bluuebunny/crossref_metadata_2025 huggingface dataset:
CNS Activity of an LHX2‐Associated Cis‐Regulatory Module
Authors: Zhang Michael , Cooper Allen M. , Britton Jessica C. , Pira Charmaine U. , Shin Alexandra , Oberg Kerby C.
Published: April 2020

Limb development can be described along three axes – proximal‐distal, anterior‐posterior, and dorsal‐ventral. Fibroblast growth factors (FGFs) from the apical ectodermal ridge (AER) coordinate growth along the proximal‐distal axis, while sonic hedgehog (SHH), secreted from the zone of polarizing activity, directs anterior‐posterior patterning and expansion. AER‐related FGFs and SHH regulate each other in a positive feedback loop. This reciprocal loop is critical for proper limb patterning, however the molecular intermediates involved in this loop are only partially characterized. Previously, we identified LIM homeobox 2 (LHX2) as a downstream target of FGF in the FGF to SHH loop and determined that FGF upregulates LHX2 in the absence of de novo protein synthesis. This suggests that LHX2, expressed in the mesoderm subjacent to the AER, is a primary response target of FGF signaling.

Cis‐regulatory modules (CRMs) within noncoding DNA can convey temporal and spatial regulation of an associated gene and are good candidates to convey the FGF‐mediated regulation of LHX2. We identified several potential CRMs (PCRMs) upstream of the LHX2 locus based on sequence conservation, active chromatin marks, and presence of transcription factor binding sites related to FGF signaling. Based on the number of active chromatin marks, we chose four of these PCRMs to investigate. We suspect that FGF regulates LHX2 through one or more of these PCRMs. Thus, we hypothesized that one or more of these PCRMs is active in the LHX2 expression domain during limb development.

To test for activity of LHX2 PCRMs we used targeted regional electroporation (TREP) to introduce PCRM‐ptk‐GFP reporter constructs into the distal mesoderm of Hamburger‐Hamilton stage 23 (HH23) chicken limb buds. Transfection efficiency was determined by co‐transfection with a b‐actin promoter‐driven RFP construct. We determined PCRM activity by fluorescence microscopy, following 24 hours of incubation after TREP.

None of the four PCRMs tested exhibited activity in the limb. However, subsequent TREP of the reporter construct containing PCRM ‐7 (~ 800 bp conserved region located 215 kb upstream of the LHX2 promoter) into the neural tube of HH10 embryos revealed green fluorescence at the midbrain‐forebrain boundary 24 hours post‐TREP. This activity suggests PCRM ‐7 may play a role in regulating LHX2 expression in the developing forebrain. Further studies are underway to correlate the activity of this CRM with expression of LHX2 or other genes in the topologically associated domain.
An ELK4 Binding Site is Critical for Activity of the LHX2‐Associated Sub‐AER Regulatory Module 1 (LASARM1)
Authors: Olafsen Christian Eric , Cooper Allen , Britton Jessica , Pira Charmaine U. , Oberg Kerby C.
Published: April 2020

Fibroblast growth factors (FGFs) secreted from the apical ectodermal ridge (AER) coordinate limb growth and proximal‐distal patterning, while sonic hedgehog (SHH) from the zone of polarizing activity directs anterior‐posterior growth and patterning. Moreover, these signaling centers maintain each other’s expression in a reciprocal feedback loop. This regulatory loop coordinates limb patterning during outgrowth. However, the molecular intermediates involved in in this loop are only partially characterized. Previously, we identified LIM homeobox 2 (LHX2), expressed in the mesoderm subjacent to the AER, as a downstream target of FGF in the FGF to SHH arm of the feedback loop.

LHX2‐associated Cis‐regulatory modules (CRMs) are reasonable candidates to convey the FGF‐mediated regulation of LHX2. We have identified a 1745 bp CRM located 483 kb upstream of the LHX2 promoter that is active in the sub‐AER region within the expression domain of LHX2. In silico analysis of this LHX2‐associated sub‐AER regulatory module 1 (LASARM1) revealed several FGF‐related transcription factor binding sites, including a site for ETS like‐4 (ELK4). We performed in situ hybridization for ELK4 mRNA and found a pattern coincident with LHX2 expression. Thus, we hypothesized that mutation of the ELK4 binding site within LASARM1 would disrupt FGF‐mediated enhancer activity.

To identify whether the putative ELK4 transcription factor binding site contributes to LASARM1 activity, we performed site‐directed mutagenesis on the ELK4 binding site in the LASARM1‐ptk‐EGFP reporter construct. We used targeted regional electroporation (TREP) to introduce control and mutated reporter constructs into the distal mesoderm of Hamburger‐Hamilton stage 23 chicken limb buds. Transfection efficiency was determined by co‐transfection with a β‐actin promoter‐driven RFP construct. After 24 hours of incubation LASARM1 activity was determined by fluorescence microscopy.

