bluuebunny/crossref_metadata_2025 huggingface dataset:
Muscle protein turnover and low-protein diets in patients with chronic kidney disease
Authors: Garibotto Giacomo , Picciotto Daniela , Saio Michela , Esposito Pasquale , Verzola Daniela
Published: March 2020

Adaptation to a low-protein diet (LPD) involves a reduction in the rate of amino acid (AA) flux and oxidation, leading to more efficient use of dietary AA and reduced ureagenesis. Of note, the concept of ‘adaptation’ to low-protein intakes has been separated from the concept of ‘accommodation’, the latter term implying a decrease in protein synthesis, with development of wasting, when dietary protein intake becomes inadequate, i.e. beyond the limits of the adaptive mechanisms. Acidosis, insulin resistance and inflammation are recognized mechanisms that can increase protein degradation and can impair the ability to activate an adaptive response when an LPD is prescribed in a chronic kidney disease (CKD) patient. Current evidence shows that, in the short term, clinically stable patients with CKD Stages 3–5 can efficiently adapt their muscle protein turnover to an LPD containing 0.55–0.6 g protein/kg or a supplemented very-low-protein diet (VLPD) by decreasing muscle protein degradation and increasing the efficiency of muscle protein turnover. Recent long-term randomized clinical trials on supplemented VLPDs in patients with CKD have shown a very good safety profile, suggesting that observations shown by short-term studies on muscle protein turnover can be extrapolated to the long-term period.
Isotopic Signatures of Carbon in the ‘Los Pobres’ Graphite Mine, Ronda, Spain
Authors: Neubeck Anna , Broman Curt , Ivarsson Magnus , Holm Nils G , Whitehouse Martin , Nilsson Sara , Geppert Wolf , Gervilla Fernando
Published: March 2020

Graphite formation temperatures in the ‘Los Pobres’ mine within the Ronda peridotite, Spain, previously reported to be between 770 and 820 °C, have been reinterpreted based on new temperature measurements using Raman spectroscopy. Additional in situ and bulk stable carbon isotopic measurements and fluid inclusion studies contributed to improved understanding of parts of the graphite formation process. Raman spectroscopy revealed that the formation of the ‘Los Pobres’ graphite extends to temperatures as low as 500 °C, indicating a broader temperature range than previously reported. Stable carbon isotopes and temperature estimates suggest two different crystallization events, followed by a late hydrothermal alteration of the host rock. The first event occurred at temperatures higher than ∼600°C, in which crystalline graphite was formed with a mixed 13C composition as a result of the mixing of two different carbon-bearing sources. The second graphite formation event took place below ∼600°C, within the same system, but with lower purity and crystallinity of the graphite. In the third event, the temperature decreased to less than 550 °C, and hydrothermal fluids altered the host rock, precipitating silica and iron oxides in veins penetrating both the host rock and the deposited graphite.
A Randomized Trial to Compare Serratus Anterior Plane Block and Erector Spinae Plane Block for Pain Management Following Thoracoscopic Surgery
Authors: Ekinci Mürsel , Ciftci Bahadir , Gölboyu Birzat Emre , Demiraran Yavuz , Bayrak Yusuf , Tulgar Serkan
Published: March 2020

Objective

Comparison of ultrasound (US)-guided erector spinae plane block (ESPB) and serratus anterior plane block (SAPB) in video-assisted thoracic surgery (VATS) patients. The primary outcome was to compare perioperative and postoperative (48 hours) opioid consumption.

Methods

A total of 60 patients were randomized into two groups (N = 30): an ESPB group and an SAPB group. All the patients received intravenous patient-controlled postoperative analgesia and ibuprofen 400 mg intravenously every eight hours. Visual analog scale (VAS) scores, opioid consumption, and adverse events were recorded.

Results

Intraoperative and postoperative opioid consumption at 0–8, 8–16, and 16–24 hours and rescue analgesic use were significantly lower in the ESPB group (P < 0.05). Static/dynamic VAS scores were significantly lower in the ESPB group (P < 0.05). There was no significant difference between static VAS scores at the fourth hour. There were no differences between adverse effects. Block procedure time and one-time puncture success were similar between groups (P  > 0.05 each).

Conclusion

US-guided ESPB may provide better pain control than SAPB after VATS.

Question

Even though there are studies about analgesia management after VATS, clinicians want to perform the technique that is both less invasive and more effective.

Findings

This randomized trial showed that US-guided ESPB provides effective analgesia compared with SAPB.

Meaning

Performing single-injection ESPB reduces VAS scores and opioid consumption compared with SAPB.
Excess Body Mass and Leisure Time Physical Activity in the Incidence and Persistence of Chronic Pain
Authors: Shiri Rahman , Lallukka Tea , Rahkonen Ossi , Leino-Arjas Päivi
Published: March 2020

Objective

To estimate the effects of excess body mass and leisure time physical activity on the incidence and persistence of chronic pain.

Design

A prospective cohort study.

Methods

As a part of the Finnish Helsinki Health Study, we included three cohorts of employees of the City of Helsinki (18,562 observations) and defined incident chronic pain as having pain in any part of the body for more than three months at follow-up in participants without chronic pain at baseline (N = 13,029 observations). Persistent chronic pain was defined as having pain for more than three months at both baseline and follow-up (N = 5,533 observations).

