bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantitative analysis of the splice variants expressed by the major hepatitis B virus genotypes
Authors: Lim Chun Shen , Sozzi Vitina , Revill Peter A. , Brown Chris M.
Published: August 2020

Hepatitis B virus (HBV) is a major human pathogen that causes liver diseases. The main HBV RNAs are unspliced transcripts that encode the key viral proteins. Recent studies show that some of the HBV spliced transcript isoforms are predictive of liver cancer, yet the roles of these spliced transcripts remain elusive. Furthermore, a total of 9 major HBV genotypes were isolated from discrete geographical regions of the world, it is likely that these genotypes may express a broad variety of spliced transcript isoforms. To systematically study the HBV splice variants, we transfected the human hepatoma cells Huh7 with 4 HBV genotypes (A2, B2, C2, and D3), followed by deep RNA-sequencing. We found that 12-25% of HBV RNAs were splice variants, which were reproducibly detected across independent biological replicates. This accounted for a total of 6 novel and 6 previously identified splice variants. In particular, 2 highly abundant novel splice variants, in which we called the putative splice variants 1 and 5 (pSP1 and pSP5), were specifically expressed at high levels in genotypes D3 and B2, respectively. In general, the HBV splicing profiles varied across the genotypes except for the known spliced pgRNAs SP1 and SP9, which were present in all 4 major genotypes. Counterintuitively, these singly spliced SP1 and SP9 had a suboptimal 5′ splice site, suggesting that splicing of HBV RNAs is tightly controlled by the viral post-transcriptional regulatory RNA element.

IMPORTANCE

HBV infection affects over 257 million people worldwide. HBV is a major cause of liver diseases including cancer and there is no cure. Some HBV RNAs are spliced variants and their roles are largely unclear, although some splice variants have been previously found to be associated with liver cancer. HBV exists as 9 genotypes worldwide with marked differences in replicative capacity and disease sequelae. Whether HBV splice variants vary for the different genotypes is yet to be investigated in depth. Here we sequenced RNAs from 4 major HBV genotypes using a cell culture system. We found 6 new and 6 previously known splice variants across these genotypes. Some novel splice variants were present at high levels, suggesting they could be functionally important. Interestingly, although HBV has adapted to human hosts for over 50,000 years, the most frequently spliced location shared little flanking sequence similarity with that of humans.
Diagnostic accuracy of B scan ultrasonography for posterior segment eye disorders in a tertiary care setting in Eastern India
Authors: Chaudhury Maheswar , Parida Bikash , Panigrahi Sandeep Kumar
Published: August 2020

Introduction

Ophthalmic ultrasound (USG) produces real time high resolution images of the eye and orbit. It can categorize and predict the location of pathology in the posterior chamber of eye very well. It is useful even in pre-operative evaluation and diagnosing posterior segment eye disorders. However, the diagnostic accuracy has usually not being studied thoroughly, with special emphasis to its probability of predicting posterior-segment eye disorders using B-scan USG.

Objectives

To find out the prevalence and pattern of posterior segment disorders using B-scan ultrasonography, and to find its diagnostic accuracy.

Materials and Methods

The study was prospective in nature and conducted in the department of radiodiagnosis and ophthalmology of a tertiary care center of Eastern India. Patients referred to the radiology department for ruling out intra-ocular pathology using B-scan ophthalmic ultrasound were included in the study, irrespective of any age and gender. Data were captured on an excel sheet and analyzed using Stata 12.1 SE.

Results

The mean age of 84 study participants was 37.4 ± 19.5 years, with maximum in between 40-50 years. Males were more (72.6%). 50% presented with low vision, and most commonly associated with cataract (45%). Prevalence of posterior segment eye disorders was 13.1%. Sensitivity and negative predictive values were 100%. Post-test probability was 95.5%. Accuracy was however very less (39.3%).

Conclusion

Using B-scan ultrasonography for pre-operative assessment and confirmation of diagnosis increases the probability of detecting presence or absence of posterior segment pathology. Absence of posterior segment disorder using this is also very helpful in ruling out disease entirely. It also a very high sensitivity and hence can be used even in rural health centers.
Assembly and symmetry of the fungal E3BP-containing core of the Pyruvate Dehydrogenase Complex
Authors: Forsberg B. O. , Aibara S. , Howard R. J. , Mortezaei N. , Lindahl E.
Published: August 2020

