bluuebunny/crossref_metadata_2025 huggingface dataset:
Operationalizing evolutionary transitions in individuality
Authors: Carmel Yohay , Shavit Ayelet
Published: February 2020

Evolutionary transitions in individuality (hereafter, ETIs), such as the transition to multi-cellularity and the transition to social colonies, have been at the centre of evolutionary research, but only few attempts were made to systematically operationalize this concept. Here, we devise a set of four indicators intended to assess the change in complexity during ETIs: system size, inseparability, reproductive specialization and non-reproductive specialization. We then conduct a quantitative comparison across multiple taxa and ETIs. Our analysis reveals that inseparability has a crucial role in the process; it seems irreversible and may mark the point where a group of individuals becomes a new individual at a higher hierarchical level. Interestingly, we find that disparate groups demonstrate a similar pattern of progression along ETIs.
Paraburkholderia madseniana sp. nov., a phenolic acid-degrading bacterium isolated from acidic forest soil
Authors: Wilhelm Roland C. , Murphy Sean J. L. , Feriancek Nicole M. , Karasz David C. , DeRito Christopher M. , Newman Jeffrey D. , Buckley Daniel H.
Published: February 2020

RP11T was isolated from forest soil following enrichment with 4-hydroxybenzoic acid. Cells of RP11T are aerobic, non-sporulating, exhibit swimming motility, and are rods (0.8 µm by 1.4 µm) that often occur as diplobacillus or in short chains (3–4 cells). Optimal growth on minimal media containing 4-hydroxybenzoic acid (µ=0.216 hr−1) occurred at 30 °C, pH 6.5 or 7.0 and 0% salinity. Comparative chemotaxonomic, genomic and phylogenetic analyses revealed the isolate was distinct from its closest relative type strains identified as

Paraburkholderia aspalathi

LMG 27731T,

Paraburkholderia fungorum

LMG 16225T and

Paraburkholderia caffeinilytica

CF1T. Strain RP11T is genetically distinct from

P. aspalathi

, its closest relative, in terms of 16S rRNA gene sequence similarity (98.7%), genomic average nucleotide identity (94%) and in silico DNA–DNA hybridization (56.7 %±2.8). The composition of fatty acids and substrate utilization pattern differentiated strain RP11T from its closest relatives, including growth on phthalic acid. Strain RP11T encoded the greatest number of aromatic degradation genes of all eleven closely related type strains and uniquely encoded a phthalic acid dioxygenase and paralog of the 3-hydroxybenzoate 4-monooxygenase. The only ubiquinone detected in strain RP11T was Q-8, and the major cellular fatty acids were C16 : 0, 3OH-C16 : 0, C17 : 0 cyclo, C19 : 0 cyclo ω8c, and summed feature 8 (C18 : 1 ω7c/ω6c). On the basis of this polyphasic approach, it was determined that strain RP11T represents a novel species from the genus

Paraburkholderia

for which the name Paraburkholderia madseniana sp. nov. is proposed. The type strain is RP11T (=DSM 110123T=LMG 31517T).
Consequences of single-locus and tightly linked genomic architectures for evolutionary responses to environmental change
Authors: Oomen Rebekah A. , Kuparinen Anna , Hutchings Jeffrey A.
Published: February 2020

Genetic and genomic architectures of traits under selection are key factors influencing evolutionary responses. Yet, knowledge of their impacts has been limited by a widespread assumption that most traits are controlled by unlinked polygenic architectures. Recent advances in genome sequencing and eco-evolutionary modelling are unlocking the potential for integrating genomic information into predictions of population responses to environmental change. Using eco-evolutionary simulations, we demonstrate that hypothetical single-locus control of a life history trait produces highly variable and unpredictable harvesting-induced evolution relative to the classically applied multi-locus model. Single-locus control of complex traits is thought to be uncommon, yet blocks of linked genes, such as those associated with some types of structural genomic variation, have emerged as taxonomically widespread phenomena. Inheritance of linked architectures resembles that of single loci, thus enabling single-locus-like modeling of polygenic adaptation. Yet, the number of loci, their effect sizes, and the degree of linkage among them all occur along a continuum. We review how linked architectures are often associated, directly or indirectly, with traits expected to be under selection from anthropogenic stressors and are likely to play a large role in adaptation to environmental disturbance. We suggest using single-locus models to explore evolutionary extremes and uncertainties when the trait architecture is unknown, refining parameters as genomic information becomes available, and explicitly incorporating linkage among loci when possible. By overestimating the complexity (e.g., number of independent loci) of the genomic architecture of traits under selection, we risk underestimating the complexity (e.g., nonlinearity) of their evolutionary dynamics.
Evidence and characteristics of human-to-human transmission of SARS-CoV-2
Authors: Kang Min , Wu Jie , Ma Wenjun , He Jianfeng , Lu Jing , Liu Tao , Li Baisheng , Mei Shujiang , Ruan Feng , Lin Lifeng , Zou Lirong , Ke Changwen , Zhong Haojie , Zhang Yingtao , Chen Xuguang , Liu Zhe , Zhu Qi , Xiao Jianpeng , Yu Jianxiang , Hu Jianxiong , Zeng Weilin , Li Xing , Liao Yuhuang , Tang Xiujuan , Xiao Songjian , Wang Ying , Song Yingchao , Zhuang Xue , Liang Lijun , Zeng Siqing , He Guanhao , Lin Peng , Deng Huihong , Song Tie
Published: February 2020

Background

On December 31, 2019, an outbreak of COVID-19 in humans was reported in Wuhan, and then spread fast to other provinces, China. We analyzed data from field investigations and genetic sequencing to describe the evidence and characteristics of human-to-human transmission in Guangdong Province.