Results

Overweight (adjusted odds ratio [OR] = 1.18, 95% confidence interval [CI] = 1.06–1.31) and obesity (OR = 1.65, 95% CI = 1.45–1.88) increased the incidence of chronic pain. Moreover, overweight (OR = 1.16, 95% CI = 1.02–1.32) and obesity (OR = 1.48, 95% CI = 1.26–1.74) increased the risk of persistent chronic pain. Vigorous leisure time physical activity reduced the incidence of chronic pain (OR = 0.85, 95% CI = 0.75–0.96). Physical activity did not influence the risk of persistent chronic pain. Furthermore, overweight/obesity modified the effect of leisure time physical activity on incident chronic pain. Inactive overweight or obese participants were at the highest risk of chronic pain (OR = 1.71, 95% CI = 1.40–2.09), while the OR dropped to 1.44 (95% CI = 1.19–1.75) in moderately active overweight or obese participants and to 1.20 (95% CI = 0.97–1.47) in highly active overweight or obese participants.

Conclusions

Obesity not only increases the risk of developing chronic pain, but also increases the risk of persistent pain, while leisure time physical activity reduces the risk of developing chronic pain.
Charged Higgs contribution on Bc → (Ds, Ds*) l+l−
Authors: Maji P , Biswas S , Nayek P , Sahoo S
Published: March 2020

In this paper, we study rare semileptonic decays of the $B_c$ meson in the context of type-I, II, and III two Higgs doublet models. We follow the relativistic quark model for parameterizing the form factors used in matrix elements of weak transitions between the corresponding meson states. We investigate observables such as branching ratio, lepton polarization asymmetry, forward–backward asymmetry, etc. and analyze the dependence of these quantities on the model parameters. We have found that there is noticeable sensitivity to these observables for the charged Higgs boson, which may provide a powerful probe to the standard model and new physics beyond it.
The effect of pre-pregnancy weight and gestational weight gain on blood pressure in children at 6 years of age
Authors: Torres Camila Honorato A , Schultz Lidiane F , Veugelers Paul J , Mastroeni Silmara S B S , Mastroeni Marco F
Published: March 2020

Background

We evaluated the effect of maternal gestational weight gain (GWG) and pre-pregnancy weight on blood pressure (BP) of children 6 years after delivery.

Methods

Cross-sectional study that compared the anthropometric measurements of 181 mothers and their children’s BP 6 years after delivery. The BP was measured by the auscultatory method. We used log-binomial regression to investigate the association of pre-pregnancy body mass index (BMI) and GWG categories with BP in mid-childhood.

Results

The prevalence of elevated BP in children was 26.5%. Maternal pre-pregnancy overweight and concurrent excessive GWG were positively associated with elevated BP at 6 years of age. Mothers with pre-pregnancy overweight and excessive GWG were more likely to have children with elevated BP at 6 years of age (OR = 2.05; P = 0.018) compared to mothers who were of normal weight pre-pregnancy and experienced appropriate GWG. We also found that mothers with pre-pregnancy BMI ≥25 kg/m2 and concurrent excessive GWG were more likely to have children with elevated diastolic blood pressure (OR = 2.72; P = 0.005).

Conclusions

Pre-pregnancy overweight/obesity had impact on BP in mid-childhood. Interventions aimed at reducing cardiovascular diseases in children should promote weight loss in women of reproductive age rather than in pregnant women.
Exact Distribution of Divergence Times from Fossil Ages and Tree Topologies
Authors: Didier Gilles , Laurin Michel
Published: March 2020

Being given a phylogenetic tree of both extant and extinct taxa in which the fossil ages are the only temporal information (namely, in which divergence times are considered unknown), we provide a method to compute the exact probability distribution of any divergence time of the tree with regard to any speciation (cladogenesis), extinction, and fossilization rates under the Fossilized Birth–Death model. We use this new method to obtain a probability distribution for the age of Amniota (the synapsid/sauropsid or bird/mammal divergence), one of the most-frequently used dating constraints. Our results suggest an older age (between about 322 and 340 Ma) than has been assumed by most studies that have used this constraint (which typically assumed a best estimate around 310–315 Ma) and provide, for the first time, a method to compute the shape of the probability density for this divergence time. [Divergence times; fossil ages; fossilized birth–death model; probability distribution.]
Combined Maternal Exposure to Cypermethrin and Stress Affect Embryonic Brain and Placental Outcomes in Mice
Authors: Elser Benjamin A , Kayali Khaled , Dhakal Ram , O’Hare Bailey , Wang Kai , Lehmler Hans-Joachim , Stevens Hanna E
Published: March 2020