The pyruvate dehydrogenase complex (PDC) is a central component of all aerobic respiration, connecting glycolysis to mitochondrial oxidation of pyruvate. Despite its central metabolic role, its precise composition and means of regulation remain unknown. To explain the variation in stoichiometry reported for the E3-recruiting protein X (PX) in the fungal PDC, we established cryo-EM reconstructions of the native and recombinant PDC from the filamentous fungus and model organismNeurospora crassa. We find that the PX C-terminal domain localizes interior to the E2 core. Critically, we show that two distinct arrangements of a trimeric oligomer exists, which both result in strict tetrahedral symmetry of the PDC core interior. Both oligomerization and volume occlusion of the PDC interior by PX appears to limit its binding stoichiometry, which explains the variety of stoichiometries found previously forS. cerevisiae. This also suggests that the PX oligomer stability and size are potential mechanisms to dynamically adjust PDC compostion in response to external cues. Moreover, we find that the site where PX binds is conserved within fungi but not mammals, suggesting that it could be therapeutically targeted. To this end, we also show that a PX knockout results in loss of activity through dysfunctional E3 recruitment, leading to severely impairedN. crassagrowth on sucrose. The fungal PDC is thus shown to be fundamentally similar to the mammalian PDC in function but subject to other conditions of possible regulation, conditioned by a steric restrictions imposed by the symmetry of the PDC and its components.
eIF2B extends lifespan through inhibition of the integrated stress response
Authors: Derisbourg Maxime , Wester Laura , Baddi Ruth , Denzel Martin S.
Published: August 2020

Protein homeostasis is modulated by stress response pathways and its deficiency is a hallmark of aging. The integrated stress response (ISR) is a conserved stress-signaling pathway that tunes mRNA translation via phosphorylation of the translation initiation factor eIF2. ISR activation and translation initiation are finely balanced by eIF2 kinases and by the eIF2 guanine nucleotide exchange factor eIF2B. However, the role of the ISR during aging remains unexplored. Using a genomic screen inCaenorhabditis elegans, we discovered a role of eIF2B and the eIF2 kinases in longevity. By limiting the ISR, these mutations enhanced protein homeostasis and increased lifespan. Consistently, full ISR inhibition using phosphorylation-defective eIF2α or pharmacological ISR inhibition prolonged lifespan. Lifespan extension through ISR inhibition occurred without changes in overall protein synthesis, and depended on enhanced translational efficiency of the kinase KIN-35. Evidently, lifespan is limited by the ISR and its inhibition may provide an intervention in aging.
Structure of the activated Roq1 resistosome directly recognizing the pathogen effector XopQ
Authors: Martin Raoul , Qi Tiancong , Zhang Haibo , Liu Furong , King Miles , Toth Claire , Nogales Eva , Staskawicz Brian J.
Published: August 2020

Plants and animals detect pathogen infection via intracellular nucleotide-binding leucine-rich repeat receptors (NLRs) that directly or indirectly recognize pathogen effectors and activate an immune response. How effector sensing triggers NLR activation remains poorly understood. Here we describe the 3.8 Å resolution cryo-electron microscopy structure of the activated Roq1, an NLR native toNicotiana benthamianawith a Toll-like interleukin-1 receptor (TIR) domain, bound to theXanthomonaseffector XopQ. Roq1 directly binds to both the predicted active site and surface residues of XopQ while forming a tetrameric resistosome that brings together the TIR domains for downstream immune signaling. Our results suggest a mechanism for the direct recognition of effectors by NLRs leading to the oligomerization-dependent activation of a plant resistosome and signaling by the TIR domain.

One Sentence Summary

Visualization of an activated plant immune receptor that triggers the immune response upon pathogen recognition.
Structural insights into the interaction of heme with protein tyrosine kinase JAK2
Authors: Schmalohr Benjamin Franz , Mustafa Al-Hassan M. , Krämer Oliver , Imhof Diana
Published: August 2020

Janus kinase 2 (JAK2) is the most important signal transducing tyrosine kinase in erythropoietic precursor cells. Its malfunction drives several myeloproliferative disorders. Heme is a small metal ion-carrying molecule, which is incorporated into hemoglobin in erythroid precursor cells to transport oxygen. In addition, heme is a signaling molecule and regulator of various biochemical processes. Here we show that heme exposure leads to hyperphosphorylation of JAK2 in a myeloid cancer cell line. Two peptides identified in JAK2 represent heme-regulatory motifs and show low micromolar affinities for heme. These peptides map to the kinase domain of JAK2, which is essential for downstream signaling. We suggest these motifs to be the interaction sites of heme with JAK2, which drive the heme-induced hyperphosphorylation. The results presented herein may facilitate the development of heme-related pharmacological tools to combat myeloproliferative disorders.
Expression of neuronal Na+ leak channel, NALCN, provides for persistent invasion of metastasizing cancer cells
Authors: Iamshanova Oksana , Gordienko Dmitri , Folcher Antoine , Bokhobza Alexandre , Shapovalov George , Kannancheri-Puthooru Dheeraj , Mariot Pascal , Allant Laurent , Desruelles Emilie , Spriet Corentin , Diez Raquel , Oullier Thibauld , Marionneau-Lambot Séverine , Brisson Lucie , Geraci Sandra , Impheng Hathaichanok , Lehenkyi V’yacheslav , Haustrate Aurelien , Mihalache Adriana , Gosset Pierre , Chadet Stéphanie , Retif Stéphanie , Laube Maryline , Sobilo Julien , Lerondel Stéphanie , Villari Giulia , Serini Guido , Pla Alessandra Fiorio , Roger Sébastien , Fromont-Hankard Gaelle , Djamgoz Mustafa , Clezardin Philippe , Monteil Arnaud , Prevarskaya Natalia
Published: August 2020

