bluuebunny/crossref_metadata_2025 huggingface dataset:
Mental health service activity during COVID-19 lockdown: South London and Maudsley data on working age community and home treatment team services and mortality from February to mid-May 2020
Authors: Stewart Robert , Martin Evangelia , Broadbent Matthew
Published: June 2020

The lockdown and social distancing policy response to the COVID-19 pandemic in the UK has a potentially important impact on provision of mental healthcare; however, there has been relatively little quantification of this. Taking advantage of the Clinical Record Interactive Search (CRIS) data resource with 24-hourly updates of electronic mental health records data, this paper describes daily caseloads and contact numbers (face-to-face and virtual) for home treatment teams (HTTs) and working age adult community mental health teams (CMHTs) from 1st February to 15th May 2020 at the South London and Maudsley NHS Trust (SLaM), a large mental health service provider for 1.2m residents in south London. In addition daily deaths are described for all current and previous SLaM service users over this period and the same dates in 2019. In summary, comparing periods before and after 16th March 2020 the CMHT sector showed relatively stable caseloads and total contact numbers, but a substantial shift from face-to-face to virtual contacts, while HTTs showed the same changeover but reductions in caseloads and total contacts (although potentially an activity rise again during May). Number of deaths for the two months between 16th March and 15th May were 2.4-fold higher in 2020 than 2019, with 958 excess deaths.
Underlying causes of death with changing mortality among adults in the United States, 2013-2017
Authors: Hu Xin , Lin Yong , Zhang Lanjing
Published: June 2020

Overall mortality among U.S. adults was stable in the past years, while racial disparity was found in 10 leading causes of death or age-specific mortality in U.S. Blacks or African Americans. However, the trends in sex- and race-adjusted age-standardized cause-specific mortality are poorly understood. This study was aimed at identifying the UCD with sex- and race-adjusted, age-standardized mortality that was changing in recent years. We extracted the data of underlying causes of death (UCD) from the Multiple Cause of Death database of the Centers for Disease Control and Prevention (CDC). Multivariable log-linear regression models were used to estimate trends in sex- and race-adjusted, age-standardized mortality during 2013-2017. A total of 31,029,133 deaths were identified. Among the list of 113 UCD compiled by the CDC, there were 29 UCD with upward trend, 33 UCD with downward trend and 56 UCD with no significant trend. The 2 UCD with largest annual percent change were both nutrition related (annual percent change= 17.73, 95% CI [15.13-20.33] for malnutrition and annual percent change= 17.49, 95% CI [14.94-20.04] for Nutritional deficiencies), followed by Accidental poisoning and exposure to noxious substances. This study thus reported the UCD with changing mortality in recent years, which was sex- and race-adjusted and age-standardized. More efforts and resources should be focused on understanding, prevention and control of the mortality linked to these UCD. Continuous monitoring of mortality trends is recommended.
Binding of Calcium and Magnesium to Cardiac Troponin C
Authors: Rayani K , Seffernick JT , Li YA , Davis JP , Spuches AM , Petegem F Van , Solaro RJ , Lindert S , Tibbits GF
Published: June 2020

Cardiac troponin C (cTnC) is the Ca2+-sensing component of the thin filament. It contains structural sites (III/IV) which bind both Ca2+and Mg2+, and a regulatory site (II) that has been thought to bind only Ca2+. The latter binding initiates a series of conformational changes that culminate in force production.

We have quantified the interaction between site II and Ca2+/Mg2+through Isothermal Titration Calorimetry and Thermodynamic Integration simulations. Direct and competitive binding titrations using wild type and a double mutant that significantly reduces binding to site II demonstrated that physiologically relevant concentrations of both Ca2+/Mg2+interact with the same locus. Cytosolic free Mg2+(~1 mM) could occupy a significant population of available site II, as this concentration of Mg2+decreased the affinity for Ca2+1.4-fold.

Interaction of Mg2+with site II of cTnC likely has important functional consequences for the heart at baseline and in diseased states which decrease or increase availability of Mg2+such as secondary hyperparathyroidism or ischemia, respectively.
An enzyme-based immunodetection assay to quantify SARS-CoV-2 infection
Authors: Conzelmann Carina , Gilg Andrea , Groß Rüdiger , Schütz Desirée , Preising Nico , Ständker Ludger , Jahrsdörfer Bernd , Schrezenmeier Hubert , Sparrer Konstantin M. J. , Stamminger Thomas , Stenger Steffen , Münch Jan , Müller Janis A.
Published: June 2020

SARS-CoV-2 is a novel pandemic coronavirus that caused a global health and economic crisis. The development of efficient drugs and vaccines against COVID-19 requires detailed knowledge about SARS-CoV-2 biology. Several techniques to detect SARS-CoV-2 infection have been established, mainly based on counting infected cells by staining plaques or foci, or by quantifying the viral genome by PCR. These methods are laborious, time-consuming and expensive and therefore not suitable for a high sample throughput or rapid diagnostics. We here report a novel enzyme-based immunodetection assay that directly quantifies the amount ofde novosynthesized viral spike protein within fixed and permeabilized cells. This in-cell ELISA enables a rapid and quantitative detection of SARS-CoV-2 infection in microtiter format, regardless of the virus isolate or target cell culture. It follows the established method of performing ELISA assays and does not require expensive instrumentation. Utilization of the in-cell ELISA allows to e.g. determine TCID50of virus stocks, antiviral efficiencies (IC50values) of drugs or neutralizing activity of sera. Thus, the in-cell spike ELISA represents a promising alternative to study SARS-CoV-2 infection and inhibition and may facilitate future research.

