bluuebunny/crossref_metadata_2025 huggingface dataset:
Non-Negative Data-Driven Mapping of Structural Connections in the Neonatal Brain
Authors: Thompson E. , Mohammadi-Nejad A.R. , Robinson E.C. , Glasser M.F. , Jbabdi S. , Bastiani M. , Sotiropoulos S.N.
Published: March 2020

Mapping connections in the neonatal brain can provide insight into the crucial early stages of neurodevelopment that shape brain organisation and lay the foundations for cognition and behaviour. Diffusion MRI and tractography provide unique opportunities for such explorations, through estimation of white matter bundles and brain connectivity. Atlas-based tractography protocols, i.e. a priori defined sets of masks and logical operations in a template space, have been commonly used in the adult brain to drive such explorations. However, rapid growth and maturation of the brain during early development make it challenging to ensure correspondence and validity of such atlas-based tractography approaches in the developing brain. An alternative can be provided by data-driven methods, which do not depend on predefined regions of interest. Here, we develop a novel data-driven framework to extract white matter bundles and their associated grey matter networks from neonatal tractography data, based on non-negative matrix factorisation that is inherently suited to the non-negative nature of structural connectivity data. We also develop a non-negative dual regression framework to map group-level components to individual subjects. Using in-silico simulations, we evaluate the accuracy of our approach in extracting connectivity components and compare with an alternative data-driven method, independent component analysis. We apply non-negative matrix factorisation to whole-brain connectivity obtained from publicly available datasets from the Developing Human Connectome Project, yielding grey matter components and their corresponding white matter bundles. We assess the validity and interpretability of these components against traditional tractography results and grey matter networks obtained from resting-state fMRI in the same subjects. We subsequently use them to generate a parcellation of the neonatal cortex using data from 323 new-born babies and we assess the robustness and reproducibility of this connectivity-driven parcellation.
In VivoTranscriptomic Profiling using Cell Encapsulation Identifies Effector Pathways of Systemic Aging
Authors: Mashinchian Omid , Hong Xiaotong , Michaud Joris , Migliavacca Eugenia , Lefebvre Gregory , Boss Christophe , De Franceschi Filippo , Le Moal Emmeran , Collerette-Tremblay Jasmin , Isern Joan , Metairon Sylviane , Raymond Frederic , Descombes Patrick , Bouche Nicolas , Muñoz-Cánoves Pura , Feige Jerome N. , Bentzinger C. Florian
Published: March 2020

Sustained exposure to a young systemic environment rejuvenates aged organisms and promotes cellular function. However, due to the intrinsic complexity of tissues it remains challenging to pinpoint niche-independent effects of circulating factors on specific cell populations. Here we describe a method for the encapsulation of human and mouse skeletal muscle progenitors in diffusible polyethersulfone hollow fiber capsules that can be used to profile systemic agingin vivoindependent of heterogeneous short-range tissue interactions. We observed that circulating long-range signaling factors in the old systemic environment lead to an activation of Myc and E2F transcription factors, induce senescence and suppress myogenic differentiation. Importantly,in vitroprofiling using young and old serum in 2D culture does not capture all pathways deregulated in encapsulated cells in aged mice. Thus,in vivotranscriptomic profiling using cell encapsulation allows for the characterization of effector pathways of systemic aging with unparalleled accuracy.
SCLC_CellMiner: Integrated Genomics and Therapeutics Predictors of Small Cell Lung Cancer Cell Lines based on their genomic signatures
Authors: Tlemsani Camille , Pongor Lorinc , Girard Luc , Roper Nitin , Elloumi Fathi , Varma Sudhir , Luna Augustin , Rajapakse Vinodh N. , Sebastian Robin , Kohn Kurt W. , Krushkal Julia , Aladjem Mirit , Teicher Beverly A. , Meltzer Paul S. , Reinhold William C. , Minna John D. , Thomas Anish , Pommier Yves
Published: March 2020

Model systems are necessary to understand the biology of SCLC and develop new therapies against this recalcitrant disease. Here we provide the first online resource, CellMiner-SCLC (https://discover.nci.nih.gov/SclcCellMinerCDB) incorporating 118 individual SCLC cell lines and extensive omics and drug sensitivity datasets, including high resolution methylome performed for the purpose of the current study. We demonstrate the reproducibility of the cell lines and genomic data across the CCLE, GDSC, CTRP, NCI and UTSW datasets. We validate the SCLC classification based on four master transcription factors: NEUROD1, ASCL1, POU2F3 and YAP1 (NAPY classification) and show transcription networks connecting each them with their downstream and upstream regulators as well as with the NOTCH and HIPPO pathways and the MYC genes (MYC, MYCL1 and MYCN). We find that each of the 4 subsets express specific surface markers for antibody-targeted therapies. The SCLC-Y cell lines differ from the other subsets by expressing the NOTCH pathway and the antigen-presenting machinery (APM), and responding to mTOR and AKT inhibitors. Our analyses suggest the potential value of NOTCH activators, YAP1 inhibitors and immune checkpoint inhibitors in SCLC-Y tumors that can now be independently validated.

