bluuebunny/crossref_metadata_2025 huggingface dataset:
Probing the thermal state of the intergalactic medium at z > 5 with the transmission spikes in high-resolution  Ly α forest spectra
Authors: Gaikwad Prakash , Rauch Michael , Haehnelt Martin G , Puchwein Ewald , Bolton James S , Keating Laura C , Kulkarni Girish , Iršič Vid , Bañados Eduardo , Becker George D , Boera Elisa , Zahedy Fakhri S , Chen Hsiao-Wen , Carswell Robert F , Chardin Jonathan , Rorai Alberto
Published: March 2020

We compare a sample of five high-resolution, high S/N  Ly α forest spectra of bright 6 < z < ∼6.5 QSOs aimed at spectrally resolving the last remaining transmission spikes at z > 5 with those obtained from mock absorption spectra from the Sherwoodand Sherwood–Relics simulation suites of hydrodynamical simulations of the intergalactic medium (IGM). We use a profile-fitting procedure for the inverted transmitted flux, 1 − F, similar to the widely used Voigt profile fitting of the transmitted flux F at lower redshifts, to characterize the transmission spikes that probe predominately underdense regions of the IGM. We are able to reproduce the width and height distributions of the transmission spikes, both with optically thin simulations of the post-reionization Universe using a homogeneous UV background and full radiative transfer simulations of a late reionization model. We find that the width of the fitted components of the simulated transmission spikes is very sensitive to the instantaneous temperature of the reionized IGM. The internal structures of the spikes are more prominent in low temperature models of the IGM. The width distribution of the observed transmission spikes, which require high spectral resolution (≤ 8  km s−1) to be resolved, is reproduced for optically thin simulations with a temperature at mean density of T0 = (11 000 ± 1600, 10 500 ± 2100, 12 000 ± 2200) K at z = (5.4, 5.6, 5.8). This is weakly dependent on the slope of the temperature-density relation, which is favoured to be moderately steeper than isothermal. In the inhomogeneous, late reionization, full radiative transfer simulations where islands of neutral hydrogen persist to z ∼ 5.3, the width distribution of the observed transmission spikes is consistent with the range of T0 caused by spatial fluctuations in the temperature–density relation.
The accuracy of post-processed nucleosynthesis
Authors: Bravo Eduardo
Published: March 2020

The computational requirements posed by multi-dimensional simulations of type Ia supernovae make it difficult to incorporate complex nuclear networks to follow the release of nuclear energy along with the propagation of the flame. Instead, these codes usually model the flame and use simplified nuclear kinetics, with the goal of determining a sufficiently accurate rate of nuclear energy generation and, afterwards, post-processing the thermodynamic trajectories with a large nuclear network to obtain more reliable nuclear yields. In this work, I study the performance of simplified nuclear networks with respect to reproduction of the nuclear yields obtained with a one-dimensional supernova code equipped with a large nuclear network. I start by defining a strategy to follow the properties of matter in nuclear statistical equilibrium (NSE). I propose to use published tables of NSE properties, together with a careful interpolation routine. Short networks (iso7 and 13α) are able to give an accurate yield of 56Ni, after post-processing, but can fail by order of magnitude in predicting the ejected mass of even mildly abundant species (>10−3 M⊙). A network of 21 species reproduces the nucleosynthesis of the Chandrasekhar and sub-Chandrasekhar explosions studied here with average errors better than 20 per cent for the whole set of stable elements and isotopes followed in the models.
A parameter survey of Sgr A* radiative models from GRMHD simulations with self-consistent electron heating
Authors: Dexter J , Jiménez-Rosales A , Ressler S M , Tchekhovskoy A , Bauböck M , de Zeeuw P T , Eisenhauer F , von Fellenberg S , Gao F , Genzel R , Gillessen S , Habibi M , Ott T , Stadler J , Straub O , Widmann F
Published: March 2020

The Galactic centre black hole candidate Sgr A* is the best target for studies of low-luminosity accretion physics, including with near-infrared (NIR) and submillimetre wavelength long baseline interferometry experiments. Here, we compare images and spectra generated from a parameter survey of general relativistic MHD simulations to a set of radio to NIR observations of Sgr A*. Our models span the limits of weak and strong magnetization and use a range of sub-grid prescriptions for electron heating. We find two classes of scenarios can explain the broad shape of the submillimetre spectral peak and the highly variable NIR flaring emission. Weakly magnetized ‘disc-jet’ models where most of the emission is produced near the jet wall, consistent with past work, as well as strongly magnetized (magnetically arrested disc) models where hot electrons are present everywhere. Disc-jet models are strongly depolarized at submillimetre wavelengths as a result of strong Faraday rotation, inconsistent with observations of Sgr A*. We instead favour the strongly magnetized models, which provide a good description of the median and highly variable linear polarization signal. The same models can also explain the observed mean Faraday rotation measure and potentially the polarization signals seen recently in Sgr A* NIR flares.
Types of erythropoiesis-stimulating agents and risk of end-stage kidney disease and death in patients with non-dialysis chronic kidney disease
Authors: Minutolo Roberto , Garofalo Carlo , Chiodini Paolo , Aucella Filippo , Del Vecchio Lucia , Locatelli Francesco , Scaglione Francesco , De Nicola Luca
Published: March 2020

Background

Despite the widespread use of erythropoiesis-stimulating agents (ESAs) to treat anaemia, the risk of adverse outcomes associated with the use of different types of ESAs in non-dialysis chronic kidney disease (CKD) is poorly investigated.

