bluuebunny/crossref_metadata_2025 huggingface dataset:
Vaping: Impact of Improving Screening Questioning in Adolescent Population: A Quality Improvement Initiative
Authors: Cano Rodriguez Zoila , Chen Yingying , Siegel Janet H. , Rousseau-Pierre Thaina
Published: December 2020

Introduction:

The use of Electronic Nicotine Delivery Systems (ENDS) increased dramatically over the past decade, making them the most common tobacco product used among youth. While physicians often screen for the use of tobacco, very few screen for vaping product usage. This quality improvement project aimed to increase the screening rate of ENDS use among adolescents to 85% to match the Healthy People 2020 screening target of 83.3% for smoking.

Method:

We collected data from weekly chart reviews of all adolescent visits with a primary care provider by using keywords such as “vapor,” “e-cigs,” and “vaping” to document screening for ENDS use. The project consisted of 4 PDSA cycles: (1) education of the Adolescent Clinic staff about screening; (2) the addition of the specific question for e-cigarette use in the facility’s Electronic Health Record; (3) house staff lecture about the importance of screening; and (4) reinforcement about screening to adolescent physicians.

Results:

The percentage of screening for traditional tobacco use was consistently higher than ENDS use in all months. ENDS use assessment increased since the first intervention, going from 0% at baseline to 90% at the end. The addition of a specific question for ENDS use in EPIC was the most significant intervention and increased the screening percentage to 78%.

Conclusions:

To adequately assess for the use of ENDS, the nonspecific question, “do you smoke?” is not sufficient. A direct approach is necessary. A specific question in the EHR is the most significant way to increase screening for ENDS use.
HIV Care Prioritization Using Phylogenetic Branch Length
Authors: Moshiri Niema , Smith Davey M. , Mirarab Siavash
Published: December 2020

Background:

The structure of the HIV transmission networks can be dictated by just a few individuals. Public health intervention, such as ensuring people living with HIV adhere to antiretroviral therapy and remain virally suppressed, can help control the spread of the virus. However, such intervention requires using limited public health resource allocations. Determining which individuals are most at risk of transmitting HIV could allow public health officials to focus their limited resources on these individuals.

Setting:

Molecular epidemiology can help prioritize people living with HIV by patterns of transmission inferred from their sampled viral sequences. Such prioritization has been previously suggested and performed by monitoring cluster growth. In this article, we introduce Prioritization using AnCesTral edge lengths (ProACT), a phylogenetic approach for prioritizing individuals living with HIV.

Methods:

ProACT starts from a phylogeny inferred from sequence data and orders individuals according to their terminal branch length, breaking ties using ancestral branch lengths. We evaluated ProACT on a real data set of 926 HIV-1 subtype B pol data obtained in San Diego between 2005 and 2014 and a simulation data set modeling the same epidemic. Prioritization methods are compared by their ability to predict individuals who transmit most after the prioritization.

Results:

Across all simulation conditions and most real data sampling conditions, ProACT outperformed monitoring cluster growth for multiple metrics of prioritization efficacy.

Conclusion:

The simple strategy used by ProACT improves the effectiveness of prioritization compared with state-of-the-art methods that rely on monitoring the growth of transmission clusters defined based on genetic distance.
Wheelchair Seated Posture and Health Outcomes of Older Veterans in Community Living Centers
Authors: Barks Lelia , Garvan Cynthia , Crane Barbara , Peterson Matthew , Brown Lisa M. , Powell-Cope Gail
Published: December 2020

Purpose

Nursing home residents sit in wheelchairs (WCs) for extended periods, often with slumped posture. They often experience pneumonia, pressure ulcers, and pain. This study described WC seated posture with its selected predictors and outcomes in the nursing home environment, throughout the daytime hours of 1 day.

Design and Methods

This observational study (n = 45) in two Veterans Administration Community Living Centers introduced a new measure of WC fit and described WC seated posture of older Veterans, with selected predictors and outcomes.

Findings

Wheelchair seated posture was predicted by cognitive status, WC fit, WC skills, and duration of sitting, but not by level of sitting ability. Poor posture measured by the Seated Posture Scale was associated with pain. Highest interface pressures measurable were seen in peak pressure index (PPI = 200 mm Hg), indicating risk of pressure injury. Veterans often denied discomfort, possibly lowering overall pain scores, while reporting severe pain in specific body parts.

Conclusions

Wheelchair seated posture was predicted by cognitive status, WC fit, WC skills, and duration of sitting. Poor posture was associated with pain, and poor posture was an outcome of poor WC fit. Poor WC fit in this study supported earlier findings in non-Veterans Administration nursing homes.
A Self-Efficacy Reinforcement Stretching Exercise Program for Community-Dwelling Older Women With Osteoarthritis: A Pilot Study
Authors: Cho Su-jin
Published: December 2020

Purpose

This study evaluated the effectiveness of the Self-Efficacy Reinforcement Stretching Exercise Program to improve osteoarthritis (OA)-related symptoms in older women with OA.

Design

A quasi-experimental design was used in this study.

Methods

The experimental group participated in the Self-Efficacy Reinforcement Stretching Exercise Program, a 6-week program composed of stretching exercises and self-efficacy reinforcement strategies, whereas the control group did not. All participants were assessed on pain; joint stiffness; physical function disability; body mass index; depression; and quality of life at the beginning, end, and 4 weeks after the program ended.