Methods

A confirmed COVID-19 case was defined if a suspected case was verified with positive of SARS-CoV-2 in throat swabs, nasal swabs, bronchoalveolar lavage fluid (BALF), or endotracheal aspirates by real-time reverse transcriptase polymerase chain reaction assay (RT-PCR) or genetic sequencing. Field investigations were conducted for each confirmed case. Clinical and demographic data of confirmed cases were collected from medical records. Exposure and travel history were obtained by interview.

Results

A total of 1,151 confirmed cases were identified as of February 10, 2020 in Guangdong Province, China. Of them, 697 (60.1%) cases were from 234 cluster infections. Two hundred and fourteen (18.6%) were secondary cases, in which 144 cases were from family cluster infections. With the epidemic continuing, although familial cluster events were dominated, community cluster events increased with a nosocomial event. The whole genomes within the same family cluster infections were identical, and presented a few unique single nucleotide variants (SNVs) compared with SARS-CoV-2 identified on December 2019 in Wuhan.

Conclusions

We observed evident human-to-human transmissions of SARS-CoV-2 in Guangdong, China. Although most of them were from family cluster infections, community and nosocomial infections were increasing. Our findings indicate that human-to-human transmission risks are transferring from family to community in Guangdong Province.
Exosome-mediated apoptosis pathway during WSSV infection in crustacean mud crab
Authors: Gong Yi , Kong Tongtong , Ren Xin , Chen Jiao , Lin Shanmeng , Zhang Yueling , Li Shengkang
Published: February 2020

MicroRNAs are regulatory molecules that can be packaged into exosomes to modulate recipient’s cellular response, while their role during viral infection is beginning to be appreciated. However, the involvement of exosomal miRNAs during immunoregulation in invertebrates has not been addressed. Here, we found that exosomes released from WSSV-injected mud crabs could suppress viral invasion by inducing apoptosis of hemocytes. Besides, miR-137 and miR-7847 were found to be less packaged in mud crab exosomes during viral infection, with both miR-137 and miR-7847 shown to be negative apoptosis regulators by targeting the apoptosis-inducing factor (AIF). Moreover, our data revealed that AIF did not only translocate to the nucleus to induce DNA fragmentation, but could also competitively bind to HSP70 to disintegrate the HSP70-Bax (Bcl-2-associated X protein) complex, which eventually activated the mitochondria apoptosis pathway via free Bax. Therefore, our findings provides a novel mechanism underlying the crosstalk between exosomal miRNAs and apoptosis pathway in innate immunity in invertebrates.
Accuracy of short tandem repeats genotyping tools in whole exome sequencing data
Authors: Halman Andreas , Oshlack Alicia
Published: February 2020

Background

Short tandem repeats are important source of genetic variation, they are highly mutable and repeat expansions are associated dozens of human disorders, such as Huntington’s disease and spinocerebellar ataxias. Technical advantages in sequencing technology have made it possible to analyse these repeats at large scale, however, accurate genotyping is still a challenging task. We compared four different short tandem repeats genotyping tools on whole exome sequencing data to determine their genotyping performance and limits which will aid other researchers to choose a suitable tool and parameters for analysis.

Methods

The analysis was performed on the Simons Simplex Collection dataset where we used a novel method of evaluation with accuracy determined by the rate of homozygous calls on the X chromosome of male samples. In total we analysed 433 samples and around a million genotypes for evaluating tools on whole exome sequencing data.

Results

We determined a relatively good performance of all tools when genotyping repeats of 3-6 bp in length which could be improved with coverage and quality score filtering. However, genotyping homopolymers was challenging for all tools and a high error rate was present across different thresholds of coverage and quality scores. Interestingly, dinucleotide repeats displayed a high error rate as well, which was found to be mainly caused by the AC/TG repeats. Overall, LobSTR was able to make the most calls and was also the fastest tool while RepeatSeq and HipSTR exhibited the lowest heterozygous error rate at low coverage.