Methods

From a pooled cohort of four observational studies, we selected CKD patients receiving short-acting (epoetin α/β; n = 299) or long-acting ESAs (darbepoetin and methoxy polyethylene glycol-epoetin β; n = 403). The primary composite endpoint was end-stage kidney disease (ESKD; dialysis or transplantation) or all-cause death. Multivariable Cox models were used to estimate the relative risk of the primary endpoint between short- and long-acting ESA users.

Results

During follow-up [median 3.6 years (interquartile range 2.1–6.3)], the primary endpoint was registered in 401 patients [166 (72%) in the short-acting ESA group and 235 (58%) in the long-acting ESA group]. In the highest tertile of short-acting ESA dose, the adjusted risk of primary endpoint was 2-fold higher {hazard ratio [HR] 2.07 [95% confidence interval (CI) 1.37–3.12]} than in the lowest tertile, whereas it did not change across tertiles of dose for long-acting ESA patients. Furthermore, the comparison of ESA type in each tertile of ESA dose disclosed a significant difference only in the highest tertile, where the risk of the primary endpoint was significantly higher in patients receiving short-acting ESAs [HR 1.56 (95% CI 1.09–2.24); P = 0.016]. Results were confirmed when ESA dose was analysed as continuous variable with a significant difference in the primary endpoint between short- and long-acting ESAs for doses >105 IU/kg/week.

Conclusions

Among non-dialysis CKD patients, the use of a short-acting ESA may be associated with an increased risk of ESKD or death versus long-acting ESAs when higher ESA doses are prescribed.
Task-Oriented Circuit Training for Mobility in Outpatient Stroke Rehabilitation in Germany and Austria: A Contextual Transferability Analysis
Authors: Diermayr Gudrun , Schomberg Maria , Greisberger Andrea , Elsner Bernhard , Gronwald Marit , Salbach Nancy M
Published: March 2020

People with stroke cite mobility deficits as one of the most burdensome limitations. National and international stroke guidelines recommend physical therapy based on task-oriented practice, with high numbers of repetitions to improve mobility. In the outpatient setting in Germany and Austria, these principles have not yet been established. The purpose of this study was to identify an evidence-based intervention that could help reduce this research-practice gap.

A stepwise approach proposed by Voigt-Radloff and colleagues and Cochrane Germany was used. First, the specific health service problem in the German and Austrian physical therapy outpatient context was identified. Second, a promising intervention was identified using a systematic search in the Cochrane Library and by grading the quality of the evidence using the Grading of Recommendations Assessment, Development and Evaluation. Finally, the transferability of the promising intervention into the local context was evaluated using predefined questions from the Cochrane guide and reports from health insurances, professional organizations, and national stroke guidelines.

Task-oriented circuit training reviewed by English and colleagues was chosen. The review showed clinically important improvements in walking distance and speed. The quality of the evidence was graded high for these 2 outcomes. We identified contextual challenges for implementation at the setting level (eg, insufficient reimbursement for group therapy by insurance companies), the participant and therapist level (eg, unknown motivation for group therapy due to the established 1:1 patient-therapist ratio), and the outcome measure level (eg, lack of standardized, cross-culturally translated manuals).

Although task-oriented circuit training is scientifically well established, barriers to implementation into routine care in Germany and Austria can be expected. In a next step, research using knowledge translation methodology will focus on the detailed evaluation of barriers and facilitators with relevant stakeholders.
World leaders’ usage of Twitter in response to the COVID-19 pandemic: a content analysis
Authors: Rufai Sohaib R , Bunce Catey
Published: March 2020

Background

It is crucial that world leaders mount effective public health measures in response to COVID-19. Twitter may represent a powerful tool to help achieve this. Here, we explore the role of Twitter as used by Group of Seven (G7) world leaders in response to COVID-19.

Methods

This was a qualitative study with content analysis. Inclusion criteria were as follows: viral tweets from G7 world leaders, attracting a minimum of 500 ‘likes’; keywords ‘COVID-19’ or ‘coronavirus’; search dates 17 November 2019 to 17 March 2020. We performed content analysis to categorize tweets into appropriate themes and analyzed associated Twitter data.

Results

Eight out of nine (88.9%) G7 world leaders had verified and active Twitter accounts, with a total following of 85.7 million users. Out of a total 203 viral tweets, 166 (82.8%) were classified as ‘Informative’, of which 48 (28.6%) had weblinks to government-based sources, while 19 (9.4%) were ‘Morale-boosting’ and 14 (6.9%) were ‘Political’. Numbers of followers and viral tweets were not strictly related.