Prenatal exposure to cypermethrin is a risk factor for adverse neurodevelopmental outcomes in children. In addition, maternal psychological stress during pregnancy has significant effects on fetal neurodevelopment and may influence end-stage toxicity to offspring by altering maternal xenobiotic metabolism. As such, this study examined effects of maternal exposure to alpha-cypermethrin and stress, alone and in combination, on offspring development, with a focus on fetal neurotoxicity. CD1 mouse dams were administered 10 mg/kg alpha-cypermethrin or corn oil vehicle via oral gavage from embryonic day 11 (E11) to E14. In addition, dams from each treatment were subjected to a standard model of restraint stress from E12 to E14. Cypermethrin treatment impaired fetal growth, reduced fetal forebrain volume, and increased ventral forebrain proliferative zone volume, the latter effects driven by combined exposure with stress. Cypermethrin also impaired migration of GABAergic progenitors, with different transcriptional changes alone and in combination with stress. Stress and cypermethrin also interacted in effects on embryonic microglia morphology. In addition, levels of cypermethrin were elevated in the serum of stressed dams, which was accompanied by interacting effects of cypermethrin and stress on hepatic expression of cytochrome P450 enzymes. Levels of cypermethrin in amniotic fluid were below the limit of quantification, suggesting minimal transfer to fetal circulation. Despite this, cypermethrin increased placental malondialdehyde levels and increased placental expression of genes responsive to oxidative stress, effects significantly modified by stress exposure. These findings suggest a role for interaction between maternal exposures to cypermethrin and stress on offspring neurodevelopment, involving indirect mechanisms in the placenta and maternal liver.
Reproducibility of the Development and Validation Process of Standard Area Diagram by Two Laboratories: An Example Using the Botrytis cinerea/Gerbera jamesonii Pathosystem
Authors: de Melo Vilma Pereira , Mendonça Ana Claudia da Silva , de Souza Hudson Sergio , Gabriel Lorrant Cavanha , Bock Clive H. , Eaton Mahogani J. , Schwan-Estrada Kátia Regina Freitas , Nunes William Mário de Carvalho
Published: March 2020

Standard area diagrams (SADs) are plant disease severity assessment aids demonstrated to improve the accuracy and reliability of visual estimates of severity. Knowledge of the sources of variation, including those specific to a lab such as raters, specific procedures followed including instruction, image analysis software, image viewing time, etc., that affect the outcome of development and validation of SADs can help improve standard operating practice of these assessment aids. As reproducibility has not previously been explored in development of SADs, we aimed to explore the overarching question of whether the lab in which the measurement and validation of a SAD was performed affected the outcome of the process. Two different labs (Lab 1 and Lab 2) measured severity on the individual diagrams in a SAD and validated them independently for severity of gray mold (caused by Botrytis cinerea) on Gerbera daisy. Severity measurements of the 30 test images were performed independently at the two labs as well. A different group of 18 raters at each lab assessed the test images first without, and secondly with SADs under independent instruction at both Lab 1 and 2. Results showed that actual severity on the SADs as measured at each lab varied by up to 5.18%. Furthermore, measurement of the test image actual values varied from 0 to up to 24.29%, depending on image. Whereas at Lab 1 an equivalence test indicated no significant improvement in any measure of agreement with use of the SADs, at Lab 2, scale shift, generalized bias, and agreement were significantly improved with use of the SADs (P ≤ 0.05). An analysis of variance indicated differences existed between labs, use of the SADs aid, and the interaction, depending on the agreement statistic. Based on an equivalence test, the interrater reliability was significantly (P ≤ 0.05) improved at both Lab 1 and Lab 2 as a result of using SADs as an aid to severity estimation. Gain in measures of agreement and reliability tended to be greatest for the least able raters at both Lab 1 and Lab 2. Absolute error was reduced at both labs when raters used SADs. The results confirm that SADs are a useful tool, but the results demonstrated that aspects of the development and validation process in different labs may affect the outcome.
A Decision Support System Based on Degree-Days to Initiate Fungicide Spray Programs for Peach Powdery Mildew in Catalonia, Spain
Authors: Marimon Neus , Eduardo Iban , Martínez-Minaya Joaquín , Vicent Antonio , Luque Jordi
Published: March 2020

The incidence of peach powdery mildew (PPM) on fruit was monitored in commercial peach orchards to i) describe the disease progress in relation to several environmental parameters and ii) establish an operating threshold to initiate a fungicide spray program based on accumulated degree-day (ADD) data. A beta-regression model for disease incidence showed a substantial contribution of the random effects orchard and year, whereas relevant fixed effects corresponded to ADD, wetness duration, and ADD considering vapor pressure deficit and rain. When beta-regression models were fitted for each orchard and year considering only ADD, disease onset was observed at 242 ± 13 ADD and symptoms did not develop further after 484 ± 42 ADD. An operating threshold to initiate fungicide applications was established at 220 ADD, coinciding with a PPM incidence in fruit around 0.05. A validation was further conducted by comparing PPM incidence in i) a standard, calendar-based program, ii) a program with applications initiated at 220 ADD, and iii) a nontreated control. A statistically relevant reduction in disease incidence in fruit was obtained with both fungicide programs, from 0.244 recorded in the control to 0.073 with the 220-ADD alert program, and 0.049 with the standard program. The 220-ADD alert program resulted in 33% reduction in fungicide applications.
Human papillomavirus type 16 infection activates the host serine arginine protein kinase 1 (SRPK1) – splicing factor axis
Authors: Mole Sarah , Faizo Arwa Ali A. , Hernandez-Lopez Hegel , Griffiths Megan , Stevenson Andrew , Roberts Sally , Graham Sheila V
Published: March 2020