Highlights

Determination of SARS-CoV-2 infection by enzymatically quantifying the expression of viral spike protein in bulk cell cultures

Targeting a highly conserved region in the S2 subunit of the S protein allows broad detection of several SARS-CoV-2 isolates in different cell lines

Screening of antivirals in microtiter format and determining the antiviral activity as inhibitory concentrations 50 (IC50)
Suppressors of mRNA decapping defects isolated by experimental evolution ameliorate transcriptome disruption without restoring mRNA decay
Authors: Kim Minseon , van Hoof Ambro
Published: June 2020

Faithful degradation of mRNAs is a critical step in gene expression, and eukaryotes share a major conserved mRNA decay pathway. In this major pathway, the two rate determining steps in mRNA degradation are the initial gradual removal of the poly(A) tail, followed by removal of the cap structure. Removal of the cap structure is carried out by the decapping enzyme, containing the Dcp2 catalytic subunit. While the mechanism and regulation of mRNA decay is well-understood, the consequences of defects in mRNA degradation are less clear. Dcp2 has been reported as either essential or nonessential. Here we clarify that Dcp2 is essential for continuous growth and use experimental evolution to identify suppressors of this essentiality. We show that null mutations in at least three different are each sufficient to restore viability to adcp2Δ, of whichkap123Δ andtl(gag)gΔ appear the most specific. Unlike previously reported suppressors of decapping defects, these suppressor do not restore decapping or mRNA decay to normal rates, but instead allow survival while only modestly affecting transcriptome homeostasis. These effects are not limited to mRNAs, but extend to ncRNAs including snoRNAs and XUTs. These results provide important new insight into the importance of decapping and resolves previously conflicting publications about the essentiality ofDCP2.
Definition of a Small Core Transcriptional Circuit Regulated by AML1-ETO
Authors: Stengel Kristy R. , Ellis Jacob , Spielman Clare , Bomber Monica , Hiebert Scott W.
Published: June 2020

Transcription factors regulate gene networks controlling normal hematopoiesis and are frequently deregulated in acute myeloid leukemia (AML). Critical to our understanding of the mechanism of cellular transformation by oncogenic transcription factors is the ability to define their direct gene targets. While this seems to be a straight forward task, gene network cascades can change within minutes to hours, making it difficult to distinguish direct from secondary or compensatory transcriptional changes by traditional methodologies. We describe an approach utilizing CRISPR-based genome editing to insert a degron tag into the endogenous AML1-ETO locus of Kasumi-1 cells, as well as overexpression of a degradable AML1-ETO protein in CD34+human cord blood cells, which is a an AML1-ETO-dependent pre-leukemia model. Upon addition of a small molecule proteolysis targeting chimera (PROTAC), the AML1-ETO protein was rapidly degraded in both systems. Furthermore, by combining rapid degradation with nascent transcript analysis (PRO-seq), RNA-seq and Cut&Run, we have defined the core AML1-ETO regulatory network, which consists of fewer than 100 direct gene targets. The ability of AML1-ETO to regulate this relatively small gene pool is critical for maintaining cells in a self-renewing state, and AML1-ETO degradation set off a cascade of transcriptional events resulting in myeloid differentiation.
A high fat containing chicken egg-only diet suppresses fatty liver induced by a lipid-rich methionine and choline deficient diet
Authors: Isobe Ken-ichi , Nishio Naomi , Kuzuya Ami , Kato Kana , Hatanaka Aki , Suzuki Rena , Kawai Miki , Kanjya Aoi , Suitou Chiaki , Nakano Yui , Nagasaki Manae
Published: June 2020

Nonalcoholic fatty liver disease (NAFLD) is a simple hepatic steatosis, which may proceed to nonalcoholic steatohepatitis (NASH) in the presence of steatosis and inflammation with hepatocyte injury. Obesity induced by a high-fat diet or high monosaccharide diet is considered a risk factor for NAFLD. A popular mouse model of NAFLD is a high-fat diet consisting of 60% energy from fat. A modified methionine and choline deficient (MCD) diet containing 60% energy from fat (CDAHFD) is a quick induction model for NAFLD. Chicken eggs also contain 60% energy from fat with very low carbohydrate. Here we compared liver pathologies in mice fed either a CDAHFD or egg-only diet. We found that a CDAHFD induced NAFLD within only two weeks.