Conclusions

Twitter may represent a powerful tool for world leaders to rapidly communicate public health information with citizens. We would urge general caution when using Twitter for health information, with a preference for tweets containing official government-based information sources.
Speculators and Middlemen: The Strategy and Performance of Investors in the Housing Market
Authors: Bayer Patrick , Geissler Christopher , Mangum Kyle , Roberts James W
Published: March 2020

Using data from the Los Angeles area from 1988 to 2012, we study the behavior and sources of returns of individual investors in the housing market. We document the existence of two distinct investor types. The first act as middlemen, purchasing substantially below and reselling above market prices throughout the cycle, improving liquidity and the existing capital stock in the process. The second act as speculators, who primarily enter during the boom, buying and selling at essentially market prices. Neither type anticipated the housing bust. We document similar behavior by speculators and middlemen in 96 other U.S. metro areas.
Neural mechanisms of self-affirmation’s stress buffering effects
Authors: Dutcher Janine M , Eisenberger Naomi I , Woo Hayoung , Klein William M P , Harris Peter R , Levine John M , Creswell John David
Published: March 2020

Self-affirmation can buffer stress responses across different contexts, yet the neural mechanisms for these effects are unknown. Self-affirmation has been shown to increase activity in reward-related neural regions, including the ventral striatum and ventromedial prefrontal cortex (VMPFC). Given that reward-related prefrontal cortical regions such as the VMPFC are involved in reducing neurobiological and behavioral responses to stress, we hypothesized that self-affirmation would activate VMPFC and also reduce neural responses to stress in key neural threat system regions such as the dorsal anterior cingulate cortex (dACC) and anterior insula (AI). We explored this hypothesis using self-affirmation and evaluative stress tasks following a within-subjects design in the fMRI scanner. Consistent with prior work, self-affirmation blocks led to lower self-reported stress and improved performance. With respect to neural activity, compared to control blocks, self-affirmation blocks led to greater VMPFC activity, and subsequently less left AI (but not dACC) activity during stress task blocks. Functional connectivity analyses revealed greater connectivity between the VMPFC and left and right AI during self-affirmation compared to control. These findings begin to articulate the neural circuits involved in self-affirmation’s effects during exposure to stressors, and more broadly specify neural reward-based responses to stressful situations.
Robust prediction of individual personality from brain functional connectome
Authors: Cai Huanhuan , Zhu Jiajia , Yu Yongqiang
Published: March 2020

Neuroimaging studies have linked inter-individual variability in the brain to individualized personality traits. However, only one or several aspects of personality have been effectively predicted based on brain imaging features. The objective of this study was to construct a reliable prediction model of personality in a large sample by using connectome-based predictive modeling (CPM), a recently developed machine learning approach. High-quality resting-state functional magnetic resonance imaging data of 810 healthy young participants from the Human Connectome Project dataset were used to construct large-scale brain networks. Personality traits of the five-factor model (FFM) were assessed by the NEO Five Factor Inventory. We found that CPM successfully and reliably predicted all the FFM personality factors (agreeableness, openness, conscientiousness and neuroticism) other than extraversion in novel individuals. At the neural level, we found that the personality-associated functional networks mainly included brain regions within default mode, frontoparietal executive control, visual and cerebellar systems. Although different feature selection thresholds and parcellation strategies did not significantly influence the prediction results, some findings lost significance after controlling for confounds including age, gender, intelligence and head motion. Our finding of robust personality prediction from an individual’s unique functional connectome may help advance the translation of ‘brain connectivity fingerprinting’ into real-world personality psychological settings.
Simulation and social behavior: an fMRI study of neural processing during simulation in individuals with and without risk for psychosis
Authors: Lincoln Sarah Hope , Germine Laura T , Mair Patrick , Hooker Christine I
Published: March 2020

Social dysfunction is a risk indicator for schizophrenia spectrum disorders, with at-risk individuals demonstrating a range of social behavior impairments. Variability in social ability may be explained by individual differences in the psychological processes of social behavior. In particular, mental simulation, the process by which an individual generates an internal representation of the thoughts or feelings of another, may explain variation in social behavior. This study investigates the neural process of simulation in healthy individuals and individuals at risk for psychosis. Using a novel fMRI pain paradigm, individuals watch videos of another person’s hand or foot experiencing pain. After each video, individuals are asked to simulate the observed painful situation on their own hand or foot. Neural activity during simulation in the somatosensory cortex was associated with real-world self-reported social behavior, such that a stronger neural response in the somatosensory cortex was associated with greater rates of positive social experiences and affective empathy across all participants. These findings suggest that the neural mechanisms that underlie simulation are important for social behavior, and may explain individual variability in social functioning in healthy and at-risk populations.
Hepatitis B cure: modeling the economics of a potential cost of a cure
Authors: Toy Mehlika , So Samuel , Hutton David W.
Published: March 2020

Purpose of review

The cure for hepatitis C virus infection has raised hope for a potential hepatitis B virus (HBV) cure, but the high price tag has led to serious questions about the affordability, and thus to access for all. This review discusses cost-effectiveness models, affordability, and access to a potential new cure for chronic HBV infection.

Recent findings

A cure does not yet exist for HBV, but the antiviral treatments that are currently available help slow down the progression of disease. There is limited research in the area of cost-effectiveness and economic analysis comparing a potential cure. Our preliminary findings from modeling and economic threshold analysis show that cure could be potentially cost-effective or cost-saving. Governments can possibly use the results of economic models for price negotiations.