The infectious life cycle of human papillomaviruses (HPVs) is tightly linked to keratinocyte differentiation. Evidence suggests a sophisticated interplay between host gene regulation and virus replication. Alternative splicing is an essential process for host and viral gene expression, and is generally upregulated by serine arginine-rich splicing factors (SRSFs). SRSF activity can be positively or negatively controlled by cycles of phosphorylation/dephosphorylation. Here we show that HPV16 infection leads to accumulation of the paradigm SRSF protein, SRSF1, in the cytoplasm in a keratinocyte differentiation-specific manner. Moreover, HPV16 infection leads to increased levels of cytoplasmic and nuclear phosphorylated SRSF1. SR protein kinase 1 (SRPK1) phosphorylates SRSF1. Similar to HPV upregulation of SRSF1, we demonstrate HPV upregulation of SRPK1 via the viral E2 protein. SRPK1 depletion or drug inhibition of SRPK1 kinase activity resulted in reduced levels of SRSF1, suggesting that phosphorylation stabilizes the protein in differentiated HPV-infected keratinocytes. Together, these data indicate HPV infection stimulates the SRPK1–SRSF axis in keratinocytes.
Integration of urine proteomics and renal single-cell genomics identifies an interferon-gamma response gradient in lupus nephritis
Authors: Fava Andrea , Buyon Jill , Mohan Chandra , Zhang Ting , Belmont H. Michael , Izmirly Peter , Clancy Robert , Trujillo Jose Monroy , Fine Derek , Zhang Yuji , Magder Laurence , Rao Deepak A. , Arazi Arnon , Berthier Celine C. , Davidson Anne , Diamond Betty , Hacohen Nir , Wofsy David ,   the Accelerating Medicines Partnership in SLE network, Raychaudhuri Soumya , Petri Michelle
Published: March 2020

Lupus nephritis, one of the most serious manifestations of systemic lupus erythematosus (SLE), has both a heterogeneous clinical and pathological presentation. For example, proliferative nephritis identifies a more aggressive disease class that requires immunosuppression. However, the current classification system relies on the static appearance of histopathological morphology which does not capture differences in the inflammatory response. Therefore, a biomarker grounded in the disease biology is needed to understand the molecular heterogeneity of lupus nephritis and identify immunologic mechanism and pathways. Here, we analyzed the patterns of 1000 urine protein biomarkers in 30 patients with active lupus nephritis. We found that patients stratify over a chemokine gradient inducible by interferon-gamma. Higher values identified patients with proliferative lupus nephritis. After integrating the urine proteomics with the single-cell transcriptomics of kidney biopsies, it was observed that the urinary chemokines defining the gradient were predominantly produced by infiltrating CD8 T cells, along with natural killer and myeloid cells. The urine chemokine gradient significantly correlated with the number of kidney-infiltrating CD8 cells. These findings suggest that urine proteomics can capture the complex biology of the kidney in lupus nephritis. Patient-specific pathways may be noninvasively tracked in the urine in real time, enabling diagnosis and personalized treatment.
If long-term suppression is not possible, how do we minimize mortality for COVID-19 and other emerging infectious disease outbreaks?
Authors: Handel Andreas , Miller Joel C. , Ge Yang , Fung Isaac Chun-Hai
Published: March 2020

As COVID-19 continues to spread, public health interventions are crucial to minimize its impact. The most desirable goal is to drive the pathogen quickly to extinction. This generally involves applying interventions as strongly as possible, which worked for SARS, but so far has failed for COVID-19. If fast eradication is not achievable, the next best goal is to delay the spread and minimize cases and burden on the health care system until suitable drugs or vaccines are available. This suppression approach also calls for strong interventions, potentially applied for a long time.
Functionally non-redundant paralogsspe-47andspe-50encode FB-MO associated proteins and interact withhim-8
Authors: Clark Jessica N. , Prajapati Gaurav , Aldaco Fermina , Sokolich Thomas J. , Keung Steven , Austin Sarojani , Valdés Ángel A. , LaMunyon Craig W.
Published: March 2020

The activation ofC. elegansspermatids to crawling spermatozoa is affected by a number of genes includingspe-47.Here, we investigate a paralog tospe-47:spe-50, which has a highly conserved sequence and expression, but which is not functionally redundant tospe-47.Phylogenetic analysis indicates that the duplication event that produced the paralogs occurred prior to the radiation of theCaenorhabditisspecies included in the analysis, allowing a long period for the paralogs to diverge in function. Furthermore, we observed that knockout mutations in both genes, either alone or together, have little effect on sperm function. However, hermaphrodites harboring both knockout mutations combined with a third mutation in thehim-8gene are nearly self-sterile due to a sperm defect, even though they have numerous apparently normal sperm within their spermathecae. We suggest that the sperm in these triple mutants are defective in fusing with oocytes, and that the effect of thehim-8mutation is due to its role in chromatin remodeling.
HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads
Authors: Nurk Sergey , Walenz Brian P. , Rhie Arang , Vollger Mitchell R. , Logsdon Glennis A. , Grothe Robert , Miga Karen H. , Eichler Evan E. , Phillippy Adam M. , Koren Sergey
Published: March 2020