Graphical Abstract

Highlights

SCLC-CellMiner provides the most extensive SCLC resource in terms of number of cell lines (118 cell lines), extensive omics data (exome, microarray, RNA-seq, copy number, methylomes and microRNA) and drug sensitivity testing.

We find evidence of distinct epigenetic profile of SCLC cell lines (global hypomethylation and histone gene methylation), which is consistent with their plasticity.

Transcriptome analyses demonstrate the coherent transcriptional networks associated with the 4 main genomic subgroups (NEUROD1, ASCL1, POU2F3 & YAP1 = NAPY classification) and their connection with the NOTCH and HIPPO signaling pathways.

SCLC-CellMiner provides a conceptual framework for the selection of therapies for SCLC in a personalized fashion allowing putative biomarkers according molecular classifications and molecular characteristics.

SCLC-Y cell lines differ from the other cancer cell lines; their transcriptome resemble NSCLC cell lines. YAP1 cell lines while being the most resistant to standard of care treatments (etoposide, cisplatin and topotecan) respond to mTOR and AKT inhibitors and present native immune predisposition suggesting sensitivity to immune checkpoint inhibitors.
Risk-based Decision Making in Rats: Modulation by Sex and Amphetamine
Authors: Islas-Preciado Dannia , Wainwright Steven R. , Sniegocki Julia , Lieblich Stephane E. , Yagi Shunya , Floresco Stan B. , Galea Liisa A. M.
Published: March 2020

Decision-making is a complex process essential to daily adaptation in many species. Risk is an inherent aspect of decision-making and it is influenced by gonadal hormones. Testosterone and 17β-estradiol may modulate decision making and impact the mesocorticolimbic dopamine pathway. Here, we explored sex differences, the effect of gonadal hormones and the dopamine agonist amphetamine on risk-based decision making. Intact or gonadectomised (GDX) male and female rats underwent to a probabilistic discounting task. High and low doses of testosterone propionate (1.0 or 0.2 mg) and 17β-estradiol benzoate (0.3 μg) were administered to assess acute effects on risk-based decision making. After 3-days of washout period, intact and GDX rats received high or low (0.5 or 0.125 mg/kg) doses of amphetamine and re-tested in the probabilistic discounting task. Under baseline conditions, males made more risky choices during probability discounting compared to female rats, particularly in the lower probability blocks, but GDX did not influence risky choice. The high, but not the low dose, of testosterone modestly reduced risky decision making in GDX male rats. Conversely, 17β-estradiol had no significant effect on risky choice regardless of GDX status in either sex. Lastly, a higher dose of amphetamine increased risky decision making in both intact males and females, but had no effect in GDX rats. These findings demonstrated sex differences in risk-based decision making, with males showing a stronger bias towards larger, uncertain rewards. GDX status influenced the effects of amphetamine, suggesting different dopaminergic regulation in risk-based choices among males and females.
Using the Price equation to detect inclusive fitness in class-structured populations
Authors: Rodrigues António M. M.
Published: March 2020

Inclusive fitness theory has transformed the study of adaptive evolution since 1964, contributing to significant empirical findings. However, its status as a theory has been challenged by the proposals of several alternative frameworks. Those challenges have been countered by analyses that use the Price equation and the regression method. The Price equation is a universal description of evolutionary change, and the partitioning of the Price equation using the regression method immediately yields Hamilton’s rule, which embodies the main tenets of inclusive fitness. Hamilton’s rule captures the intensity and direction of selection acting on social behaviour and its underlying causal structure. Recent work, however, has suggested that there is an anomaly in this approach: in some cases, the regression method fails to estimate the correct values of the variables in Hamilton’s rule and the causal structure of the behaviour. Here, I address this apparent anomaly. I argue that the failure of the simple regression method occurs because social players vary in baseline fecundity. I reformulate the Price equation and regression method to recover Hamilton’s rule and I show that the method correctly estimates its key variables. I show that games where baseline fecundity varies among individuals represent a more general set of games that unfold in class-structured populations. This framework supports the robustness and validity of inclusive fitness.
Axial skeleton anterior-posterior patterning is regulated through feedback regulation between Meis transcription factors and retinoic acid
Authors: López-Delgado Alejandra C. , Delgado Irene , Cadenas Vanessa , Sánchez-Cabo Fátima , Torres Miguel
Published: March 2020