The fluorescence of LASARM1mutELK4 was markedly reduced relative to the LASARM1control. Our findings suggest that FGF signaling utilizes the ELK4 transcription factor to regulate LHX2 expression through the LASARM1 enhancer. Further work is needed to confirm this connection.
MicroRNAs and Their Potential Role as Biomarkers in Canine COngestive Heart Failure
Authors: Zepeda Anthony , Bohan Amy
Published: April 2020

Myxomatous mitral valvular degeneration (MMVD) is the most common heart disease in dogs, accounting for more than 70% of canine heart disease cases. It primarily affects middle‐aged small dogs, though, any dog can develop MMVD. It can affect all heart valves but is usually detected in mitral valves. Degenerative processes cause mitral valves to thicken and retract, creating an unwanted hole which blood can flow through. Tearing of mitral valves can lead to blood overflow and later, CHF in the heart’s left‐side. Currently, there are no medications proven to prevent, slow, or reverse the development of MMVD. Because of limited knowledge on MMVD, heart murmurs and coughing are the earliest means of detection. A microRNA (miRNA) is a small non‐coding RNA molecule, about 22 nucleotides long. We would test miRNA‐21, miRNA‐29a‐3p, miRNA‐210, and miRNA‐133a. If said miRNA significantly upregulated in CHF‐positive dog plasma, then upregulation of those miRNA could indicate development of MMVD. Plasma would be collected from dogs at an animal shelter. Plasma RNA would be purified using QIAzol Lysis Reagent. RT‐PCR would be used to reverse transcribe RNA to cDNA. SYBR Green (fluorescent dye) would detect miRNA amplification. If we can determine which miRNAs have a significantly high concentration in CHF‐positive dog plasma, we would be able to detect MMVD in pre‐developmental stages. For example, if a dog’s blood screening results show abnormal upregulation of miRNA precursor to MMVD, inhibitors of said miRNA could administered as a preventative measure.
MicroRNAs as a Potential Biomarker in Feline Kidney Disease
Authors: Bateman Taylor
Published: April 2020

Kidney failure is a very common disease in felines, more so than many may have thought. Due to there being very little research on kidney failure in felines there is not much understanding to what causes it and how it can be prevented. Since this disease in felines is quite similar to kidney failure in humans, this research may benefit further research on kidney failure. Therefore, it is important to identify the causes of kidney failure in felines in order to treat all patients at the earliest detectable stage. MicroRNAs are small, non‐coding RNAs that can down‐regulate the expression of protein coding genes by binding to the 3′UTR sites in their messenger RNAs. Prior research shows that kidney failure can be detected by microRNAs, making microRNAs a useful biomarker to kidney failure. The microRNAs may also help detect the early stages of kidney failure in felines making it easier to diagnose this disease. Our proposal is to test that circulating microRNAs may be useful biomarkers for detection of kidney failure. Liquid biopsies, blood samples, were collected in EDTA tubes from 8 healthy felines with no prior history of kidney failure and 8 felines who were diagnosed with kidney failure. Total serum RNS was isolated using miRNeasy Serum/Plasma kit. Isolated RNA was then reverse transcribed using miScript II RT Kit and lastly, miRNA was quantified using miScript SYBR green PCR Kit, along with miScript miRNA PCR Arrays.
Using Alu Elements to Identify Orthologous Chromosomes Across Primates
Authors: Mehra Mehul , Sood Nitish , Mittal Anav , Bates Christopher
Published: April 2020

Orthologous chromosome identification provides a basis for detecting the chromosomal locations of various genes between species. In non‐human primates, this information is instrumental to model organism research and pharmacogenetics. Thus far, ascertaining orthologous chromosome pairings between primate species has been constrained by resource and time‐intensive biochemical or bioinformatic approaches. As such, current methods have had only limited progress in identifying orthologous chromosomes in primates. Large‐scale genetic sequence analysis remains impractical, largely due to the computational overload associated with simultaneously analyzing millions of nucleotides. As such, an accurate and efficient strategy to identify orthologous chromosomes remains to be developed. Such a strategy would ideally compare short, rapidly diverging genetic sequences that originated preceding speciation. In addition, these sequences should be easily distinguishable from surrounding DNA, have a unidirectional mode of evolution, and be homoplasy‐free. These characteristics best describe Short Interspersed Nuclear Elements (SINEs). Yet, comparative analysis of primate SINEs has traditionally been limited to a binary state, detecting merely the presence or lack of a specific transposable element. Here, we propose a novel strategy to identify orthologous chromosomes in primates by analyzing the divergence of Alu sequences, a ubiquitous primate SINE. Alu elements were first obtained from the University of California Santa Cruz Genome Table Browser for 11 distinct primate species. Each parent sequence in a given species was then aligned using the Smith‐Waterman algorithm to all other sequences of the same subfamily in a second species. The sequence with the highest Smith‐Waterman score was assigned to be homologous to the parent sequence. The chromosome number of the parent and homologous sequences were recorded. After over 5 million sequences were analyzed, the results were tabulated to determine which chromosomes had the highest frequency of homologous pairings across any two compared primate species. This approach allowed us to determine orthologous chromosomes between two primates with a minimum z score of 2.5 (p < 0.007) and regularly above 4 (p < 1e–4). A sample of our results was compared with previously published lists of orthologous chromosomes, and a near‐perfect match verified the validity of our methodology. Our next goal is to generate a publicly available interactive repository of primate orthologous chromosome pairings.
Metformin enhances nigrostriatal dopaminergic tone via activation of atypical protein kinase ζ
Authors: Choi Dong-Young
Published: April 2020