Complete and accurate genome assemblies form the basis of most downstream genomic analyses and are of critical importance. Recent genome assembly projects have relied on a combination of noisy long-read sequencing and accurate short-read sequencing, with the former offering greater assembly continuity and the latter providing higher consensus accuracy. The recently introduced PacBio HiFi sequencing technology bridges this divide by delivering long reads (>10 kbp) with high per-base accuracy (>99.9%). Here we present HiCanu, a significant modification of the Canu assembler designed to leverage the full potential of HiFi reads via homopolymer compression, overlap-based error correction, and aggressive false overlap filtering. We benchmark HiCanu with a focus on the recovery of haplotype diversity, major histocompatibility complex (MHC) variants, satellite DNAs, and segmental duplications. For diploid human genomes sequenced to 30× HiFi coverage, HiCanu achieved superior accuracy and allele recovery compared to the current state of the art. On the effectively haploid CHM13 human cell line, HiCanu achieved an NG50 contig size of 77 Mbp with a per-base consensus accuracy of 99.999% (QV50), surpassing recent assemblies of high-coverage, ultra-long Oxford Nanopore reads in terms of both accuracy and continuity. This HiCanu assembly correctly resolves 337 out of 341 validation BACs sampled from known segmental duplications and provides the first preliminary assemblies of 9 complete human centromeric regions. Although gaps and errors still remain within the most challenging regions of the genome, these results represent a significant advance towards the complete assembly of human genomes.

Availability

HiCanu is implemented within the Canu assembly framework and is available fromhttps://github.com/marbl/canu.
In-hospital Death Following Successful OHCA Resuscitation: Causes of early and late mortality and the impact of withdrawal of care
Authors: Li Shu , Lazaridis Christos , Goldenberg Fernando D. , Shah Atman P. , Tataris Katie , Beiser David G. , Sharp Willard W.
Published: March 2020

Objective

In-hospital mortality in patients successfully resuscitated following out-of-hospital cardiac arrest (OHCA) is high. The factors and timings of these deaths is not well known. To better understand in hospital post-OHCA mortality we developed a novel categorization system of in hospital death and studied the factors and timings associated with these deaths.

Methods

This was a single-centered retrospective observational human study in adult non-traumatic OHCA patients in a university affiliated hospital. Through an expert consensus process, a novel classification system of hospital death was developed.

Results

Two hundred and forty-one patients were enrolled in the study. Death was categorized as due to withdrawal of life sustaining treatment (WOLST) 159 (66.0%), recurrent in-hospital cardiac arrest 51 (21.1%), or due to neurological criteria 31 (12.9%). Subcategorization of factors associated with WOLST into 7 categories was done by defined criteria. Inter-reliability of this system was 0.858. 50% of WOLST decisions were due to neurological injury. Early death (≤ 3 days) was associated with recurrent in-hospital cardiac arrest and WOLST in the setting of refractory shock or multi-organ injury. Late in-hospital death (> 3 days) was primarily due to WOLST decisions in the setting of isolated neurological injury.

Conclusions

OHCA in hospital mortality occurred in a bimodal pattern with early deaths due to recurrent arrest and multiorgan injury while late deaths were due to isolated neurological injury. The majority of deaths occurred in the setting of WOLST decisions. Further study of the influence of these factors on post OHCA survival are needed.
V367F mutation in SARS-CoV-2 spike RBD emerging during the early transmission phase enhances viral infectivity through increased human ACE2 receptor binding affinity
Authors: Ou Junxian , Zhou Zhonghua , Dai Ruixue , Zhao Shan , Wu Xiaowei , Zhang Jing , Lan Wendong , Cui Lilian , Wu Jianguo , Seto Donald , Chodosh James , Zhang Gong , Zhang Qiwei
Published: March 2020

The current global pandemic of COVID-19 is caused by a novel coronavirus SARS-CoV-2. The SARS-CoV-2 spike protein receptor-binding domain (RBD) is the critical determinant of viral tropism and infectivity. To investigate whether naturally occurring mutations in the RBD have altered the receptor binding affinity and infectivity, firstly we analyzed in silico the binding dynamics between mutated SARS-CoV-2 RBDs and the human ACE2 receptor. Among 1609 genomes of SARS-CoV-2 strains isolated during the early transmission phase, 32 non-synonymous RBD mutants were identified and found clustered into nine mutant types under high positive selection pressure. Applying molecular dynamics simulations, three mutant types (V367F, W436R, N354D/D364Y) displayed higher binding affinity to human ACE2, likely due to the enhanced structural stabilization of the RBD beta-sheet scaffold. The increased infectivity of one mutant (V367F) circulating worldwide was further validated by performing receptor-ligand binding ELISA, surface plasmon resonance, and pseudotyped virus assays. Genome phylogenetic analysis of V367F mutants showed that during the early transmission phase, most V367F mutants clustered more closely with the SARS-CoV-2 prototype strain than the dual-mutation variants (V367F + D614G), which emerged later and formed a distinct sub-cluster. The analysis of critical RBD mutations provides further insights into the evolutionary trajectory of SARS-CoV-2 under high selection pressure and supports the continuing surveillance of spike mutations to aid in the development of COVID-19 drugs and vaccines.
Rapidly induced drug adaptation mediates escape from BRAF inhibition in single melanoma cells
Authors: Yang Chen , Tian Chengzhe , Hoffman Timothy E. , Jacobsen Nicole K. , Spencer Sabrina L.
Published: March 2020