Conclusions

All tools have different strengths and weaknesses and the choice may depend on the type of analysis. In this analysis we demonstrated the effect of using different filtering parameters and offered recommendations based on the trade-off between the best accuracy of genotyping and the highest number of calls.
ZipSeq : Barcoding for Real-time Mapping of Single Cell Transcriptomes
Authors: Hu Kenneth H. , Eichorst John P. , McGinnis Chris S. , Patterson David M. , Chow Eric D. , Kersten Kelly , Jameson Stephen C. , Gartner Zev J. , Rao Arjun A. , Krummel Matthew F.
Published: February 2020

Spatial transcriptomics seeks to integrate single-cell transcriptomic data within the 3-dimensional space of multicellular biology. Current methods use glass substrates pre-seeded with matrices of barcodes or fluorescence hybridization of a limited number of probes. We developed an alternative approach, called ‘ZipSeq’, that uses patterned illumination and photocaged oligonucleotides to serially print barcodes (Zipcodes) onto live cells within intact tissues, in real-time and with on-the-fly selection of patterns. Using ZipSeq, we mapped gene expression in three settings: in-vitro wound healing, live lymph node sections and in a live tumor microenvironment (TME). In all cases, we discovered new gene expression patterns associated with histological structures. In the TME, this demonstrated a trajectory of myeloid and T cell differentiation, from periphery inward. A variation of ZipSeq efficiently scales to the level of single cells, providing a pathway for complete mapping of live tissues, subsequent to real-time imaging or perturbation.
Prestimulus alpha power is related to the strength of stimulus representation
Authors: Barne Louise C. , de Lange Floris P. , Cravo André M.
Published: February 2020

Spatial attention can modulate behavioural performance and is associated with several electrophysiological markers. In this study, we used multivariate pattern analysis in electrophysiology data to investigate the effects of covert spatial attention on the quality of stimulus processing and underlying mechanisms. Our results show that covert spatial attention led to (i) an anticipatory alpha power desynchronization; (ii) enhanced stimuli identity information. Moreover, we found that alpha power fluctuations in anticipation of the relevant stimuli boosted and prolonged the coding of stimulus identity.
Multiple links between 5-methylcytosine content of mRNA and translation
Authors: Schumann Ulrike , Zhang He-Na , Sibbritt Tennille , Pan Anyu , Horvath Attila , Gross Simon , Clark Susan J , Yang Li , Preiss Thomas
Published: February 2020

5-methylcytosine (m5C) is a prevalent base modification in tRNA and rRNA but it also occurs more broadly in the transcriptome, including in mRNA, where it serves incompletely understood molecular functions. In pursuit of potential links of m5C with mRNA translation, we performed polysome profiling of human HeLa cell lysates and subjected RNA from resultant fractions to efficient bisulfite conversion followed by RNA sequencing (bsRNA-seq). Bioinformatic filters for rigorous site calling were devised to reduce technical noise. We obtained ∼1,000 candidate m5C sites in the wider transcriptome, most of which were found in mRNA. Multiple novel sites were validated by amplicon-specific bsRNA-seq in independent samples of either human HeLa, LNCaP and PrEC cells. Furthermore, RNAi-mediated depletion of either the NSUN2 or TRDMT1 m5C:RNA methyltransferases showed a clear dependence on NSUN2 for the majority of tested sites in both mRNAs and noncoding RNAs. Candidate m5C sites in mRNAs are enriched in 5’UTRs and near start codons, and are commonly embedded in a local context reminiscent of the NSUN2-dependent m5C sites found in the variable loop of tRNA. Analysing mRNA sites across the polysome profile revealed that modification levels, at bulk and for many individual sites, were inversely correlated with ribosome association. Altogether, these findings emphasise the major role of NSUN2 in making this mark transcriptome-wide and further substantiate a functional interdependence of cytosine methylation level with mRNA translation.
Impact of an Oomen feeding with a neonicotinoid on daily activity and colony development of honeybees assessed with an AI based monitoring device
Authors: Gonsior Gundula , Tausch Frederic , Schmidt Katharina , Knäbe Silvio
Published: February 2020

Feeding experiments are standard tools in the pollinator risk assessment. The design (Oomen et al 1992) was developed to test insect growth regulators and herbicides. In recent years there was an update (Lückmann & Schmitzer 2015) on the outline in order to also focus on the advantage of different rates making a dose response design possible where exposure levels are known. Additionally, this design gives the possibility to test different rates for honey bee colonies foraging in the same landscape.

The main objective of the experiment presented here was to determine the natural variability of foragers losses of hives fed with a sub-lethal neonicotinoid concentration compared to an untreated control. Other objectives were to see if the neurotoxic exposure results in any observable sub-lethal effects and to find out if losses can be correlated to hive development. This was assessed with traditional methods and a novel, visual monitoring device.
Testing structural identifiability by a simple scaling method
Authors: Castro Mario , de Boer Rob J.
Published: February 2020

Successful mathematical modeling of biological processes relies on the expertise of the modeler to capture the essential mechanisms in the process at hand and on the ability to extract useful information from empirical data. The very structure of the model limits the ability to infer numerical values for the parameters, a concept referred to as structural identifiability. Most of the available methods to test the structural identifiability of a model are either too complex mathematically for the general practitioner to be applied, or require involved calculations or numerical computation for complex non-linear models. In this work, we present a new analytical method to test structural identifiability of models based on ordinary differential equations, based on the invariance of the equations under the scaling transformation of its parameters. The method is based on rigorous mathematical results but it is easy and quick to apply, even to test the identifiability of sophisticated highly non-linear models. We illustrate our method by example and compare its performance with other existing methods in the literature.

