bluuebunny/crossref_metadata_2025 huggingface dataset:
Topology-based Sparsification of Graph Annotations
Authors: Danciu Daniel , Karasikov Mikhail , Mustafa Harun , Kahles André , Rätsch Gunnar
Published: November 2020

Since the amount of published biological sequencing data is growing exponentially, efficient methods for storing and indexing this data are more needed than ever to truly benefit from this invaluable resource for biomedical research. Labeled de Bruijn graphs are a frequently-used approach for representing large sets of sequencing data. While significant progress has been made to succinctly represent the graph itself, efficient methods for storing labels on such graphs are still rapidly evolving. In this paper, we present RowDiff, a new technique for compacting graph labels by leveraging expected similarities in annotations of vertices adjacent in the graph. RowDiff can be constructed in linear time relative to the number of vertices and labels in the graph, and in space proportional to the graph size. In addition, construction can be efficiently parallelized and distributed, making the technique applicable to graphs with trillions of nodes. RowDiff can be viewed as an intermediary sparsification step of the original annotation matrix and can thus naturally be combined with existing generic schemes for compressed binary matrices. Experiments on 10,000 RNA-seq datasets show that RowDiff combined with Multi-BRWT results in a 30% reduction in annotation footprint over Mantis-MST, the previously known most compact annotation representation. Experiments on the sparser Fungi subset of the RefSeq collection show that applying RowDiff sparsification reduces the size of individual annotation columns stored as compressed bit vectors by an average factor of 42. When combining RowDiff with a Multi-BRWT representation, the resulting annotation is 26 times smaller than Mantis-MST.
Signatures Of Tspan8 Variants Associated With Human Metabolic Regulation And Diseases
Authors: De Tisham , Goncalves Angela , Speed Doug , Froguel Phillipe ,   NFBC consortium, Gaffney Daniel , Johnson Michael R. , Jarvelin Maarjo-Riitta , Coin Lachlan JM
Published: November 2020

Here, with the example of common copy number variation (CNV) in the TSPAN8 gene, we present an important piece of work in the field of CNV detection, CNV association with complex human traits such as1H NMR metabolomic phenotypes and an example of functional characterization of CNVs among human induced pluripotent stem cells (HipSci). We report TSPAN8 exon 11 as a new locus associated with metabolomic regulation and show that its biology is associated with several metabolic diseases such as type 2 diabetes (T2D), obesity and cancer. Our results further demonstrate the power of multivariate association models over univariate methods and define new metabolomic signatures for several new genomic loci, which can act as a catalyst for new diagnostics and therapeutic approaches.
Functional traits predict species responses to environmental variation in a California grassland annual plant community
Authors: Kandlikar Gaurav S. , Kleinhesselink Andew R. , Kraft Nathan J.B.
Published: November 2020

Turnover in species composition and community-wide functional traits across environmental gradients is a ubiquitous pattern in ecology, and is generally assumed to reflect shifts in trait optima across these gradients. However, the demographic processes that give rise to these trait turnover patterns at the community level remain unclear.

We asked whether shifts in the community-weighted means of three key functional traits across an environmental gradient in a southern California grassland reflect variation in the trait-performance relationship across the landscape.

We planted seeds of 17 annual plant species in cleared patches with no competitors, and quantified the lifetime seed production of 1360 individuals. We then asked whether models that included trait-environment interactions help explain interspecific variation in demographic responses to the environment. This allowed us to evaluate whether observed shifts in community-weighted mean traits matched the direction of any trait-environment interactions detected in the plant performance experiment.

Our results indicate that commonly-measured plant functional traits help explain variation in species responses to the environment – for example, high-SLA species had a demographic advantage in soils with high soil Ca:Mg levels, while low-SLA species had an advantage in low Ca:Mg soils. We also found that shifts in community-weighted mean traits often reflect the direction of these trait-environment interactions, though not all trait-environment relationships at the community level reflect interactive effects of traits and environment on species performance.

Our results support the value of plant functional traits for predicting species responses to environmental variation, and highlight a need for more detailed evaluation of how trait-performance relationships change across environments to improve such predictions.
First record of the Australian redclaw crayfishCherax quadricarinatus(von Martens 1868) in Hong Kong, China
Authors: Sze-man YAU , Anthony LAU
Published: November 2020

Invasive freshwater crayfish are spreading rapidly across the world. Here, we report the first record of Australian redclaw crayfish,Cherax quadricarinatus(von Martens 1868) in Hong Kong, China. Identification of the captured crayfish was confirmed using external morphological features and molecular analyses. A total of 49 crayfish were captured from a stream pool and a reservoir in Pok Fu Lam Country Park using dip nets and funnel traps. The capturedC. quadricarinatusranged from 17.20 mm to 56.40 mm (mean = 30.70) in carapace length and the sex ratio was 1:1. Since this species is globally recognized as an invasive species, a comprehensive survey on its status and invasion front, an investigation into its potential ecological impacts, as well as the formulation of a monitoring and removal strategy, are warranted.
Circulating tumor fraction analyses with ultra-low pass whole genome sequencing predict response to chemoradiation and recurrence in stage IV small cell carcinoma of the cervix: a longitudinal case study
Authors: Abbas Ata , Gruner Morgan , Karohl Jennifer , Rose Peter G. , Joehlin-Price Amy , Al-Sudani Hussein , Stover Daniel , Mahdi Haider
Published: November 2020