Findings

After participation, the experimental group had significantly less joint stiffness, physical function disability, and depression scores and significantly higher self-efficacy and quality of life than the control group.

Conclusions

This intervention program led to an improvement in OA-related symptoms, self-efficacy, and quality of life in older women with OA.

Clinical Relevance

The sustained effects of acquired exercise behaviors that persisted up to 4 weeks after the program ended could be of interest to rehabilitation nurses and other healthcare professionals.
Quantitative Assessment of Intraoperative Laser Fluorescence Angiography With Indocyanine Green Predicts Early Graft Function After Kidney Transplantation
Authors: Gerken Andreas L.H. , Nowak Kai , Meyer Alexander , Weiss Christel , Krüger Bernd , Nawroth Nina , Karampinis Ioannis , Heller Katharina , Apel Hendrik , Reissfelder Christoph , Schwenke Kay , Keese Michael , Lang Werner , Rother Ulrich
Published: December 2020

Objective:

This study was designed to demonstrate the predictive ability of quantitative indocyanine green (ICG) fluorescence angiography for the short-term postoperative outcome, the occurrence of delayed graft function (DGF), and long-term graft survival.

Summary Background Data:

DGF is a relevant problem after kidney transplantation; sufficient microperfusion of the allograft is crucial for postoperative organ function. Fluorescence angiography with ICG can serve as an intraoperative quality control of microperfusion.

Methods:

This prospective diagnostic study, conducted in 2 German transplantation centers from November 2015 to October 2018, included 128 consecutive kidney transplantations. Intraoperative assessment of the allograft microperfusion was performed by near-infrared fluorescence angiography with ICG; a software was used for quantitative analysis. The associations between perfusion parameters (eg, ICG Ingress) and donor, recipient, peri-procedural, and postoperative characteristics were evaluated.

Results:

DGF occurred in 23 (24%) kidney recipients from deceased donors. ICG Ingress (P = 0.0027), donor age (P = 0.0452), recipient age (P = 0.0139), and recipient body mass index (P = 0.0017) were associated with DGF. ICG Ingress correlated significantly with recipient age (r = −0.27662, P = 0.0016), cold and warm ischemia time (r = −0.25204, P = 0.0082; r = −0.19778, P = 0.0283), operating time (r = −0.32208, P = 0.0002), eGFR on postoperative days 1 (r =+0.22674, P = 0.0104) and 7 (r = +0.33189, P = 0.0001). The cutoff value for ICG Ingress was 106.23 AU with sensitivity of 78.3% and specificity of 80.8% (P < 0.0001) for the prediction of DGF.

Conclusion:

Fluorescence angiography with ICG allows intraoperative quantitative assessment of microperfusion during kidney transplantation. The parameter ICG Ingress reflects recipient and procedure characteristics and is able to predict the incidence of DGF.

Trial registration:

Clinicaltrials.gov: NCT-02775838
Prediction of Abdominal Aortic Aneurysm Growth Using Geometric Assessment of Computerized Tomography Images Acquired During the Aneurysm Surveillance Period
Authors: Chandrashekar Anirudh , Handa Ashok , Lapolla Pierfrancesco , Shivakumar Natesh , Ngetich Elisha , Grau Vicente , Regent Lee
Published: December 2020

Objective:

We investigated the utility of geometric features for future AAA growth prediction.

Background:

Novel methods for growth prediction of AAA are recognized as a research priority. Geometric feature have been used to predict cerebral aneurysm rupture, but not examined as predictor of AAA growth.

Methods:

Computerized tomography (CT) scans from patients with infra-renal AAAs were analyzed. Aortic volumes were segmented using an automated pipeline to extract AAA diameter (APD), undulation index (UI), and radius of curvature (RC). Using a prospectively recruited cohort, we first examined the relation between these geometric measurements to patients' demographic features (n = 102). A separate 192 AAA patients with serial CT scans during AAA surveillance were identified from an ongoing clinical database. Multinomial logistic and multiple linear regression models were trained and optimized to predict future AAA growth in these patients.

Results:

There was no correlation between the geometric measurements and patients' demographic features. APD (Spearman r = 0.25, P < 0.05), UI (Spearman r = 0.38, P < 0.001) and RC (Spearman r =–0.53, P < 0.001) significantly correlated with annual AAA growth. Using APD, UI, and RC as 3 input variables, the area under receiver operating characteristics curve for predicting slow growth (<2.5 mm/yr) or fast growth (>5 mm/yr) at 12 months are 0.80 and 0.79, respectively. The prediction or growth rate is within 2 mm error in 87% of cases.

Conclusions:

Geometric features of an AAA can predict its future growth. This method can be applied to routine clinical CT scans acquired from patients during their AAA surveillance pathway.
Prophylactic Mesh Reinforcement for Prevention of Midline Incisional Hernias
Authors: Olavarria Oscar A. , Dhanani Naila H. , Bernardi Karla , Holihan Julie L. , Bell Cynthia S. , Ko Tien C. , Liang Mike K.
Published: December 2020

Objective:

To systematically review the published literature on the use of prophylactic mesh reinforcement of midline laparotomy closures for prevention of VIH

Summary of Background Data:

VIH are common complications of abdominal surgery. Prophylactic mesh has been proposed as an adjunct to prevent their occurrence.