Parkinson’s disease (PD) is the second most common neurodegenerative disease characterized by the progressive loss of the dopaminergic neurons in the substantia nigra leading to a decrease in the striatal dopamine. In our previous study, we demonstrated that metformin upregulated dopamine in the mouse brain, thus we designed this study to investigate the molecular mechanism behind such pharmacological effects. Here, we found that metformin enhanced the phosphorylation of tyrosine hydroxylase (TH) which was accompanied by increased expression of BDNF, GDNF, and activated their common signaling pathways in the nigrostriatal pathway. These effects were recapitulated in SH‐SY5Y cells suggesting a plausible role of neurotrophic factors in the activation of TH. Indeed, both BDNF and GDNF were essential for metformininduced TH activation. Importantly, we found that AMPK/aPKCζ/CREB pathway was required for metformin induced GDNF upregulation and TH activation. Our research is the first to reveal the critical role of DA‐upregulating effect of metformin via TH activation that critically requires neurotrophic factor induction. These results potentiate the candidacy of metformin not only as a neuroprotective agent but also as a restorative therapy for the treatment of PD.

Support or Funding Information

This research was supported by Basic Science Research Program through the Natonal Research Foundation of Korea funded by the Ministry of Education (2018R1D1A3B07049570).
MINER2.0 Combines ImageJ and R for Fast Nearest Neighbour Colocalization of 2D Multi‐Channel Fluorescence Images
Authors: Poburko Damon , dos Santos Anita , Jensen Gabrille , Kim BaRun , Pauls Andrew D. , Shalchy-Tabrizi Sophia , Ng Irvin
Published: April 2020

Introduction

Colocalization analysis has become a common tool of microscopic subcellular localization studies. There are many tools and packages available for colocalization analyses. MINER2.0 differs from many other packages by providing user‐friendly, highly customizable and scalable Nearest Neighbour analyses, drawing on principles of centroid localization used in single molecule imaging.

Methods and Results

To circumvent issues related to colocalization indices that rely on (often) arbitrarily thresholding color channels, our analysis pipeline compares predefined sets of regions of interest (ROIs) or can perform a de novo search for the K‐Nearest Neighbours (KNN) around the predefined ROIs. The algorithm calculates and reports: puncta area, mean intensities, full‐width‐half‐max sizes and intensity, and distances between the centroid or perimeter of reference ROIs and the centers of ROIs in up to two comparator ROI sets. Users can define ROI centroids as center of mass, geometric center or the biaxial Gaussian fit of the puncta. This latter method can statistically detect differences in distances between centroids in separate image channels of 1.4 pixels. At higher magnifications this allows detection of distances separating centroids in separate color channels at <90 nm, below the diffraction limit of optical microscopy. The pipeline is written as a user‐friendly macro for ImageJ/Fiji to ease of access. New in version 2.0, we moved from a brute force KNN calculation in ImageJ with an O(n2) time complexity to a Kd‐tree calculation in R with O(nLog(n)) complexity. This reduces the KNN calculation for large ROI sets (i.e. >1000 ROIs) from hours in ImageJ to typically <10 s in R. This enables batched analysis of large image sets on standard desktop computers (e.g. 36,000 ROIs in six 2048 × 2048 pixel images analyzed in <1.5 hours). We discuss three use cases: (1) the analysis of anti‐colocalization of the vesicular nucleotide transporter with diverse vesicle and lysosomal markers in Neuro2A cells, (2) analysis of the decrease of mitochondria containing mitochondrial DNA in A7r5 cells treated with diverse stressors including angiotensin II, 5,6‐dideoxycytidine, rotenone and hydrogen peroxide, and (3) the prevalence of micronuclei as markers of genotoxic stress in A7r5 cells expressing loss‐of‐function variants of polymerase gamma that is responsible for replicating mitochondrial DNA.

Conclusion

MINER2.0 provides a user‐friendly interface for fast batch processing of spatial colocalization analyses with minimal subjective bias. It provides users with extensive output parameters to allow detailed understanding of the spatial relationships of fluorescently labelled structures within cells.

Support or Funding Information

Natural Sciences and Engineering Research Council of Canada
A low cost electromechanical device injury model for hind limb murine muscles
Authors: Perez-Hernandez Daniel , Segura-Alegria Bertha , Garcia-Pelagio Karla
Published: April 2020

In daily life, muscle injuries due to accidents, sports, traumatic events or pathological conditions are constantly occurring. Not knowing the forces involved or the torque or the angle at which the injury was caused represent a challenging clinical problem limiting appropriate treatment protocols. In here, we design, developed, built and validated a reproducible well‐characterized injury device for small species at low cost using Arduino platform. The device can perform two types of injuries while varying speed, angle and frequencies; the first one generated by eccentric contractions and the second one by doing torsions. Briefly, under anesthesia the animal is placed in a pre‐warmed bed, then one leg is secured to a foot plate attached to an electric steeper motor providing a torque of 48 N‐m controlled by Arduino. Two electrodes are placed in the rat’s gastrocnemius to generate the injury. For eccentric contraction type of injury, the foot plate moves backward and forward causing dorsi and plantarflexion intermittently at a certain angle and speed. As the bed can rotate 180° fibrillar and tendon ruptures can be determined. The torsion type of injury mimics an ankle sprain at controlled force and speed. This is intended to study joint and tendon damage by mechanical analysis. The instantaneous speed of the movement is measured with an electronic gyroscope attached to the axis of the bed. Torque, isometric and isotonic stimulation can be measured as well. With this, the mechanisms of hypertrophy and muscular strengthening can be studied by measuring their progress with the aim of generating adequate physiotherapy therapies. We are currently validating the device in small species animals. Results will be shown.