Neuroendocrine carcinoma of the cervix is a rare and aggressive form of cervical cancer that presents with frequent metastasis at diagnosis and high recurrence rates. Primary treatment is multimodal, which often includes chemotherapy with or without radiation therapy. There is no data available to guide treatment for recurrence, and second-line therapies are extrapolated from small cell lung carcinoma data. Close monitoring of these patients for recurrence is paramount. Evaluation of circulating tumor DNA (ctDNA) in the peripheral blood is an attractive approach due to its noninvasive nature. Ultra-low pass whole genome sequencing (ULP-WGS) can assess tumor burden, response to therapy, and predict recurrence; however, data are lacking regarding the role of ULP-WGS in small cell carcinoma of the cervix. This study demonstrates a patient whose response to chemotherapy and cancer recurrence was accurately monitored by ctDNA using ULP-WGS testing and confirmed with radiologic imaging findings.
Genome-wide association study of febrile seizures identifies seven new loci implicating fever response and neuronal excitability genes
Authors: Skotte Line , Fadista João , Bybjerg-Grauholm Jonas , Appadurai Vivek , Hildebrand Michael S , Hansen Thomas F , Banasik Karina , Grove Jakob , Climent Clara A , Geller Frank , Bjurström Carmen F , Vilhjálmsson Bjarni J , Coleman Matthew , Damiano John A , Burgess Rosemary , Scheffer Ingrid E , Vesterager Pedersen Ole Birger , Erikstrup Christian , Westergaard David , René Nielsen Kaspar , Sørensen Erik , Bruun Mie Topholm , Liu Xueping , Hjalgrim Henrik , Pers Tune H , Mortensen Preben Bo , Mors Ole , Nordentoft Merete , Dreier Julie W , Børglum Anders , Christensen Jakob , Hougaard David M , Buil Alfonso , Hviid Anders , Melbye Mads , Ullum Henrik , Berkovic Samuel F , Werge Thomas , Feenstra Bjarke
Published: November 2020

Febrile seizures represent the most common type of pathological brain activity in young children and are influenced by genetic, environmental, and developmental factors. While usually benign, in a minority of cases, febrile seizures precede later development of epilepsy. Here, we conducted a genome-wide association study of febrile seizures with 7,635 cases and 93,966 controls identifying and replicating seven new loci, all with P < 5 × 10−10. Variants at two loci were functionally related to altered expression of the fever response genes PTGER3 and IL10, and four other loci harbored genes (BSN, ERC2, GABRG2, HERC1) influencing neuronal excitability by regulating neurotransmitter release and binding, vesicular transport or membrane trafficking at the synapse. GABRG2 is a well-established epilepsy gene comprising variants associated with febrile seizures, and overall we found positive genetic correlations with epilepsies (rg = 0.39, P = 1.68 × 10−4). Finally, a polygenic risk score based on all genome-wide significant loci was associated within patients with number of hospital admissions with febrile seizures and age at first admission, suggesting potential clinical utility of improved genetic understanding of febrile seizure genesis.
REACT-1 round 6 updated report: high prevalence of SARS-CoV-2 swab positivity with reduced rate of growth in England at the start of November 2020
Authors: Riley Steven , Ainslie Kylie E. C. , Eales Oliver , Walters Caroline E. , Wang Haowei , Atchison Christina , Fronterre Claudio , Diggle Peter J. , Ashby Deborah , Donnelly Christl A. , Cooke Graham , Barclay Wendy , Ward Helen , Darzi Ara , Elliott Paul
Published: November 2020

Background

England is now in the midst of its second wave of the COVID-19 pandemic. Multiple regions of the country are at high infection prevalence and all areas experienced rapid recent growth of the epidemic during October 2020.

Methods

REACT-1 is a series of community surveys of SARS-CoV-2 RT-PCR swab-positivity in England designed to monitor the spread of the epidemic and thus increase situational awareness. Round 6 of REACT-1 commenced swab-collection on 16th October. A prior interim report included data from 16th to 25th October for 85,971 participants. Here, we report data for the entire round on 160,175 participants with swab results obtained up to 2nd November 2020.

Results

Overall weighted prevalence of infection in the community in England was 1.3% or 130 people per 10,000 infected, up from 60 people per 10,000 in the round 5 report (18th September to 5th October 2020), doubling every 24 days on average since the prior round. The corresponding R number was estimated to be 1.2. Prevalence of infection was highest in North West (2.4%, up from 1.2%), followed by Yorkshire and The Humber (2.3% up from 0.84%), West Midlands (1.6% up from 0.60%), North East (1.5% up from 1.1%), East Midlands (1.3% up from 0.56%), London (0.97%, up from 0.54%), South West (0.80% up from 0.33%), South East (0.69% up from 0.29%), and East of England (0.69% up from 0.30%). Rapid growth in the South observed in the first half of round 6 was no longer apparent in the second half of round 6. We also observed a decline in prevalence in Yorkshire and The Humber during this period. Comparing the first and second halves of round 6, there was a suggestion of decline in weighted prevalence in participants aged 5 to 12 years and in those aged 25 to 44 years. While prevalence remained high, in the second half of round 6 there was suggestion of a slight fall then rise that was seen nationally and also separately in both the North and the South.