Methods:

PubMed, Embase, Scopus, and Cochrane were reviewed for RCTs that compared prophylactic mesh reinforcement versus conventional suture closure of midline abdominal surgery. Primary outcome was the incidence of VIH at postoperative follow-up ≥24 months. Secondary outcomes included surgical site infection and surgical site occurrence (SSO). Pooled risk ratios were obtained through random effect meta-analyses and adjusted for publication bias. Network meta-analyses were performed to compare mesh types and locations.

Results:

Of 1969 screened articles, 12 RCTs were included. On meta-analysis there was a lower incidence of VIH with prophylactic mesh [11.1% vs 21.3%, Relative risk (RR) = 0.32; 95% confidence interval (CI) = 0.19–0.55, P < 0.001), however, publication bias was highly likely. When adjusted for this bias, prophylactic mesh had a more conservative effect (RR = 0.52; 95% CI = 0.39–0.70). There was no difference in risk of surgical site infection (9.1% vs 8.9%, RR = 1.08, 95% CI = 0.82–1.43; P = 0.118), however, prophylactic mesh increased the risk of SSO (14.2% vs 8.9%, RR = 1.57, 95% CI = 1.19–2.05; P < 0.001).

Conclusion:

Current RCTs suggest that in mid-term follow-up prophylactic mesh prevents VIH with increased risk for SSO. There is limited long-term data and substantial publication bias.
Ethnicity-dependent effects of Zinc finger 804A variant on schizophrenia: a systematic review and meta-analysis
Authors: Wang Dandan , Wang Yewei , Chen Yan , Yu Lingfang , Fang Xinyu , Liu Ruimei , Wu Zenan , Zhang Chen
Published: December 2020

Objectives

Previous studies and meta-analysis indicated that rs1344706 was associated with schizophrenia in European population, whereas the conclusions in other populations were disputed. To further explore whether the allele A of rs1344706 would increase the risk of schizophrenia in different populations and update the original meta-analysis, we conducted a systematic review and meta-analysis worldwide.

Methods

A literature search was performed in PubMed, Embase, Cochrane Library, PsycINFO and Web of Science (up to 10 July 2019) according to the inclusion criteria.

Results

A total of 27 articles were included. Our meta-analysis showed an association between rs1344706 and schizophrenia in total populations [P = 0.000; odds ratio (OR) = 1.105; 95% confidence interval (CI), 1.048–1.165], Europe population (P = 0.025; OR = 1.108; 95% CI, 1.013–1.222) and Asian population(P = 0.005; OR = 1.094; 95% CI, 1.027–1.164).

Conclusions

Our findings suggested that the risk of single nucleotide polymorphism rs1344706 A-allele may increase the risk of schizophrenia worldwide. Also, this ethnicity-dependent effects of ZNF804A variant on schizophrenia may be related to the opposite allele direction. But to elucidate the underlying biological mechanism, further studies with large participant populations are needed.
Acceptable Performance of the Abbott ID NOW Among Symptomatic Individuals with Confirmed COVID-19
Authors: Stokes William , Berenger Byron M. , Singh Takshveer , Adeghe Ifueko , Schneider Angela , Portnoy Danielle , King Teagan , Scott Brittney , Pabbaraju Kanti , Shokoples Sandy , Wong Anita A. , Gill Kara , Turnbull LeeAnn , Hu Jia , Tipples Graham
Published: December 2020

INTRODUCTION

Point of care diagnostic tests for SARS-CoV-2, such as the ID NOW, have great potential to help combat the COVID-19 pandemic. The ID NOW is approved by the United States Food and Drug Administration (FDA) for the detection of SARS-CoV-2 in symptomatic individuals within the first 7 days of symptom onset for COVID-19 if tested within 1 hour of specimen collection. However, clinical data on the performance of the ID NOW is limited, with many studies deviating from the manufacturer’s instructions and/or having small sample size.

METHODS

Adults with COVID-19 in the community or hospital were recruited into the study. Paired throat swabs were collected, with one throat swab transported immediately in an empty sterile tube to the laboratory for ID NOW testing, and the other transported in universal transport media and tested by an in-house SARS-CoV-2 RT-PCR assay targeting the E-gene. Positive percent agreement (PPA) was calculated.

RESULTS

133 individuals were included in the study. 129 samples were positive on either the ID NOW and/or RT-PCR. Assuming any positive result on either assay represents a true positive, PPA of the ID NOW compared to RT-PCR with 95% confidence intervals was 89.1% [82.0% - 94.1%] and 91.6% [85.1% - 95.9%], respectively. When analyzing individuals with symptoms ≤ 7 days and who had the ID NOW performed within an hour, ID NOW PPA increased to 98.2%.