Despite increasing numbers of effective anti-cancer therapies, successful treatment is limited by the development of drug resistance. While the contribution of genetic factors to drug resistance is undeniable, little is known about how drug-sensitive cells first evade drug action to proliferate in drug. Here we track the response of thousands of single melanoma cells to BRAF inhibitors and show that a subset escapes drug within the first 3 days of treatment. Cell-cycle re-entry occurs via a non-genetic mechanism involving activation of mTORC1 and ATF4, validated in cultures of patient biopsies. These escapees cycle periodically in drug, incur significant DNA damage, and out-proliferate non-escapees over extended treatment. Our work reveals a mutagenesis-prone, expanding subpopulation of early drug escapees that may seed development of permanent drug resistance.
Glycolytic metabolism of pathogenic T cells enables early detection of GvHD by13C-MRI
Authors: Assmann Julian C. , Farthing Don E. , Saito Keita , Maglakelidze Natella , Oliver Brittany , Warrick Kathrynne A. , Sourbier Carole , Ricketts Christopher J. , Meyer Thomas J. , Pavletic Steven Z. , Linehan W. Marston , Krishna Murali C. , Gress Ronald E. , Buxbaum Nataliya P.
Published: March 2020

Graft-versus-host disease (GvHD) is a prominent barrier to allogeneic hematopoietic stem cell transplantation (HSCT). Definitive diagnosis of GvHD is invasive and biopsies of involved tissues pose a high risk of bleeding and infection. Our previous studies in a chronic GvHD mouse model demonstrated that alloreactive CD4+T cells are distributed to target organs ahead of overt symptoms, meanwhile CD4+T cell activation is tied to increased glycolysis. Thus, we hypothesized that metabolic imaging of glycolysis would allow non-invasive detection of insipient GvHD in target organs infiltrated by glycolytic effector memory CD4+T cells. We metabolically characterized CD4+T cell subsets on day 14 post-transplant before the onset of chronic GvHD in a pre-clinical mouse model and performed13C hyperpolarized magnetic resonance imaging (MRI) to quantify glycolytic activity in the liver of mice over the course of the disease. Intracellular metabolic screening andex vivometabolic profiling of CD4+T cell subsets at day 14 confirmed that activated CD4+T cells were highly glycolytic. Concurrently, hyperpolarized13C-pyruvate MRI of the liver showed high conversion of pyruvate to lactate, indicative of increased glycolytic activity, that distinguished allogeneic from syngeneic HSCT recipients prior to the development of overt chronic GvHD. Furthermore, single cell sequencing of T cells in patients undergoing allogeneic HSCT indicated that similar metabolic changes may play a role in acute GvHD, providing a rationale for testing this imaging approach in the clinical post-HSCT setting. Our imaging approach is amenable to clinical translation and may allow early, non-invasive diagnosis of GvHD.
Testing the efficacy of lionfish traps in the northern Gulf of Mexico
Authors: Harris Holden E. , Fogg Alexander Q. , Gittings Stephen R. , Ahrens Robert N. M. , Allen Micheal S. , Patterson William F.
Published: March 2020

Spearfishing is currently the primary approach for removing invasive Indo-Pacific lionfish(Pterois volitans/milescomplex) to mitigate their impacts to western Atlantic marine ecosystems. However, a substantial portion of lionfish spawning biomass is beyond the depth limits of SCUBA. Innovative technologies may offer an alternative means to target lionfish and allow for the development of a deepwater lionfish trap fishery, but the removal efficiency and potential environmental impacts of traps have not been evaluated. We tested a collapsible non-containment trap (the ‘Gittings trap’) near artificial reefs in the northern Gulf of Mexico. A total of 327 lionfish and 28 native fishes (4 of which regulated species) recruited to traps (i.e., number of fish observed within the trap footprint) during 82 trap sets, catching 144 lionfish and 29 native species. Lionfish recruitment was highest for single (versus paired) traps deployed <15 m from reefs with a 1-day soak time, for which mean lionfish and native species recruitment per trap were approximately 5 and 0.1, respectively. Gittings traps selected for larger lionfish (mean size 277 mm total length) compared to spearfishing (mean size 258 mm). Community impacts from Gittings traps appeared minimal given recruitment patterns and catch rates were >10X higher for lionfish versus native fishes. Gittings traps did not move on the bottom during two major storm events; however, further testing will be necessary to test trap movement with surface buoys. Additional research should also focus on design and operational modifications to improve Gittings trap deployment success (68% successfully opened on the seabed) and reduce lionfish escapement (56% escaped from traps upon retrieval). While removal efficiency for lionfish (12–24%) was far below that of spearfishing, study results demonstrate Gittings traps are suitable for future testing on deepwater natural reefs, which constitute >90% of the region’s reef habitat.
Meta Gene Regulatory Networks in Maize Highlight Functionally Relevant Regulatory Interactions
Authors: Zhou Peng , Li Zhi , Magnusson Erika , Gomez Cano Fabio , Crisp Peter A. , Noshay Jaclyn M. , Grotewold Erich , Hirsch Candice N. , Briggs Steven P. , Springer Nathan M.
Published: March 2020