The highest burden of the HBV infection is in low and middle-income countries. Given that the cost of current treatment has dropped dramatically in recent years as the first line treatments have come off patent, the price for a HBV cure needs to be reasonable and affordable to all people.
A Venous Mesenteric Ischemia Revealing a Protein C Deficiency
Authors: Abdel-Nacer Nefis , Jaoued Oussamma , Rejeb Manel Ben , Hassen Mohamed Fekih
Published: March 2020

In this case, we reported a 9-year-old girl who presented with a superior mesenteric venous thrombosis secondary to Protein C deficiency. This condition of venous thrombosis secondary to Protein C deficiency is rare. Symptoms are not specific and may include vomiting, nausea, and abdominal pain. The article describes the case of a familial disorder. Treatment included anticoagulation to prevent further thrombotic events and a resection of the necrotic bowel segment.
Long-term Change in the Speech Perception Ability in Pediatric Cochlear Implants and the Effect of the Age at Implantation
Authors: Kwak Min Young , Lee Jee Yeon , Kim Yehree , Seo Ji Won , Lee Je Yeon , Kang Woo Seok , Ahn Joong Ho , Chung Jong Woo , Park Hong Ju
Published: March 2020

Objective:

We analyzed the long-term changes in speech perception ability of pediatric cochlear implants (CIs) to evaluate the effect of the age at the time of surgery.

Study Design:

Retrospective.

Setting:

Tertiary care academic center.

Patients:

One hundred fourteen prelingually deaf children with CI use duration >10 years.

Main Outcome Measures:

Categories of auditory performance (CAP) scores and monosyllabic word recognition scores using the Asan-Samsung Korean word list (ASK-WRS) and a conventional word list (KS-WRS) were the main outcomes. Outcomes were compared according to the age at surgery (group I, 1–2 yr; II, 2.1–3 yr; III, 3.1–7 yr; IV, 7.1–13 yr).

Results:

CAP scores reached plateaus at 2.6 to 3.3 years post-CI; groups I to III showed better scores than group IV. The maximum CAP score was obtained in all children of groups I to III and in 65% of group IV. ASK-WRSs reached plateaus at 3.2 to 4.8 years post-CI. Younger patients at CI operation showed better ASK-WRSs (97, 93, 90, and 54% in groups I–IV, respectively), but the differences were not significant (I versus II and II versus III). Ceiling effect (perfect score) was observed in early groups (67, 44, 30, and 0% in groups I–IV). KS-WRSs, which is a challenging test, reached plateaus at 7.2 to 8.4 years postsurgery with no ceiling effect. Early implantees showed significantly better scores (88, 82, 73, and 46% in groups I–IV).

Conclusions:

Speech perception ability after CI showed audiological age-specific improvement evaluated by various test methods. The most challenging test demonstrated long-term performance differences by the age at CI operation.
Narcissism and Quality of Life
Authors: Ellison William D. , Acuff M. Chase , Kealy David , Joyce Anthony S. , Ogrodniczuk John S.
Published: March 2020

Pathological narcissism is associated with decreased quality of life, even when accounting for psychiatric comorbidity, but the processes behind this association are unclear. Here, we evaluate whether disturbed relatedness accounts for the negative association between narcissistic pathology and quality of life. Patients in day hospital treatment for personality pathology (N = 218, 70% female; mean age, 37.3 years) completed measures of personality disorder features, quality of life, and global symptoms before beginning treatment. Quality of object relations was assessed through semistructured interviews. Regression-based mediation analyses showed that narcissistic personality traits relate to quality of life through quality of object relations, controlling for other personality disorders and psychiatric distress. These results highlight the importance of problematic relationship patterns for the low quality of life associated with pathological narcissism. Clinicians working with narcissistic individuals should consider psychotherapies that promote mature relatedness and should attend to facilitating the quality of patients' relationships.
Chest X-ray Sizing for Lung Transplants Reflects Pulmonary Diagnosis and Body Composition and Is Associated With Primary Graft Dysfunction Risk
Authors: Li David , Weinkauf Justin , Hirji Alim , Nagendran Jayan , Kapasi Ali , Lien Dale , Halloran Kieran
Published: March 2020

Background.

Donor-recipient oversizing based on predicted total lung capacity (pTLC) is associated with a reduced risk of primary graft dysfunction (PGD) following lung transplant but the effect varies with the recipient’s diagnosis. Chest x-ray (CXR) measurements to estimate actual total lung capacity (TLC) could account for disease-related lung volume changes, but their role in size matching is unknown.

Methods.

We reviewed adult double lung transplant recipients 2007–2016 and measured apex-to-costophrenic-angle distance (=lung height) on pretransplant donor and recipient CXRs (oversized donor-recipient ratio >1; undersized ≤1]. We tested the relationship between recipient lung height to actual TLC; between lung height ratio and donor/recipient characteristics; and between both lung height ratio or pTLC ratio and grade 3 PGD with logistic regression.

Results.