DISCUSSION

In this study, SARS-CoV-2 results from the ID NOW were reliable, especially when testing was adhered to manufacturer’s recommendations.
Effects of climatic warming on spring phenology in subtropical trees: process-based modelling with experiments designed for model development
Authors: Zhang Rui , Lin Jianhong , Wang Fucheng , Hänninen Heikki , Wu Jiasheng
Published: December 2020

To project the effects of climatic warming on the timing of spring leafout and flowering in trees, process-based tree phenology models are often used nowadays. Unfortunately, the biological realism of the models is often compromised because the model development has often been based on various assumptions and indirect methods. We developed process-based tree phenology models for four subtropical tree species, and for the first time for these trees, we based the model development on explicit experimental work particularly designed to address the processes being modelled. For all the four species, a model of seedling leafout was developed, and forTorreya grandis, a model for female flowering in adult trees was additionally developed. The models generally showed reasonable accuracy when tested against two sources of independent data: observational phenological records and leafout data from a whole-tree chamber warming experiment. In scenario simulations, the models projected an advanced spring phenology under climatic warming for 2020 – 2100. For the leafout of seedlings, the advancing rates varied between 4.7 and 5.9 days per one °C warming, with no major differences found between the climatic scenarios RCP4.5 and RCP8.5. ForTorreyaflowering, less advancing was projected, and the projected advancing per one °C warming was less for RCP8.5 (0.9 days / °C) than for RCP4.5 (2.3 days / °C). The low advancing rates ofTorreyaflowering were caused by reduced chilling under the warming climate and by the particular temperature responses found forTorreyaflowering. For instance, our results show that inTorreyaflower buds, no rest break (endodormancy release) is seen at +15 °C, whereas in the seedlings of all four species, +15 °C has a clear rest-breaking effect. These findings highlight the need to base the model development on explicit experiments particularly designed to address the process being modelled.
Direct measurement of B lymphocyte gene expression biomarkers in peripheral blood enables early prediction of seroconversion after vaccination
Authors: Huang Dan , Liu Alex YN , Leung K.S. , Tang Nelson LS
Published: December 2020

Vaccination is a common and efficient means to reduce the mortality and morbidity of emerging infectious diseases. Among responders, injected antigen induces acquired immunity pathways and leads to the final production of antigen-specific antibodies. The whole process may take weeks to months, depending on the antigen. Typically, seroconversion to influenza vaccine is expected after one month with a responder rate of ~50%.

An early biomarker to predict response is desirable. Peripheral blood gene expression (or transcript abundance, TA) datasets in the public domain were analyzed for early biomarkers among responders. As peripheral blood samples (such as peripheral blood mononuclear cells, PBMC) are cell mixture samples containing various blood cell-types (leukocyte subpopulations, LS). We first develop a model that enables the determination of TA in B lymphocytes of certain genes directly in PBMC samples without the need of prior cell isolation. These genes are called B cell informative genes. Then a ratio of two B cell informative genes (a target gene and a stably expressed reference gene) measured in PBMC was used as a new biomarker to gauge the target gene expression in B lymphocytes. This method having an obvious advantage over conventional methods by eliminating the tedious procedure of cell sorting and enables directly determining TA of a leukocyte subpopulation in cell mixture samples is calledDirect LS-TA method.

By using a B lymphocyte-specific gene such as TNFRSF17 or TXNDC5 as target genes with either TNFRSF13C or FCRLA as reference genes, the B cell biomarkers were determined directly in PBMC which was highly correlated with TA of target genes in purified B lymphocytes. These Direct LS-TA biomarkers in PBMC increased significantly early after vaccination in both the discovery dataset and a meta-analysis of 7 datasets. Responders had almost a 2-fold higher Direct LS-TA biomarker level of TNFRSF17 (SMD=0.84, 95% CI=0.47-1.21 after log2). And Direct LS-TA biomarkers of TNFRSF17 and TXNDC5 measured at day 7 predict responder with sensitivity values of higher than 0.7. The Area-under curves (AUC) in receiver operation curve (ROC) analysis were over 0.8.

Here, we report a straightforward approach to directly analyses B lymphocyte gene expression in PBMC, which could be used in a routine clinical setting as it avoids the labor-intensive procedures of B lymphocyte isolation. And the method allows the practice of precision medicine in the prediction of vaccination response.

Furthermore, response to vaccination could be predicted as early as on day 7. As vaccination response is based on the similar acquired immunology pathway in the upcoming worldwide vaccination campaign against COVID-19, these biomarkers could also be useful to predict seroconversion for individuals.
Integrating central and peripheral neurons in elongating multi-lineage-organized gastruloids
Authors: Olmsted Zachary T. , Paluh Janet L.
Published: December 2020

Human stem cell technologies including self-assembling 3D tissue models provide unprecedented access to early neurodevelopment and enable fundamental insights into neuropathologies. Gastruloid models have yet to be used to investigate the developing nervous system. Here we generate elongating multi-lineage-organized (EMLO) gastruloids with trunk identity that co-develop central and peripheral nervous system (CNS, PNS) correlates. We track migrating neural crest cells that differentiate to form peripheral neurons integrated with an upstream spinal cord region. This follows initial EMLO polarization events, and is coordinated with primitive gut tube elongation and cardiomyocyte differentiation. By immunofluorescence of multi-lineage and functional biomarkers, we evaluate EMLOs over a twenty-two day period, and apply them to investigate the impact of mu opioid receptor modulation on neuronal activity. This comprehensive study demonstrates a novel combined CNS-PNS model of early organogenesis and integration events in the trunk to benefit human biomedical research.
The Broad Role of Nkx3.2 in the Development of the Zebrafish Axial Skeleton
Authors: Waldmann Laura , Leyhr Jake , Zhang Hanqing , Öhman-Mägi Caroline , Allalou Amin , Haitina Tatjana
Published: December 2020