Conclusion

The impact of the second national lockdown in England is not yet known. We provide here a detailed description of swab-positivity patterns at national, regional and local scales for the period immediately preceding lockdown, against which future trends in prevalence can be evaluated.
Quantifying Covid19-Vaccine Location Strategies For Germany
Authors: Leithäuser Neele , Schneider Johanna , Johann Sebastian , Krumke Sven O. , Schmidt Eva , Streicher Manuel , Scholz Stefan
Published: November 2020

Abstract

Background

Vaccines are an important tool to limit the health and economic damage of the Covid-19 pandemic. Several vaccine candidate already provided promising effectiveness data, but it is crucial for an effective vaccination campaign that people are willing and able to get vaccinated as soon as possible. Taking Germany as an example, we provide insights of using a mathematical approach for the planning and location of vaccination sites to optimally administer vaccines against Covid-19.

Methods

We used mathematical programming for computing an optimal selection of vaccination sites out of a given set (i.e., university hospitals, health department related locations and general practices). Different patient-to-facility assignments and doctor-to-facility assignments and different constraints on the number of vaccinees per site or maximum travel time are used.

Results

In order to minimize the barriers for people to get vaccinated, i.e., limit the one-way travel journey (airline distance) by around 35 km for 75 % of the population (with a maximum of 70 km), around 80 well-positioned facilities can be enough. If only the 38 university hospitals are being used, the 75 % distance increases to around 50 km (with a maximum of 145 km). Using all 400 health departments or all 56 000 general practices can decrease the journey length significantly, but comes at the price of more required staff and possibly wastage of only partially used vaccine containers.

Conclusions

In the case of free assignments, the number of required physicians can in most scenarios be limited to 2 000, which is also the minimum with our assumptions. However, when travel distances for the patients are to be minimized, capacities of the facilities must be respected, or administrative assignments are prespecified, an increased number of physicians is unavoidable.
Type I PRMTs and PRMT5 Independently Regulate Both snRNP Arginine Methylation and Post-Transcriptional Splicing
Authors: Maron Maxim I. , Burgos Emmanuel S. , Gupta Varun , Casill Alyssa D. , Kosmyna Brian , Chen Hongshan , Gamble Matthew J. , Query Charles C. , Shechter David
Published: November 2020

Protein argininemethyltransferases (PRMTs) methylate histones, splicing factors, and many other nuclear proteins. Type I enzymes (PRMT1-4,6,8) catalyze mono- (Rme1/MMA) and asymmetric (Rme2a/ADMA) dimethylation; Type II enzymes (PRMT5,9) catalyze mono- and symmetric (Rme2s/SDMA) dimethylation. Misregulation of PRMTs in multiple types of cancers is associated with aberrant gene expression and RNA splicing. To understand the specific mechanisms of PRMT activity in splicing regulation, we treated cells with the PRMT5 inhibitor GSK591 and the Type I inhibitor MS023 and probed their transcriptomic consequences. We discovered that Type I PRMTs and PRMT5 inversely regulate core spliceosomal Sm protein Rme2s and intron retention. Loss of Sm Rme2s is associated with the accumulation of polyadenylated RNA containing retained introns and snRNPs on chromatin. Conversely, increased Sm Rme2s correlates with decreased intron retention and chromatin-association of intron-containing polyadenylated RNA. Using the newly developed SKaTER-seq model, comprehensive and quantitative analysis of co-transcriptional splicing revealed that either Type I PRMT or PRMT5 inhibition resulted in slower splicing rates. Surprisingly, altered co-transcriptional splicing kinetics correlated poorly with ultimate changes in alternatively spliced mRNA. Quantitation of retained intron decay following inhibition of nascent transcription revealed that Type I PRMTs and PRMT5 reciprocally regulate post-transcriptional splicing efficiency.
Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance
Authors: Fareh Mohamed , Zhao Wei , Hu Wenxin , Casan Joshua ML , Kumar Amit , Symons Jori , Voskoboinik Ilia , Ekert Paul G , Rudraraju Rajeev , Lewin Sharon R , Trapani Joseph A
Published: November 2020

Mutation-driven evolution of SARS coronavirus-2 (SARS-CoV-2) highlights the need for innovative approaches that simultaneously suppress viral replication and circumvent viral escape routes from host immunity and antiviral therapeutics. Here, we employed genome-wide computational prediction and singlenucleotide resolution screening to reprogram CRISPR-Cas13b against SARS-CoV-2 genomic and subgenomic RNAs. Reprogrammed Cas13b effectors targeting accessible regions of Spike and Nucleocapsid transcripts achieved >98% silencing efficiency in virus free-models. Further, optimized and multiplexed gRNAs suppressed viral replication by up to 90% in mammalian cells infected with replication-competent SARS-CoV-2. Unexpectedly, the comprehensive mutagenesis of guide-target interaction demonstrated that single-nucleotide mismatches do not impair the capacity of a potent single gRNA to simultaneously suppress ancestral and mutated SARS-CoV-2 in infected mammalian cells, including the highly infectious and globally disseminated Spike D614G mutant. The specificity, efficiency and rapid deployment properties of reprogrammed Cas13b described here provide a molecular blueprint of antiviral therapeutics to simultaneously suppress a wide range of SARS-CoV-2 mutants, and is readily adaptable to other emerging pathogenic viruses.
A precise measure of the impact of the first wave of Covid-19 on life expectancy. Regional differentials in Switzerland
Authors: Wanner Philippe
Published: November 2020

Based on publicly available data supplied by the Swiss Federal Statistical Office (FSO), we calculated life tables by sex and by week for seven major regions of Switzerland in 2020, up to October 26th. These life tables provide information on the trends of life expectancy at birth and at the age of 65 years during the first wave of the coronavirus disease 2019 (COVID-19) epidemic.