Two hundred six patients were included and 32 (16%) developed grade 3 PGD at 48 or 72 hours. Recipient lung height was related to TLC (r
2=0.7297). Pulmonary diagnosis, donor BMI, and recipient BMI were the major determinants of lung height ratio (AUC 0.9036). Lung height ratio oversizing was associated with increased risk of grade 3 PGD (odds ratio, 2.51; 95% confidence interval, 1.17-5.47; P = 0.0182) in this cohort, while pTLC ratio oversizing was not.

Conclusions.

CXR lung height estimates actual TLC and reflects pulmonary diagnosis and body composition. Oversizing via CXR lung height ratio increased PGD risk moreso than pTLC-based oversizing in our cohort.
The role of oxygen transport in atherosclerosis and vascular disease
Authors: Tarbell John , Mahmoud Marwa , Corti Andrea , Cardoso Luis , Caro Colin
Published: March 2020

Atherosclerosis and vascular disease of larger arteries are often associated with hypoxia within the layers of the vascular wall. In this review, we begin with a brief overview of the molecular changes in vascular cells associated with hypoxia and then emphasize the transport mechanisms that bring oxygen to cells within the vascular wall. We focus on fluid mechanical factors that control oxygen transport from lumenal blood flow to the intima and inner media layers of the artery, and solid mechanical factors that influence oxygen transport to the adventitia and outer media via the wall's microvascular system—the vasa vasorum (VV). Many cardiovascular risk factors are associated with VV compression that reduces VV perfusion and oxygenation. Dysfunctional VV neovascularization in response to hypoxia contributes to plaque inflammation and growth. Disturbed blood flow in vascular bifurcations and curvatures leads to reduced oxygen transport from blood to the inner layers of the wall and contributes to the development of atherosclerotic plaques in these regions. Recent studies have shown that hypoxia-inducible factor-1α (HIF-1α), a critical transcription factor associated with hypoxia, is also activated in disturbed flow by a mechanism that is independent of hypoxia. A final section of the review emphasizes hypoxia in vascular stenting that is used to enlarge vessels occluded by plaques. Stenting can compress the VV leading to hypoxia and associated intimal hyperplasia. To enhance oxygen transport during stenting, new stent designs with helical centrelines have been developed to increase blood phase oxygen transport rates and reduce intimal hyperplasia. Further study of the mechanisms controlling hypoxia in the artery wall may contribute to the development of therapeutic strategies for vascular diseases.
Lysinimonas yzui sp. nov., isolated from cattail root soil from mine tailings
Authors: Mei Lijuan , Piao Zhe , Hu Jian , Shi Linlin , Bai Yanchao , Yin Shixue
Published: March 2020

A yellow-pigmented, Gram-stain-negative, aerobic, non-motile rod shaped, mesophilic bacterium, designated strain N7XX-4T, was isolated from cattail root grown on the mine tailings of Phoenix mountain, Tongling city, Anhui Province (PR China). Analysis of the 16S rRNA gene sequence revealed that the strain represented a novel member of the family

Microbacteriaceae

. The nearest phylogenetic neighbour was

Lysinimonas kribbensis

MSL-13T (97.8 % 16S rRNA gene sequence similarity). The most abundant fatty acid in whole cells of N7XX-4T was anteiso-C15 : 0 (29.9 %). The predominant menaquinones were MK-12(H2), MK-13(H2) and MK-11(H2). The peptidoglycan type of the isolate was B1δ with l-Lys as the diagnostic cell-wall diamino acid. On the basis of differences in phenotypic and genotypic characteristics, strain N7XX-4T (=CGMCC 1.16548T=DSM 106791T=JCM 32630T) is designated as the type strain of a novel species of the genus

Lysinimonas

, for which the name Lysinimonas yzui sp. nov. is proposed.
Streptomyces lasalocidi sp. nov. (formerly ‘Streptomyces lasaliensis’), an actinomycete isolated from soil which produces the polyether antibiotic lasalocid
Authors: Erwin Gary S. , Heikkinen Jouni , Halimaa Pauliina , Haber Christopher L.
Published: March 2020

Strain ATCC 31180T was isolated from soil collected in Hyde Park, Massachusetts (USA), and found to produce the polyether antibiotic lasalocid. The name ‘Streptomyces lasaliensis’ has been in common use since 1974, without a recognized taxonomic description. The most closely related type cultures determined by rRNA gene sequence similarity were

Streptomyces longwoodensis

DSM 41677T (100 %) and

Streptomyces galbus

DSM 40089T (100 %). OrthoANI values with

S. longwoodensis

and

S. galbus

were 95.50 and 94.41 %, respectively. Chemotaxonomic characteristics supported inclusion within the genus

Streptomyces

. The cell wall peptidoglycan contained ll-diaminopimelic acid, and the major whole-cell sugars were glucose and ribose. Polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, phosphatidylglycerol, one unidentified lipid and one unidentified glycolipid. The major menaquinones detected were MK9(H4), MK9(H6) and MK9(H8). The major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0, iso-C15 : 0 and anteiso-C17 : 1. Its DNA had a G+C content of 72.6 %. Differentiation of ATCC 31180T from the closely related species was evident from digital DNA–DNA hybridization values of 61.80 and 56.90 % for