The regulation of gene expression is central to many biological processes. Gene regulatory networks (GRNs) link transcription factors (TFs) to their target genes and represent maps of potential transcriptional regulation. Here, we analyzed a large number of publically available maize (Zea mays) transcriptome data sets including >6000 RNA sequencing samples to generate 45 coexpression-based GRNs that represent potential regulatory relationships between TFs and other genes in different populations of samples (cross-tissue, cross-genotype, and tissue-and-genotype samples). While these networks are all enriched for biologically relevant interactions, different networks capture distinct TF-target associations and biological processes. By examining the power of our coexpression-based GRNs to accurately predict covarying TF-target relationships in natural variation data sets, we found that presence/absence changes rather than quantitative changes in TF gene expression are more likely associated with changes in target gene expression. Integrating information from our TF-target predictions and previous expression quantitative trait loci (eQTL) mapping results provided support for 68 TFs underlying 74 previously identified trans-eQTL hotspots spanning a variety of metabolic pathways. This study highlights the utility of developing multiple GRNs within a species to detect putative regulators of important plant pathways and provides potential targets for breeding or biotechnological applications.
A comparison of bank and credit union growth around the financial crisis
Authors: Lu Wenling , Swisher Judith
Published: March 2020

Purpose

The purpose of this research is to examine the growth rates of commercial banks and credit unions around the financial crisis and recovery. Credit unions are analyzed as a group and by field of membership. Specifically, this research analyzes the growth rates of assets, deposits, and loans.

Design/methodology/approach

This research employs univariate tests of differences to examine the median growth rates for commercial banks and credit unions. Unbalanced pool regressions analyze growth rates during the pre-crisis, crisis, and recovery periods, controlling for size, net charge-offs, and unemployment.

Findings

Univariate test results that control for size show that banks grow at faster rates than credit unions for most of the pre-crisis years. However, medium sized credit unions grow at faster rates for most of the crisis and recovery years. Results of unbalanced pool regressions suggest that, overall, credit unions grow at slower rates than do banks. However, during the crisis and recovery, credit union growth is significantly greater than that of banks, after controlling for net charge-offs, size, and unemployment. Credit union growth varies by field of membership type.

Originality/value

Although a large volume of research examines commercial bank performance around the financial crisis, only a few papers assess the performance of credit unions. And very few papers compare commercial banks and credit unions. This paper explores how the recent financial crisis influenced the growth of commercial banks and credit unions from 2005 to 2013.
A qualitative study investigating food choices and perceived psychosocial influences on eating behaviours in secondary school students
Authors: Calvert Sian , Dempsey Robert C. , Povey Rachel
Published: March 2020

Purpose

Childhood obesity is a major global health concern. Understanding children's and adolescent’s eating behaviours and promoting healthier behaviours is key for reducing the negative health outcomes associated with obesity. The current study explored the perceptions of healthy eating behaviours and the influences on eating behaviours amongst 11-to-13-year-old secondary school students.

Design/methodology/approach

Nine semi-structured same-sex focus group discussions were conducted in schools located in deprived areas of England, with the discussions subjected to a thematic framework analysis.

Findings

Three main constructs were identified in the analysis as follows: (1)eating patterns and lifestyle, (2)social influencesand (3)environmental influences. Participants understood what healthy eating behaviours are and the benefits of eating healthy; yet, they reported irregular mealtimes and consuming unhealthy snacks. Students reported that their parents and fellow student peers were strong influences on their own eating behaviours, with girls subjected to being teased by male students for attempting to eat healthily. Finally, students perceived that unhealthy foods were cheaper, tasted better and were readily available in their social environments compared to healthier options, making healthier behaviours less likely to occur.

Originality/value

Findings indicate that students had a good understanding of healthy eating behaviours but did not always practise them and are seemingly influenced by their social and environmental context. The promotion of healthier eating in this age group needs to challenge the misperceptions associated with the accessibility and social acceptability of unhealthy food items.
Scholarly publication venue recommender systems
Authors: Dehdarirad Hossein , Ghazimirsaeid Javad , Jalalimanesh Ammar
Published: March 2020

Purpose

The purpose of this investigation is to identify, evaluate, integrate and summarize relevant and qualified papers through conducting a systematic literature review (SLR) on the application of recommender systems (RSs) to suggest a scholarly publication venue for researcher's paper.

Design/methodology/approach

To identify the relevant papers published up to August 11, 2018, an SLR study on four databases (Scopus, Web of Science, IEEE Xplore and ScienceDirect) was conducted. We pursued the guidelines presented by Kitchenham and Charters (2007) for performing SLRs in software engineering. The papers were analyzed based on data sources, RSs classes, techniques/methods/algorithms, datasets, evaluation methodologies and metrics, as well as future directions.