Author summary

Theoretical Biology is a useful approach to explain, generate hypotheses, or discriminate among competing theories. A well-formulated model has to be complex enough to capture the relevant mechanisms of the problem, and simple enough to be fitted to data. Structural identifiability tests aim to recognize, in advance, if the structure of the model allows parameter fitting even with unlimited high-quality data. Available methods require advanced mathematical skills, or are too costly for high-dimensional non-linear models. We propose an analytical method based on scale invariance of the equations. It provides definite answers to the structural identifiability problem while being simple enough to be performed in a few lines of calculations without any computational aid. It favorably compares with other existing methods.
Exon 13-skipped USH2A protein retains functional integrity in mice, suggesting an exo-skipping therapeutic approach to treat USH2A-associated disease
Authors: Pendse Nachiket , Lamas Veronica , Maeder Morgan , Pawlyk Basil , Gloskowski Sebastian , Pierce Eric A. , Chen Zheng-Yi , Liu Qin
Published: February 2020

Mutations in theUSH2Agene are the most common cause of non-syndromic inherited retinal degeneration and Usher syndrome, which is characterized by congenital deafness and progressive vision loss. Development of a vector mediated therapy forUSH2A-associated disease has been challenging due to its large size of coding sequence (~15.6kb). Therefore, there is an unmet need to develop alternative therapeutic strategies. The USH2A protein (Usherin) contains many repetitive domains, and it has been hypothesized that some domains may be dispensable with regard to protein function. Here, we show that skipping of exon 13 of the humanUSH2Agene or the equivalent exon 12 of the mouseUsh2agene results in an in-frame transcript that produces functional Usherin protein. This nearly full length Usherin rescues the ciliogenesis inUsh2anull cells as well as the cochlear and retinal phenotypes inUsh2anull mice. Together, our results support the development of exon-skipping strategies to treat both visual and hearing loss in patients withUSH2A-associated disease due to mutations in exon 13.
Warm periods in repeated cold stresses protectDrosophilaagainst ionoregulatory collapse, chilling injury, and reproductive deficits
Authors: El-Saadi Mahmoud I. , Ritchie Marshall W. , Davis Hannah E. , MacMillan Heath A.
Published: February 2020

In many insects, repeated cold stress, characterized by warm periods that interrupt cold periods, have been found to yield survival benefits over continuous cold stress, but at the cost of reproduction. During cold stress, chill susceptible insects likeDrosophila melanogastersuffer from a loss of ion and water balance, and the current model of recovery from chilling posits that re-establishment of ion homeostasis begins upon return to a warm environment, but that it takes minutes to hours for an insect to fully restore homeostasis. Following this ionoregulatory model of chill coma recovery, we predicted that the longer the duration of the warm periods between cold stresses, the better a fly will recover from a subsequent chill coma event and the more likely they will be to survive, but at the cost of fewer offspring. Here, femaleD. melanogasterwere treated to a long continuous cold stress (25 h at 0°C), or experienced the same total time in the cold with repeated short (15 min), or long (120 min) breaks at 23°C. We found that warm periods in general improved survival outcomes, and individuals that recovered for more time in between cold periods had significantly lower rates of injury, faster recovery from chill coma, and produced greater, rather than fewer, offspring. These improvements in chill tolerance were associated with mitigation of ionoregulatory collapse, as flies that experienced either short or long warm periods better maintained low hemolymph [K+]. Thus, warm periods that interrupt cold exposures improve cold tolerance and fertility inD. melanogasterfemales relative to a single sustained cold stress, potentially because this time allows for recovery of ion and water homeostasis.
Genetic Disruption of Serine Biosynthesis is a Key Driver of Macular Telangiectasia Type 2 Etiology and Progression
Authors: Bonelli Roberto , Ansell Brendan R E , Lotta Luca , Scerri Thomas , Clemons Traci E , Leung Irene ,   The MacTel Consortium, Peto Tunde , Bird Alan C , Sallo Ferenc B , Langenberg Claudia , Bahlo Melanie
Published: February 2020

Purpose

Macular telangiectasia type 2 (MacTel) is a rare, heritable and largely untreatable retinal disorder, often comorbid with diabetes. Genetic risk loci subtend retinal vascular calibre, and glycine/serine/threonine metabolism genes. Serine deficiency may contribute to MacTel via neurotoxic deoxysphingolipid production, however, an independent vascular contribution is also suspected. Here we use statistical genetics to dissect the causal mechanisms underpinning this complex disease.

Methods

We integrated genetic markers for MacTel, vascular, and metabolic traits, and applied Mendelian randomization, MTAG, and conditional/interaction genome-wide association analysis to discover causal contributors to both disease, and spatial retinal imaging sub-phenotypes.

Results

Serine was a key causal driver of disease occurrence and progression, with a lesser contribution to type 2 diabetes risk. Conversely, glycine, threonine and retinal vascular traits are unlikely to be causal for MacTel. Conditional regression analysis resolved three novel disease loci independent of endogenous serine biosynthetic capacity. By aggregating retinal phenotypes into endophenotypes, we demonstrate that SNPs constituting independent risk loci act via related endophenotypes.