S. longwoodensis

and

S. galbus

respectively. Significant differences were seen in the polyphasic phenotypic analyses. ATCC 31180T produced lasalocid, grew from 10 to 45 °C, pH4-8 and in the presence of 0–10 % NaCl, 0.01 % NaN3 and 1 % phenol. Melanin was produced; H2S and indole were not. Nitrate was not reduced. Spore chains were retinaculum-apertum and spore surfaces were smooth. Spore colour, mycelia colour and soluble pigment production were medium-dependent. The proposed name is Streptomyces lasalocidi sp. nov.; the type strain being ATCC 31180T (=NRRL 3382T=DSM 46487T).
General Model for COVID-19 Spreading with Consideration of Intercity Migration, Insufficient Testing and Active Intervention: Application to Study of Pandemic Progression in Japan and USA
Authors: Zhan Choujun , Tse Chi K. , Lai Zhikang , Chen Xiaoyun , Mo Mingshen
Published: March 2020

A new Susceptible-Exposed-Infected-Confirmed-Removed (SEICR) model with consideration of intercity travel and active intervention is proposed for predicting the spreading progression of the 2019 New Coronavirus Disease (COVID-19). The model takes into account the known or reported number of infected cases being fewer than the actual number of infected individuals due to insufficient testing. The model integrates intercity travel data to track the movement of exposed and infected individuals among cities, and allows different levels of active intervention to be considered so that realistic prediction of the number of infected individuals can be performed. The data of the COVID-19 infection cases and the intercity travel data for Japan (January 15 to March 20, 2020) and the USA (February 20 to March 20, 2020) are used to illustrate the prediction of the pandemic progression in 47 regions of Japan and 50 states (plus a federal district) in the USA. By fitting the model with the data, we reveal that, as of March 19, 2020, the number of infected individuals in Japan and the USA could be twenty-fold and five-fold as many as the number of confirmed cases, respectively. Moreover, the model generates future progression profiles for different levels of intervention by setting the parameters relative to the values found from the data fitting. Results show that without tightening the implementation of active intervention, Japan and the USA will see about 6.55% and 18.2% of the population eventually infected, and with drastic ten-fold elevated active intervention, the number of people eventually infected can be reduced by up to 95% in Japan and 70% in the USA. Finally, an assessment of the relative effectiveness of active intervention and personal protective measures is discussed. With a highly vigilant public maintaining personal hygiene and exercising strict protective measures, the percentage of population infected can be further reduced to 0.23% in Japan and 2.7% in the USA.
Online narrative guides for illuminating tissue atlas data and digital pathology images
Authors: Rashid Rumana , Chen Yu-An , Hoffer John , Muhlich Jeremy L. , Lin Jia-Ren , Krueger Robert , Pfister Hanspeter , Mitchell Richard , Santagata Sandro , Sorger Peter K.
Published: March 2020

The recent development of highly multiplexed tissue imaging promises to substantially accelerate research into basic biology and human disease. Concurrently, histopathology in a clinical setting is undergoing a rapid transition to digital methods. Online tissue atlases involving highly multiplexed images of research and clinical specimens will soon join genomics as a systematic source of information on the molecular basis of disease and therapeutic response. However, even with recent advances in machine learning, experience with anatomic pathology shows that there is no immediate substitute for expert visual review, annotation, and description of tissue images. In this perspective we review the ecosystem of software available for analysis of tissue images and identify a need for interactive guides or “digital docents” that allow experts to help make complex images intelligible. We illustrate this idea usingMinervasoftware and discuss how interactive image guides are being integrated into multi-omic browsers for effective dissemination of atlas data.
A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage
Authors: Deng Xianding , Gu Wei , Federman Scot , Plessis Louis du , Pybus Oliver G. , Faria Nuno , Wang Candace , Yu Guixia , Pan Chao-Yang , Guevara Hugo , Sotomayor-Gonzalez Alicia , Zorn Kelsey , Gopez Allan , Servellita Venice , Hsu Elaine , Miller Steve , Bedford Trevor , Greninger Alexander L. , Roychoudhury Pavitra , Starita Lea M. , Famulare Michael , Chu Helen Y. , Shendure Jay , Jerome Keith R. , Anderson Catie , Gangavarapu Karthik , Zeller Mark , Spencer Emily , Andersen Kristian G. , MacCannell Duncan , Paden Clinton R. , Li Yan , Zhang Jing , Tong Suxiang , Armstrong Gregory , Morrow Scott , Willis Matthew , Matyas Bela T. , Mase Sundari , Kasirye Olivia , Park Maggie , Chan Curtis , Yu Alexander T. , Chai Shua J. , Villarino Elsa , Bonin Brandon , Wadford Debra A. , Chiu Charles Y.
Published: March 2020