The transcription factor Nkx3.2 (Bapx1) is an important chondrocyte maturation inhibitor. PreviousNkx3.2knock-down and overexpression studies in non-mammalian gnathostomes have focused on its role in primary jaw joint development, while little is known about the function of this gene in broader skeletal development. We generated CRISPR/Cas9 knockout ofnkx3.2in zebrafish and applied a range of techniques to characterize skeletal phenotypes at developmental stages from larva to adult, revealing fusions in bones of the occiput, the loss or deformation of bony elements derived from basiventral cartilages of the vertebrae, and an increased length of the proximal radials of the dorsal and anal fins. These phenotypes are reminiscent ofNkx3.2knockout phenotypes in mammals, suggesting that the function of this gene in axial skeletal development is ancestral to osteichthyans. Our results highlight the broad role ofnkx3.2in zebrafish skeletal development and its context-specific functions in different skeletal elements.
The Heterochromatin protein 1 is a master regulator in RNA splicing precision deficient in ulcerative colitis
Authors: Mata-Garrido Jorge , Xiang Yao , Chang-Marchand Yunhua , Reisacher Caroline , Ageron-ardila Elisabeth , Guerrera Chiara , Casafont Inigo , Bruneau Aurelia , Cherbuy Claire , Treton Xavier , Dumay Anne , Ogier-Denis Eric , Batsche Eric , Costallat Mickael , Revêchon Gwladys , Eriksson Maria , Muchardt Christian , Arbibe Laurence
Published: December 2020

Defects in RNA splicing have been linked to numerous human disorders, but remain poorly explored in inflammatory bowel disease (IBD). Here, we report that, in the gut epithelium of patients with ulcerative colitis (UC), the expression of the chromatin and alternative splicing regulator HP1γ is strongly reduced. Accordingly, inactivation of the HP1γ gene in the mouse gut triggered several IBD-like traits, including inflammation and dysbiosis. In parallel, we discovered that its loss of function broadly increased splicing noise, reducing requirement for canonical splicing consensus sequences, and favoring the usage of cryptic splice sites at numerous genes with key functions in gut biology. This notably resulted in the production of progerin, a noncanonical toxic splice variant of prelamin A mRNA, responsible for the Hutchinson Gilford Progeria Syndrome (HGPS) of premature aging. Likewise, production of progerin transcript was found to be a signature of colonic cells from UC patients. Thus, our study identifies HP1γ as a regulator of RNA metabolismin vivo, providing a unique mechanism linking anti-inflammation and accuracy of RNA splicing in the gut epithelium. HP1 defect may confer a general disturbance in RNA splicing precision to scrutinize in IBD and more generally in accelerating aging diseases.
Structural basis of meiotic chromosome synaptic elongation through hierarchical fibrous assembly of SYCE2-TEX12
Authors: Dunce James M. , Salmon Lucy J. , Davies Owen R.
Published: December 2020

The synaptonemal complex (SC) is a supramolecular protein assembly that mediates synapsis between homologous chromosomes during meiosis. SC elongation along the chromosome length (up to 24 μm) depends on its midline α-fibrous component SYCE2-TEX12. Here, we report X-ray crystal structures of SYCE2-TEX12 as an individual building-block and upon assembly within a fibrous lattice. We combine these structures with mutagenesis, biophysics and electron microscopy to reveal the hierarchical mechanism of SYCE2-TEX12 fibre assembly. SYCE2-TEX12’s building-blocks are 2:2 coiled-coils which dimerise into 4:4 hetero-oligomers and interact end-to-end and laterally to form 10-nm fibres, which intertwine within 40-nm bundled micrometre-long fibres that define the SC’s midline structure. This assembly mechanism bears striking resemblance with intermediate filament proteins vimentin, lamin and keratin. Thus, SYCE2-TEX12 exhibits behaviour typical of cytoskeletal proteins to provide an α-fibrous SC backbone that structurally underpins synaptic elongation along meiotic chromosomes.
Glycolysis downregulation is a hallmark of HIV-1 latency and sensitizes infected cells to oxidative stress
Authors: Shytaj Iart Luca , Procopio Francesco Andrea , Tarek Mohammad , Carlon-Andres Irene , Tang Hsin-Yao , Goldman Aaron R. , Munshi MohamedHusen , Forcato Mattia , Leskov Konstantin , Ye Fengchun , Lucic Bojana , Cruz Nicolly , Singh Amit , Bicciato Silvio , Padilla-Parra Sergi , Lusic Marina , Diaz Ricardo Sobhie , Alvarez-Carbonell David , Savarino Andrea
Published: December 2020