Support or Funding Information

Supported partially by UNAM‐PAPIIT IA210320 and CONACyT AI‐S‐17636 to KPGP.
Regulator of G protein signaling 6 (RGS6) is a critical modulator of reward behavior and dopamine signaling in the mesolimbic circuit
Authors: Spicer Mackenzie Marie , Weber Matthew A. , Luo Zili , Yang Jianqi , Narayanan Kumar , Fisher Rory A.
Published: April 2020

Alcohol (EtOH) is the most commonly abused drug worldwide and chronic EtOH consumption often leads to development of dependence and abuse. EtOH dependence is a progressive, neurological disorder characterized by an accumulation of neuroadaptations resulting from chronic EtOH exposure. The neurobiological mechanisms underlying EtOH‐seeking behavior and dependence are not fully understood. As a result, there are limited therapeutics designed to reduce alcohol cravings or withdrawal symptomology, and abstinence remains the only effective way to prevent alcohol use disorders (AUDs). Previously, we showed that RGS6 deficiency in mice leads to reduced EtOH seeking and reward behaviors. Reduced EtOH seeking in RGS6−/− mice was partially reversed by GABAB and D2 autoreceptor (D2R) antagonism and completely reversed by singular inhibition of DAT. These findings, together with the observed reduction in striatal DA content in RGS6−/− mice, led us to hypothesize that RGS6 functions to promote mesolimbic DA transmission by suppressing GPCR‐Gαi/o‐mediated upregulation of DAT. To investigate this possibility, we examined the effects of RGS6 loss on DAT expression in VTA cell bodies and synaptic terminals in the nucleus accumbens (NAcc). In addition, we examined the effects of RGS6 loss on mesolimbic DA transmission using optogenetic stimulated release of DA and c‐Fos staining in the NAcc. We observed robust expression of RGS6 in VTA cell bodies and terminals where its loss led to upregulated expression of DAT. These findings suggest that RGS6 functions to promote EtOH seeking and reward behavior by promoting DA neurotransmission in the mesolimbic circuit by suppressing GPCR‐Gαi/o‐DAT upregulation.

Support or Funding Information

National Institutes of Health [AA025919]; the Michael J. Fox Foundation [1151]; and University of Iowa Pharmacological Sciences Training Grant [T32GM067795].
Internal carotid artery blood flow response to cognitive task is similar between young and older adults
Authors: Asahara Ryota , Ishii Kei , Izaki Tsubasa , Iwaki Sunao , Komine Hidehiko
Published: April 2020

Previous studies reported that the increase in the middle cerebral artery blood flow velocity during cognitive task was greater in older adults than in young adults, suggesting age‐related differences in cerebral blood flow responses to cognitive task. However, previous studies utilized transcranial Doppler ultrasound and thereby information regarding arterial diameter, blood volume flow, and vascular conductance was lacking. On the other hand, Doppler ultrasonography can assess blood volume flow in the internal carotid artery (ICA), which provides the blood supply to a large portion of the cerebral cortex. To date, it remains to be determined whether ICA blood flow response to cognitive task is different between young and older adults. The present study examined the ICA blood flow and blood pressure (BP) responses to 20 s of task switching in 6 young (30 ± 3 yr) and 6 older (66 ± 3 yr) subjects. The ICA blood flow and BP did not change significantly during task switching in young subjects. In older subjects, significant ICA blood flow response was not found, while BP increased (p<0.05) slightly and transiently during the first 10 s of the task. In both subjects, vascular conductance of the ICA was unaltered during task switching. Our present findings suggest that the ICA blood flow response to task switching was similar between young and older subjects.

Support or Funding Information

Grant‐in‐Aid for Research Activity start‐up from the Japan Society for the Promotion of Science (19K24333)
Computational Modeling of Attentional Impairments in Disruptive Mood Dysregulation and Attention Deficit/Hyperactivity Disorder
Authors: Haller Simone P. , Stoddard Joel , Pagliaccio David , Bui Hong , MacGillivray Caroline , Joes Matt , Brotman Melissa A.
Published: April 2020

Objective

Computational models provide information about cognitive components underlying behavior. When applied to psychopathology-relevant processes, they offer additional insight to observed differences in behavioral performance. Drift diffusion models have been successfully applied to investigate processing efficiency during binary choice tasks. Using these, we examine the association between psychopathology (irritability and inattention) and processing efficiency under different attentional demands.

Method

187 youth with ADHD, DMDD, both disorders, or no major psychopathology (M age=13.09, SD=2.55; 34% female) completed an Eriksen Flanker task. Of these, 87 provided complete data on dimensional measures of the core symptom of DMDD, irritability, and those of ADHD, inattention and hyperactivity.