The results show a strong cyclical decrease in life expectancy, particularly in Ticino, where this variable has decreased by almost 6 years compared to the 2019 life expectancy, and in the Lake Geneva region. The other regions of Switzerland observed more modest decreases during the first wave, generally not exceeding a 2-year reduction. This decrease can be explained to some extent by seasonal variations in this indicator.

In conclusion, the very sharp decrease in the average lifespan observed in the two regions mentioned above suggests that the first wave of the epidemic had a significant impact. It also reflects an unfavourable health situation. The life expectancy at the age of 65 years observed at the end of March 2020 in Ticino corresponded to the average life expectancy observed in Switzerland forty years ago.

The calculated indicators have the advantage of accounting for the age structures of the respective populations. They therefore demonstrate their usefulness in monitoring during a pandemic, such as the one occurring currently.
Screening & diagnosing errors in longitudinal measures of body size
Authors: Wills AK
Published: November 2020

This paper presents a novel multi-step automated algorithm to screen for errors in longitudinal height and weight data and describes the frequency and characteristics of errors in three datasets. It also offers a taxonomy of published cleaning routines from a scoping review.

Illustrative data are from three Norwegian retrospective cohorts containing 87,792 assessments (birth to 14y) from 8,428 children. Each has different data pipelines, quality control and data structure. The algorithm contains 43 steps split into 3 sections; (a) dates, (b) Identifiable data entry errors, (c) biologically impossible/ implausible change, and uses logic checks, and cross-sectional and longitudinal routines. The WHO cross-sectional approach was also applied as a comparison.

Published cleaning routines were taxonomized by their design, the marker used to screen errors, the reference threshold and how threshold was selected. Fully automated error detection was not possible without false positives or reduced sensitivity. Error frequencies in the cohorts were 0.4%, 2.1% and 2.4% of all assessments, and the percentage of children with ≥1 error was 4.1%, 13.4% and 15.3%. In two of the datasets, >2/3s of errors could be classified as inliers (within ±3SD scores). Children with errors had a similar distribution of HT and WT to those without error. The WHO cross-sectional approach lacked sensitivity (range 0-55%), flagged many false positives (range: 7-100%) and biased estimates of overweight and thinness.

Elements of this algorithm may have utility for built-in data entry rules, data harmonisation and sensitivity analyses. The reported error frequencies and structure may also help design more realistic simulation studies to test routines. Multi-step distribution-wide algorithmic approaches are recommended to systematically screen and document the wide range of ways in which errors can occur and to maximise sensitivity for detecting errors, naive cross-sectional trimming as a stand-alone method may do more harm than good.
Ultrafast Brownian-ratchet mechanism for protein translocation by a AAA+ machine
Authors: Mazal Hisham , Iljina Marija , Riven Inbal , Haran Gilad
Published: November 2020

AAA+ ring-shaped machines, such as ClpB and Hsp104, mediate substrate translocation through their central channel by a set of pore loops. Recent structural studies suggested a universal hand-over-hand translocation mechanism, in which pore loops are moving rigidly in tandem with their corresponding subunits. However, functional and biophysical studies are in discord with this model. Here, we directly measure the real-time dynamics of the pore loops of ClpB and their response to substrate binding, using single-molecule FRET spectroscopy. All pore loops undergo large-amplitude fluctuations on the microsecond timescale, and change their conformation upon interaction with substrate proteins. Pore-loop conformational dynamics are modulated by nucleotides and strongly correlate with disaggregation activity. The differential behavior of the pore loops along the axial channel points to a fast Brownian-ratchet translocation mechanism, which likely acts in parallel to the much slower hand-over-hand process.
Generation of two Multipotent Mesenchymal Progenitor Cell Lines Capable of Osteogenic, Mature Osteocyte, Adipogenic, and Chondrogenic Differentiation
Authors: Prideaux Matthew , Wright Christian S. , Noonan Megan L. , Yi Xin , Clinkenbeard Erica L. , Mevel Elsa , Wheeler Jonathan A. , Byers Sharon , Sankar Uma , White Kenneth E. , Atkins Gerald J. , Thompson William R.
Published: November 2020