Cytosolic Ca2+ oscillations provide signaling input to several effector systems of the cell. These include neuronal development, migration and networking. Although similar signaling events are hijacked by highly aggressive cancer cells, the complexity of the ‘neuron-like’ remodeling in metastasis remains to be explored. Here, using a variety of in vitro and in vivo techniques we show that strongly metastatic prostate cancer cells acquire specific Na+/Ca2+ signature required for persistent invasion. We identify the ‘neuronal’ Na+ leak channel, NALCN, at the hot spots of the Ca2+ wave initiation and invadopodia formation. Mechanistically, NALCN associates functionally with plasmalemmal and mitochondrial Na+/Ca2+ exchangers, reactive oxygen species and store-operated channels to generate intracellular Ca2+ oscillations. In turn, this stimulates the activity of protooncogene Src kinase co-localized with NALCN, actin remodeling and secretion of proteolytic enzymes, thus increasing an invasive potential of the cancer cells and metastatic lesions in vivo (accessed in pre-clinical models). Overall, our findings provide new insight into the signaling pathway specific for metastatic cells where NALCN plays the role of the persistent invasion “launcher and controller”.
Retention of Lumpy Skin Disease Virus inStomoxysSpp (Stomoxys Calsitrans, Stomoxys Sitiens, Stomoxys Indica) following intrathoracic inoculation, Diptera: Muscidae
Authors: Issimov Arman , Kutumbetov Lespek , Zhanabayev Assylbek , Kazhgaliyev Nurlybay , Nurgaliyev Birzhan , Zhubantayev Izimgali , Akhmetaliyeva Aliya , Shalmenov Malik , Kereyev Abzal , White Peter J.
Published: August 2020

Lumpy skin disease (LSD) is an emerging disease in cattle in Kazakhstan and the means of transmission remains uncertain. In the current study, acquisition of Lumpy Skin Disease Virus (LSDV) byStomoxysspecies following intrathoracic inoculation was demonstrated under laboratory conditions. Flies were injected with a virulent LSDV strain into the thorax region to bypass the midgut barrier. The fate of pathogen in the hemolymph of the flies was further examined using PCR and Virus isolation tests. LSDV was isolated from all threeStomoxysspecies immediately and up to 24h post intrathoracic inoculation while virus DNA was detectable up to 7d post intrathoracic inoculation.
Sero-Prevalence and Associated Risk Factors of Bovine Brucellosis in Sendafa, Oromia Special Zone Surrounding Addis Ababa, Ethiopia
Authors: Bifo Hadji , Gugsa Getachew , Kifleyohannes Tsegabirhan , Abebe Engidaw , Ahmed Meselu
Published: August 2020

Bovine brucellosis is an infectious bacterial disease caused by members of genus Brucella, affecting both animals and humans, and resulting in a serious economic loss in animal production sector and deterioration of public health. This cross-sectional study was conducted from November 2014 to April 2015 to determine the sero-prevalence and associated risk factors of bovine brucellosis in Sendafa, Oromia special Zone, Ethiopia. A total of 503 blood samples were collected using simple random sampling technique from dairy cattle of above 6 months of age with no history of previous vaccination against brucellosis. All sera samples were demonstrated using both Rose Bengal Plate Test for screening and Compliment Fixation Test for confirmation. Accordingly, the overall sero-prevalence of bovine brucellosis in this area was 0.40%. The result showed that the sero-prevalence of bovine brucellosis in the study area was not statistically significant with all proposed risk factors. Thus, the study revealed the absence of significant statistical variation in the sero-prevalence of bovine brucellosis in different age, sex groups, breeding method and history of previous abortions (P>0.05). No reactors were observed in male animals. Sero-prevalence of 0.40% was observed in animals without previous history of abortion. Moreover, information was gathered on individual animal and farm-level risk factors and other farm characteristics using a questionnaire. The awareness among the society was poor, so the positive animals can be a potential hazard to animals and humans in the study area. Therefore, public education should be done in order to improve the awareness of people on bovine brucellosis and its public health impact with due consideration on the safely consumption of food of animal origin.
Integrating Non-Spiking Interneurons in Spiking Neural Networks
Authors: Strohmer Beck , Stagsted Rasmus Karnøe , Manoonpong Poramate , Larsen Leon Bonde
Published: August 2020

Researchers working with neural networks have historically focused on either non-spiking neurons tractable for running on computers or more biologically plausible spiking neurons typically requiring special hardware. However, in nature homogeneous networks of neurons do not exist. Instead, spiking and non-spiking neurons cooperate, each bringing a different set of advantages. A well researched biological example of such a mixed network is the sensorimotor pathway, responsible for mapping sensory inputs to behavioral changes. This pathway is also well researched in robotics where it is applied to achieve closed-loop operation of legged robots by adapting amplitude, frequency, and phase of the motor output. In this paper we investigate how spiking and non-spiking neurons can be combined to create a sensorimotor neuron pathway capable of shaping network output based on analog input. We propose sub-threshold operation of an existing spiking neuron model to create a non-spiking neuron able to interpret analog information and communicate with spiking neurons. The validity of this methodology is confirmed through a simulation of a closed-loop amplitude regulating network. Additionally, we show that non-spiking neurons can effectively manipulate post-synaptic spiking neurons in an event-based architecture. The ability to work with mixed networks provides an opportunity for researchers to investigate new network architectures for adaptive controllers, potentially improving locomotion strategies of legged robots.
A comparative analysis of automated MRI brain segmentation in a large longitudinal dataset: Freesurfer vs. FSL
Authors: Quilis-Sancho Javier , Fernandez-Blazquez Miguel A. , Gomez-Ramirez J
Published: August 2020