Findings

A total of 32 papers were identified. The most data sources exploited in these papers were textual (title/abstract/keywords) and co-authorship data. The RS classes in the selected papers were almost equally used. DBLP was the main dataset utilized. Cosine similarity, social network analysis (SNA) and term frequency–inverse document frequency (TF–IDF) algorithm were frequently used. In terms of evaluation methodologies, 24 papers applied only offline evaluations. Furthermore, precision, accuracy and recall metrics were the popular performance metrics. In the reviewed papers, “use more datasets” and “new algorithms” were frequently mentioned in the future work part as well as conclusions.

Originality/value

Given that a review study has not been conducted in this area, this paper can provide an insight into the current status in this area and may also contribute to future research in this field.
Kinh and ethnic tourism stakeholder participation and collaboration in tourism planning in Sapa, Vietnam
Authors: Nguyen Huy Van , Diane Lee , Newsome David
Published: March 2020

Purpose

This paper aims to explore the Kinh and ethnic stakeholders’ participation and collaboration in tourism planning in Sapa, Vietnam.

Design/methodology/approach

The primary data collection involved semi-structured interviews with 33 key tourism stakeholders, and data were analyzed using qualitative content analysis.

Findings

The findings reveal that in terms of participation and collaboration in tourism planning, there is little difference between the Kinh and ethnic groups. Tourism planning is viewed as a top-down approach, and both groups at the community level have very limited participation in tourism planning activities. However, at the on-site management level, there are opposing views between high (Kinh) and low (ethnic) management levels about participation in tourism planning. Both groups recognize the need for interdependence regarding collaboration in tourism planning. They also share similar aspects in regard to facilitating and hindering their participation in tourism planning.

Research limitations/implications

The limitations of this study include the use of a qualitative method, which limited the number of respondents. Future research could benefit from the application of quantitative research methods to include a greater number of local tourism stakeholders.

Practical implications

This study contributes to a better understanding of tourism planning in the Vietnamese context and has some practical implications for destination management and policymaking.

Originality/value

This is the first study to investigate the perspectives of Kinh and ethnic groups in term of participation and collaboration in tourism planning in the Vietnamese context.
Mechanisms of labour exploitation: the case of Pakistan
Authors: Arslan Muhammad
Published: March 2020

Purpose

The issue of exploitative labour practices has been a persistent and recurring problem in the textile and garment industry. Despite increased media, policy and practitioners attention the evidence base remains unexplored. The International Labour Organization (ILO) has acknowledged the presence of labour exploitation in global supply chains because of private sectors’ employment practices. The purpose of this study is to apprehend views of multilevel stakeholders to explore the nature and driving mechanisms of exploitation.

Design/methodology/approach

Semi-structured interviews were conducted with 76 respondents from 25 factories from 3 cities of Pakistan i.e. Faisalabad, Lahore and Gujranwala. Convenient and snowball sampling techniques were used because of the complexity of research settings. Transcribed data was analysed with the help of NVivo.

Findings

Drawing on qualitative evidence, the study reveals that workers experience a range of exploitation at the workplace, which is unlikely to fall within the scope of severe exploitation. The findings reveal that three types of exploitation exist in Pakistan’s textile and garment industry such as financial, physiological and psychological. Power inequality is the foundation and a fundamental cause of the endurance of exploitation. The study found three mechanisms that facilitate the endurance of exploitation, i.e. distance, profit and oppression.

Research limitations/implications

The study contributes to supply chain literature by exemplifying power inequality. It is crucial for the government to step up efforts to stipulate a minimum wage rate in the textile and garment industry to alleviate labour exploitation. The findings provide motivation for policy and decision-makers to implement incremental changes to global supply chains to protect the rights and welfare of workers, according to the standards of social accountability 8000, the ILO and other world trade stakeholders.

Originality/value

This study argues that the international and local instruments do not specifically address the severe labour exploitation in Pakistan textile and garment industry. Therefore, the need arises to develop a specific instrument to address the problem. In the absence of such an instrument, there is a piecemeal approach by international and local bodies towards the regulation of labour exploitation.
Transformational leadership and service quality in e-commerce businesses
Authors: Mahdikhani Mehri , Yazdani Bita
Published: March 2020

Purpose

The purpose of this paper is to examine the transformational leadership and service quality in the businesses active in the field of e-commerce with the mediating role of trust and team performance.

Design/methodology/approach

Survey questionnaires were administered on a 384-subject sample of the employees of the teams working in electronic businesses in Iran. The structural equation modeling and partial least square techniques were used to analyze the data.

Findings

The results showed that transformational leadership has a positive impact on service quality and improves team performance. The effect of transformational leadership on the interpersonal trust and the trust on the team performance are also positive and significant. In summary, the improved performance also has a positive impact on service quality.

Research limitations/implications

The main limitation is the assessment by questionnaire because the questionnaires measure the attitudes of individuals, not the facts as they are, and the attitudes of individuals usually involve personal judgments and prejudices in the research. Also, examining the research model in different cultural domains may provide different results because of being influenced by different cultures. Hence, the authors recommend that the findings should be examined in other communities with different cultures.

Originality/value

Evaluating the impact of the transformational leadership on service quality (SERVPERF scale) by a survey of team trust and performance in e-business is an innovation in the influence assessment of these variables. The present research is considered applicable to the management science as new findings in organizational behavior studies and recognition of transformational leaders, as well as the positive impacts of the characteristics of them on individuals and followers.