Ballooning of hepatocytes with an of immune cell appearance in the liver and high serum ALT and AST indicated that the mice fed CDAHFD developed NAFLD, which could proceed to NASH. However, mice fed an egg-only diet did not develop NAFLD even after 7 weeks. These mice showed normal liver histology with normal ALT and AST. The mice fed an egg-only diet showed high blood ketone bodies and normal blood glucose. Furthermore we found that the mice fed a combination CDAHFD /egg diet or mice fed an egg-only diet after two weeks of CDAHFD diet showed almost normal ALT and AST with reduced levels of fat bodies in the liver. These results indicate that an egg-only diet strongly inhibits high fat and carbohydrates induced NAFLD.
Genome-wide identification of long non-coding RNAs in the gravid ectoparasiteVarroa destructor
Authors: Lin Zheguang , Liu Yibing , Chen Xiaomei , Han Cong , Wang Wei , Ke Yalu , Su Xiaoling , Chen Heng , Xu Hao , Chen Guohong , Ji Ting
Published: June 2020

Long non-coding RNAs (lncRNAs) emerge as critical regulators with various biological functions in living organisms. However, to date, no systematic characterization of lncRNAs has been investigated in the ectoparasitic miteVarroa destructor, the most severe biotic threat to honey bees worldwide. Here, we performed an initial genome-wide identification of lncRNAs inV. destructorvia high-throughput sequencing technology and reported, for the first time, the transcriptomic landscape of lncRNAs in the devastating parasite. By means of a lncRNA identification pipeline, 6,645 novel lncRNA transcripts, encoded by 3,897 gene loci, were identified, including 2,066 sense lncRNAs, 2,772 lincRNAs, and 1,807 lncNATs. Compared with protein-coding mRNAs,V. destructorlncRNAs are shorter in terms of full length, as well as of the ORF length, contain less exons, and express at lower level. GO term and KEGG pathway enrichment analyses of the lncRNA target genes demonstrated that these predicted lncRNAs are likely to play key roles in cellular processes, genetic information processing and environmental responses. To our knowledge, this is the first catalog of lncRNA profile in the parasitiformes species, providing a valuable resource for genetic and genomic studies. Understanding the characteristics and features of lncRNAs inV. destructorwould promote sustainable pest control.
Biosystematic Studies on the Status ofSolanum chilense(Dunal) Reiche
Authors: Raduski Andrew R. , Igić Boris
Published: June 2020

Abstract

Members ofSolanumsect.Lycopersicumare commonly used as a source of exotic germplasm for improvement of the cultivated tomato, and are increasingly employed in basic research. Although it experienced significant early and ongoing work, the taxonomic status of many wild species in this section has undergone a number of significant revisions, and remains uncertain.

Here, we examine the taxonomic status of obligately outcrossing Chilean wild tomato (Solanum chilense) using reduced-representation sequencing (RAD-seq), a range of phylogenetic and population genetic analyses, crossing data, and morphological data.

Overall, each of our analyses provides some weight of evidence that the Pacific coastal populations and Andean inland populations of the currently describedS. chilenserepresent separately evolving populations.

Despite its vast economic importance,Solanumsect.Lycopersiconstill exhibits considerable taxonomic instability. A pattern of under-recognition of outcrossing species may be common across flowering plants. We discuss the possible causes and implications of this observation, with a focus on macroevolutionary inference.
Air Quality and COVID-19 Prevalence/Fatality
Authors: Takagi Hisato , Kuno Toshiki , Yokoyama Yujiro , Ueyama Hiroki , Hari Yosuke , Ando Tomo
Published: June 2020

To investigate the association of real-time/observed ozone/PM2.5 levels with COVID-19 prevalence/fatality, meta-regression of data from the Northeast megalopolis was conducted. Daily Air Quality Index (AQI) values based on available ozone/PM2.5 data in these counties/cities (3/15/2020–5/31/2020) were extracted from US Environmental Protection Agency and World Air Quality Project. In each county/city, total confirmed COVID-19 cases/deaths (5/31/2020) were available from Johns Hopkins Coronavirus Resource Center, and total population was extracted from US Census Bureau. Random-effects meta-regression was performed using OpenMetaAnalyst. A meta-regression graph depicted COVID-19 prevalence and fatality (plotted as logarithm-transformed prevalence/fatality on the y-axis) as a function of mean ozone/PM2.5 AQI (plotted on the x-axis). Coefficients were not statistically significant for ozone (P = 0.212/0.814 for prevalence/fatality) and PM2.5 (P = 0.986/0.499). Although multivariable analysis had been planned, it was not performed because of non-significant covariates of interest in the univariable model. In conclusion, ozone/PM2.5 may be unassociated with COVID-19 prevalence/fatality.
Explore the Possible Impact of BCG Vaccination Policy on the Morbidity, Mortality, and Recovery Rates due to COVID-19 Infection
Authors: Chang Chuan-Hsin , Chang Yue-Cune
Published: June 2020

BACKGROUND

The Coronavirus Disease-19 (COVID-19) is the new form of an acute infectious respiratory disease and has quickly spread over most continents in the world. Recently, it has been shown that Bacille Calmette-Guerin (BCG) might protect against COVID-19. This study aims to investigate the possible correlation between BCG vaccination and morbidity/mortality/recovery rate associated with COVID-19 infection.

METHODS

Data of COVID-19 confirmed cases, deaths, recoveries, and population were obtained fromhttps://www.worldometers.info/coronavirus/(Accessed on 12 June, 2020). To have meaningful comparisons among countries’ mortality and recovery rates, we only choose those countries with COVID-19 infected cases at least 200. The Poisson regression and logistic regression were used to explore the relationship between BCG vaccination and morbidity, mortality and recovery rates.