The study of brain volumetry and morphology of the different brain structures can determine the diagnosis of an existing disease, quantify its prognosis or even help to identify an early detection of dementia. Manual segmentation is an extremely time consuming task and automated methods are thus, gaining importance as clinical tool for diagnosis. In the last few years, AI-based segmentation has delivered, in some cases, superior results than manual segmentation, in both time and accuracy. In this study we aim at performing a comparative analysis of automated brain segmentation. In order to test the performance of automated segmentation methods, the two most commonly used software libraries for brain segmentation Freesurfer and FSL, were put to work in each of the 4028 MRIs available in the study. We find a lack of linear correlation between the segmentation results obtained from Freesurfer and FSL. On the other hand. Freesurfer volume estimates of subcortical brain structures tends to be larger than FSL estimates of same areas. The study builds on an uniquely large, longitudinal dataset of over 4,000 MRIs, all performed with identical equipment to help researchers understand what to expect from fully automated segmentation procedures.
Culture volume influences the dynamics of adaptation under long-term stationary phase
Authors: Gross Jonathan , Avrani Sarit , Katz Sophia , Hershberg Ruth
Published: August 2020

Escherichia coliand many other bacterial species, which are incapable of sporulation, can nevertheless survive within resource exhausted media by entering a state termed long-term stationary phase (LTSP). We have previously shown thatE. colipopulations adapt genetically under LTSP in an extremely convergent manner. Here we examine how the dynamics of LTSP genetic adaptation are influenced by varying a single parameter of the experiment - culture volume. We find that culture volume affects survival under LTSP, with viable counts decreasing as volumes increase. Across all volumes, mutations accumulate with time, and the majority of mutations accumulated demonstrate signals of being adaptive. However, positive selection appears to affect mutation accumulation more strongly at higher, compared to lower volumes. Finally, we find that several similar genes are likely involved in adaptation across volumes. However, the specific mutations within these genes that contribute to adaptation can vary in a consistent manner. Combined, our results demonstrate how varying a single parameter of an evolutionary experiment can substantially influence the dynamics of observed adaptation.
FGF signaling induces mesoderm in members of Spiralia
Authors: Andrikou Carmen , Hejnol Andreas
Published: August 2020

FGF signaling is involved in mesoderm induction in deuterostomes, but not in flies and nematodes, where it has a role in mesoderm patterning and migration. However, comparable studies in other protostomic taxa are missing in order to decipher whether this mesoderm-inducing function of FGF extends beyond the lineage of deuterostomes. Here, we investigated the role of FGF signaling during mesoderm development in three species of lophophorates, a clade within the protostome group Spiralia. Our gene expression analyses show that the molecular patterning of mesoderm development is overall conserved between brachiopods and phoronids, but the spatial and temporal recruitment of transcription factors differs significantly. Moreover, inhibitor experiments demonstrate that FGF signaling is involved in mesoderm formation, morphogenetic movements of gastrulation and posterior axial elongation. Our findings suggest that the inductive role of FGF in mesoderm possibly predates the origin of deuterostomes.
Use of target-displaying magnetized yeast in screening mRNA display peptide libraries to identify ligands
Authors: Bowen John , Bacon Kaitlyn , Reese Hannah , Rao Balaji M. , Menegatti Stefano
Published: August 2020

This work presents the first use of yeast-displayed protein targets for screening mRNA display libraries of cyclic and linear peptides. The WW domains of Yes-Associated Protein 1 (WW-YAP) and mitochondrial import receptor subunit TOM22 were adopted as protein targets. Yeast cells displaying WW-YAP or TOM22 were magnetized with iron oxide nanoparticles to enable the isolation of target-binding mRNA-peptide fusions. Equilibrium adsorption studies were conducted to estimate the binding affinity (KD) of selected WW-YAP-binding peptides: KD values of 37 μM and 4 μM were obtained for cyclo[M-AFRLC-K] and its linear cognate, and 40 μM and 3 μM for cyclo[M-LDFVNHRSRG-K] and its linear cognate, respectively. TOM22-binding peptide cyclo[M-PELNRAI-K] was conjugated to magnetic beads and incubated with yeast cells expressing TOM22 and luciferase. A luciferase-based assay showed a 4.5-fold higher binding of TOM22+ yeast compared to control cells. This work demonstrates that integrating mRNA and yeast display accelerates the discovery of biospecific peptides.
Open Science Saves Lives: Lessons from the COVID-19 Pandemic
Authors: Besançon Lonni , Peiffer-Smadja Nathan , Segalas Corentin , Jiang Haiting , Masuzzo Paola , Smout Cooper , Billy Eric , Deforet Maxime , Leyrat Clémence
Published: August 2020