The COVID-19 pandemic caused by the novel coronavirus SARS-CoV-2 has spread globally, resulting in >300,000 reported cases worldwide as of March 21st, 2020. Here we investigate the genetic diversity and genomic epidemiology of SARS-CoV-2 in Northern California using samples from returning travelers, cruise ship passengers, and cases of community transmission with unclear infection sources. Virus genomes were sampled from 29 patients diagnosed with COVID-19 infection from Feb 3rd through Mar 15th. Phylogenetic analyses revealed at least 8 different SARS-CoV-2 lineages, suggesting multiple independent introductions of the virus into the state. Virus genomes from passengers on two consecutive excursions of the Grand Princess cruise ship clustered with those from an established epidemic in Washington State, including the WA1 genome representing the first reported case in the United States on January 19th. We also detected evidence for presumptive transmission of SARS-CoV-2 lineages from one community to another. These findings suggest that cryptic transmission of SARS-CoV-2 in Northern California to date is characterized by multiple transmission chains that originate via distinct introductions from international and interstate travel, rather than widespread community transmission of a single predominant lineage. Rapid testing and contact tracing, social distancing, and travel restrictions are measures that will help to slow SARS-CoV-2 spread in California and other regions of the USA.
Predicting the evolution and control of COVID-19 pandemic in Portugal
Authors: Pais Ricardo J. , Taveira Nuno
Published: March 2020

The Coronavirus (COVID-19) is a world pandemic that has been affecting Portugal since 2 of March 2020. Portuguese government has been making efforts to contradict the exponential growth through social isolation measures. We have developed a mathematical model to predict the impact of such measures in the number of infected cases and peak of infection. We estimate the peak to be around 2 million infected cases by the beginning of May if no additional measures are taken. The model shows that current measures effectively isolated 25-30% of the population, contributing for some reduction on the infection peak. Importantly, our simulations show that the infection burden can be further reduced with higher isolation degree, providing information for a second intervention.
SCHNEL: Scalable clustering of high dimensional single-cell data
Authors: Abdelaal Tamim , de Raadt Paul , Lelieveldt Boudewijn P.F. , Reinders Marcel J.T. , Mahfouz Ahmed
Published: March 2020

Motivation

Single cell data measures multiple cellular markers at the single-cell level for thousands to millions of cells. Identification of distinct cell populations is a key step for further biological understanding, usually performed by clustering this data. Dimensionality reduction based clustering tools are either not scalable to large datasets containing millions of cells, or not fully automated requiring an initial manual estimation of the number of clusters. Graph clustering tools provide automated and reliable clustering for single cell data, but suffer heavily from scalability to large datasets.

Results

We developed SCHNEL, a scalable, reliable and automated clustering tool for high-dimensional single-cell data. SCHNEL transforms large high-dimensional data to a hierarchy of datasets containing subsets of data points following the original data manifold. The novel approach of SCHNEL combines this hierarchical representation of the data with graph clustering, making graph clustering scalable to millions of cells. Using seven different cytometry datasets, SCHNEL outperformed three popular clustering tools for cytometry data, and was able to produce meaningful clustering results for datasets of 3.5 and 17.2 million cells within workable timeframes. In addition, we show that SCHNEL is a general clustering tool by applying it to single-cell RNA sequencing data, as well as a popular machine learning benchmark dataset MNIST.

Availability and Implementation

Implementation is available on GitHub (https://github.com/paulderaadt/HSNE-clustering)

Contact

a.mahfouz@lumc.nl

Supplementary information

Supplementary data are available atBioinformaticsonline.
Retromer forms low order oligomers on supported lipid bilayers
Authors: Deatherage Catherine L. , Nikolaus Joerg , Karatekin Erdem , Burd Christopher G.
Published: March 2020

Retromer is a protein sorting device that orchestrates the selection and export of integral membrane proteins from the endosome via retrograde and plasma membrane recycling pathways. Long standing hypotheses regarding the Retromer sorting mechanism posit that oligomeric interactions between Retromer and associated accessory factors on the endosome membrane drives clustering of Retromer-bound integral membrane cargo prior to its packaging into a nascent transport carrier. To test this hypothesis, we examined interactions between the components of the SNX3-Retromer sorting pathway using quantitative single particle fluorescence microscopy of a reconstituted system comprising a supported bilayer, Retromer, a model cargo protein, the accessory proteins SNX3, RAB7, and the Retromer-binding segment of the WASHC2C subunit of the WASH complex. The predominant species of membrane associated Retromer are low order: monomers (∼18%), dimers (∼35%), trimers (∼24%) and tetramers (∼24%). Unexpectedly, neither cargo nor accessory factors promote Retromer oligomerization on a supported bilayer. The results indicate that Retromer has an intrinsic propensity to form low order oligomers and that neither membrane association nor accessory factors potentiate oligomerization. Hence, Retromer is a minimally concentrative sorting device adapted to bulk membrane trafficking from the endosomal system.
Oil India Limited – overcoming the challenges in competency planning
Authors: Kumar Abhishek , Jaisinghani Dinesh , Tiwari Shailesh
Published: March 2020

Learning outcomes

The case highlights the initiatives that can be taken by the management of a large organization to bring more objectivity in promotion policies and to make the process of succession management more scientific. After completing the case, the following teaching objectives should be achieved. Students should be able to comprehend the industrial structure and the key challenges faced by oil and gas industry in an emerging economy – India; students should understand how a large organization can bring objectivity and transparency in its promotion policy by focussing on merit; students can analyse the challenges faced by a large organization in implementing changes in its promotion policy; and students should be able to understand the mechanism of alignment of assessment centres with the promotion policy.