Differentiation of multi-potent mesenchymal progenitor cells give rise to several tissue types including bone, cartilage, and adipose. In addition to the complication arising from the numerous spatial, temporal, and hormonal factors that regulate lineage allocation, targeting of these cellsin vivois challenging, making mesenchymal progenitor cell lines valuable tools to study both tissue development and the differentiated cell types. Mesenchymal stem cells (MSCs) can be isolated from humans and animals; however, obtaining homogenous, responsive cells in a reproducible fashion can be problematic. As such, we have developed two novel mesenchymal progenitor cell (MPC) lines, MPC1 and MPC2, which were generated from the bone marrow of male C57BL/6 mice. These cells were immortalized using the temperature sensitive large T-antigen, allowing for thermal control of proliferation and differentiation. Both MPC1 and MPC2 cell lines are capable of osteogenic, adipogenic, and chondrogenic differentiation. Under osteogenic conditions both cell lines formed discrete mineralized nodules, staining for alizarin red and alkaline phosphatase, while expressing high levels of osteogenic genes includingSost,Fgf23, andDmp1.SostandDmp1mRNA levels were drastically reduced with parathyroid hormone, thus recapitulatingin vivoresponses. MPC cells secreted both the intact (iFGF23) andC-terminal (cFGF23) forms of endocrine hormone FGF23, which was upregulated in the presence of 1,25 dihydroxy vitamin D (1,25D). In addition to osteogenic differentiation, both cell lines also rapidly entered the adipogenic lineage, expressing several adipose markers after only 4 days in adipogenic media. MPC cells were also capable of chondrogenic differentiation, displaying increased expression of common cartilage genes including aggrecan, sox9, and cartilage oligomeric matrix protein. With the ability to differentiate into multiple mesenchymal lineages and mimic in vivo responses of key regulatory genes/proteins, MPC cells are a valuable model to study factors that regulate mesenchymal lineage allocation as well as the mechanisms that dictate transcription, protein modification, and secretion of these factors.
The structural mechanism underlying the antithetic effect of homologous RND1 and RhoD GTPases in plexin regulation
Authors: Liu Yanyan , Ke Pu , Kuo Yi-chun , Wang Yuxiao , Zhang Xuewu , Song Chen , Shan Yibing
Published: November 2020

Plexins are semaphorin receptors that play essential roles in neuronal axon guidance and in many other important biological processes. Plexin signaling depends on a semaphorin-induced dimerization mechanism, and is modulated by small signaling GTPases of the Rho family, of which RND1 serves as a plexin activator yet its close homolog RhoD an inhibitor. Using molecular dynamics (MD) simulations we showed that RND1 reinforces plexin dimerization interface whereas RhoD destabilizes it due to their differential interaction with cell membrane. Upon binding plexin dimers at the Rho-GTPase binding (RBD) domains, RND1 and RhoD interact differently with the inner leaflet of cell membrane, and exert opposite effects on the dimerization interface via an allosteric network involving the RBD domain, RBD linkers, and a buttress segment adjacent to the dimerization interface. The differential membrane interaction is attributed to the fact that, unlike RND1, RhoD features a short C-terminal tail and a positively-charged membrane interface.
SERCA activity is reduced inDJ-1mutant flies and human cells due to oxidative modification
Authors: Solana-Manrique Cristina , Muñoz-Soriano Verónica , Sanz Francisco José , Paricio Nuria
Published: November 2020

DJ-1is a causative gene for familial Parkinson’s disease (PD) with different functions, standing out its role against oxidative stress (OS). Accordingly, PD model flies harboring a mutation in theDJ-1βgene (theDrosophilaortholog of humanDJ-1) show high levels of OS markers like protein carbonylation, a common post-translational modification that may alter protein function. To increase our understanding of PD pathogenesis as well as to discover potential therapeutic targets for pharmacological intervention, we performed a redox proteomic assay inDJ-1βmutant flies. Among the proteins that showed increased carbonylation levels in PD model flies, we found SERCA, an endoplasmic reticulum Ca2+channel that plays an important role in Ca2+homeostasis. Several studies have supported the involvement of Ca2+dyshomeostasis in PD. Interestingly, a functional link betweenDJ-1and Ca2+homeostasis maintenance was previously reported. Thus, we decided to study the relation between SERCA activity and PD physiopathology. Our results showed that SERCA enzymatic activity is significantly reduced inDJ-1βmutant flies, probably as a consequence of OS-induced carbonylation, as well as in a human cell PD model based onDJ-1-deficiency. Indeed, higher carbonylation levels of SERCA were also observed inDJ-1-deficient SH-SY5Y neuron-like cells compared to controls. In addition, we demonstrated that SERCA activity was increased in both PD models after treatment with a specific activator of this protein, CDN1163. Consistently, CDN1163 was also able to restore PD-related phenotypes in PD model flies and to increase viability in the human cell PD model. Taken together, our results indicate that impaired SERCA activity in both familial PD models may play a role in PD physiopathology. In addition, we demonstrate that therapeutic strategies addressing SERCA activation could be beneficial to treat this disease as shown for CDN1163.
Efficacy and safety of colchicine for the treatment of osteoarthritis: protocol for a systematic review and meta-analysis of intervention trials
Authors: Molina-Garcia Pablo , Singh Ambrish , Hussain Salman , Das Sidharth , Antony Benny
Published: November 2020

Colchicine, in the form of Colchicum autumnale, has been used to treat joint swelling for centuries. The anti-inflammatory action o colchicine and the higher prevalence of calcium pyrophosphate crystal deposition (CPPD) in osteoarthritis (OA) joints have led to th use of colchicine as a potential treatment for OA, however, the quality of the evidence on this regards is still limited. The curren protocol aims to conduct a systematic review and meta-analysis proving the efficacy and safety of colchicine for the treatment of adul patients with OA. For that purpose, Scopus®, Web of Sciences®, Medline® and Cochrane Library® will be inspected for the availabl trials testing the efficacy and safety of colchicine for the treatment of any type of OA (e.g., hand, knee or hip). Cochrane tool will b used to assess the risk of bias of included trials. A meta-analysis of dichotomous (e.g., adverse events) or continuous data (e.g., mea difference in pain scale) will be performed depending on the data reporting. Review Manager 5 (RevMan) and RStudio Version 1.2.133 will be used to conduct the statistical analysis.
Structure and stability of γ1-AuZn2.1: a γ-brass-related complex phase in the Au–Zn System
Authors: Koley Biplab , Thimmaiah Srinivasa , Lidin Sven , Jana Partha P.
Published: November 2020