Results

In a categorical analysis (n=187), we found a ADHD-by-DMDD-by task condition interaction on processing efficiency (b=−1.07, p=.01, 95%CI=[−1.89,−.24]), where increases in processing efficiency for non-conflict conditions were larger in youth without psychopathology relative to patients. Analysis of symptom severity (n=87) across diagnosis was consistent with the above analysis, revealing an interaction between symptom dimensions and task condition on processing efficiency (b=−0.10, p=.018, 95%CI[−.18, −.02]). Inattention, and its combined effect with irritability, predicted the magnitude of difference in processing efficiency between conflict and non-conflict conditions.

Discussion

Reduced processing efficiency may represent a shared cognitive endophenotype between ADHD and DMDD. Youth high in irritability or inattention may have difficulty adjusting processing efficiency to changing task demands possibly reflecting impairments in cognitive flexibility.
Trends and prediction in daily incidence and deaths of COVID-19 in the United States: a search-interest based model
Authors: Yuan Xiaoling , Xu Jie , Hussain Sabiha , Wang He , Gao Nan , Zhang Lanjing
Published: April 2020

Background and Objectives

The coronavirus disease 2019 (COVID-19) infected more than 586,000 patients in the U.S. However, its daily incidence and deaths in the U.S. are poorly understood. Internet search interest was found correlated with COVID-19 daily incidence in China, but not yet applied to the U.S. Therefore, we examined the association of internet search-interest with COVID-19 daily incidence and deaths in the U.S.

Methods

We extracted the COVDI-19 daily incidence and death data in the U.S. from two population-based datasets. The search interest of COVID-19 related terms was obtained using Google Trends. Pearson correlation test and general linear model were used to examine correlations and predict future trends, respectively.

Results

There were 555,245 new cases and 22,019 deaths of COVID-19 reported in the U.S. from March 1 to April 12, 2020. The search interest of COVID, “COVID pneumonia,” and “COVID heart” were correlated with COVDI-19 daily incidence with ∼12-day of delay (Pearson’s r=0.978, 0.978 and 0.979, respectively) and deaths with 19-day of delay (Pearson’s r=0.963, 0.958 and 0.970, respectively). The COVID-19 daily incidence and deaths appeared to both peak on April 10. The 4-day follow-up with prospectively collected data showed moderate to good accuracies for predicting new cases (Pearson’s r=-0.641 to −0.833) and poor to good accuracies for daily new deaths (Pearson’s r=0.365 to 0.935).

Conclusions

Search terms related to COVID-19 are highly correlated with the trends in COVID-19 daily incidence and deaths in the U.S. The prediction-models based on the search interest trend reached moderate to good accuracies.
COVID-19 outbreak in Greece has passed its rising inflection point and stepping into its peak
Authors: Georgiou Harris V.
Published: April 2020

Since the beginning of 2020, COVID-19 is the most urgent and challenging task for the international scientific community, in order to identify its behaviour, track its progress and plan effective mitigation policies. In this study, Greece is the main focus for assessing the national outbreak and estimating the general trends and outlook of it. Multiple data analytics procedures, spectral decomposition and curve-fitting formulations are developed based on the data available at hand. Standard SIEQRDP epidemic modelling is applied for Greece and for the general region around it, providing hints for the outbreak progression in the mid- and long-term, for various infections under-reporting rates. The overall short-term outlook for Greece seems to be towards positive, with a downward trend in infections rate daily increase (i.e., now beyond the exponential growth rate), a possible peak within a few days beyond April 14th, as well as the high availability level of ICU w.r.t. expected demand at peak. On the negative side, the fade-out period seems to be in the order of several months, with high probability of recurrent surges of the outbreak. The mitigation policies for the ‘next day’ should be focused on close tracking of the epidemic via large-scale tests, strict border checking in international travelling and an adaptive plan for selective activation of mitigation measures when deemed necessary.

Significance Statement

This study focuses on the COVID-19 outbreak in Greece and provides data-driven epidemic modelling and experimental results regarding the current state. Based on these results, the overall short-term outlook for Greece seems to be towards positive, having recently passed the rising inflection point and approaching the peak of the infections, and most probably capable of covering the projected ICU demand peak by a large margin. On the downside, the fade-out period seems to be in the order of several months, with high probability of recurrent surges of the outbreak. The ‘next day’ mitigation policies need to be carefully planned, highly adaptive and based on close tracking of the outbreak via large-scale testing in the general population.
How deadly is COVID-19? A rigorous analysis of excess mortality and age-dependent fatality rates in Italy
Authors: Modi Chirag , Böhm Vanessa , Ferraro Simone , Stein George , Seljak Uroš
Published: April 2020