Discussion

Our findings will aid in early diagnosis and accurate prognosis of MacTel, and improve prospects for effective therapeutic intervention. Our integrative genetics approach also serves as a useful template for post-GWAS analyses in other disorders.
Generating Digital Twins with Multiple Sclerosis Using Probabilistic Neural Networks
Authors: Walsh Jonathan R. , Smith Aaron M. , Pouliot Yannick , Li-Bland David , Loukianov Anton , Fisher Charles K. ,   for the Multiple Sclerosis Outcome Assessments Consortium
Published: February 2020

Multiple Sclerosis (MS) is a neurodegenerative disorder characterized by a complex set of clinical assessments. We use an unsupervised machine learning model called a Conditional Restricted Boltzmann Machine (CRBM) to learn the relationships between covariates commonly used to characterize subjects and their disease progression in MS clinical trials. A CRBM is capable of generating digital twins, which are simulated subjects having the same baseline data as actual subjects. Digital twins allow for subject-level statistical analyses of disease progression. The CRBM is trained using data from 2395 subjects enrolled in the placebo arms of clinical trials across the three primary subtypes of MS. We discuss how CRBMs are trained and show that digital twins generated by the model are statistically indistinguishable from their actual subject counterparts along a number of measures.
Chromonomer: a tool set for repairing and enhancing assembled genomes through integration of genetic maps and conserved synteny
Authors: Catchen Julian , Amores Angel , Bassham Susan
Published: February 2020

The pace of the sequencing and computational assembly of novel reference genomes is accelerating. Though DNA sequencing technologies and assembly software tools continue to improve, biological features of genomes such as repetitive sequence as well as molecular artifacts that often accompany sequencing library preparation can lead to fragmented or chimeric assemblies. If left uncorrected, defects like these trammel progress on understanding genome structure and function, or worse, positively mislead such research. Fortunately, integration of additional, independent streams of information, such as a genetic map – particularly a marker-dense map from RADseq, for example – and conserved orthologous gene order from related taxa can be used to scaffold together unlinked, disordered fragments and to restructure a reference genome where it is incorrectly joined. We present a tool set for automating these processes, one that additionally tracks any changes to the assembly and to the genetic map, and which allows the user to scrutinize these changes with the help of web-based, graphical visualizations. Chromonomer takes a user-defined reference genome, a map of genetic markers, and, optionally, conserved synteny information to construct an improved reference genome of chromosome models: a “chromonome”. We demonstrate Chromonomer’s performance on genome assemblies and genetic maps that have disparate characteristics and levels of quality.
Structures of α-synuclein filaments from multiple system atrophy
Authors: Schweighauser Manuel , Shi Yang , Tarutani Airi , Kametani Fuyuki , Murzin Alexey G. , Ghetti Bernardino , Matsubara Tomoyasu , Tomita Taisuke , Ando Takashi , Hasegawa Kazuko , Murayama Shigeo , Yoshida Mari , Hasegawa Masato , Scheres Sjors H.W. , Goedert Michel
Published: February 2020

Synucleinopathies are human neurodegenerative diseases that include multiple system atrophy (MSA), Parkinson’s disease, Parkinson’s disease dementia (PDD) and dementia with Lewy bodies (DLB) (1). Existing treatments are at best symptomatic. These diseases are characterised by the presence in brain cells of filamentous inclusions of α-synuclein, the formation of which is believed to cause disease (2, 3). However, the structures of α-synuclein filaments from human brain are not known. Here we show, using electron cryo-microscopy, that α-synuclein inclusions from MSA are made of two types of filaments, each of which consists of two different protofilaments. Non-proteinaceous molecules are present at the protofilament interfaces. By two-dimensional class averaging, we show that α-synuclein filaments from the brains of patients with MSA and DLB are different, suggesting that distinct conformers (or strains) characterise synucleinopathies. As was the case of tau assemblies (4–9), the structures of α-synuclein filaments extracted from the brains of individuals with MSA differ from those formedin vitrousing recombinant proteins, with implications for understanding the mechanisms of aggregate propagation and neurodegeneration in human brain. These findings have diagnostic and potential therapeutic relevance, especially in view of the unmet clinical need to be able to image filamentous α-synuclein inclusions in human brain.
Interplay between compartmentalized NAD+ synthesis and consumption: a focus on the PARP family
Authors: Cohen Michael S.
Published: February 2020