γ1-AuZn2.1in the Au–Zn binary system has been synthesized and its structure analyzed by single-crystal X-ray diffraction. It crystallizes in the trigonal space groupP31m(No. 157) with ∼227 atoms per unit cell and represents a \surd3a× \surd3a×csuperstructure of rhombohedrally distorted γ-Au5–xZn8+y. The structure is largely tetrahedrally closed packed. The formation of γ1-AuZn2.1can be understood within the framework of a Hume-Rothery stabilization mechanism with a valence electron concentration of 1.68 e/a (valence electrons per atom).
Single crystals of ferroelectric lithium niobate–tantalate LiNb1–x
Ta

x

O3 solid solutions for high-temperature sensor and actuator applications
Authors: Roshchupkin Dmitry , Emelin Evgenii , Plotitcyna Olga , Rashid Fahrtdinov , Irzhak Dmitry , Karandashev Vasilii , Orlova Tatiana , Targonskaya Natalya , Sakharov Sergey , Mololkin Anatolii , Redkin Boris , Fritze Holger , Suhak Yuri , Kovalev Dmitry , Vadilonga Simone , Ortega Luc , Leitenberger Wolfram
Published: November 2020

Ferroelectric LiNb1–x
Ta
x
O3 solid solutions with various Nb/Ta ratio were grown from the melt by the Czochralski method. The exact composition of the grown crystals was determined by inductively coupled plasma atomic mass spectrometry. The dependence of the crystal composition on the composition of the initial melt was obtained and explained by a wide separation between the phase boundaries of the liquid and solid phases on the LiNbO3–LiTaO3 phase diagram. Using high-resolution X-ray diffraction, the parameters a and c of a crystal unit cell were determined (LiNb0.88Ta0.12O3: a = 5.1574 Å and c = 13.8498 Å). Further, the Curie temperature T
C of the crystals was measured using the differential scanning calorimetry technique. T
C was found to depend on the composition of the crystals that allowed conditions for the monodomainization of the grown crystals to be defined (LiNb0.88Ta0.12O3: T
C = 1102°C; LiNb0.33Ta0.67O3: T
C = 794°C). Finally, the velocity of surface acoustic waves was determined by scanning electron microscopy and X-ray diffraction techniques (YZ-cut of a LiNb0.88Ta0.12O3 crystal: V = 3440 m s−1).
Unexpected synthesis and crystal structure of N-{2-[2-(2-acetylethenyl)phenoxy]ethyl}-N-ethenyl-4-methylbenzenesulfonamide
Authors: Temesgen Ayalew W. , Luong Minh Duc , Truong Hong Hieu , Nguyen Van Tuyen , Dang Thi Tuyet Anh , Le Tuan Anh , Tskhovrebov Alexander G. , Khrustalev Victor N.
Published: November 2020

The title compound, C21H23NO4S, obtained by alkaline treatment of 1,5-bis(1-phenoxy)-3-azapentane at moderate heating, is a N-tosylated secondary vinylamine. An intramolecular S=O...H—C hydrogen bond generates a 13-membered ring. The benzalacetone moiety adopts a trans conformation with respect to the C=C double bond, which is slightly longer than usual due to the conjugation with a neighbouring acetyl group. Theoretical predictions of potential biological activities were performed, suggesting that the title compound can inhibit gluconate 2-dehydrogenase (85% probability), as well as to act as a mucomembranous protector (73%).
An analytical study of stakeholders relevance based on their perceived preference in terms of climate strategy proactivity (CSP)
Authors: Kant Nikhil
Published: November 2020

Purpose

The purpose of this study is to evaluate empirically the perceptions of the stakeholder regarding their relevance based on their perceived preference in terms of climate strategy proactivity (CSP) which is an outcome of the importance and influence of the category of the stakeholders of Indian companies. Revolutionized by the liberalization–privatization–globalization, the practices and strategies of the companies in the developing country such as India have been marked by dynamic changes in the several past decades. In these circumstances, it has become imperative to understand the relevance of the stakeholders in terms of CSP displayed by these companies to seek help in developing appropriate strategies in the emerging competitive market.

Design/methodology/approach

This paper used a research design comprising descriptive analytical method using non-probability purposive sampling method to collect data from a sampled 701 respondents representing eleven categories stakeholders, with the help of a cross-sectional, self-administered online survey questionnaire.

Findings

The findings of the study detail the evaluation of the stakeholders relevance based on their perceived preference in terms of CSP attaching significance to the stakeholders’ perception as a useful tool. While the findings hint at the incessant growth of stakeholder awareness urging corporations to analyze effects and adopt appropriate strategies in developing countries, they also evaluate empirically the perceptions of the stakeholder regarding their relevance based on their perceived preference in terms of CSP which is an outcome of the importance and influence enjoyed by the category of the stakeholders of Indian companies. The findings confirmed the adequate level of awareness of the stakeholders of Indian companies responsible for making them adopt CSP.