We perform a counterfactual time series analysis on 2020 mortality data from towns in Italy using data from the previous five years as control. We find an excess mortality that is correlated in time with the official COVID-19 death rate, but exceeds it by a factor of at least 1.5. Our analysis suggests that there is a large population of predominantly older people that are missing from the official fatality statistics. We estimate that the number of cOvID-19 deaths in Italy is 49,000-53,000 as of May 9 2020, as compared to the official number of 33,000. The Population Fatality Rate (PFR) has reached 0.26% in the most affected region of Lombardia and 0.58% in the most affected province of Bergamo. These PFRs constitutes a lower bound to the Infection Fatality Rate (IFR). We combine the PFRs with the Test Positivity Ratio to derive the lower bound of 0.61% on the IFR for Lombardia. We further estimate the IFR as a function of age and find a steeper age dependence than previous studies: we find 17% of COVID-related deaths are attributed to the age group above 90, 7.5% to 80-89, declining to 0.04% for age 40-49 and 0.01% for age 30-39, the latter more than an order of magnitude lower than previous estimates. We observe that the IFR traces the Yearly Mortality Rate (YMR) above ages of 60 years, which can be used as a model to estimate the IFR for other populations and thus other regions in the world. We predict an IFR lower bound of 0.5% for NYC and that 27% of the total COVID-19 fatalities in NYC should arise from the population below 65 years. This is in agreement with the official NYC data and three times higher than the percentage observed in Lombardia. Combining the PFR with the Princess Diamond cruise ship IFR for ages above 70 we estimate the infection rates (IR) for regions in Italy. These peak in Lombardia at 26% (13%-47%, 95% c.l.), and for provinces in Bergamo at 69% (35%-100%, 95% c.I.). These estimates suggest that the number of infected people greatly exceeds the number of positive tests, e.g., by a factor of 35 in Lombardia.*
“Genomic and phenotypic characterization of Investigator Global Assessment (IGA) scale based endotypes in atopic dermatitis”
Authors: Smieszek Sandra P , Przychodzen Bartlomiej , Welsh Sarah E , Brzezynski Jennifer , Kaden Alyssa , Mohrman Michael , Wang Jingyuan , Xiao Changfu , Ständer Sonja , Birznieks Gunther , Polymeropoulos Christos , Polymeropoulos Mihael H
Published: April 2020

ABTRACT

Background

Atopic dermatitis (AD) is a heritable and heterogeneous inflammatory chronic skin disorder. Utilizing decision tree/supervised learning of extensive clinical, molecular and genetic data, we aimed to define distinct AD endotypes.

Methods

Deep phenotyping and whole-genome sequencing was performed on samples obtained from participants of EPIONE, a randomized-controlled phase III study in AD patients with severe pruritus comprising mild (23%), moderate (64%) and severe (13%) AD as determined by AD Investigator Global Assessment scale. Three categories of analysis were performed: clinical associations, lab value associations (EOS, IgE, cytokines) and genetic analysis of whole-genome sequencing data

Results

Based on a decision tree, we found that five clinical features from the SCORing Atopic Dermatitis (SCORAD) Index can accurately differentiate between IGA severities. We observe a significant difference between severity and eosinophil counts (p<0.001), IgE (p<0.001) and Filaggrin (FLG) LOF frequency (OR 2.3, CI 1.6-3.2, p<0.0001) as well as interleukin pathway genes, specifically IL5RA variants differentiating the groups.

Conclusion

Our results suggest significant differences between severity groups across a number of features appear to constitute distinct endotypes with likely distinct causative factors. Differing underlying pathophysiology’s indicate endotype knowledge is critical to help guide therapeutic approaches to AD.

Capsule summary

AD is a heritable and heterogeneous skin disorder that makes the ‘one size fits all’ therapeutic approach suboptimal for patients with AD.

We attempted to define AD endotypes based on clinical, molecular, and genetic characteristics. Clinical, CBC, and genetic associations all tend to suggest existence of separate endotypes.
Rapid development of an inactivated vaccine for SARS-CoV-2
Authors: Gao Qiang , Bao Linlin , Mao Haiyan , Wang Lin , Xu Kangwei , Yang Minnan , Li Yajing , Zhu Ling , Wang Nan , Lv Zhe , Gao Hong , Ge Xiaoqin , Kan Biao , Hu Yaling , Liu Jiangning , Cai Fang , Jiang Deyu , Yin Yanhui , Qin Chengfeng , Li Jing , Gong Xuejie , Lou Xiuyu , Shi Wen , Wu Dongdong , Zhang Hengming , Zhu Lang , Deng Wei , Li Yurong , Lu Jinxing , Li Changgui , Wang Xiangxi , Yin Weidong , Zhang Yanjun , Qin Chuan
Published: April 2020

The COVID-19 pandemic caused by SARS-CoV-2 has brought about an unprecedented crisis, taking a heavy toll on human health, lives as well as the global economy. There are no SARS-CoV-2-specific treatments or vaccines available due to the novelty of this virus. Hence, rapid development of effective vaccines against SARS-CoV-2 is urgently needed. Here we developed a pilot-scale production of a purified inactivated SARS-CoV-2 virus vaccine candidate (PiCoVacc), which induced SARS-CoV-2-specific neutralizing antibodies in mice, rats and non-human primates. These antibodies potently neutralized 10 representative SARS-CoV-2 strains, indicative of a possible broader neutralizing ability against SARS-CoV-2 strains circulating worldwide. Immunization with two different doses (3μg or 6 μg per dose) provided partial or complete protection in macaques against SARS-CoV-2 challenge, respectively, without any antibody-dependent enhancement of infection. Systematic evaluation of PiCoVacc via monitoring clinical signs, hematological and biochemical index, and histophathological analysis in macaques suggests that it is safe. These data support the rapid clinical development of SARS-CoV-2 vaccines for humans.