Vertebrate axial skeletal patterning is controlled by coordinated collinear expression ofHoxgenes and axial level-dependent activity of Hox protein combinations. Transcription factors of the Meis family act as cofactors of Hox proteins and profusely bind to Hox complex DNA, however their roles in mammalian axial patterning have not been established. Similarly, retinoic acid (RA) is known to regulate axial skeletal element identity through the transcriptional activity of its receptors, however, whether this role is related to Meis/Hox activity in axial patterning remains unknown. Here we study the role of Meis in axial skeleton formation and its relationship to the RA pathway by characterizingMeis1,Meis2andRaldh2mutant mice. Meis elimination produces axial skeleton defects without affecting Hox gene transcription, including vertebral homeotic transformations and rib mis-patterning associated to defects in the hypaxial myotome. While Raldh2 and Meis positively regulate each other,Raldh2elimination largely recapitulates the defects associated to Meis-deficiency and Meis overexpression rescues the axial skeletal defects inRaldh2mutants. We propose a Meis-RA positive feedback loop whose output is Meis levels and is essential to establish anterior-posterior identities and pattern of the vertebrate axial skeleton.
Transcriptomic characterization of tuberculous sputum reveals a host Warburg effect and microbial cholesterol catabolism
Authors: Lai Rachel PJ , Cortes Teresa , Marais Suzaan , Rockwood Neesha , Burke Melissa L , Garza-Garcia Acely , Horswell Stuart , O’Garra Anne , Young Douglas B , Wilkinson Robert J
Published: March 2020

The crucial transmission phase of tuberculosis (TB) relies on infectious sputum yet cannot easily be modeled. We applied one-step RNA-Sequencing to sputum from infectious TB patients to investigate the host and microbial environments underlying transmission ofMycobacterium tuberculosis(Mtb). In such TB sputa, compared to non-TB controls, transcriptional upregulation of inflammatory responses and a metabolic shift towards glycolysis was observed in the host. Amongst all bacterial sequences in the sputum, only less than 1.5% originated fromMtband its abundance is associated with HIV-1 coinfection status. The transcriptome of sputumMtbmore closely resembled aerobic replication and was characterized by evidence of cholesterol utilization, zinc deprivation and reduced expression of the virulence-associated PhoP regulon. Our study provides a comprehensive analysis of the transcriptional landscape associated with infectious sputum and demonstrates the feasibility of applying advanced sequencing technology to readily accessible pathological specimens in the study of host-pathogen adaptation.
Oculomotor-related measures but not distance visual acuity are predictive of reading ability in first graders
Authors: Portnoy Avi , Gilaie-Dotan Sharon
Published: March 2020

Vision screening in junior schools around the globe are often limited to distance visual acuity (dVA). Oculomotor dysfunction (OMD) is an umbrella term that includes abnormalities in comfortable and accurate control of the oculomotor system (fixation, pursuits and saccades) and can exist despite normal dVA. Since we assumed that a basic prerequisite for successful reading is that the ocular sensory-motor functions perform in flawless harmony with effortless automaticity, we hypothesized that OMD but not dVA would have profound effect on comfortable and efficient acquisition of effective reading skills. Consequently, we retrospectively compared independently obtained (double blind) reading evaluations and extensive optometric screening examinations of a class of 28 first graders. We found, as we hypothesized, that performance on optometric oculomotor tests, but not dVA, were predictive of reading test performance (both speed and accuracy) according to the standardized national reading norms. Our results suggest reevaluating the effectiveness of dVA as a marker of visual readiness for scholastic achievements. We propose including OMD related assessments as part of a paradigm shift in both vision screening in early readers as well as potential treatment protocols for those pupils struggling to acquire efficient reading skills.
Host species determine symbiotic community composition in Antarctic sponges (Porifera: Demospongiae)
Authors: Sacristán-Soriano Oriol , Criado Natalia Pérez , Avila Conxita
Published: March 2020

The microbiota of four Antarctic sponges,Dendrilla antarctica, Sphaerotylus antarcticus, Mycale acerata, andHemigellius pilosus, collected at two South Shetland Islands and at two locations in the Antarctic Peninsula separated by ca. 670 km, were analyzed together with surrounding seawater. We used high throughput sequencing of the V4 region of the 16S rRNA gene common to Bacteria and Archaea to investigate the microbial diversity and community composition. Our study reveals that sponge-associated prokaryote communities are consistently detected within a particular sponge species regardless of the collection site. Their community structure and composition are typical of low microbial abundance (LMA) sponges. We conclude that prokaryote communities from Antarctic sponges are less diverse and differ in their composition compared to those in the water column. Microbiome analysis indicates that Antarctic sponges harbor a strict core consisting of seven OTUs, and a small variable community comprising several tens of OTUs. Two abundant prokaryotes from the variable microbiota that are affiliated to the archaeal and bacterial phyla Thaumarchaeota and Nitrospirae may be involved in the sponge nitrification process and might be relevant components of the nitrogen cycling in Antarctica. The likely generalist nature of dominant microbes and the host-specific structure of symbiont communities suggest that these Antarctic sponges represent different ecological niches for particular microbial enrichments.
Resistance to Ceftazidime/Avibactam Plus Meropenem/Vaborbactam When Both are Used Together Achieved in Four Steps From Metallo-β-Lactamase NegativeKlebsiella pneumoniae
Authors: Dulyayangkul Punyawee , Douglas Edward J. A. , Lastovka Filip , Avison Matthew B.
Published: March 2020