Research limitations/implications

This study had the limitations such as collection of information through a self-reported questionnaire which might have the impact of self-bias despite all the preventive and corrective measures, and the risk of creation of a subjective viewpoint due to the assessment of the perceptions of varied stakeholders. Nonetheless, meeting the objective of this study, the study succeeds in providing a stakeholder perspective to the existing body of knowledge with respect to CSP, a stakeholders-centric concept which is in infancy in the context of developing countries and their corporations.

Originality/value

The paper is original as it adds value by providing empirical evidence from the perspective of different stakeholders, including but not limited to managers or shareholders only, like majority of previous studies. By doing so, it successfully attempts to contextualize them indicating the need to unlock huge potentialities and substantial significance for other developing countries.
Exploring the magnitude of inclusion of Indian youth in the world of work based on choices of educational attainment
Authors: Bisht Nitin , Pattanaik Falguni
Published: November 2020

Purpose

This study attempts to investigate the interrelationship between choice-based educational achievement and employability prospects across the skill-based occupations amongst the youth in India.

Design/methodology/approach

This study relies on the use of National Sample Survey (NSS) data on employment and unemployment for the 68th round (2011–2012) and the Periodic Labour Force Survey (PLFS) (2017–2018). To estimate the relative contributions of choice-based educational attainment affecting the skill-based employment of youth in a different category of occupations ( high/medium/low skilled), the multinomial logistic regression and its marginal effects have been used.

Findings

The study finds educational attainment both as an opportunity (improvising employability in the high and medium skill occupation) and a challenge (highest unemployment amongst the educated) while ensuring skill-based youth employability. Despite the growing enrolment of youth in education, youth from a general education background does not find sustained employability prospects in high-skill occupations.

Research limitations/implications

Vocational education highlights a brighter employability prospect but the acceptability of the same amongst the youth needs a policy intervention.

Practical implications

Educational choices need an intervention based on market-driven apprenticeships and training.

Social implications

The decline of overall employability in the low-skill occupation raises a threat to inclusive development as such youth results to Not in Employment, Education or Training (NEET), better identified as the unproductive economic youth.

Originality/value

This study attempts to investigate that “how far the choice of educational attainment (general/technical/vocational) is able to make youth a fit in the world of work?” in the Indian context, where the youth constitute the highest share in the population.
Challenges in abrasive jet machining of fiber-reinforced polymeric composites – a review
Authors: Madhu S. , Balasubramanian M.
Published: November 2020

Purpose

The purpose of this study is for solving many issues in production that includes processing of complex-shaped profile, machining of high-strength materials, good surface finish with high-level precision and minimization of waste. Among the various advanced machining processes, abrasive jet machining (AJM) is one of the non-traditional machining techniques used for various applications such as polishing, deburring and hole making. Hence, an overview of the investigations done on carbon fiber-reinforced polymer (CFRP) and glass fiber-reinforced polymer (GRFP) composites becomes important.

Design/methodology/approach

Discussion on various approaches to AJM, the effect of process parameters on the glass fiber and carbon fiber polymeric composites are presented. Kerf characteristics, surface roughness and various nozzle design were also discussed.

Findings

It was observed that abrasive jet pressure, stand-off distance, traverse rate, abrasive size, nozzle diameter, angle of attack are the significant process parameters which affect the machining time, material removal rate, top kerf, bottom kerf and kerf angle. When the particle size is maximum, the increased kinetic energy of the particle improves the penetration depth on the CFRP surface. As the abrasive jet pressure is increased, the cutting process is enabled without severe jet deflection which in turn minimizes the waviness pattern, resulting in a decrease of the surface roughness.

Research limitations/implications

The review is limited to glass fiber and carbon fiber polymeric composites.

Practical implications

In many applications, the use of composite has gained wide acceptance. Hence, machining of the composite need for the study also has gained wide acceptance.

Social implications

The usage of composites reduces the usage of very costly materials of high density. The cost of the material also comes down.

Originality/value

This paper is a comprehensive review of machining composite with abrasive jet. The paper covers in detail about machining of only GFRP and CFRP composites with various nozzle designs, unlike many studies which has focused widely on general AJM of various materials.
The anaerobic survival mechanism of Schizophyllum commune 20R‐7‐F01, isolated from deep sediment 2 km below the seafloor
Authors: Zain Ul Arifeen Muhammad , Chu Chen , Yang Xinyi , Liu Junzhong , Huang Xin , Ma Yunan , Liu Xuan , Xue Yarong , Liu Changhong
Published: November 2020

Fungi dominated the eukaryotic group in the anaerobic sedimentary environment below the ocean floor where they play an essential ecological role. However, the adaptive mechanism of fungi to these anaerobic environments is still unclear. Here, we reported the anaerobic adaptive mechanism of Schizophyllum commune 20R‐7‐F01, isolated from deep coal‐bearing sediment down to ~2 km below the seafloor, through biochemical, metabolomic and transcriptome analyses. The fungus grows well, but the morphology changes obviously and the fruit body develops incompletely under complete hypoxia. Compared with aerobic conditions, the fungus has enhanced branched‐chain amino acid biosynthesis and ethanol fermentation under anaerobic conditions, and genes related to these metabolisms have been significantly up‐regulated. Additionally, the fungus shows novel strategies for synthesizing ethanol by utilizing both glycolysis and ethanol fermentation pathways. These findings suggest that the subseafloor fungi may adopt multiple mechanisms to cope with lack of oxygen.
Trends in Market Concentration of Australian Industries
Authors: Bakhtiari Sasan
Published: November 2020