HIV-1 infects lymphoid and myeloid cells, which can harbor a latent proviral reservoir responsible for maintaining lifelong infection. Glycolytic metabolism has been identified as a determinant of susceptibility to HIV-1 infection, but its role in the development and maintenance of HIV-1 latency has not been elucidated. By combining transcriptomic, proteomic and metabolomic analysis, we here show that transition to latent HIV-1 infection downregulates glycolysis, while viral reactivation by conventional stimuli reverts this effect. Decreased glycolytic output in latently infected cells is associated with downregulation of NAD+/NADH. Consequently, infected cells rely on the parallel pentose phosphate pathway and its main product, the antioxidant NADPH, fueling antioxidant pathways maintaining HIV-1 latency. Of note, blocking NADPH downstream effectors, thioredoxin and glutathione, favors HIV-1 reactivation from latency in lymphoid and myeloid cellular models. This provides a “shock and kill effect” decreasing proviral DNA in cells from people-living-with-HIV/AIDS. Overall, our data show that downmodulation of glycolysis is a metabolic signature of HIV-1 latency that can be exploited to target latently infected cells with eradication strategies.
Molecular Noise-Filtering in theβ-adrenergic Signaling Network by Phospholamban Pentamers
Authors: Koch Daniel , Alexandrovich Alexander , Funk Florian , Schmitt Joachim P. , Gautel Mathias
Published: December 2020

Phospholamban (PLN) is an important regulator of calcium handling in cardiomyocytes due to its ability to inhibit the sarco(endo)plasmic reticulum calcium-ATPase (SERCA)β-adrenergic stimulation reverses SERCA inhibition via PLN phosphorylation and facilitates fast calcium reuptake PLN also forms pentamers whose physiological significance has remained elusive Using biochemical experiments and mathematical modeling, we show that pentamers regulate both the dynamics and steady-state levels of monomer phosphorylation Substrate competition by pentamers and a feed-forward loop involving inhibitor-can delay monomer phosphorylation by protein kinase A (PKA) Steady-state phosphorylation of PLN is predicted to be bistable due to cooperative dephosphorylation of pentamers Both effects act as complementary noise-filters which can reduce the effect of random fluctuations in PKA activity Pentamers thereby ensure consistent monomer phosphorylation and SERCA activity in spite of noisy upstream signals Preliminary analyses suggest that the PLN mutation R del could impair noise-filtering, offering a new perspective on how this mutation causes cardiac arrhythmias.
Computational quantification of global effects induced by mutations and drugs in signaling networks of colorectal cancer cells
Authors: Sommariva Sara , Caviglia Giacomo , Ravera Silvia , Frassoni Francesco , Benvenuto Federico , Tortolina Lorenzo , Castagnino Nicoletta , Parodi Silvio , Piana Michele
Published: December 2020

Colorectal cancer (CRC) is one of the most deadly and commonly diagnosed tumors worldwide. Several genes are involved in its development and progression. The most frequent mutations concern APC, KRAS, SMAD4, and TP53 genes, suggesting that CRC relies on the alteration of different pathways. However, with classic molecular approaches, it is not easy to simultaneously analyze the interconnections between these pathways. For this reason, we propose a computational model based on a huge chemical reaction network to simulate the effects induced on the global signaling associated with CRC by single or multiple concurrent mutations or by drug treatment. This approach displays several advantages. The model can quantify the alteration in the concentration of the proteins connected with the examined mutation. Moreover, working on the global signaling of CRC, it is possible to disclose unexpected interactions between the involved pathways, representing new therapeutic targets.

Highlights

Colorectal cancer relates to defects in many different pathways within cell signaling

Cell signaling is modeled as a chemical ration network with 10 interacting pathways

Global effects induced by single or multiple concurrent mutations are quantified

A possible extension of the model to account for a targeted drug is discussed
Association ofIRS1(Gly972Arg) andIRS2(Gly1057Asp) genes polymorphisms with OSA and NAFLD in Asian Indians
Authors: Bhatt Surya Prakash , Randeep Guleria DM
Published: December 2020

Aim and Objective

The aim of the study was to investigate the relationships between insulin receptor substrate (IRS) 1 (Gly972Arg) andIRS2(Gly1057Asp) genes with obstructive sleep apnea (OSA) and non-alcoholic fatty liver disease (NAFLD) in Asian Indians.

Method

A total of 410 overweight/obese subjects (130 with OSA with NAFLD, 100 with OSA without NAFLD, 95 without OSA and with NAFLD and 85 without OSA and without NAFLD) were recruited. Degree of NAFLD was based on liver ultrasound and of OSA on overnight polysomnography.

Result

InIRS1gene, the genotype frequency (%) of Arg/Arg was significantly higher in NAFLD and OSA subjects. In addition, Gly/Arg genotype ofIRS1gene was associated with significantly higher body mass index, fat mass, %body fat, triglycerides, cholesterol, alkaline phosphate, aspartate transaminase, fasting insulin and HOMA-IR levels in OSA and NAFLD subjects. No significant difference in genotype frequencies ofIRS2was observed between four groups. Further we found that subjects carryingIRS1Gly/Arg (OR 4.49, 95% C.I. 1.06-12.52, p=0.002) genotype possess a much higher risk of OSA and NAFLD compared toIRS2Gly/Asp (OR 1.01, 95% C.I. 0.8-2.56, p=0.05).