Serine cephalosporinases and carbapenemases are dominant causes of critically important β-lactam resistance inKlebsiella pneumoniae. This has led to the recent clinical deployment of new serine β-lactamase inhibitors used in combination with β-lactams. Starting with clinicalK. pneumoniaeisolates and adding plasmids carrying the OXA-48-like class D carbapenemase, OXA-232, the class A carbapenemase KPC-3, the class A cephalosporinase CTX-M-14 and mutant derivatives of these enzymes, we set out to identify the steps required to give resistance to the recently approved β-lactam/β-lactamase inhibitor pairs ceftazidime/avibactam and meropenem/vaborbactam when both are used together. We show that four steps:ompK36andramRloss-of-function plus carriage of OXA-232 and KPC-3-D178Y, all of which have been observed in clinical isolates, allowK. pneumoniaeto resist the combined use of both β-lactam/β-lactamase inhibitor pairs. These findings have implications for decision making about sequential and combinatorial use of β-lactam/β-lactamase inhibitor pairs to treatK. pneumoniaeinfections, and suggest simple surveillance activities that might identify intermediate stages in resistance acquisition and therefore guide therapy to reduce the emergence of dual resistant strains.
Episodic evolution of coadapted sets of amino acid sites in mitochondrial proteins
Authors: Neverov A.D. , Fedonin G.G. , Cheremukhin E.A. , Klink G.V. , Popova A.V. , Bazykin G.A.
Published: March 2020

The rate of evolution differs between protein sites and changes with time. However, the link between these two phenomena remains poorly understood. Here, we design a phylogenetic approach for distinguishing pairs of amino acid sites that undergo coordinated evolution, i.e., such that substitutions at one site trigger subsequent substitutions at the other; and also pairs of sites that undergo discordant evolution, so that substitutions at one site impede subsequent substitutions at the other. We distinguish groups of amino acid sites that undergo coordinated evolution and evolve discordantly from other such groups. In mitochondrially encoded proteins of metazoans and fungi, we show that concordantly evolving sites are clustered in protein structures. Moreover, the substitution rates within individual concordant groups themselves change in the course of evolution, and phylogenetic positions of these changes are consistent between proteins, suggesting common selective forces underlying them.

Author summary

Evolution in most protein sites is constrained by alleles in other sites, this phenomena is called epistasis. Generally, newly arisen allele, if it would not be lost, increases its fitness with time due to adaptive mutations occurred in other sites in the process called the entrenchment. Thus, we expect that the evolution of sites would be coordinated, such that mutations in sites rapidly follow each other on phylogenetic lineages. Indeed, we have observed such coordinated evolution of sites in five proteins encoded in the mitochondria genomes of metazoan and fungi. Unexpectedly, coordinated evolution is observed only for nearby sites on protein structures, such that each protein could be partitioned into several groups of concordantly evolving sites. Evolution of sites from different groups is discordant, i.e. their mutations repel each other into different phylogenetic lineages or clades. Thus, the proteins encoded in mitochondrial genome consist of the sort of structural blocks like elements of the LEGO kit. Some of them have functional specialization, e.g. some blocks are associated with interfaces between proteins composing respiratory complexes.
Unravelling the effects of methylphenidate on the dopaminergic and noradrenergic functional circuits
Authors: Dipasquale Ottavia , Martins Daniel , Sethi Arjun , Veronese Mattia , Hesse Swen , Rullmann Michael , Sabri Osama , Turkheimer Federico , Harrison Neil A , Mehta Mitul A , Cercignani Mara
Published: March 2020

Functional magnetic resonance imaging (fMRI) can be combined with drugs to investigate the system-level functional responses in the brain to such challenges. However, most psychoactive agents act on multiple neurotransmitters, limiting the ability of fMRI to identify functional effects related to actions on discrete pharmacological targets. We recently introduced a multimodal approach, REACT (Receptor-Enriched Analysis of functional Connectivity by Targets), which offers the opportunity to disentangle effects of drugs on different neurotransmitters and clarify the biological mechanisms driving clinical efficacy and side effects of a compound. Here, we focus on methylphenidate (MPH), which binds to the dopamine transporter (DAT) and the norepinephrine transporter (NET), to unravel its effects on dopaminergic and noradrenergic functional circuits in the healthy brain at rest. We then explored the relationship between these target-enriched resting state functional connectivity (FC) maps and inter-individual variability in behavioural responses to a reinforcement-learning task encompassing a novelty manipulation to disentangle the molecular systems underlying specific cognitive/behavioural effects.

Results showed a significant MPH-induced FC increase in sensorimotor areas in the functional circuit associated with DAT. We also found that MPH-induced variations in DAT-and NET-enriched FC were significantly correlated with inter-individual differences in effects of MPH on key behavioural responses associated with the reinforcement-learning task.