Nicotinamide adenine dinucleotide (NAD+) is an essential cofactor for redox enzymes, but also moonlights as a substrate for signaling enzymes. When used as a substrate by signaling enzymes, it is consumed, necessitating the recycling of NAD+ consumption products (i.e., nicotinamide) via a salvage pathway in order to maintain NAD+ homeostasis. A major family of NAD+ consumers in mammalian cells are poly-ADP-ribose-polymerases (PARPs). PARPs comprise a family of 17 enzymes in humans, 16 of which catalyze the transfer of ADP-ribose from NAD+ to macromolecular targets (namely, proteins, but also DNA and RNA). Because PARPs and the NAD+ biosynthetic enzymes are subcellularly localized, an emerging concept is that the activity of PARPs and other NAD+ consumers are regulated in a compartmentalized manner. In this review, I discuss NAD+ metabolism, how different subcellular pools of NAD+ are established and regulated, and how free NAD+ levels can control signaling by PARPs and redox metabolism.
The full-length transcriptome of C. elegans using direct RNA sequencing
Authors: Roach Nathan P. , Sadowski Norah , Alessi Amelia F. , Timp Winston , Taylor James , Kim John K.
Published: February 2020

Current transcriptome annotations have largely relied on short read lengths intrinsic to the most widely used high-throughput cDNA sequencing technologies. For example, in the annotation of the Caenorhabditis elegans transcriptome, more than half of the transcript isoforms lack full-length support and instead rely on inference from short reads that do not span the full length of the isoform. We applied nanopore-based direct RNA sequencing to characterize the developmental polyadenylated transcriptome of C. elegans. Taking advantage of long reads spanning the full length of mRNA transcripts, we provide support for 23,865 splice isoforms across 14,611 genes, without the need for computational reconstruction of gene models. Of the isoforms identified, 3452 are novel splice isoforms not present in the WormBase WS265 annotation. Furthermore, we identified 16,342 isoforms in the 3′ untranslated region (3′ UTR), 2640 of which are novel and do not fall within 10 bp of existing 3′-UTR data sets and annotations. Combining 3′ UTRs and splice isoforms, we identified 28,858 full-length transcript isoforms. We also determined that poly(A) tail lengths of transcripts vary across development, as do the strengths of previously reported correlations between poly(A) tail length and expression level, and poly(A) tail length and 3′-UTR length. Finally, we have formatted this data as a publicly accessible track hub, enabling researchers to explore this data set easily in a genome browser.
Crystal structure of 2-methyl-1,2,3,4-tetrahydroisoquinoline trihydrate
Authors: Langenohl Felix , Otte Felix , Strohmann Carsten
Published: February 2020

The crystal structure of the title compound, C10H13N·3H2O, a heterocyclic amine, was determined in the presence of water. The compound co-crystallizes with three water molecules in the asymmetric unit, which leads to the formation of hydrogen bonding in the crystal.
What is the structural chemistry of the living organism at its temperature and pressure?
Authors: Helliwell John R.
Published: February 2020

The three probes of the structure of matter (X-rays, neutrons and electrons) in biology have complementary properties and strengths. The balance between these three probes within their strengths and weaknesses is perceived to change, even dramatically so at times. For the study of combined states of order and disorder, NMR crystallography is also applicable. Of course, to understand biological systems the required perspectives are surely physiologically relevant temperatures and relevant chemical conditions, as well as a minimal perturbation owing to the needs of the probe itself. These remain very tough challenges because, for example, cryoEM by its very nature will never be performed at room temperature, crystallization often requires nonphysiological chemical conditions, and X-rays and electrons cause beam damage. However, integrated structural biology techniques and functional assays provide a package towards physiological relevance of any given study. Reporting of protein crystal structures, and their associated database entries, could usefully indicate how close to the biological situation they are, as discussed in detail in this feature article.
Entrepreneurial framework conditions and business sustainability among the youth and women entrepreneurs
Authors: Orobia Laura A. , Tusiime Immaculate , Mwesigwa Rogers , Ssekiziyivu Bob
Published: February 2020

Purpose

This study aims to investigate the relationship between entrepreneurial framework conditions (EFCs) and business sustainability among youth and women entrepreneurs using the institutional theory.

Design/methodology/approach

This study is cross-sectional and follows an explanatory research design using 390 youth and women entrepreneurs in Mbarara district (Uganda). A principal factor analysis was conducted to single out the particular constructs of business sustainability and EFC. Inferential analysis was conducted to test the relationships.

Findings

First, the constructs of business sustainability are stakeholder engagements, people and skills, ecosystem management, market and sales and innovation. Second, the constructs of EFC are education, government program and policies, IT infrastructure, market openness and finance. Finally, finance and IT infrastructure are significant predictors of business sustainability among the youth and women entrepreneurs.

Research limitations/implications

The examination of EFCs from the perspective of the consumers/beneficiaries can offer reasonable results when compared to the national expert perspective.

Originality/value

This study generates initial evidence on the applicability of EFCs from the perspective of the individuals as opposed to the national experts.
Small-scale private equity: demand versus supply
Authors: Dwyer Bruce , Duncan Keith , Southam Colette
Published: February 2020

Purpose

This paper aims to bridge the gap between theoretical dissertations on the demand and supply for equity by Australian small and medium-sized enterprises (SMEs) and the reality of the capital raising markets.

Design/methodology/approach

The mixed-methods approach includes questions integrated into a survey of 26,000 SMEs paired with semi-structured interviews with the CEOs or Chairs of the 15 Australian small-scale private equity (SSPE) firms.