Conclusion

We concluded that Asian Indian subject carrying the allele Gly972Arg polymorphism ofIRS1is predisposed to develop OSA and NAFLD.
Complete mitochondrial genome sequence of Bos frontalis (Gayal) from Bangladesh
Authors: Deb GK , Khatun R , Hossain SMJ , Rahman SS , Bhuiyan MAB , Mobassirin S , Afrin S , Billah M , Baten A , Sarker NR , Bhuyian MSA , Siddiki AMAMZ
Published: December 2020

The Gayal is a large-sized endangered semi-domesticated bovine species belonging to the family Bovidae, tribe Bovini, group Bovina, genus Bos, and species Bos frontalis. It is also called the Mithan or Mithun. Mitochondrial genome is considered as an important tool for species identification and monitoring the populations of conservation concern and therefore it becomes an obligation to sequence the mitochondrial genome of Bagladeshi gayal. We want to identify some important genes related to a particular trait such as those associated with adaptation, muscle strength, or prolificacy. The data will help explore evolutionary relationships with closely related species. The mitogenome ofBos frontalisis 16,347 bp in length and nucleotide composition is AT-based (60.21%), contains 37 genes including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region.
Exploring Fayol's management process in a traditional Mayan dance (Pochó Dance): an ethnographic study
Authors: Suarez-Barraza Manuel F. , Miguel Davila Jose Angel
Published: December 2020

Purpose

Well into the 21st century, it is difficult to deny the contribution that Mayan culture has made to the history of the world, and not only because of its contribution to universal culture with its architecture, astronomy and mathematics. Understanding the management practices of a Mayan dance (the dance of the Pochó) that has transcended over the years can give us an idea of the management practices carried out by an ancestral culture such as the Maya. The purpose of this article is to establish an initial conceptual relationship between the management process proposed by Henry Fayol (1916) and the management of a Mayan dance that has survived to the present day.

Design/methodology/approach

A specific ethnographic study was carried out in the municipality of Tenosique, Tabasco (Mexico) for two consecutive years. Research methods such as direct observation, researcher diaries, in-depth interviews and photographs were utilized that allowed a study of management practices.

Findings

Thanks to the cross-checking of the data obtained, it was possible to determine a theoretical-conceptual relationship between Fayol's management process and the Mayan dance studied. In fact, 12 specific management practices found in the four phases of the process were identified. In addition, with the ethnographic study it was possible to determine the levels of intensity and impact regarding the satisfaction of those attending and performing the dance.

Research limitations/implications

Research limitations are due to result from the fact that the analysis corresponds to a single Mayan dance in a specific place (Tenosique) in the state of Tabasco, Mexico.

Practical implications

To understand the management practices of the Mayan culture through the study of a dance that has remained alive until our days; this might be useful for the management practices of today's companies.

Originality/value

It is a pioneering study that analyzes a Mayan dance through the optics of management sciences.
The informal city and the future of our cities: towards a manifesto
Authors: Mostafa Magda
Published: December 2020

Purpose

The New Urban Agenda has catalyzed discussion across academia and practice on how to responsibly position ourselves as key players in the making of the future of our cities. With questions such as what is the right to the city? Who has those rights? What is a city? What is formal and who defines informal? These questions may prompt a need for departure from, or at least a reconsideration of the narrative surrounding formal and informal urbanism. This paper presents a pedagogical approach to addressing these and other questions within the framework of the new agenda. It reviews pedagogical approaches to understanding and learning to design within an informal context. It also foregrounds the process with the theoretical framing of Christopher Alexander's Pattern Language and Timeless way of Building as lenses through which to understand and identify common languages and intersections across the global spectrum of representations of informal urbanism. It then outlines the resultant process and products of a one-week intensive master-class and design charette of international scholars and students focusing on the Informal City.

Design/methodology/approach

It reviews pedagogical approaches to understanding and learning to design within an informal context. It also foregrounds the process with the theoretical framing of Christopher Alexander's Pattern Language and Timeless way of Building as lenses through which to understand and identify common languages and intersections across the global spectrum of representations of informal urbanism. It then outlines the resultant process and products of a one-week intensive master-class and design charette of international scholars and students focusing on the Informal City.

Findings

The paper conclusively presents new nomenclature for informality that strives to shift the semantic lens from its current negative connotations to more productive, proactive and positive ones. It also presents an Informal City Manifesto, a call to arms of theoretical framing of how we think about the formal informal divide.

Research limitations/implications

The paper, in part, outlines the results of a single studio with a small student number. Although diverse in its composition the student body is small.

Originality/value

This new framing could potentially allow us to best leverage lessons and mitigate challenges of the informal city condition, as our human settlements continue to urbanize.
Impact of COVID-19 on undergraduate business students: a longitudinal study on academic motivation, engagement and attachment to university
Authors: Pasion Rita , Dias-Oliveira Eva , Camacho Ana , Morais Catarina , Campos Franco Raquel
Published: December 2020

Purpose

This study aims to explore whether the COVID-19-related circumstances hindered these academic-related variables.

Design Methodology Approach

The authors surveyed two groups of undergraduate business students (42% male) who completed the questionnaires at the beginning and at the end of the semester. One group of students attended only face-to-face classes in the 2018/2019 academic year (n = 126) and the other group transitioned to online classes because of the COVID-19 outbreak in the 2019/2020 academic year (n = 99).