Our findings show that MPH-related FC changes are specifically associated with DAT and provide evidence that when compounds have mixed pharmacological profiles, REACT may be able to capture regional functional effects that are underpinned by the same cognitive mechanism but are related to distinct molecular targets.
Quantifying temperature compensation of Bicoid gradients with a fast T-tunable microfluidic device
Authors: Zhu H. , Cui Y. , Luo C. , Liu F.
Published: March 2020

As a reaction-diffusion system strongly affected by temperature, the early fly embryos surprisingly show highly reproducible and accurate developmental patterns during embryogenesis under temperature perturbations. To reveal the underlying temperature compensation mechanism, it is important to overcome the challenge in quantitative imaging on fly embryos under temperature perturbations. Inspired by a microfluidics generating temperature steps on fly embryos, here we design a microfluidic device capable of ensuring the normal development of multiple fly embryos as well as achieving real-time temperature control and fast temperature jumps for quantitative live imaging with a home-built two-photon microscope. We apply this system to quantify the temperature compensation of the morphogen Bicoid (Bcd) gradient in fly embryos. The length constant of the exponential Bcd gradient reaches the maximum at 25 °C within the measured temperatures of 18-29 °C and gradually adapts to the corresponding value at new temperatures upon a fast temperature switch. Such an adaption decreases to a less degree if temperature is switched in a later developmental stage. This age-dependent temperature compensation could not be explained with the traditional synthesis-diffusion-degradation (SDD) model assuming the static parameters but an extended SDD model incorporating the dynamic change of the parameters controlling the formation of Bcd gradients.

SIGNIFICANCE

Thermal robustness is important for biological systems experiencing temperature fluctuations. To reveal the temperature compensation mechanism, the fruit fly embryo is an ideal model system. It is intriguing how the early fly embryo achieves highly reproducible and accurate patterning despite it is a reaction-diffusion system strongly affected by temperature. However, it has been challenging to quantitatively measure the developmental patterns in fly embryos under temperature perturbations. To overcome this problem, we construct a fast temperature tunable microfluidic device for fly embryos. Combining quantitative imaging with this device and mathematical modeling, we successfully quantify the temperature response of the morphogen Bicoid (Bcd) gradient and reveal that the temperature compensation for the Bcd gradient is stronger in the later developmental stage.
Stigma Receptivity is controlled by Functionally Redundant MAPK Pathway Components in Arabidopsis
Authors: Jamshed Muhammad , Sankaranarayanan Subramanian , Abhinandan Kumar , Samuel Marcus A.
Published: March 2020

In angiosperms, the process of pollination relies on species-specific interaction and signaling between the male (pollen) and female (pistil) counterparts where the interplay between several pollen and stigma proteins decides the fate of the pollen. In Brassicaceae, the dry stigmatic papillary cells control pollen germination by releasing resources only to compatible pollen thereby allowing pollen to hydrate and germinate. Despite the identification of a number of stigmatic proteins that facilitate pollination responses, the signaling mechanisms that regulate functions of these proteins have remained unknown. Here we show that, in Arabidopsis, an extremely functionally redundant mitogen-activated protein kinase (MAPK) cascade is required for maintaining stigma receptivity to accept compatible pollen. Our genetic analyses demonstrate that in stigmas, five MAPK kinases (MKKs), MKK1/2/3/7/9 are required to transmit upstream signals to two MPKs, MPK3/4, to mediate compatible pollination. Compromised functions of these fiveMKKsin the quintuple mutant (mkk1/2/3RNAi/mkk7/9) phenocopied pollination defects observed in thempk4RNAi/mpk3double mutant. We further show that this MAPK nexus converges on Exo70A1, a previously identified stigmatic compatibility factor essential for pollination. Given that pollination is the crucial initial step during plant reproduction, understanding the mechanisms that govern successful pollination could lead to development of strategies to improve crop yield.
Comparative characterisation ofPlasmodium falciparumHsp70-1 relative toE. coliDnaK reveals functional specificity of the parasite chaperone
Authors: Lebepe Charity Mekgwa , Matambanadzo Pearl Rutendo , Makhoba Xolani Henry , Achilonu Ikechukwu , Zininga Tawanda , Shonhai Addmore
Published: March 2020

Hsp70 is one of the most prominent molecular chaperones. Although Hsp70s from various organisms are generally conserved, they exhibit specialised cellular functions. It remains to be fully understood how these highly conserved molecules exhibit specialised functional features.Plasmodium falciparumHsp70-1 (PfHsp70-1) is a cytosol localised molecular chaperone that is implicated in the cyto-protection and pathogenicity of the malaria parasite. In the current study, we investigated the comparative structure-function features of PfHsp70-1 relative to its homologue,E. coliHsp70 (DnaK) and a chimeric protein, KPf, that was constituted by the ATPase domain of DnaK and the substrate binding domain (SBD) of PfHsp70-1. Recombinant forms of all the three Hsp70s exhibited similar secondary and tertiary structural fold. We further established that compared to DnaK, both KPf and PfHsp70-1 were more stable to heat stress and exhibited higher basal ATPase activity. A recombinantP. falciparumHsp40 (PfHsp40) stimulated the ATPase activities of all the three Hsp70s. In addition, both PfHsp70-1 and KPf exhibited preference for asparagine rich peptides as opposed to DnaK. Furthermore, all the three proteins exhibited self-association capabilities in vitro. RecombinantP. falciparumadenosylmethionine decarboxylase (PfAdoMetDC) co-expressed inE. coliwith either KPf or PfHsp70-1 was produced as a fully folded product. On the other hand, co-expression of PfAdoMetDC with heterologous DnaK inE. colidid not promote folding of the former. These findings demonstrated that the SBD of PfHsp70-1 regulates several functional features of the protein and that this molecular chaperone is tailored to facilitate folding of plasmodial proteins.
Genomic loci susceptible to systematic sequencing bias in clinical whole genomes
Authors: Freeman Timothy M. ,   Genomics England Research Consortium, Wang Dennis , Harris Jason
Published: March 2020

