bluuebunny/crossref_metadata_2025 huggingface dataset:
A case of recurrent takotsubo-like cardiomyopathy associated with pheochromocytoma exhibiting different patterns of left ventricular wall motion abnormality and coronary vasospasm: a case report
Authors: Sato Koichi , Takahashi Jun , Amano Keiko , Shimokawa Hiroaki
Published: May 2020

Background

Takotsubo-like cardiomyopathy associated with pheochromocytoma (Pheo-TTS) is a recognized but uncommon disorder. While Pheo-TTS might more often recur and the pattern of left ventricular (LV) wall motion abnormality is more diverse compared with primary TTS, it remains to be elucidated whether coronary functional abnormalities are also involved.

Case summary

A 50-year-old woman was referred with a chief complaint of transient chest pain, dyspnoea, and paroxysmal thyroid swelling that usually developed after meals. In the past, she had been admitted to emergency rooms three times due to pulmonary oedema following the above attacks. Serial cardiac catheterizations showed normal coronary arteries and morphologically different types of LV dysfunction each time; apical LV ballooning at the first, basal LV ballooning at the second, and diffuse LV hypokinesis at the last admission. Acetylcholine (ACh) provocation testing for coronary vasospasm was negative at the second admission. During hospitalization in our department, abdominal ultrasonography for screening detected a right adrenal mass and the urinary normetanephrine level was increased. The adrenal tumour was urgently removed surgically and finally she was diagnosed as having norepinephrine-secreting pheochromocytoma. Acetylcholine testing was again performed just after the operation, showing both epicardial and microvascular coronary spasms. Since the operation, she has been free of symptoms. Importantly, ACh testing at 1-year follow-up showed that epicardial spasm was no longer noted, whereas coronary microvascular spasm persisted.

Discussion

Adrenal pheochromocytoma could cause recurrent attacks of catecholamine surges with different patterns of LV dysfunction, where coronary vasospasm may also be involved along the coronary arteries.
The Human Right to Science and Its Relationship to International Environmental Law
Authors: Hubert Anna-Maria
Published: May 2020

This article explores the potential contribution of international human rights law – specifically, the oft-neglected ‘right to science’ – to the interpretation, operation and progressive development of international environmental law. Science and its applications play a critical role in environmental protection. At the same time, society faces persistent controversies at this interface. Environmental regimes may lack sufficient norms and tools for regulating upstream science and innovation processes because they tend to focus narrowly on physical harms to the environment and may not address the wider ethical, legal, social and political concerns. The human right to science, which is codified in various international and regional human rights instruments, may serve to augment international environmental law and contribute to more effective, equitable and democratically legitimate and accountable processes and outcomes in relation to the application of science and technology in environmental regimes. The article begins by outlining the scope and contents of, as well as the limitations on, the right to science, focusing on Article 15(1)(b) of the International Covenant on Economic, Social and Cultural Rights (ICESCR) and its overlaps with the norms of international environmental law.1 It then analyses the ways in which the right to science may influence the development of international environmental law by elucidating mechanisms for the integration of a human rights perspective in science and technology and by outlining its potential substantive contributions to the development of international environmental law.
Timing of intervention in asymptomatic patients with valvular heart disease
Authors: Baumgartner Helmut , Iung Bernard , Otto Catherine M
Published: May 2020

Current management of valvular heart disease (VHD) seeks to optimize long-term outcome by timely intervention. Recommendations for treatment of patients with symptoms due to severe valvular disease are based on a foundation of solid evidence. However, when to intervene in asymptomatic patients remains controversial and decision requires careful individual weighing of the potential benefits against the risk of intervention and its long-term consequences. The primary rationale for earlier intervention is prevention of irreversible left ventricular (LV) myocardial changes that might result in later clinical symptoms and adverse cardiac events. A number of outcome predictors have been identified that facilitate decision-making. This review summarizes current recommendations and discusses recently published data that challenge them suggesting even earlier intervention. In adults with asymptomatic aortic stenosis (AS), emerging risk markers include very severe valve obstruction, elevated serum natriuretic peptide levels, and imaging evidence of myocardial fibrosis or increased extracellular myocardial volume. Currently, transcatheter aortic valve implantation (TAVI) is not recommended for treatment of asymptomatic severe AS although this may change in the future. In patients with aortic regurgitation (AR), the potential benefit of early intervention in preventing LV dilation and dysfunction must be balanced against the long-term risk of a prosthetic valve, a particular concern because severe AR often occurs in younger patients with a congenital bicuspid valve. In patients with mitral stenosis, the option of transcatheter mitral balloon valvotomy tilts the balance towards earlier intervention to prevent atrial fibrillation, embolic events, and pulmonary hypertension. When chronic severe mitral regurgitation is due to mitral valve prolapse, anatomic features consistent with a high likelihood of a successful and durable valve repair favour early intervention. The optimal timing of intervention in adults with VHD is a constantly changing threshold that depends not only on the severity of valve disease but also on the safety, efficacy, and long-term durability of our treatment options.
Orthologous Divergence and Paralogous Anticonvergence in Molecular Evolution of Triplicated Green Opsin Genes in Medaka Fish, Genus Oryzias
Authors: Matsumoto Yoshifumi , Oda Shoji , Mitani Hiroshi , Kawamura Shoji
Published: May 2020