Findings

The findings show no statistically significant group differences between the pre- and post-test in students’ intrinsic and extrinsic motivation, feelings of attachment to the university and engagement dimensions of absorption and vigour. Nevertheless, a moderate negative effect was found in the dedication engagement dimension.

Practical Implications

The authors discuss the main results in terms of some practices that may contribute towards attenuating the effects of future emerging pandemics in the higher education setting.

Originality Value

The COVID-19 pandemic imposed a rapid transition to online instruction in education institutions worldwide. However, it remains unclear to date how students’ engagement, motivation and attachment to the university were negatively affected by the first COVID-19 outbreak.
How trust was maintained in Scandinavia through the first crisis of modernity
Authors: Dahlen Øystein Pedersen , Skirbekk Helge
Published: December 2020

Purpose

The aim of this article is to explain why there is a higher degree of trust in some countries compared to others – and which are the main historical factors that explain these differences. The main focus is on how governments relate to and communicate with its citizens in the times of crises.

Design/methodology/approach

The analysis is based on comparative historical sociology with a modernity perspective with a special focus on Norway and Scandinavia. The authors do a parallel demonstration of history to confirm and expand the theories that could explain the high level of trust in these countries. The authors also bring in the Spanish experience in order to testify how governmental reactions affected the different levels of trust.

Findings

Scandinavian governments allowed open communication between different social classes on difficult and important issues, in contrast to Spain in the same period. These two factors therefore expand the understanding of the development of trust: (1) The establishment of the nation state as the organising concept and all-encompassing container of the other institutions (democracy, parliamentarism, trade unions, etc.); (2) The open hand strategy in dealing with deviant opinions, based on democratic compromises and a policing of consent ideology.

Originality/value

The article combines the understanding of the first crisis of modernity and the development of trust and contain a comparative analysis of the development of trust in four different countries. The investigation thus clarifies the correlation between specific historical factors and the levels of trust.
Image reconstruction by solving the inverse problem in ultrasonic transmission tomography system
Authors: Rymarczyk Tomasz , Kania Konrad , Gołąbek Michał , Sikora Jan , Maj Michał , Adamkiewicz Przemysław
Published: December 2020

Purpose

The purpose of this study is to develop a reconstruction and measurement system for data analysis using ultrasonic transmission tomography. The problem of reconstruction from the projection is encountered in practical implementation, which consists in reconstructing an image that is an estimation of an unknown object from a finite set of projection data. Reconstructive algorithms used in transmission tomography are based on linear mathematical models, which makes it necessary to process non-linear data into estimates for a finite number of projections. The application of transformation methods requires building a mathematical model in which the projection data forming the known and unknown quantities are functions with arguments from a continuous set of real numbers, determining the function describing the unknown quantities sought in the form of inverse relation and adapting it to operate on discrete and noisy data. This was done by designing a tomographic device and proprietary algorithms capable of reconstructing two-dimensional images regardless of the size, shape, location or number of inclusions hidden in the examined object.

Design/methodology/approach

The application consists of a device and measuring sensors, as well as proprietary algorithms for image reconstruction. Ultrasonic transmission tomography makes it possible to analyse processes occurring in an object without interfering with the examined object. The proposed solution uses algorithms based on ray integration, the Fermat principle and deterministic methods. Two applications were developed, one based on C and implemented on the embedded device, while the other application was made in Matlab.

Findings

Research shows that ultrasonic transmission tomography provides an effective analysis of tested objects in closed tanks.

Research limitations/implications

In the presented technique, the use of ultrasonic absorption wave has been limited. Nevertheless, the effectiveness of such a solution has been confirmed.

Practical implications

The presented solution can be used for research and monitoring of technological processes.

Originality/value

Author’s tomographic system consisting of a measuring system and image reconstruction algorithms.
Development of mathematical model and circuit emulators for four lobe memristive behaviour
Authors: Bhardwaj Kapil , Srivastava Mayank
Published: December 2020

Purpose

This paper aims to develop a mathematical model for four-lobe memristor (FLM) element. The four-lobe memristive behaviour can be used in realization of hyperchaotic oscillators and implementation of multi-bit memories. For verification of the developed mathematical framework, two FLM circuit emulators have been presented using VDCC and IC LM13700, respectively.

Design/methodology/approach

A mathematical model for FLM has been developed in which, the condition for the existence of symmetrical four lobes, instances and coordinates of the end points of lobes has been derived and presented. Using this mathematical framework, a FLM emulator based on VDCC has been developed. To validate the possibility of practical implementation of FLM concept, an IC LM13700-based circuit has also been developed. The workability of VDCC based circuit has been verified by running simulations in PSPICE environment using CMOS VDCC model. Similarly, the behaviour of LM13700 IC-based circuit has been confirmed by SPICE model of LM13700 IC.

Findings

It has been shown mathematically that under certain conditions, third-order flux dependent equation of memductance can be used to generate four lobes on the transient v-i plane. Also, two FLM emulators without using any voltage multiplier circuit/IC have been reported.

Originality/value

From the best knowledge of the authors, there are no such FLM emulators that have been reported in literature so far, which operates at practical operating frequencies.