In the last decade Open Science principles have been successfully advocated for and are being slowly adopted in different research communities. In response to the COVID-19 pandemic many publishers and researchers have sped up their adoption of Open Science practices, sometimes embracing them fully and sometimes partially or in a sub-optimal manner. In this article, we express concerns about the violation of some of the Open Science principles and its potential impact on the quality of research output. We provide evidence of the misuses of these principles at different stages of the scientific process. We call for a wider adoption of Open Science practices in the hope that this work will encourage a broader endorsement of Open Science principles and serve as a reminder that science should always be a rigorous process, reliable and transparent, especially in the context of a pandemic where research findings are being translated into practice even more rapidly. We provide all data and scripts athttps://osf.io/renxy/.
Immunoreactive peptide maps of SARS-CoV-2 and other human coronaviruses
Authors: Mishra Nischay , Huang Xi , Joshi Shreyas , Guo Cheng , Ng James , Thakkar Riddhi , Wu Yongjian , Dong Xin , Li Qianlin , Pinapati Richard , Sullivan Eric , Caciula Adrian , Tokarz Rafal , Briese Thomas , Lu Jiahai , Lipkin W. Ian
Published: August 2020

Serodiagnosis of SARS-CoV-2 infection is impeded by immunological cross-reactivity to the human coronaviruses (HCoV) SARS-CoV-2, SARS-CoV-1, MERS-CoV, OC43, 229E, HKU1, and NL63. Here we report the identification of humoral immune responses to SARS-CoV-2 and other HCoV peptides that can be used to detect asymptomatic, mild and, severe SARS-CoV-2 infections, and may enable the discovery of biomarkers for immunity following infection or vaccination.
Homologous recombination defects in Shwachman-Diamond syndrome and Diamond-Blackfan anemia
Authors: Asik Elif , Chatterjee Nimrat , Bertuch Alison A.
Published: August 2020

Shwachman-Diamond syndrome (SDS) and Diamond-Blackfan anemia (DBA) are ribosomopathies characterized by impaired hematopoiesis and cancer predisposition. The mechanisms underlying cancer predisposition in these disorders are not well understood. We found that LCLs derived from patients with SDS or DBA had a prolonged DNA damage response and hypersensitivity to ionizing radiation, suggesting impaired DNA double strand break (DSB) repair. Consistent with this, depletion of SBDS and RPS19, the most common etiologic factors in SDS and DBA, respectively, resulted in reduced homologous recombination (HR) in HCT116 and U2OS cells. Surprisingly, depletion of EFL1, which functions with SBDS in ribosome biogenesis, did not impair HR and depletion of eIF6, which restores ribosome joining in SBDS-depleted cells, did not rescue the HR defect associated with SBDS depletion. Instead, we found SBDS and RPS19 recruitment to sites of DSBs suggesting that SBDS and RPS19 have more proximate roles in regulating HR, independent of their ribosomal functions. We propose that reduced HR shifts DSB repair toward error-prone NHEJ and this may contribute to oncogenesis in SDS and DBA. Additionally, we found SBDS and RPS19 depleted cells were hypersensitive to PARP inhibition, potentially uncovering a therapeutic target for SDS- and DBA-associated malignancies.
Conditional resampling improves calibration and sensitivity in single-cell CRISPR screen analysis
Authors: Barry Timothy , Wang Xuran , Morris John A. , Roeder Kathryn , Katsevich Eugene
Published: August 2020

Single-cell CRISPR screens are the most promising biotechnology for mapping regulatory elements to their target genes at genome-wide scale. However, the analysis of these screens presents significant statistical challenges. For example, technical factors like sequencing depth impact not only expression measurement but also perturbation detection, creating a confounding effect. We demonstrate on two recent high multiplicity of infection single-cell CRISPR screens how these challenges cause calibration issues among existing analysis methods. To address these challenges, we propose SCEPTRE: analysis of single-cell perturbation screens via conditional re-sampling. This methodology, designed to avoid calibration issues due to technical confounders and expression model misspecification, infers associations between perturbations and expression by resampling the former according to a working model for perturbation detection probability in each cell. SCEPTRE demonstrates excellent calibration and sensitivity on the CRISPR screen data and yields hundreds of new regulatory relationships, supported by orthogonal functional evidence.
Machine learning reveals time-varying microbial predictors with complex effects on glucose regulation
Authors: Aasmets Oliver , Lüll Kreete , Lang Jennifer M. , Pan Calvin , Kuusisto Johanna , Fischer Krista , Laakso Markku , Lusis Aldons J. , Org Elin
Published: August 2020