Gene duplication of green (RH2) opsin genes and their spectral differentiation are well documented in many teleost fish. However, their evolutionary divergence or conservation patterns among phylogenetically close but ecologically diverse species is not well explored. Medaka fish (genus Oryzias) are broadly distributed in fresh and brackish waters of Asia, with many species being laboratory-housed and feasible for genetic studies. We previously showed that a Japan strain (HNI) of medaka (Oryzias latipes) possessed three RH2 opsin genes (RH2-A, RH2-B, and RH2-C) encoding spectrally divergent photopigments. Here, we examined the three RH2 opsin genes from six Oryzias species representing three species groups: the latipes, the celebensis, and the javanicus. Photopigment reconstitution revealed that the peak absorption spectra (λmax) of RH2-A were divergent among the species (447–469 nm), whereas those of RH2-B and RH2-C were conservative (516–519 and 486–493 nm, respectively). For the RH2-A opsins, the largest spectral shift was detected in the phylogenetic branch leading to the latipes group. A single amino acid replacement T94C explained most of the spectral shift. For RH2-B and -C opsins, we detected tracts of gene conversion between the two genes homogenizing them. Nevertheless, several amino acid differences were maintained. We showed that the spectral difference between the two opsins was attributed to largely the E/Q amino acid difference at the site 122 and to several sites with individually small spectral effects. These results depict dynamism of spectral divergence of orthologous and paralogous green opsin genes in phylogenetically close but ecologically diverse species exemplified by medaka.
A Systematic Review of Frailty Trajectories: Their Shape and Influencing Factors
Authors: Welstead Miles , Jenkins Natalie D , Russ Tom C , Luciano Michelle , Muniz-Terrera Graciela
Published: May 2020

Background and Objectives

Frailty describes an increased vulnerability to adverse events such as disease or injury. Combating this state remains a major challenge for geriatric research. By exploring how and why frailty changes throughout later life we will be better positioned to improve ways of identifying and treating those at high risk.

Research Design and Methods

We systematically reviewed publications that captured rate of frailty progression over time and established any associated risk or protective factors that affected this progression. We included longitudinal observational studies which quantified frailty trajectories in adults aged 50+ using any validated continuous frailty measurement tool.

Results

After screening 8,318 publications, 25 met our criteria. Findings show that despite a great degree of heterogeneity in the literature, progression of frailty is unquestionably affected by numerous risk and protective factors, with particular influence exhibited by social demographics, brain pathology, and physical comorbidities.

Discussion and Implications

Findings that the gradient of frailty progression is affected by various influencing factors are valuable to clinicians and policymakers as they will help identify those at highest frailty risk and inform prevention strategies. However, the heterogeneous methodological approaches of the publications included in this review highlight the need for consensus within the field to promote more coordinated research. Improved consistency of methods will enable further data synthesis and facilitate a greater understanding of the shape of frailty over time and the influencing factors contributing to change, the results of which could have crucial implications for frailty risk reduction.
TinderMIX: Time-dose integrated modelling of toxicogenomics data
Authors: Serra Angela , Fratello Michele , del Giudice Giusy , Saarimäki Laura Aliisa , Paci Michelangelo , Federico Antonio , Greco Dario
Published: May 2020

Background

Omics technologies have been widely applied in toxicology studies to investigate the effects of different substances on exposed biological systems. A classical toxicogenomic study consists in testing the effects of a compound at different dose levels and different time points. The main challenge consists in identifying the gene alteration patterns that are correlated to doses and time points. The majority of existing methods for toxicogenomics data analysis allow the study of the molecular alteration after the exposure (or treatment) at each time point individually. However, this kind of analysis cannot identify dynamic (time-dependent) events of dose responsiveness.