RESULTS

Among those 158 countries with at least 200 COVID-19 infected cases, there were 141 countries with BCG vaccination information available. The adjusted rates ratio of COVID-19 confirmed cases for Current BCG vaccination vs. non-Current BCG vaccination was 0.339 (with 95% CI= (0.338,0.340)). Moreover, the adjusted odds ratio (OR) of death and recovery after coronavirus infected for Current BCG vaccination vs. non-Current BCG vaccination were 0.258 (with 95% CI= (0.254,0.261)) and 2.151 (with 95% CI= (2.140,2.163)), respectively.

CONCLUSIONS

That data in this study show the BCG might provide the protection against COVID-19, with consequent less COVID-19 infection and deaths and more rapid recovery. BCG vaccine might bridge the gap before the disease-specific vaccine is developed, but this hypothesis needs to be further tested in rigorous randomized clinical trials.
NECo: A node embedding algorithm for multiplex heterogeneous networks
Authors: Dursun Cagatay , Smith Jennifer R. , Hayman G. Thomas , Kwitek Anne E. , Bozdag Serdar
Published: June 2020

Complex diseases such as hypertension, cancer, and diabetes cause nearly 70% of the deaths in the U.S. and involve multiple genes and their interactions with environmental factors. Therefore, identification of genetic factors to understand and decrease the morbidity and mortality from complex diseases is an important and challenging task. With the generation of an unprecedented amount of multi-omics datasets, network-based methods have become popular to represent the multilayered complex molecular interactions. Particularly node embeddings, the low-dimensional representations of nodes in a network are utilized for gene function prediction. Integrated network analysis of multi-omics data alleviates the issues related to missing data and lack of context-specific datasets. Most of the node embedding methods, however, are unable to integrate multiple types of datasets from genes and phenotypes. To address this limitation, we developed a node embedding algorithm called Node Embeddings of Complex networks (NECo) that can utilize multilayered heterogeneous networks of genes and phenotypes. We evaluated the performance of NECo using genotypic and phenotypic datasets from rat (Rattus norvegicus) disease models to classify hypertension disease-related genes. Our method significantly outperformed the state-of-the-art node embedding methods, with AUC of 94.97% compared 85.98% in the second-best performer, and predicted genes not previously implicated in hypertension.

Availability and implementation

The source code is available on GitHub athttps://github.com/bozdaglab/NECo.
Mobile element warfare via CRISPR and anti-CRISPR inPseudomonas aeruginosa
Authors: Leon Lina M. , Park Allyson E. , Borges Adair L. , Zhang Jenny Y. , Bondy-Denomy Joseph
Published: June 2020

Bacteria deploy multiple defense mechanisms to prevent the invasion of mobile genetic elements (MGEs). CRISPR-Cas systems use RNA-guided nucleases to target MGEs, which in turn produce anti-CRISPR (Acr) proteins that inactivate Cas protein effectors. The minimal component Type I-C CRISPR-Cas subtype is highly prevalent in bacteria, and yet a lack of a tractablein vivomodel system has slowed its study, the identification of cognate Acr proteins, and thus our understanding of its true role in nature. Here, we describe MGE-MGE conflict between a mobilePseudomonas aeruginosaType I-C CRISPR-Cas system always encoded on pKLC102-like conjugative elements, which are large mobile islands, and seven new Type I-C anti-CRISPRs (AcrIF2*, AcrIC3-IC8) encoded by phages, other mobile islands, and transposons. TheP. aeruginosaType I-C system possesses a total of 300 non-redundant spacers (from 980 spacers total) across the 42 genomes analyzed, predominantly targetingP. aeruginosaphages. Of the seven new Type I-C anti-CRISPRs, all but one are highly acidic, and four have surprisingly broad inhibition activity, blocking multiple distantly relatedP. aeruginosaType I CRISPR system subtypes (e.g. I-C and I-F, or I-C and I-E), including AcrIF2 (now, AcrIF2*), a previously described DNA mimic. Anti-type I-C activity of AcrIF2* was far more sensitive to mutagenesis of acidic residues in AcrIF2* than anti-type I-F activity, suggesting distinct binding mechanisms for this highly negatively charged protein. Five of the seven Acr proteins block DNA-binding, while the other two act downstream of DNA-binding, likely by preventing Cas3 recruitment or activity. For one such Cas3 inhibitor (AcrIC3), we identify a novel anti-CRISPR evasion strategy: acas3-cas8gene fusion, which also occurs in nature. Collectively, the Type I-C CRISPR spacer diversity and corresponding anti-CRISPR response, all occurring onPseudomonasMGEs, demonstrates an active co-evolutionary battle between parasitic elements.
Impact of bead-beating intensity on microbiome recovery in mouse and human stool:Optimization of DNA extraction
Authors: Zhang Bo , Brock Matthew , Arana Carlos , Dende Chaitanya , Hooper Lora , Raj Prithvi
Published: June 2020