Accurate massively parallel sequencing (MPS) of genetic variants is key to many areas of science and medicine, such as cataloging population genetic variation and diagnosing genetic diseases. Certain genomic positions can be prone to higher rates of systematic sequencing and alignment bias that limit accuracy, resulting in false positive variant calls. Current standard practices to differentiate between loci that can and cannot be sequenced with high confidence utilize consensus between different sequencing methods as a proxy for sequencing confidence. These practices have significant limitations, and alternative methods are required to overcome them. We have developed a novel statistical method based on summarizing sequenced reads from whole-genome clinical samples and cataloging them in “Incremental Databases” that maintain individual confidentiality. Allele statistics were cataloged for each genomic position that consistently showed systematic biases with the corresponding MPS sequencing pipeline. We found systematic biases present at ∼1%–3% of the human autosomal genome across five patient cohorts. We identified which genomic regions were more or less prone to systematic biases, including large homopolymer flanks (odds ratio = 23.29–33.69) and the NIST high confidence genomic regions (odds ratio = 0.154–0.191). We confirmed our predictions on a gold-standard reference genome and showed that these systematic biases can lead to suspect variant calls within clinical panels. Our results recommend increased caution to address systematic biases in whole-genome sequencing and alignment. This study provides the implementation of a simple statistical approach to enhance quality control of clinically sequenced samples by flagging variants at suspect loci for further analysis or exclusion.
Redetermination of the crystal structure of R
5Si4 (R = Pr, Nd) from single-crystal X-ray diffraction data
Authors: Yokota Kaori , Watanuki Ryuta , Nakashima Miki , Uehara Masatomo , Gouchi Jun , Uwatoko Yoshiya , Umehara Izuru
Published: March 2020

The crystal structures of praseodymium silicide (5/4), Pr5Si4, and neodymium silicide (5/4), Nd5Si4, were redetermined using high-quality single-crystal X-ray diffraction data. The previous structure reports of Pr5Si4 were only based on powder X-ray diffraction data [Smith et al. (1967). Acta Cryst.
22 940–943; Yang et al. (2002b). J. Alloys Compd.
339, 189–194; Yang et al., (2003). J. Alloys Compd.
263, 146–153]. On the other hand, the structure of Nd5Si4 has been determined from powder data [neutron; Cadogan et al., (2002). J. Phys. Condens. Matter, 14, 7191–7200] and X-ray [Smith et al. (1967). Acta Cryst.
22 940–943; Yang et al. (2002b). J. Alloys Compd.
339, 189–194; Yang et al., (2003). J. Alloys Compd.
263, 146–153] and single-crystal data with isotropic atomic displacement parameters [Roger et al., (2006). J. Alloys Compd.
415, 73–84]. In addition, the anisotropic atomic displacement parameters for all atomic sites have been determined for the first time. These compounds are confirmed to have the tetragonal Zr5Si4-type structure (space group: P41212), as reported previously (Smith et al., 1967). The structure is built up by distorted body-centered cubes consisting of Pr(Nd) atoms, which are linked to each other by edge-sharing to form a three-dimensional framework. This framework delimits zigzag channels in which the silicon dimers are situated.
The first coordination compound of 6-fluoronicotinate: the crystal structure of a one-dimensional nickel(II) coordination polymer containing the mixed ligands 6-fluoronicotinate and 4,4′-bipyridine
Authors: Politeo Nives , Pisačić Mateja , Đaković Marijana , Sokol Vesna , Kukovec Boris-Marko
Published: March 2020

A one-dimensional nickel(II) coordination polymer with the mixed ligands 6-fluoronicotinate (6-Fnic) and 4,4′-bipyridine (4,4′-bpy), namely, catena-poly[[diaquabis(6-fluoropyridine-3-carboxylato-κO)nickel(II)]-μ-4,4′-bipyridine-κ2
N:N′] trihydrate], {[Ni(6-Fnic)2(4,4′-bpy)(H2O)2]·3H2O}
n
, (1), was prepared by the reaction of nickel(II) sulfate heptahydrate, 6-fluoronicotinic acid (C6H4FNO2) and 4,4′-bipyridine (C10H8N2) in a mixture of water and ethanol. The nickel(II) ion in 1 is octahedrally coordinated by the O atoms of two water molecules, two O atoms from O-monodentate 6-fluoronicotinate ligands and two N atoms from bridging 4,4′-bipyridine ligands, forming a trans isomer. The bridging 4,4′-bipyridine ligands connect symmetry-related nickel(II) ions into infinite one-dimensional polymeric chains running in the [1\overline{1}0] direction. In the extended structure of 1, the polymeric chains and lattice water molecules are connected into a three-dimensional hydrogen-bonded network via strong O—H...O and O—H...N hydrogen bonds, leading to the formation of distinct hydrogen-bond ring motifs: octameric R
8
8(24) and hexameric R
8
6(16) loops.
Comparing the measures of consumer knowledge calibration
Authors: Pillai Kishore Gopalakrishna , Hofacker Charles F.
Published: March 2020