Findings

Contrary to capital structure theory expectations, 46 per cent of Australian SMEs are interested in equity funding, despite a stated ability to acquire additional debt. The authors reveal a mismatch between supply and demand for SSPE with few SMEs able to meet private equity (PE) firms’ stringent investment criteria.

Research limitations/implications

The population of Australian SSPE firms is small and interviewee responses are qualitative and are not easily replicated.

Practical implications

To improve SSPE market liquidity, SMEs must overcome severe information asymmetry to demonstrate their quality and reduce the cost of due diligence for PE firms. One relatively easy step is for SMEs to voluntarily adopt auditable financial controls on SMEs similar to publicly traded firms.

Originality/value

Few studies focus on small firm equity, which is essential to economic growth and innovation. The authors use a large data set of Australian SMEs and unique informationally rich interview data on the population of Australian firms in SSPE, an industry known for its lack of transparency.
Getting CFO on board – its impact on firm performance and earnings quality
Authors: Duong Lien , Evans John , Truong Thu Phuong
Published: February 2020

Purpose

This paper aims to investigate the impact of Australian Chief Financial Officers (CFOs) as board insiders on firm performance and earnings quality with reference to agency theory and theory of friendly board.

Design/methodology/approach

The ordinary least square, two-stage least-squares and propensity score matching regressions are performed with various proxies for firm performance and accruals quality.

Findings

Firms with CFOs as board insiders experience significantly lower firm performance and earnings quality. In firms with powerful CEOs, the negative impact of CFO board membership on earnings quality is further magnified. Additionally, the negative impact of CFO board membership on firm values and earnings quality is only present in firms with bigger boards or firms with less outside directors. The findings are consistent with the agency perspective and in sharp contrast to the US market.

Originality/value

This is the first Australian study to examine the impact of CFO board membership on firm performance and earnings quality. The findings suggest that the monitoring of executives is best done by a small or independent board and that the insider board membership should be optimised.
Numerical study on convective flow and heat transfer in 3D inclined enclosure with hot solid body and discrete cooling
Authors: Alshomrani Ali S. , Sivasankaran S. , Ahmed Amer Abdulfattah
Published: February 2020

Purpose

This study aims to deal the numerical simulation on buoyant convection and energy transport in an inclined cubic box with diverse locations of the heater and coolers.

Design/methodology/approach

The left/right walls are cooled partially whereas the other walls are kept adiabatic. In the left/right walls, three different locations of the cooler are examined, whereas heater moves in three locations in the middle of the enclosed box. The governing models are numerically solved using the finite-element method.

Findings

The simulations are done on several values of the Rayleigh number and cavity inclination angles and different locations of the heater and coolers. The results are presented in the form of streamlines, isosurfaces and Nusselt numbers for different values of parameter involved here. It is recognized that the inclination of the box and the locations of the coolers strongly influence the stream and energy transport inside the enclosed domain.

Research limitations/implications

The present investigation is conducted for steady, laminar, three-dimensional natural convective flow in a box for different locations of cooler and tilting angles of a cavity. The study might be useful to the design of solar collectors, room ventilation systems and electronic cooling systems.

Originality/value

This work examines the effects of different locations of cooler and tilting angles of a cavity on convective heat transfer in a 3D cavity. The study is useful for thermal engineering applications.
Remote teaching for equal and inclusive education in rural areas? An analysis of teachers’ perspectives on remote teaching
Authors: Stenman Saga , Pettersson Fanny
Published: February 2020

Purpose

The aim of this study is to explore equality and inclusion as an aspect of remote teaching in rural areas. Moreover, the aim is to explore teachers' pedagogical digital competence (PDC) and school organizational support as conditions for developing remote teaching.

Design/methodology/approach

A mixed method approach with both qualitative and quantitative data was used.

Findings

According to this study, remote teaching can solve many problems for school organizations and offer pupils new opportunities to learn in rural areas. Remote teaching expands the learning environment and provides pupils with equal access to qualified teachers and a wider range of learning solutions for different needs. However, the learning context needs to be redesigned with flexibility to meet the needs of individual pupils, whereas the remote teaching format itself can contribute to difficulties in teachers' flexibility. In meeting these challenges teachers' PDC and digital relational competencies are becoming increasingly important. Moreover, teachers' access to communities and school contexts where remote teaching is collaboratively discussed and elaborated on.

Research limitations/implications

The study is limited to a region in Sweden, with ten participants.

Practical implications

The practical implications are that equal and inclusive remote teaching is dependent on technological as well as pedagogical competence from teachers as well as from organizations.

Social implications

If sufficient professional development for teachers is provided as well as organizational structure are in place, remote teaching is an option for equal access to education in sparsely populated areas. This means inclusive education can be provided to areas otherwise lacking in teacher competence.

Originality/value

The study is one of few that investigates how remote teaching teachers perceive the teaching form and the competencies and support required to develop and use it in rural areas.
Expatriate assignments: the “same” job may require different tasks
Authors: Martin Scott , James Reynold
Published: February 2020

Purpose

Given a specific job, this paper aims to examine if the tasks change when moving from one country to another, and if so, whether such changes are at least partly a function of environmental factors.