One Sentence Summary

A purified inactivated SARS-CoV-2 virus vaccine candidate (PiCoVacc) confers complete protection in non-human primates against SARS-CoV-2 strains circulating worldwide by eliciting potent humoral responses devoid of immunopathology
A calcium-based plasticity model predicts long-term potentiation and depression in the neocortex
Authors: Chindemi Giuseppe , Abdellah Marwan , Amsalem Oren , Benavides-Piccione Ruth , Delattre Vincent , Doron Michael , Ecker Andras , King James , Kumbhar Pramod , Monney Caitlin , Perin Rodrigo , Rössert Christian , Van Geit Werner , DeFelipe Javier , Graupner Michael , Segev Idan , Markram Henry , Muller Eilif
Published: April 2020

Long-term potentiation (LTP) and long-term depression (LTD) of pyramidal cell connections are among the key mechanisms underlying learning and memory in the brain. Despite their important role, only a few of these connections have been characterized in terms of LTP/LTD dynamics, such as the one between layer 5 thick-tufted pyramidal cells (L5-TTPCs). Comparing the available evidence on different pyramidal connection types reveals a large variability of experimental outcomes, possibly indicating the presence of connection-type-specific mechanisms. Here, we show that a calcium-based plasticity rule regulating L5-TTPC synapses holds also for several other pyramidal-to-pyramidal connections in a digital model of neocortical tissue. In particular, we show that synaptic physiology, cell morphology and innervation patterns jointly determine LTP/LTD dynamics without requiring a different model or parameter set for each connection type. We therefore propose that a similar set of plasticity mechanisms is shared by seemingly very different neocortical connections and that only a small number of targeted experiments is required for generating a complete map of synaptic plasticity dynamics in the neocortex.
The ΔF508 CFTR defect: molecular mechanism of suppressor mutation V510D and the contribution of transmembrane helix unraveling
Authors: Simon Kailene S. , Nagarajan Karthi , Mechin Ingrid , Duffy Caroline , Manavalan Partha , Altmann Steve , Majewski Aliza , Foley Joseph , Kaczmarek J. Stefan , Bercury Scott , Maderia Matthew , Hilbert Brendan , Batchelor Joseph D. , Ziegler Robin , Bajko Jeffrey , Kothe Michael , Scheule Ronald K. , Nair Anil , Hurlbut Gregory D.
Published: April 2020

Cystic fibrosis (CF) results from mutations within the gene encoding the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR), a transmembrane chloride channel found on the apical surface of epithelial cells. The most common CF-causing mutation results in a deletion of phenylalanine 508 (ΔF508-CFTR), a residue normally found within the NBD1 domain. Loss of F508 causes NBD1 to be less thermodynamically stable and prevents proper tertiary folding of CFTR. As a result, CFTR is not properly trafficked to the cell surface. Recently, progress has been made towards the development of small molecule “correctors” that can restore CFTR tertiary structure and stabilize the channel to overcome the instability inherent in ΔF508-CFTR. However, the resultant improvement in channel activity has been modest, and the need for potent correctors remains. To fully inform such efforts, a better understanding of the molecular pathology associated with ΔF508-CFTR is required. Here we present a comprehensive study of the impact of F508 deletion on both purified NBD1 and full-length CFTR. Through the use of homology modeling, molecular dynamics simulations, mutational analysis, biochemical, biophysical and functional characterization studies, we obtained insight into how the ΔF508 mutation may lead to helical unraveling of transmembrane domains 10 and 11 (TM10, TM11), and how the known suppressor mutations V510D and R1070W, as well as novel second site suppressor mutations (SSSMs) identified in this work, may act to rescue ΔF508-CFTR maturation and trafficking.
Complete characterization of the human immune cell transcriptome using accurate full-length cDNA sequencing
Authors: Cole Charles , Byrne Ashley , Adams Matthew , Volden Roger , Vollmers Christopher
Published: April 2020

The human immune system relies on highly complex and diverse transcripts and the proteins they encode. These include transcripts encoding human leukocyte antigen (HLA) receptors as well as B cell and T cell receptors (BCR and TCR). Determining which alleles an individual possesses for each HLA gene (high-resolution HLA typing) is essential to establish donor–recipient compatibility in organ and bone marrow transplantations. In turn, the repertoires of millions of unique BCR and TCR transcripts in each individual carry a vast amount of health-relevant information. Both short-read RNA-seq-based HLA typing and BCR/TCR repertoire sequencing (AIRR-seq) currently rely on our incomplete knowledge of the genetic diversity at HLA and BCR/TCR loci. Here, we generated over 10,000,000 full-length cDNA sequences at a median accuracy of 97.9% using our nanopore sequencing-based Rolling Circle Amplification to Concatemeric Consensus (R2C2) protocol. We used this data set to (1) show that deep and accurate full-length cDNA sequencing can be used to provide isoform-level transcriptome analysis for more than 9000 loci, (2) generate accurate sequences of HLA alleles, and (3) extract detailed AIRR data for the analysis of the adaptive immune system. The HLA and AIRR analysis approaches we introduce here are untargeted and therefore do not require prior knowledge of the composition or genetic diversity of HLA and BCR/TCR loci.
Elucidating salespeople's market orientation, proactive service behavior and organizational culture in the B2B banking sector: a Malaysian perspective
Authors: Hamzah Muhammad Iskandar , Othman Abdul Kadir , Hassan Faridah
Published: April 2020

Purpose

Considering that little is known on market orientation at the individual level, this study investigates the effects of individual market orientation on proactive service behavior, and subsequently, sales performance among business-to-business salespeople. Based on social cognitive theory and competing values framework, this paper also examines the interaction effects of organizational culture on the link between individual market orientation and proactive service behavior.