Purpose

Studies on consumer knowledge calibration have used different measures of calibration. The purpose of this paper is to undertake a comparative assessment of important measures. In addition, it seeks to identify the best performing measure.

Design/methodology/approach

The paper reports on three studies. The first study uses eight survey data sets. The second and third studies use experiments.

Findings

The study found that the Brier score component measure is most responsive to feedback and is the most suitable measure of knowledge calibration. The results also indicate that researchers should use measures that use item-level confidence judgements, as against an overall confidence judgement.

Research limitations/implications

By documenting the relationship between the different measures of knowledge calibration, the study enables proper interpretation and accumulation of results of various studies that have used different measures. The study also provides guidance to researchers in psychology and education where this issue has been noted.

Practical implications

The study provides guidance to managers in knowledge intensive industries, such as finance and insurance, interested in understanding their consumers’ knowledge calibration.

Originality/value

This is the first study in consumer research that examines this issue.
Asymmetric information linkages across select futures and spot indices
Authors: Siddiqui Saif , Roy Preeti
Published: March 2020

Purpose

The study investigates the amplitude and direction of the movement of information between spot and futures indices. The study progresses to account for the investor's heterogeneity and compare the evolving structure of investors in emerging and developed economies. Further, the structural linkages in terms of returns and variance have been explored for the futures indices to contribute to meteor shower literature as explained by Engle et al. (1990); Yarovaya et al. (2017).

Design/methodology/approach

To facilitate the purpose, the Indian and Chinese markets were selected to represent emerging economies and the United States for developed one. The bivariate wavelet cum BEKK-GARCH (1,1) model was estimated.

Findings

For the developed markets, like the United States, the spot market improves its information transmission role with time horizon while exactly opposite holds for the Chinese market. A bidirectional overnight information spillover was found for all three pairs. The Indian futures market was vulnerable to bad news from the other two markets. Evidence suggesting the dominance of institutional investors in the Chinese futures market and retail investors in the Indian futures market is found.

Originality/value

The spot–futures relation has been studied on both the time and frequency domains considering different investment horizons. Due consideration has been taken to account for the overlapping trading hours.
Determinants of the result of new rural development program in Vietnam
Authors: Hoang Quang Vu
Published: March 2020

Purpose

The purpose of this paper is to identify the determinants of the proportion of communes that met all national new rural criteria (hereafter NRD communes).

Design/methodology/approach

First, the method of propensity score (PS) stratification is used to classify 63 provinces into the subgroups. Second, the ordinary least squares (OLS) model is used with the subgroups classified from the PS stratification method as one of explicative variables. The dependent variable in the OLS model is the proportion of NRD communes.

Findings

With the sample of 63 provinces of Vietnam, the author found that per capita income growth rate, high growth of gross regional domestic product (GRDP) and effort of the provincial authority have positive impact on the proportion of NRD communes.

Practical implications

This research suggests that the provincial authority should actively participate in the NRD program, and the economic development is key factor for success implementation of the NRD program.

Originality/value

This research contributes to understand the factors impacting the result of the NRD program and then help to identify the measures to support this program.
Risk-adjusted efficiency and bank size in a developing economy: an analysis of Vietnamese banks
Authors: Le Minh , Hoang Viet-Ngu , Wilson Clevo , Ngo Thanh
Published: March 2020

Purpose

There is ample empirical evidence to show that larger banks are more efficient than smaller banks in developed countries. However, there is very little empirical evidence to show that in small developing economies, such as Vietnam, bank size is associated with increased risk, especially credit risk. This paper aim to provide empirical evidence to fill in this gap. This paper employs a slack-based directional distance function using the intermediation approach in measuring the inefficiency of banks in Vietnam during the period 2006–2015. Non-performing loans are used as an undesirable output to capture credit risk. The results show that small banks are more efficient than large banks at the mean level and across the entire distributions of inefficiency of the two groups. Input waste, output shortage and risk surplus of big banks are nearly three times higher than those of small banks. The results are robust under constant and variable returns to scale for production technologies. The study’s empirical results contribute to the ongoing debate on the merits of enlarging bank size in a small transitional economy and suggest that policy makers should pay attention to the risk and inefficiency of large banks to enhance the performance of Vietnam's banking system as a whole.