Design/methodology/approach

A mixed-method approach (surveys and interviews) with professional-level expatriates based in the UAE.

Findings

The results indicated that the “same” job often required different tasks depending on the country. Given a matching job between home and host countries, 66 per cent of respondents indicated that the job was different and on average, 20 per cent of the job was perceived to be different. Environmental forces did account for meaningful task differences. Legal and regulatory forces were a particularly important driver of task differences.

Practical implications

It is important to consider potential task differences in connection with expatriate assignments. Attending to task differences can have a positive impact on staffing, development and management processes.

Originality/value

Given the “same” job, the specific tasks may be different depending on the country.
A hybrid approach for modeling the key performance indicators of information facilitated product recovery system
Authors: Dwivedi Ashish , Madaan Jitender
Published: February 2020

Purpose

This study aims to propose a comprehensive framework among Key Performance Indicators (KPIs) for analyzing the Information Facilitated Product Recovery System (IFPRS) on the basis of feedback captured from the industry experts and researchers.

Design/methodology/approach

Total Interpretive Structural Modeling (TISM) methodology interspersed with fuzzy MICMAC is used to extract the interrelationships and develop a hierarchical structure among the identified KPIs. Further, the Fuzzy Decision-Making Trial and Evaluation Laboratory (F-DEMATEL) method has been enforced to determine the intensity of these relationships and identify the most influential KPIs among identified KPIs from literature review and expert opinions. The outcome indicates that “information sharing,” “technology capacity” and “technology standards such as EDI, RFID” are the KPIs that have attained highest driving power.

Findings

This study has identified 15 KPIs of IFPRS and developed an integrated model using TISM and the fuzzy MICMAC approach, which is helpful to describe and organize the important KPIs and reveal the direct and indirect effects of each KPI on the IFPRS implementation. The integrated approach is developed, as the TISM model provides only binary relationship among KPIs, while fuzzy MICMAC analysis provides explicit analysis related to driving and dependence power of KPIs.

Research limitations/implications

Structural Equation Modeling (SEM) analysis can be performed based on the adequate number of responses collected using structured questionnaire. More qualitative techniques like ELECTRE, TOPSIS, etc. can be used to establish the strength of relationship among the KPIs and ranking them to focus on the few critical KPIs.

Practical implications

The proposed modeling could empower various governmental and non-governmental regulatory bodies in formulation of policies to effectively tackle the problem related to product recovery systems. This study has strong practical implications, for both practitioners as well as academicians. The practitioners need to concentrate on identified KPIs more cautiously during IFPRS implementation in their organizations and the top management could formulate strategy for implementing these KPIs obtained.

Originality value

There is a lack of studies related to the modeling of KPIs of IFPRS. As vast information is essential about the products returned during different product recovery stages, this study bridges the gap in literature by providing a framework for KPIs related to IFPRS. It is expected that the results originated will assist the experts to relevantly identify the significant and drop insignificant KPI for successful product recovery implementation and performance improvement of IFPRS.
Resilient supplier selection to mitigate uncertainty: soft-computing approach
Authors: Pramanik Dipika , Mondal Samar Chandra , Haldar Anupam
Published: February 2020

Purpose

In recent years, determining the effective and suitable supplier in the supply chain management (SCM) has become a key strategic consideration to the success of any manufacturing organization in terms of business intelligence (BI), as many quantitative and qualitative critical factors are measured from big data. In today’s competitive business scenario, the main purpose of this study is to determine suitable and sustainable suppliers during supplier selection process is to reduce the risk of investment along with maximize overall value to the customer and develop closeness and long-term relationships between customers and suppliers to build a resilient SCM to mitigate uncertainty for automotive organizations.

Design/methodology/approach

As these types of decisions generally involve more than a few criteria and often necessary to compromise among possibly conflicting factors, the multiple-criteria decision-making becomes a useful approach to solve this kind of problem. Considering both tangible and intangible criteria, the aim of this paper is the presentation of a new integrated fuzzy analytic hierarchy process and fuzzy additive ratio assessment method with fuzzy entropy using linguistic values to solve the supplier selection problem to build the resilient SCM under uncertain data. Fuzzy entropy is used to obtain the entropy weights of the criteria.

Findings

Organizations gather massive amounts of information known as BD on the basis of historical records of uncertainties from several internal and external sources to manage uncertainty to improve the overall performance of organizations using BI strategy for analyzing and making effective decision to support the managements of automotive manufacturing organizations in an information system.

Research limitations/implications

Although this study tries to represent a full analysis on suitable and resilient global supplier selection under various types of uncertainty, still there are some improvements that can be made in the future by developing a more refined and more sophisticated approach to further enhance the performance of the proposed scheme to calculate overall rating scores of the alternatives.

Originality/value

The novelty of this paper is to propose a framework of BI in SCM to determine a suitable and resilient global supplier where all the meaningful information, relevant knowledge and visualization retrieved by analyzing the huge and complex set of data or data streams, i.e. BD based on decision-making, to develop any manufacturing organizational performance worldwide.