The incidence of type 2 diabetes (T2D) has been increasing globally and a growing body of evidence links type 2 diabetes with altered microbiota composition. Type 2 diabetes is preceded by a long pre-diabetic state characterized by changes in various metabolic parameters. We tested whether the gut microbiome could have predictive potential for T2D development during the healthy and pre-diabetic disease stages. We used prospective data of 608 well-phenotyped Finnish men collected from the population-based Metabolic Syndrome In Men (METSIM) study to build machine learning models for predicting continuous glucose and insulin measures in a shorter (1.5 year) and longer (4.5 year) period. Our results show that the inclusion of gut microbiome improves prediction accuracy for modelling T2D associated parameters such as glycosylated hemoglobin and insulin measures. We identified novel microbial biomarkers and described their effects on the predictions using interpretable machine learning techniques, which revealed complex linear and non-linear associations. Additionally, the modelling strategy carried out allowed us to compare the stability of model performances and biomarker selection, also revealing differences in short-term and long-term predictions. The identified microbiome biomarkers provide a predictive measure for various metabolic traits related to T2D, thus providing an additional parameter for personal risk assessment. Our work also highlights the need for robust modelling strategies and the value of interpretable machine learning.

Importance

Recent studies have shown a clear link between gut microbiota and type 2 diabetes. However, current results are based on cross-sectional studies that aim to determine the microbial dysbiosis when the disease is already prevalent. In order to consider microbiome as a factor in disease risk assessment, prospective studies are needed. Our study is the first study that assesses the gut microbiome as a predictive measure for several type 2 diabetes associated parameters in a longitudinal study setting. Our results revealed a number of novel microbial biomarkers that can improve the prediction accuracy for continuous insulin measures and glycosylated hemoglobin levels. These results make the prospect of using microbiome in personalized medicine promising.
Longitudinal metatranscriptomic analysis of a meat spoilage microbiome detects abundant continued fermentation and environmental stress responses during shelf life and beyond
Authors: Hultman Jenni , Johansson Per , Björkroth Johanna
Published: August 2020

Microbial food spoilage is a complex phenomenon associated with the succession of the specific spoilage organisms (SSO) over the course of time. We performed a longitudinal metatranscriptomic study on a modified atmosphere packaged (MAP) beef product to increase understanding of the longitudinal behavior of a spoilage microbiome during shelf life and onward. Based on the annotation of the mRNA reads, we recognized three stages related to the active microbiome that were descriptive for the sensory quality of the beef: acceptable product (AP), early spoilage (ES) and late spoilage (LS). Both the 16S RNA taxonomic assignments from the total RNA and functional annotations of the active genes showed that these stages were significantly different from each other. However, the functional gene annotations showed more pronounced difference than the taxonomy assignments. Psychrotrophic lactic acid bacteria (LAB) formed the core of the SSO according to the transcribed reads.Leuconostocspecies were the most abundant active LAB throughout the study period, whereas the activity of Streptococcaceae (mainlyLactococcus) increased after the product was spoiled. In the beginning of the experiment, the community managed environmental stress by cold-shock responses which were followed by the expression of the genes involved in managing oxidative stress. Glycolysis, pentose phosphate pathway and pyruvate metabolism were active throughout the study at a relatively stable level. However, the proportional activity of the enzymes in these pathways changed over time. For example, acetate kinase activity was characteristic for the AP stage whereas formate C-acetyltransferase transcription was associated with spoilage.

Importance

It is generally known which organisms are the typical SSO in foods, whereas the actively transcribed genes and pathways during microbial succession are poorly understood. This knowledge is important since better approaches to food quality evaluation and shelf life determination are needed. Thus, we conducted this study to find longitudinal markers that are connected to quality deterioration. These kind of RNA markers could be used to develop novel type of rapid quality analysis tools in the future. New tools are needed since even though SSO can be detected and their concentrations determined using the current microbiological methods, results from these analyses cannot predict how close timewise a spoilage community is from production of clear sensory defects. Main reason for this is that the species composition of a spoilage community does not change dramatically during late shelf life, whereas the ongoing metabolic activities lead to the development of notable sensory deterioration.
Estimating Prevalence and time Course of Sars-Cov-2 Based on new Hospital Admissions and PCR Tests: Relevance to Vaccination Program Tactical Planning
Authors: Gonzalez Jose E.
Published: August 2020

Data posted in the COVID 19 tracking website for RT-PCR (PCR) results and hospital admissions are used to estimate the time course of the SARS-CoV-2 pandemic in the United States (1) and individual states. Hospital admissions mitigate positive sampling bias in PCR tests since these were limited in numbers initially. Additionally, their intent was as a diagnostic rather than a surveying tool.

By September 17, the United States’ cumulative recovered population is estimated at 45% or 149 million. The remaining susceptible population is 55%, or 50%, excepting the currently infected 5% population. The estimated mortality rate of the cumulative of the total affected population is 0.13% death.

States have followed diverse epidemic time courses. New Jersey and New York show SARS-CoV-2 prevalence of 95% and 82%, respectively. Likewise, each state exhibits relatively low current positive PCR results at 1.2 % and 0.8%. Also, these states show about twice the mortality rate of the nation. By comparison, Florida, California, and Texas showed recovered populations percent around 50%, and higher current PCR positive test results ranging from 5% to 9%.