A host of industrialised countries have seen concentration in their industries grow. This trend is fuelling concerns about falling competition. This article focuses on the changing pattern of market concentration in Australia from 2002 to 2017. On average, market concentration has been rising. However, beneath the aggregate statistics, the pattern is rather mixed, with concentration falling in several sectors. The study also detects a pattern of strong productivity growth alongside a shift towards capital intensive operation and increasing trade where concentration is growing. Overall, the implications of these findings point to the possibility that rising market concentration in some industries is technology driven and not due to a lack of competition.
Evaluation of fermented African yam bean flour composition and influence of substitution levels on properties of wheat bread
Authors: Chinma Chiemela Enyinnaya , Azeez Shakirah Omotoke , Sulayman Hudah Tahirah , Alhassan Khadizat , Alozie Sharon Nelson , Gbadamosi Hammed Dada , Danbaba Nahemiah , Oboh Henrietta Ayodele , Anuonye Julian Chukwuemeka , Adebo Oluwafemi Ayodeji
Published: November 2020

The composition (proximate, amino acids, in vitro protein digestibility [IVPD]), antinutritional factors (ANFs), functional properties, and antioxidant activity of fermented African yam bean flour (FAYBF) were determined in this study, and the effect of substituting FAYBF on the properties (nutritional, physical, and functional) of bread was investigated. Fermentation significantly (P ≤ 0.05) increased the levels of nutrients, IVPD, total phenolic content (TPC), and antioxidant activity in the flour, with significant (P ≤ 0.05) reduction in ANFs. The water absorption capacity (WAC) and oil absorption capacity (OAC), and swelling capacity of the flour increased after fermentation, while bulk density decreased. Substitution of wheat flour with FAYBF increased WAC and OAC, while peak viscosity decreased. Composite breads had higher nutritional, IVPD, TPC, and antioxidant activity than 100% wheat bread. The study demonstrates that FAYBF could be explored for the preparation of wheat‐based bread, with reduced gluten levels.

Practical Application

Bread is a staple food and this study can assist in increasing the utilization of neglected leguminous crops as well as addressing the challenge of malnutrition, prevalent in developing countries.
Practice guidance for diagnosis and treatment of pancreatitis‐related splanchnic vein thrombosis (Shenyang, 2020)
Authors:   Pancreas Study Group, Chinese Society of Gastroenterology, Chinese Medical Association
Published: November 2020

Splanchnic vein thrombosis is a severe complication of pancreatitis. To date, no consensus over the management of pancreatitis‐related splanchnic vein thrombosis has been established. Based on the consensus of multidisciplinary experts, this practice guidance systematically reviewed the epidemiology, anatomy, pathophysiology, risk assessment and clinical presentations of splanchnic vein thrombosis, and formulated a diagnosis and treatment strategy for providing guidance in clinical practice for this disease.
Does inpatient hyperglycemia predict a worse outcome in COVID‐19 intensive care unit patients?
Authors: Saand Aisha R. , Flores Monica , Kewan Tariq , Alqaisi Sura , Alwakeel Mahmoud , Griffiths Lori , Wang Xiaofeng , Han Xiaozhen , Burton Robert , Al‐Jaghbeer Mohammed J. , Abi Fadel Francois
Published: November 2020

Background

We undertook this study to evaluate the association between hyperglycemia and outcomes in patients with coronavirus disease 2019 (COVID‐19) admitted to the intensive care unit (ICU).

Methods

We conducted a multicenter retrospective study involving all adults with COVID‐19 admitted to the ICU between March and May 2020. Patients were divided into normoglycemic (average blood glucose <140 mg/dL) and hyperglycemic (average blood glucose ≥140 mg/dL) groups. Outcomes such as mortality, need and duration of mechanical ventilation, and length of hospital and ICU stays were measured.

Results

Among 495 patients, 58.4% were male with a median age of 68 years (interquartile range [IQR]: 58.00‐77.00), and baseline average blood glucose was 186.6 (SD ± 130.8). Preexisting diabetes was present in 35.8% of the studied cohort. Combined ICU and hospital mortality rates were 23.8%; mortality and mechanical ventilation rates were significantly higher in the hyperglycemic group with 31.4% vs 16.6% (P = .001) and 50.0% vs 37.2% (P = .004), respectively. Age above 60 years (hazard ratio [HR] 3.21; 95% CI 1.78, 5.78) and hyperglycemia (HR 1.79; 95% CI 1.14, 2.82) were the only significant predictors of in‐hospital mortality. Increased risk for hyperglycemia was found in patients with steroid use (odds ratio [OR] 1.521; 95% CI 1.054, 2.194), triglycerides ≥150 mg/dL (OR 1.62; 95% CI 1.109, 2.379), and African American race (OR 0.79; 95% CI 0.65, 0.95).

Conclusions

Hyperglycemia in patients with COVID‐19 is significantly associated with a prolonged ICU length of stay, higher need of mechanical ventilation, and increased risk of mortality in the critical care setting. Tighter blood glucose control (≤140 mg/dL) might improve outcomes in COVID‐19 critically ill patients; evidence from ongoing clinical trials is needed.