subjects with confirmed diagnosis of epilepsy.

Results

This study included 16 676 subjects with 8827 men (52.93%) and 7849 women (47.07%). Majority of the study subjects included were of Han Chinese (N = 13 145, 78.83%), and the remaining were of Li minority ethnicity. The incidence of epilepsy was 0.24 per 1000, and the total prevalence of active epilepsy was 2.33 per 1000. The prevalence of epilepsy in the Han and Li nationalities was 3.27 and 2.27 per 1000, respectively, which was shown to be higher in people aged ≥ 60. The initial onset of epilepsy tended to trigger among children aged between 0 and 9 years old. Initial assessment revealed that the treatment gap for active epilepsy was 58.97%, and stroke is shown as the most common cause of symptomatic epilepsy.

Significance

The prevalence and incidence of epilepsy in tropical rural areas of Hainan Province were close to those of the earlier findings that are reported in other regions of China and lower than those remaining in the tropical areas around the world. There exists a huge treatment gap for active epilepsy, which indicates an urgent need for a rational intervention strategy.
Utilization of electric vehicles in combined voltage‐frequency control of multi‐area thermal‐combined cycle gas turbine system using two degree of freedom tilt‐integral‐derivative controller
Authors: Ramoji Satish Kumar , Saikia Lalit Chandra
Published: February 2021

This paper conveys the unified control pattern of frequency and voltage of interconnected multi‐area power system through the automatic load frequency control (ALFC) loop and automatic voltage regulator (AVR) loop. Each area includes a single‐stage reheat thermal plant, combined cycle gas turbine (CCGT) plant, and electric vehicles (EVs). Pertinent generation rate constraint for thermal and CCGT plant and governor dead band for the thermal plant is considered. A maiden attempt has been made to introduce the two degree of freedom tilt‐integral‐derivative (2DOFTID) controller for both the ALFC and AVR loops. In this study, a meta‐heuristic algorithm called Harris Hawks optimization (HHO) is implemented to optimize the controller parameters. Study divulges that performance of the 2DOFTID controller predominates when compared with TID and proportional‐integral‐derivative with filter (PIDF) controller apropos time‐domain indices. By juxtaposition, the superiority of the proposed algorithm and performance index is observed. Also, improved system dynamics were independently exhibited by the influence of the lumped EV model and AVR. For the predominance of the 2DOFTID controller, different patterns of disturbances such as random and sinusoidal varying load perturbation have been investigated. Eventually, the sensitivity studies were accomplished to determine the sturdiness of the proposed controller for substantial variations in the system parameters.
Preparation of a ternary hybrid of P‐g‐C3N4@PGS‐Ti and its enhancement of the flame retardancy of epoxy resins
Authors: Hua Fenglin , Wei Hong , Ren Fupeng , Wang Mingming , Li Li , Lv Bolin , Wang Huan , Yang Zhiwang , Lei Ziqiang
Published: February 2021

A novel ternary hybrid flame retardant named P‐g‐C3N4@PGS‐Ti was prepared through step‐by‐step method. First, titanium dioxide was loaded on PGS to make PGS‐Ti (where PGS = palygorskite), and then, PGS‐Ti was decorated by phosphor‐doped g‐C3N4 (abbreviated as P‐g‐C3N4) to prepare a ternary flame retardant of P‐g‐C3N4@PGS‐Ti. It showed that P‐g‐C3N4@PGS‐Ti could efficiently improve the flame retardancy of epoxy resins (EP). The structure and the morphology of P‐C3N4@PGS‐Ti were characterized by Fourier transform infrared spectroscopy, X‐ray diffraction, scaanning electron microscopy and hermogravimetric analysis (TGA). The flame retardancy and the burning behavior of 5 wt% P‐g‐C3N4@PGS‐Ti composited EP were well investigated through TGA, limiting oxygen index (LOI), cone calorimeter test (CCT) and vertical burning test (UL‐94 standard). It was found that the peak heat releasing (pk‐HRR) of the EP/P‐g‐C3N4@PGS‐Ti composite reduced 36% (from 1459 to 852 kW/m2) with the addition of 5 wt% of P‐g‐C3N4@PGS‐Ti flame retardant to the matrix of EP. The combustion residue analysis showed that the EP/P‐g‐C3N4@PGS‐Ti composite gained the most continuous and firmest char yield due to the synergistic effect of PGS, TiO2 and the introducing of P element. The mechanism proved that the combination of gas phase and condensed phase flame‐retardant processes were well coordinated to improve the fire retardancy for EP. We tested and studied the mechanical properties of EP/P‐g‐C3N4@PGS‐Ti composites. Only 2.4% decreasing of flexural strength and 23.5% decreasing of impact strength in EP/P‐g‐C3N4@PGS‐Ti composites compared to pure EP, respectively. But according to the test results of EP/P‐g‐C3N4@PGS‐Ti composite material and the control sample in the system, EP/P‐g‐C3N4@PGS‐Ti composite material had the highest flexural modulus and impact strength.
Fabrication and properties of PEI/APP layer‐by‐layer coated ramie fabric combined with low‐temperature plasma treatment
Authors: Wang Huaqing , Yan Hongqiang , Fang Zhengping
Published: February 2021

The present work demonstrates a surface pretreatment of reducing assembly layers for flame retardant modification of ramie fabric used by layer‐by‐layer (LbL) assembly. In order to achieve this goal, low‐temperature plasma (LTP) pretreatment was chosen. Attenuated total reflection Fourier transform infrared spectroscopy (ATR‐FTIR) and scanning electron microscope (SEM) were used to confirm the effect of LTP pretreatment on polyethylenimine/ammonium polyphosphate (PEI/APP) flame retardant coating constructed on the surface of ramie fabric using LbL assembly. The thermal property and flame retardancy of PEI/APP coated ramie fabrics were analyzed by TG, LOI, UL94 vertical burning, and cone calorimeter tests. The results indicated that the decomposition rate of ramie fabrics was reduced and the char forming ability at high temperature was improved by PEI/APP coating on the ramie surface. Its LOI increased markedly to 30.6% and ramie fabric achieved self‐extinguishing effect. Meanwhile, LTP‐O2‐(PEI/APP)20 ramie fabric exhibited the low flammability and high fire safety. It was proved that LTP pretreatment under oxygen atmosphere could endow ramie fabric with better flame retardancy due to more PEI/APP adsorbed on its surface. These findings have significant implications for the application of LTP pretreatment to flame retardant modification of ramie fabric by LbL assembly.