DNA extraction methods play an important role in the acquisition of accurate and reproducible 16S sequencing data in microbiome studies. In this study, we assessed the impact of bead-beating intensity during DNA extraction on microbiome recovery in mouse and human stool. We observed a higher DNA yield, better DNA integrity, higherShannon’s entropyandSimpson’s indexin samples beaten for 4 and 9 minutes as compared to unbeaten samples. 16S sequencing data showed that bead beating has a statistically-significant (p<0.05) impact on the recovery of many clinically relevant microbes that live in the mouse and human gut, includingBifidobacterium, SutterellaandVeillonella.It was observed that 4 minutes of bead beating promotes recovery of about 70% of OTUs in mouse and human stool, while the remaining 30% requires longer bead beating. In conclusion, our study indicates adjustments in bead beating treatment based on the composition of the specimen and the targeted bacteria.
The long noncoding RNAMeg3regulates myoblast plasticity and muscle regeneration through epithelial-mesenchymal transition
Authors: Dill Tiffany L. , Carroll Alina , Gao Jiachen , Naya Francisco J.
Published: June 2020

Formation of skeletal muscle is among the most striking examples of cellular plasticity in animal tissue development, where mononucleated, lineage-restricted progenitor cells are reprogrammed by epithelial-mesenchymal transition (EMT) to produce multinucleated myofibers. While some mediators of EMT have been shown to function in muscle formation, the regulation of this process in this tissue remains poorly understood. The long noncoding RNA (lncRNA)Meg3is processed from the >200 kbDlk1-Dio3polycistron that we have previously shown is involved in skeletal muscle differentiation and regeneration. Here, we demonstrate thatMeg3regulates EMT in myoblast differentiation and skeletal muscle regeneration. Chronic inhibition ofMeg3in C2C12 myoblasts promoted aberrant EMT activation, and suppressed cell state transitions required for fusion and myogenic differentiation. Furthermore, adenoviralMeg3knockdown compromised muscle regeneration, which was accompanied by abnormal mesenchymal gene expression and interstitial cell proliferation in the regenerating milieu. Transcriptomic and pathway analyses ofMeg3-depleted C2C12 myoblasts and injured skeletal muscle revealed a significant dysregulation of EMT-related genes, and identified TGFβ as a key upstream regulator. Importantly, chemical inhibition of TGFβR1, as well as its downstream effectors ROCK1/2 and p38 MAPK, restored many aspects of myogenic differentiation inMeg3-depleted myoblastsin vitro. Thus,Meg3regulates myoblast identity to maintain proper cell state for progression into differentiation.

Summary statement

Muscle differentiation and regeneration are regulated by an evolutionarily conserved long noncoding RNA that restricts gene expression to coordinate cell state transitions
Enhancing Mask Activity in Dopaminergic Neurons Extends Lifespan in Flies
Authors: Tian Xiaolin
Published: June 2020

Dopaminergic neurons (DANs) are essential modulators for brain functions involving memory formation, reward processing, and decision making. Here I demonstrate a novel and important function of the DANs in regulating aging and longevity. Overexpressing the putative scaffolding protein Mask in two small groups of DANs in flies can significantly extend the lifespan in flies and sustain adult locomotor and fecundity at old ages. Such a Mask-induced beneficial effect requires dopaminergic transmission but cannot be recapitulated by elevating dopamine production in the DANs. Independent activation of Gαsin the same two groups of DANs via the drug-inducible DREADD system also extends fly lifespan, further indicating the connection of specific DANs to aging control. The Mask-induced lifespan extension appears to depend on the function of Mask to regulate microtubule (MT) stability. A structure-function analysis demonstrated that the ankyrin repeats domain in the Mask protein is both necessary for regulating MT stability (when expressed in muscles and motor neurons) and sufficient to prolong longevity (when expressed in the two groups of DANs). Furthermore, DAN-specific overexpression of Unc-104 or knockdown of p150Glued, two independent interventions previously shown to impact MTs dynamics, also extend lifespan in flies. Together these data demonstrated a novel DANs-dependent mechanism that, upon neuronal cell-type specific tuning of MT dynamics, modulates systemic aging and longevity in flies.
Linking Cerebellar Functional Gradients to Transdiagnostic Behavioral Dimensions of Psychopathology
Authors: Dong Debo , Guell Xavier , Genon Sarah , Wang Yulin , Chen Ji , Eickhoff Simon B. , Luo Cheng , Yao Dezhong
Published: June 2020

High co-morbidity and substantial overlap across psychiatric disorders encourage a transition in psychiatry research from categorical to dimensional approaches that integrate neuroscience and psychopathology. Cerebellum is involved in a wide range of nonmotor cognitive functions and mental disorders. An important question thus centers on the extent to which cerebellar function can be linked to transdiagnostic dimensions of psychopathology. Here, this question is investigated using partial least squares to identify latent dimensions linking cerebellar connectome properties as assessed by macroscale spatial gradients of connectivity to a large set of clinical and behavioral measures in 198 participants across diagnostic categories. This analysis reveals significant correlated patterns of cerebellar connectivity gradients and behavioral measures that could be represented into four latent dimensions: general psychopathology, general lack of attention regulation, internalizing symptoms, and dysfunctional memory. Each dimension is associated with a distinct spatial pattern of cerebellar connectivity gradients. These findings highlight the relevance of cerebellar connectivity as a necessity for the study and classification of transdiagnostic dimensions of psychopathology.
Interspecies comparative metagenomics reveals correlated gut microbiome functional capacities among vertebrates
Authors: Gaulke Christopher A. , Armour Courtney R. , Humphreys Ian R. , Beaver Laura M. , Barton Carrie L. , Carbone Lucia , Ho Emily , Tanguay Robyn L. , Jiang Yuan , Sharpton Thomas
Published: June 2020