This novel approach provides an improved source of information on the pandemic’s full-time course in terms of precision and accuracy in contrast to serological testing, which only views a narrow time slice of its history due to the transient nature of the antibody response and its graduated expression dependency on the severity of the disease. The deficiency of serological testing to estimate the recovered population is made even more acute due to the large proportion of asymptomatic and sub-clinical cases in the COVID-19 pandemic (2,3). T-cell testing, reputedly capable of long-term detection of previously infected individuals, will provide a complete view of the recovered population when it becomes available for large scale use.

This New Hospital Admission based method informs a more effective and efficient deployment of a vaccination program since it provides not only a reliable estimate of the susceptible population by state, but it can also provide visibility down to the county level based on COVID-19 hospitalization record independent of PCR testing.
Grazing-incidence X-ray diffraction investigation of the coincidence site lattice of the Ge/Si(001) system
Authors: Barnscheidt Yvo , Schmidt Jan , Osten H. Jörg
Published: August 2020

The Ge/Si(001) system has been analysed by grazing-incidence X-ray diffraction on a standard laboratory X-ray diffraction tool. A periodic array of interfacial edge dislocations forms a coincidence site lattice (CSL) which yields equidistantly spaced satellite peaks close to Bragg peaks of the Ge layer and Si substrate. The diffraction behaviour of the CSL was analysed using 2θ/φ scans along [100], [110] and [310] directions as well as azimuthal φ scans which revealed a 90° angular symmetry of the CSL. Additionally, different layer thicknesses, from 10 to 580 nm, were analysed, focusing on the dependence of layer thickness on the glancing angles of the satellite peaks. This method provides the ability to analyse whether or not epitaxially grown layers exhibit a periodic array of dislocations, and gain information about the orientation of the interfacial edge dislocations.
Simulation of X-ray diffraction in a cylindrical crystal
Authors: Punegov Vasily I. , Kolosov Sergey I.
Published: August 2020

Using the two-dimensional recurrence relations of X-ray dynamical diffraction, a numerical simulation of reflection and transmission intensity in a cylindrical crystal has been performed. It is shown that for crystals with a small radius Bragg diffraction is realized. For crystals of large radius, Bragg–Laue diffraction occurs, which is characterized by Bragg diffraction on the upper part of the crystal, as well as the presence of Pendellösung oscillations inside the cylindrical crystal. The reciprocal space maps of dynamical and kinematical diffraction have been calculated.
“Come together”: a thematic analysis of experiences with belonging
Authors: Ogundipe Esther , Sælør Knut Tore , Dybdahl Kenneth , Davidson Larry , Biong Stian
Published: August 2020

Purpose

The purpose of this paper is to explore, describe and interpret two research questions: How do persons with co-occurring mental health and substance abuse problems, living in supportive housing, experience belonging? How do residential support staff experience promoting a sense of belonging for persons with co-occurring mental health and substance abuse problems, living in a supportive housing?

Design/methodology/approach

Individual semi-structured interviews were conducted with five persons with co-occurring mental health and substance abuse problems living in supportive housing in a Norwegian district. In addition, one semi-structured focus group was conducted with nine residential support staff. All interviews were transcribed verbatim and analyzed using thematic analysis.

Findings

Analysis resulted in three main themes: “I do not go to sleep in my pajamas”, “Do I have a choice?” and “Be kind to each other”.

Research limitations/implications

More research on how inclusive practices that are commonly described in guidelines actually affect the experience of residents and residential support staff is needed.

Practical implications

Practices that incorporate a communal and contextual understanding when assigning supportive housing are warranted.

Originality/value

By paying attention to the components of social recovery, this paper provides a nuanced understanding of how persons with co-occurring mental health and substance abuse problems, living in supportive housing, experience belonging. In addition, residential support staffs’ experiences with promoting a sense of belonging for this group are explored.
New novel food regulation and collaboration for innovation
Authors: Grimsby Sveinung
Published: August 2020

Purpose

The purpose of this paper was to study the novel food (NF) industry in Europe and how regulations have affected companies' collaboration and openness towards other actors during new product development. The research question, therefore, was “How do the European NF regulations affect radical innovation in the food industry?”.

Design/methodology/approach

A multiphase mixed-methods design was used to combine three sets of data as follows: the NF applications and copies of these from 1997 to 2018; the applications in the first 18 months of the revised NF regulation period after 2018 and interviews with six NF applicant companies and seven experts on NF.

Findings

Interactions with research and development (R&D) suppliers appear to be common during development of NF products for companies of all sizes. Ownership of knowledge and a conscious intellectual property rights strategy are important for companies' openness during radical innovation and collaboration. The decentralised NF regulations from 1997 to 2017, with reduced possibilities for data protection, prevented innovation. However, both old and new NF regulations facilitate easy routes for second-to-market approach. Companies of all sizes apply for NF-approved products under the new NF regulations, which ensure data protection.

Practical implications

Future NF pioneers, food R&D suppliers and food-industry policymakers will benefit from open innovation and NF insights by gaining an understanding of NF regulations and insight into how a policy with open governance affects collaboration and co-creation.