Case overview/synopsis

The case deals with bringing change in the competency planning in a large organization. The focus of the case is to explain how a large organization can bring about a radical change in promotion policy especially for employees at the senior positions. The key issue highlighted in the case relates to building competency and linking rewards with merit. The case also highlights the kind of resistance by the stakeholders while enforcing the changes in the organization.

Complexity academic level

MBA and other similar programmes at the post-graduation level.

Supplementary materials

Teaching Notes are available for educators only.

Subject code

CSS 6: Human resource management.
Credit access, tax structure and the performance of Malaysian manufacturing SMEs
Authors: Cheong Calvin W.H. , Lee Miin Huui , Weissmann Marc Arul
Published: March 2020

Purpose

This study investigates the effects of credit access and tax structures on the performance of Manufacturing SMEs in Malaysia.

Design/methodology/approach

This study uses the dynamic panel system generalized method of moments, controlling for firm-specific as well as macroeconomic effects

Findings

The paper finds that (1) debt funding is not conducive to SME performance; (2) access to non-bank credit sources and tax incentives support SME performance by lowering opportunity costs of riskier projects; (3) existing tax structures in Malaysia inhibit SME growth and encourage manipulation of accounts; and (4) investors in Malaysia prefer SMEs that are more conservative in their accounting and taxation practices.

Research limitations/implications

Access to Malaysian SME data is restricted. Although robust methods are used, there is a chance that different conclusions may arise with a much larger sample.

Practical implications

The findings provide clear direction in the discussion and enactment of new policies that support SME growth especially in support of non-bank credit sources instead of revising tax policies. The paper also contributes by providing guidance to future SME studies that are inhibited by limited access to data.

Originality/value

SME-related studies on credit access and tax structures have often relied on traditional metrics (e.g. total amount of bank loans; tax expenses) to measure its impact on entrepreneurial/SME performance. Although relevant to the past, financial policies have evolved to embrace Industrial Revolution 4.0. This paper is a shift from the traditional by investigating the impact of new and innovative sources of funding such as incubators and crowdfunding. Also, since one cannot exist without the other, examining the joint impact of credit access and tax structures provides a more holistic view on policy-making, something prior studies have not addressed.
Motor carrier spot market: trust-building in public e-marketplaces
Authors: Collignon Stephane , Cook Deborah F. , Li Yuhong
Published: March 2020

Purpose

This research aims at understanding the routes public e-marketplaces take, in the motor carrier spot market, to generate trust among participants.

Design/methodology/approach

This work borrows cue signaling theory and an e-marketplace content analysis instrument from information systems literature. Our primary data captures differences in usage of a broad spectrum of cues between motor carrier spot e-marketplaces and a control sample.

Findings

Transportation e-marketplaces use graphical cues more frequently than the control sample, display these cues on their “operational path” (where users click to conduct transactions) and try to generate beliefs in participants' integrity and competence.

Research limitations/implications

The motor carrier online spot market constitutes a relevant test bed for trust-related theories. Several levels of trust-building conceptualizations are tested; the cue level shows the most potential. This paper extends cue signaling theory in the transportation e-marketplace context and calls for further work on operational path cues to enrich swift trust theories.

Practical implications

This study helps e-marketplace designers by identifying essential and facultative cues for the motor carrier spot market.

Originality/value

Research on public spot e-marketplaces in the motor carrier context is scant. The context is described in detail to show its specificities in structures and behaviors. This helps to contribute to both practice and research. By evolving an existing research instrument from information systems literature, this study ensures replicability (problematic in academic research) .
Fandom, forgiveness and future support: YouTube apologies as crisis communication
Authors: Kelso Sandlin Jean , Gracyalny Monica L.
Published: March 2020

Purpose

This study examined how audience characteristics and attitudes relate to their perceptions of sincerity and forgiveness of apologies by public figures posted on YouTube.

Design/methodology/approach

Four hundred twenty-seven adult participants recruited through Amazon's Mechanical Turk completed an online survey via Qualtrics. Participants were randomly assigned to view two of four public figure apologies posted on YouTube.

Findings

Results indicated that audience fandom and perceived reputation and attractiveness of the public figure were related to perceptions of sincerity and forgiveness; and perceptions of sincerity and forgiveness were related to intentions of future support.

Research limitations/implications

“Sameness” between the public figure and audience did not garner a more favorable response to the apology, and this is not consistent with earlier studies. For race similarity, the results could have been a reflection of the low number of non-White participants. However, results could indicate that “sameness” is not as simplistic as demographic sameness, such as race, sex or age.

Practical implications

The authors’ findings elevate the importance of gathering and benchmarking pre-crisis attitudinal research to better equip and inform communication professionals for crisis response. In addition, the study suggests that a public figure's strong reputation and fanbase provide a type of inoculation, lessening reputational damage.

Social implications

The finding that perceived attractiveness relates positively to perceptions of sincerity and forgiveness is consistent with psychological research indicating attractiveness has many positive social implications – even in mediated communication.

Originality/value

Evidence suggests social media apologies matter. Communication professionals need to approach apology opportunities with a keen awareness that relational outcomes and intentions of future support can shift based on social media audiences' attitudes related to the public figure.