While recent research reveals that the gut microbiome drives vertebrate health, little is known about whether the mechanisms these microbes employ to interact with physiology are consistent across host species. To help close this knowledge gap, we compared gut metagenomes across 10 vertebrate species, including biomedical animal models, to define the inter-species variation in the biochemical pathways encoded by gut microbiota. Doing so revealed gut-enriched pathways conserved across vertebrates, as well as pathways that vary concordantly with host evolutionary history. Overall, the functional capacity of the non-human gut microbiome generally reflects that of humans, though a subset of the pathways encoded by human gut microbiota are not well represented in non-human microbiomes. Collectively, these results support the use of animal models to study the mechanisms through which gut microbes impact human health, but suggest that researchers should cautiously consider which model will optimally represent a specific mechanism of interest.

Significance

Efforts to understand how the gut microbiome interacts with human physiology frequently relies on the use of animal models. However, it is generally not understood if the biochemical pathways encoded in gut microbiomes of these different animal models – which define the routes of interaction between gut microbes and their hosts – reflect those found in the human gut. To address this question, we compared gut metagenomes generated 10 different vertebrate lineages. In so doing, our study revealed that non-human gut metagenomes generally encode a set of pathways that are consistent with those found in the human gut. However, some human metagenome pathways are poorly represented in non-human guts, including pathways implicated in disease. Moreover, our analysis identified pathways that appear to be conserved across vertebrates, as well as pathways that are linked to the evolutionary history of their hosts, observations that hold potential to clarify the basis for phylosymbiosis.
Molecular underpinning of intracellular pH regulation on TMEM16F
Authors: Liang Pengfei , Yang Huanghe
Published: June 2020

TMEM16F, a dual functional phospholipid scramblase and ion channel, is important in blood coagulation, skeleton development, HIV infection and cell fusion. Despite the advances in understanding its structure and activation mechanism, how TMEM16F is regulated by intracellular factors remains largely elusive. Here we report that TMEM16F lipid scrambling and ion channel activities are strongly influenced by intracellular pH (pHi). We find that low pHiattenuates whereas high pHipotentiates TMEM16F activation. Our biophysical characterizations pinpoint that the pHiregulatory effects on TMEM16F stem from protonation and deprotonation of the Ca2+binding sites, which in turn reduces and enhances Ca2+binding affinity, respectively. We further demonstrate that intracellular alkalization of 0.5 pHican significantly promote TMEM16F activities in a choriocarcinoma cell line. Our findings thus uncover a regulatory mechanism of TMEM16F by pHiand shine light on understanding the pathophysiological roles of TMEM16F in diseases with dysregulated pHiincluding cancer.
The factor structure of attention-deficit/hyperactivity disorder in schoolchildren
Authors: Arildskov Trine Wigh , Virring Anne , Lambek Rikke , Carlsen Anders Helles , Sonuga-Barke Edmund J.S. , Østergaard Søren D. , Thomsen Per Hove
Published: June 2020

This study investigated the factor structure of attention-deficit/hyperactivity disorder (ADHD) by comparing the fit of a single-factor model, a correlated model with two or three factors, and a bifactor model with one general and two or three specific factors. Different three-factor solutions that varied with regard to the specification of the item “talks excessively” as impulsivity or hyperactivity were also tested. Parent ratings on the ADHD-Rating Scale (ADHD-RS-IV) were collected in a sample of 2044 schoolchildren (1st to 3rd grade) from the general population and in a clinical sample of 165 children and adolescents with ADHD referred to a public regional child and adolescent psychiatric hospital. Confirmatory factor analyses found a satisfactory fit for most models in both samples. However, a correlated three-factor model where “talks excessively” was included as an indicator of impulsivity and especially the bifactor version of this model with one general and three specific factors fit the data slightly better in the general population. In the clinical sample, a number of models performed equally well (the same version of the correlated three-factor model and all the bifactor models). Overall, the factor structure of ADHD seems to be better characterized by a bifactor model with a strong general factor and two or three weaker specific factors. Due to the strong general factor, we suggest emphasizing the ADHD-RS-IV total score rather than the subscale scores in clinical practice.
Lichtenberg optimization algorithm applied to crack tip identification in thin plate-like structures
Authors: Pereira João Luiz Junho , Chuman Matheus , Cunha Jr Sebastião Simões , Gomes Guilherme Ferreira
Published: June 2020

Purpose

This study aims to develop a numerical identification and characterization of crack propagation through the use of a new optimization metaheuristics called Lichtenberg optimization.

Design/methodology/approach

The damage-identification problem is treated as an inverse problem, which combines finite element methods with intelligent computational methods to obtain the best possible response. To optimize the objectives, the Lichtenberg algorithm is applied, which includes concepts of random cluster growth in nature.

Findings

The simulations show that it is possible to determine the Lichtenberg spectrum algorithm a part of the structure to be removed and replaced in this case to stop the propagation.