Design/methodology/approach

The study sampled 539 business-to-business salespeople from 18 corporate banks in Kuala Lumpur by using a questionnaire survey.

Findings

The results of the study show that adhocracy culture strengthens the effects of information acquisition on proactive service behavior, while at the same time weakens the impact of coordination of strategic response on the same outcome. Meanwhile, rational culture displayed negative contingent effects of information dissemination on proactive service behavior.

Practical implications

Given its link to sales performance and proactive service behavior, banks should motivate their employees to embrace market orientation as individual competencies. This research outcome will aid managers in developing strategies and inculcating the right culture to ensure the market-oriented behaviors are internalized and transpired into positive outcomes.

Originality/value

This paper contributes to the enrichment of the existing market orientation frameworks by offering underlying mechanisms (cultural environment and proactive service behavior) through which market-oriented behaviors contribute to the sales performance of business-to-business salespeople within the financial service industry. It is also among the earliest studies that examine the influence of individual market orientation and organizational culture on proactive service behavior.
Influence of failure factors on entrepreneurial resilience in Angolan micro, small and medium-sized enterprises
Authors: Franco Mário , Haase Heiko , António Dalne
Published: April 2020

Purpose

The purpose of this study is to analyse the influence of failure factors on entrepreneurial resilience in micro-, small- and medium-sized enterprises (MSMEs).

Design/methodology/approach

To achieve this goal, a quantitative and cross-sectional study was carried out. Using a snowball sampling technique, 133 Angolan MSMEs founders responded to a questionnaire.

Findings

The results indicate that entrepreneurs attribute the failure of their activities to financial and external environmental factors such as the economic crisis and changes in the country’s laws. However, these entrepreneurs are considered resilient, as they have enough capacity to resist the national market and have a strong sense of optimism.

Practical implications

Based on the empirical evidence, this study shows that the failure factors of the MSMEs studied have a significant influence on some of the dimensions of entrepreneurial resilience. At the practical level, the study can be also seen as a tool to support decision making in allocating resources to improve entrepreneurial resilience in developing economies.

Originality/value

This study contributes to the field of research on MSMEs in an innovative way, through triangulation of the factors of business failure and entrepreneurial resilience. Furthermore, it makes some contributions to developing the theory in entrepreneurship, which has been associated with various studies about business failure.
Calculation method for comprehensive damping of ball bearings based on multigrid method
Authors: Sun Peng , Chen Weifang , Shen Yusu , Wang Dan
Published: April 2020

Purpose

As an important part of the rotor system, the damping coefficient of ball bearing has a great influence on the dynamic characteristics of the system. This study aims to propose a theoretical calculation method and an experimental test method to obtain the damping coefficient of ball bearing.

Design/methodology/approach

Based on Hertzian contact theory and elastohydrodynamic lubrication theory, the point contact oil film damping analysis model of ball bearing is established. The comprehensive damping calculation method considering external radial load, centrifugal force, ball spin, rotational speed and lubricating oil film is derived. The multigrid method is used to obtain the oil film pressure and thickness distribution in the contact zone. The variation trend of comprehensive damping with bearing radial load, rotational speed, oil film thickness and viscosity is analyzed. The test platform is designed and the influencing factors of damping are tested.

Findings

The validity of the model and reliability of the test device are verified by comparing the good consistency obtained in the work. The results show that the comprehensive damping of ball bearing increases with the increase of radial load and decreases with the increase of rotational speed.

Originality/value

At present, the existing bearing damping model can achieve approximate calculation of damping, but the factors considered in these models are not comprehensive enough. Besides, few studies exist regarding test platform of bearing damping, and a perfect test plan has not yet been formed. In this paper, the comprehensive damping calculation model of ball bearing is improved, and a complete experimental scheme is proposed to provide reference for the comprehensive damping theory and experimental research of bearing.

Peer review

The peer review history for this article is available at: https://publons.com/publon/10.1108/ILT-08-2019-0342/
Investigation on fretting wear of Al-Li alloy
Authors: Xiao Teng , Wen Daosheng , Wang Shouren , Zhang Mingyuan , Kong Beibei , Yu Qiqi
Published: April 2020

Purpose

This paper aims to investigate the fretting wear mechanism of an Al-Li alloy at room temperature, the tangential fretting wear tests were carried out.

Design/methodology/approach

The effects of displacement amplitude and fretting frequency on the tangential fretting wear characteristics were mainly investigated. The experimental data obtained are analyzed and compared.

Findings

The results indicated that the fretting friction coefficient increased with the increase of displacement amplitude. As the displacement amplitude increased, the wear scar morphology changed significantly, mainly in terms of delamination debris and furrow scratches. The wear mechanism changed from initial mild wear to more severe oxidative wear, adhesive wear and abrasive wear.

Originality/value

This paper extends the knowledge into mechanical tight connections. The conclusions can provide theoretical guidance for the fretting of mechanical tight connections in the field of automotive lightweight and aerospace.

Peer review

The peer review history for this article is available at: https://publons.com/publon/10.1108/ILT-11-2019-0490/