Design/methodology/approach

This paper uses the non-radial slack-based directional technology distance function developed by Färe and Grosskopf (2010) to estimate the efficiency of banks using the data envelopment analysis technique. Data for 44 commercial banks are used.

Findings

The empirical results of the paper contribute to the ongoing debate on the merits of enlarging bank size in a small transitional economy and suggest that policy makers should pay attention to the risk and inefficiency of large banks to improve the performance of Vietnam's banking system as a whole.

Originality/value

This paper extends the extant literature by examining whether efficiency is associated with size in a typical transitional developing economy. The classic Cournot model, the structure-conduct-performance and the efficiency structure hypotheses state that larger banks are more efficient than smaller banks (Bikker and Bos, 2008). Empirical studies of Berger (2003), Mester (2005), Wheelock and Wilson (2012) lend support to the statement in developed countries. However, not much empirical literature focuses on small developing economies such as Vietnam to show that bank size is associated with increased risk, especially credit risk. The study’s empirical results show that size enlargement is not positively associated with risk-adjusted efficiency. Input waste, output shortage and risk surplus of big banks are nearly three times higher than those of small banks. The results are robust under constant and variable returns to scale for production technologies.
Making and breaking the manual – a case of tests and rapport in an interdisciplinary team
Authors: Ilkjær Helene , Madsen Mette My
Published: March 2020

Purpose

This article engages the concept of tests–here understood as social tests of collaborative abilities in the interdisciplinary teamwork–to examine how they are central to an applied anthropologist's positioning and influence within an organization.

Design/methodology/approach

Presented as an auto-ethnographic methodological exploration, the article takes its point of departure in ethnographic material from the work by Helene Ilkjær as an Industrial Postdoc with an interdisciplinary team of engineers, scientists and designers in a Danish technology start-up company.

Findings

Within this ethnographic context, the article examines not only the case of “the manual” to unfold how the dynamics of careful development but also notorious circumvention of manuals came to serve as social tests–moments that fundamentally changed the anthropologist's position within the interdisciplinary team. Analytically, the manual serves as a prism through which it explores the slippery and negotiable nature of the anthropologist's professional position as an Industrial Postdoc–suspended between anthropology “for” and “of” the company, officially employed by the company while also engaged in academic research.

Originality/value

The article offers anthropologists a tool to visualize the different movements and placements within continua of professional positionality while working as applied researchers with(in) private sector organizations.
Hypnosis as performance autoethnography in qualitative sociological research
Authors: Entwistle Paul Andrew
Published: March 2020

Purpose

The purpose of this paper is to introduce to sociologists the concept of dissociative hypnosis and to demonstrate the potential that this discipline has for obtaining or deriving biographical narratives in ethnographic and autoethnographic studies.

Design/methodology/approach

The paper presents brief comparative histories of the development of hypnosis and of performance autoethnography to highlight the degree of consonance between these apparently, disparate modalities, in their struggle for acceptance and respectability. The intensely introspective, emotional and experiential nature of hypnosis and self-hypnosis narratives is then compared with the personal descriptions and applications of the autoethnographic process as depicted in the sociological literature, to illustrate the parallels between the two modalities. The paper concludes with a review of the potential problems and limitations inherent in using hypnosis as a memory recall modality in sociological research studies.

Findings

This paper argues that the exploratory and revelatory nature of information accrual during dissociative altered-state hypnosis closely resembles that during performance autoethnography, and that hypnosis could therefore be usefully employed as an additional and novel (ethno-) autobiographical tool in sociological and ethnographic research.

Originality/value

Performative autoethnography has now become a firmly established route to obtaining a valid and intensely personal autobiographical history of individuals or groups of individuals. However this is the first publication to propose hypnosis as an alternative approach to deriving ethnographic and autoethnographic biographical narratives.
Sports video games participation: what can we learn for esports?
Authors: García Jaume , Murillo Carles
Published: March 2020

Purpose

This study investigates three issues associated with playing sports video games: the correlates of participation (and its intensity) in this type of activity, their complementarity with traditional sports and their perception as sport. Given the scarcity of data on esports participation, these results can be seen as an initial approach to these issues with regard to esports.

Design/methodology/approach

Sequential, two-part and regression models are estimated using a sample of 11,018 individuals from the Survey of Sporting Habits in Spain 2015.

Findings

First, the association of the correlates follows different patterns for participation in sports video games and its intensity. Second, complementarity with traditional sports is found using different approaches. Third, young people consider this activity as a dimension of their overall interest in sports.

Practical implications

The different association of the correlates with participation in esports and its intensity can be used to define marketing and brand investment strategies. The complementarity between esports and traditional sports should influence how the actual stakeholders in sport define future strategies to favour the growth of both industries. Finally, the increasing perception of esports as a sport should influence the future organisation of multi-sport events like the Olympic Games.

Originality/value

Using sports video games participation as a proxy of esports participation, this study is the first to provide empirical evidence of the relevance of distinguishing between participation in esports and its intensity, their complementarity with traditional sports and their perception as sport.