Originality/value

The results show a very good crack identification in plates-like structures using the Lichtenberg algorithm (LA) based only in strain fields. Although many studies have reported on damage-identification-based optimization methods, very few have focused on the crack tip modeling and LA as the main solver.
Supply chain quality management performance measurement: systematic review
Authors: Karamouz Seyedeh Soudeh , Ahmadi Kahnali Reza , Ghafournia Mohamad
Published: June 2020

Purpose

This study aims at investigating the existing knowledge in the literature on quality management performance measurement in order to identify performance measures in the field of total quality management and classify measures according to the three levels of supplier, customer and company.

Design/methodology/approach

A systematic literature review is conducted at the intersection of performance measurement and total quality management fields. Four databases including Web of Sciences, Scopus, Emerald and Google Scholar were searched up to 2018. A final sample of 24 articles was selected based on the inclusion/exclusion criteria that constitutes the knowledge base of the study.

Findings

One of the problems that many organizations face is the lack of knowledge and resources on how to evaluate, improve and manage the quality performance. Through analysis and synthesis of the literature, the study revealed the measures for assessing quality performance at three levels of supplier, customer and company.

Research limitations/implications

This study focuses only on four databases, which may have limited the number of the databases included and thus the scope of this investigation to a certain extent.

Originality/value

The present study aimed to identify and classify different performance measures through a systematic literature review framework classifying these measures into three groups. The article brings together fragmented literature from multiple studies to categorize research output regarding performance measurement of supply chain quality. The paper shows the state of the performance measurement in total quality management in supply chain.
Managing the professional mobility of the Russian youth: specifics of scientific discourse and methodological landmarks
Authors: Mishschenko Dmitry N. , Vereshchagina Anna V. , Magomedov Magomed G. , Mareev Vladimir I. , Kumykov Ayes M.
Published: June 2020

Purpose

The purpose of the paper is to determine the specifics of scientific discourse in the sphere of managing professional mobility of the Russian youth and to develop a cognitive scheme of sociological research of this problem.

Design/methodology/approach

The authors use the potential of the stratification and activity approaches, the theory of multiplicity of professionalization, and multidimensional analysis as the most perspective method for sociological measuring of phenomena and processes in the professional sphere in the conditions of society's transformation.

Findings

The authors determine and study the key directions in the sphere of studying the professional mobility of the Russian youth and managing this process; substantiate the conceptual and methodological underdevelopment of this problem and offer the proprietary methodological strategy of its sociological study through distinguishing three stages of professional development of youth; substantiate the perspectives of its usage in studying the professional mobility of youth and constructing the effective policy of managing this process; outline the role of state and education in overcoming crisis factors of professional development of youth in the context of domination in the modern world and among the Russian youth.

Research limitations/implications

Importance of this research is predetermined by the need for theoretical consideration of top-priority directions in studying professional mobility of youth and the means of managing this process in view of the factors of crisis professionalization, unpreparedness of youth to adapt in spontaneous and quickly changing conditions of the labor market and absence of the conceptual sociological developments in this sphere.

Originality/value

The materials of the research and the offered cognitive scheme are aimed at formation of the methodological basis of studying the problem of managing the professional mobility of the Russian youth for the purpose of overcoming the crisis trajectory of professionalization of the Russian youth and increasing the effectiveness of its professional mobility in the conditions of increased mobility of the whole modern world.
How to use fuzzy screening system and data envelopment analysis for clustering sustainable suppliers? A case study in Iran
Authors: Izadikhah Mohammad , Farzipoor Saen Reza , Ahmadi Kourosh , Shamsi Mohadeseh
Published: June 2020

Purpose

The aim of this paper is to classify suppliers into some clusters based on sustainability factors. However, there might be some unqualified suppliers and we should identify and remove those suppliers before clustering.

Design/methodology/approach

First, using fuzzy screening system, the authors identify and remove the unqualified suppliers. Then, the authors run their proposed clustering method. This paper proposes a data envelopment analysis (DEA) algorithm to cluster suppliers.

Findings

This paper presents a two-aspect DEA-based algorithm for clustering suppliers into clusters. The first aspect applied DEA to consider efficient frontiers and the second aspect applied DEA to consider inefficient frontiers. The authors examine their proposed clustering approach by a numerical example. The results confirmed that their method can cluster DMUs into clusters.

Originality/value

The main contributions of this paper are as follows: This paper develops a new clustering algorithm based on DEA models. This paper presents a new DEA model in inefficiency aspect. For the first time, the authors’ proposed algorithm uses fuzzy screening system and DEA to select suppliers. Our proposed method clusters suppliers of MPASR based on sustainability factors.
Cosmopolitanism, self-identity, online communities and green apparel perception
Authors: Khare Arpita , Kautish Pradeep
Published: June 2020

Purpose

The research examined the influence of cosmopolitanism, global self-identity and online communities on Indian consumers’ green knowledge and consequently, its effect on the perception of green apparel product attributes.

Design/methodology/approach

A mall intercept technique was used for data collection in four cities in India. The hypothesized relationships were examined through structural equation modeling.

Findings

Cosmopolitanism, global self-identity and online communities influenced green knowledge. Green knowledge influenced Indian consumers’ perception of green apparel. The results indicate that social conformance and identification with online communities predicted consumers’ understanding of green apparel.

Research limitations/implications

The research focused on green knowledge, cosmopolitanism, online communities and consumers’ perception of green apparel. The role of demographics, culture and product attributes like price, quality, promotions and design were not considered and may provide valuable insights.