Originality/value

The NF regulations and their effect on radical food innovation have not previously been studied according to innovation management theory. Understanding various forms of selective partnership and collaboration among actors in the food industry is valuable for future growth.
News media influence on public trust in bike-sharing operators in Singapore
Authors: Wong Leonard , Tan Lyon , Wong Rachel , Yeo Su Lin
Published: August 2020

Purpose

The overnight introduction of tens of thousands of dockless bike-share bicycles in Singapore with its indiscriminate parking drew the attention of the media, which generated extensive news reports on the activities carried out by bike-sharing operators. Given the meteoric rise and fall of the industry, this study examines the influence of agenda-setting of news reporting on the public’s perception of the industry and the impact on the firms’ corporate reputation.

Design/methodology/approach

Utilizing the Reputation Quotient Index, the study content analyzed 147 textual data of online reports which were crawled over two years between 2017 and 2018 from six mainstream news organizations.

Findings

Our findings showed that the news reports carried more negative frames in the headlines and body content. It also found that only five out of six dimensions of the Index were emphasized with varying degrees of importance, indicating that the corporate reputation as determined by the media reports did not collectively represent the operators’ past actions and results with valued outcomes.

Practical implications

Practical implications discussed included the need to integrate corporate strategies into public relations programs and the importance of engaging the media to demonstrate congruence between business objectives and positive social impact on society.

Originality/value

Although the study limited its data collection only to online media reports, it is one of the few research to provide empirical evidence concerning the media’s influence on the public’s perceptions and reputation of the nascent bike-sharing industry.
The strategic corporate social responsibility (CSR) quandary: an instructional case
Authors: Bhatia Sandhya , Gupta Gaurav , Tripathy Arindam
Published: August 2020

Learning outcomes

Recognize the interest groups of the business as stakeholders and shareholders. Understand the role of strategic corporate social responsibility (CSR) in attaining competitive advantage for the firm. Apply the techniques of financial statement analysis such as common-sized financial statements and ratio analysis. Analyze the overall financial position of the company such as its liquidity, solvency and profitability position. Evaluate the appropriateness of various CSR activities given the size of the company, its business model and financial position. Create a suitable CSR policy draft incorporating the critical elements of a CSR policy that enables the firm to operationalize it and fulfill the disclosure norms.

Case overview/synopsis

The management of Ball Industry Limited (BIL) had overlooked the mandatory requirement of CSR policy formulation. The company had not yet spent anything on CSR since the regulation had come into force. The company’s financial position was not healthy. Still, it fell under the regulatory clause as a borderline case and must spend 2% of its average three years’ profit on CSR activities. The company had previously ignored the requirement of formally drafting a CSR policy and deciding about the actions it might want to carry out. Now that the regulator had started sending show-cause notices to several companies who had not yet begun CSR, BIL was under immense time pressure to draft its CSR policy and initiate the relevant CSR activities. Emily, the chief operating officer of BIL, was assigned the task of preparing the blueprint of the CSR policy of the company and made it available for discussion in the upcoming meeting. The task at hand was to formulate a sound CSR policy under the constrained financial state considering its strategic planning, including the SWOT analysis, competitive environment and the overall general market and economic conditions. She submitted that rather than a vanilla CSR activity, strategic CSR would support the firm to differentiate itself from competitors. She was struggling to formulate a CSR strategy that could achieve both economic and social goals.

Complexity academic level

The case will be most suitable for use in undergraduate and graduate courses.

Supplementary materials

Teaching notes are available for educators only.

Subject code

CSS 1: Accounting and finance.
The impact of national social capital on business creation rates in the formal vs informal sectors
Authors: Thai Mai Thi Thanh , Turkina Ekaterina , Simba Amon
Published: August 2020

Purpose

Through utilizing social capital as an overarching concept, the purpose of this article is to investigate cross-country rates of business formation in the formal vs informal sectors. Plus, empirically assess the impact of social capital constructs on the national rates of entrepreneurship.

Design/methodology/approach

Adopting a regression-oriented methodology, partial least squares (PLS), the study used a sample comprising 50 nations. National rates of registered and nonregistered business creation were utilized as endogenous variables. To determine the indigenous variables, constructs of social capital were measured which is consistent with the World Value Survey (WWS).

Findings

The results of this study show that in the formal and the informal sectors, social networking enables business creation with varying levels of impact. It establishes that institutional trust has a negative effect on informal business creation and a positive effect on business registration; interpersonal trust drives entrepreneurship in the informal sector but has less impact on business registration; norms of trustworthiness are related to business registration than informal business creation.

Practical implications

The findings of this research have theoretical and practical implications. They stimulate academic debate on the application of social capital constructs at the national level. The indications that social capital promotes business formation in both the informal and formal sectors can influence entrepreneurship policy development in many countries.

Originality/value

The originality of the results of this study lies in how it conceptualizes social capital as having direct impact on business creation in the informal vs formal sector. Thus, the findings elevated the conceptualization of social capital to the national level thereby enhancing knowledge on the entrepreneurship process as well as developmental economics.