Practical implications

Green apparel manufacturers can communicate about the product attributes by linking it with growing global environmental consciousness, cosmopolitanism and global self-identity traits that focus on green consumption. Online communities can be used to inform, educate and promote green apparel.

Social implication

The study will pave the way forward to explore green consumption paradigms among fashion-oriented consumers in the Indian market who drive sustainable behavior.

Originality/value

The research suggested that conformance with global values and identification with online communities can be critical in helping consumers understand green apparel. It examined the importance of offline and online social conformance in evaluating green apparel.
Limit order books: a systematic review of literature
Authors: Tripathi Abhinava , Vipul Vipul , Dixit Alok
Published: June 2020

Purpose

This study aims to provide a systematic literature review of the research study in the area of limit order book (LOB) mechanism of trading and its implications for market efficiency. The study attempts to document the recent theoretical developments and empirical findings from the literature exhaustively and identifies the research gaps for future research.

Design/methodology/approach

The study uses seven reputable databases to select 2,514 research studies spanning over 1981-2018 (finally compressed to a pool of 103 articles, based on relevance and impact). The study uses bibliometric network visualization and text analytics to categorize and examine the literature. The chosen articles are compiled and analyzed to provide a comprehensive account of the current research on LOBs.

Findings

The recent LOB literature is summarized on various criteria as follows: sub-areas, the types of economies and markets, methodologies and the LOB measures. The review identifies a dearth of studies on the LOBs in emerging markets. It suggests the potential research areas as intraday studies in emerging LOB markets; application of market indicators based on deeper levels of LOB, beyond the best prices; market fragmentation, order routing decision and its impact on order execution quality; optimal display of LOB levels; liquidity dynamics in quote-driven markets vis-à-vis LOB markets; effect of high-frequency trading on market microstructure; application of advanced techniques (e.g. machine learning models, zero-intelligent models); relationship between the trading speed, order aggressiveness, shape and resilience of the order book and informed trading; and information content of the auxiliary order submission strategies, including cancellation, amendments and hidden orders.

Originality/value

For the past 15 years, to the best of the knowledge, a comprehensive review of the literature on LOBs has not been published. The financial markets have transformed significantly over this period, driven by the adoption of LOBs, low latency trading and technological advancements in information dissemination. This article provides an extensive collection and classification of the literature on LOBs. This would be useful for the practitioners, future researchers and academics in the area of financial markets.
Reproductive characteristics that favor invasiveness inLeonotis nepetifolia(L.) R. Br.
Authors: Díaz‐Segura Omar , Golubov Jordan , Mandujano María C. , Zavala‐Hurtado José Alejandro
Published: June 2020

Reproductive systems are life attributes important in defining the demography and genetic constitution of invasive alien species populations. We describe the phenology, floral behavior and floral visitors in Mexican populations ofLeonotis nepetifoliaconsidered invasive in America, Asia and Oceania. The mating system was determined through pollination experiments and, with a morphological analysis of flowers (outcrossing index, OCI) and pollen/ovule ratio, the breeding system was evaluated. Germination of 1 and 2‐year‐old seeds was tested to assess the potential characteristics of germination.Leonotis nepetifoliawas reproductive for 7 months (June to December) and tended towards a specific season during autumn. Anthesis lasted 36 hr with protogyny and no hercogamy, with floral visitors of Apodiformes, Hymenoptera, Lepidoptera and Thysanoptera. Pollination experiments indicated a mixed mating system, whereas the OCI and the pollen/ovule ratio pointed towards a facultative xenogamous breeding system. Seed production was high (1,445 ± 132 seeds/plant); the seeds had potential longevity and were neutral photoblastic. One‐year‐old seeds germinated slightly later (= 2.6 ± 0.11 days) than 2‐year‐old seeds (= 1.9 ± 0.02 days), both synchronously (IS1yr= 0.88 ± 0.03 and IS2yr= 0.82 ± 0.02). Germination percentage for 1‐year‐old seeds was lower (55.33 ± 4.40%) than that of 2‐year‐old seeds (94.18 ± 0.59%), suggesting a potential longevity of the seeds in an optimal environment. Reproductive characteristics, such as wide reproductive period, mixed breeding system, copious seed production, seeds with potential longevity, and quick and synchronic germination in different light conditions, favor the invasive capacity ofLeonotis nepetifolia.
Australian Housing Market Booms: Fundamentals or Speculation?*
Authors: Shi Shuping , Rahman Arafat , Wang Ben Zhe
Published: June 2020

This paper investigates the presence of housing bubbles in Australia at the national, capital city and local government area (LGA) levels. We control for housing market demand and supply fundamentals using the technique of Shi (2017), and employ the recursive evolving method proposed by Phillips et al. (2015a,b) for the detection of explosive bubbles. While the national‐level analysis suggests a short‐lived bubble episode (2017Q3) over the entire sample period from 1999 to 2017, the results from the capital‐city‐level data reveal substantial heterogeneity across cities, with only short‐lived and isolated bubbles identified for Sydney and Melbourne during the recent rapid housing price expansions from 2013 to 2017. The LGA‐level analysis suggests that only a small percentage of LGA housing markets are identified to be speculative in Sydney and Melbourne from 2013 to 2017.