Results

We propose TinderMIX, an approach that simultaneously models the effects of time and dose on the transcriptome to investigate the course of molecular alterations exerted in response to the exposure. Starting from gene log fold-change, TinderMIX fits different integrated time and dose models to each gene, selects the optimal one, and computes its time and dose effect map; then a user-selected threshold is applied to identify the responsive area on each map and verify whether the gene shows a dynamic (time-dependent) and dose-dependent response; eventually, responsive genes are labelled according to the integrated time and dose point of departure.

Conclusions

To showcase the TinderMIX method, we analysed 2 drugs from the Open TG-GATEs dataset, namely, cyclosporin A and thioacetamide. We first identified the dynamic dose-dependent mechanism of action of each drug and compared them. Our analysis highlights that different time- and dose-integrated point of departure recapitulates the toxicity potential of the compounds as well as their dynamic dose-dependent mechanism of action.
Bacterial Mucosa-associated Microbiome in Inflamed and Proximal Noninflamed Ileum of Patients With Crohn’s Disease
Authors: Olaisen Maya , Flatberg Arnar , Granlund Atle van Beelen , Røyset Elin Synnøve , Martinsen Tom Christian , Sandvik Arne Kristian , Fossmark Reidar
Published: May 2020

Background

Microbiota is most likely essential in the pathogenesis of Crohn’s disease (CD). Fecal diversion after ileocecal resection (ICR) protects against CD recurrence, whereas infusion of fecal content triggers inflammation. After ICR, the majority of patients experience endoscopic recurrence in the neoterminal ileum, and the ileal microbiome is of particular interest. We have assessed the mucosa-associated microbiome in the inflamed and noninflamed ileum in patients with CD.

Methods

Mucosa-associated microbiome was assessed by 16S rRNA sequencing of biopsies sampled 5 and 15 cm orally of the ileocecal valve or ileocolic anastomosis.

Results

Fifty-one CD patients and forty healthy controls (HCs) were included in the study. Twenty CD patients had terminal ileitis, with endoscopic inflammation at 5 cm, normal mucosa at 15 cm, and no history of upper CD involvement. Crohn’s disease patients (n = 51) had lower alpha diversity and separated clearly from HC on beta diversity plots. Twenty-three bacterial taxa were differentially represented in CD patients vs HC; among these, Tyzzerella 4 was profoundly overrepresented in CD. The microbiome in the inflamed and proximal noninflamed ileal mucosa did not differ according to alpha diversity or beta diversity. Additionally, no bacterial taxa were differentially represented.

Conclusions

The microbiome is similar in the inflamed and proximal noninflamed ileal mucosa within the same patients. Our results support the concept of CD-specific microbiota alterations and demonstrate that neither ileal sublocation nor endoscopic inflammation influence the mucosa-associated microbiome.
Dynamic Distribution and Postmortem Redistribution of Tramadol in Poisoned Rats
Authors: Su Hongliang , Li Yongjun , Wu Miaomiao , Sun Tingting , Niu Weifen , Jia Juan , Wei Zhiwen , Yun Keming
Published: May 2020

In the past dozen years, the cases of tramadol intoxication have become frequent in many countries. Most previous studies focused on tramadol’s pharmacology, such as pharmacokinetics, pharmacodynamics and pharmacogenetics. However, the dynamic distribution and postmortem redistribution (PMR) of tramadol remain unclear. Our study aimed to investigate these two issues systematically in various specimens of 216 poisoned male rats. A validated gas chromatography–mass spectrometry method was used in this study to measure the concentrations of tramadol. In the first part, 66 tramadol poisoned rats were sacrificed at 11 different time points and their organs were collected separately for the study of tramadol’s dynamic distribution, which made it feasible to investigate its PMR later on. The results of this part showed that tramadol’s concentrations varied according to the organ and time, and peaked 2 h after intragastric administration in the specimens of liver, kidney, spleen, lung, brain and heart-blood (except stomach and heart). Based on the results of the first part, the concentration of tramadol peaked 2 h in most tissues. Therefore, this time point was used for the study of tramadol’s PMR. In the second part, the remaining 150 rats were sacrificed 2 h after intragastric administration of tramadol, and the carcasses were stored under three different conditions (−20, 4 and 20°C). The autopsy was carried out at eight different time points and their organs were collected separately. The results of this part showed that under storage temperatures of −20 and 4°C, the concentrations of tramadol in individual organs showed no significant changes at different time points whereas under a storage temperature of 20°C, the concentrations in certain organs (liver, kidney, spleen, lung, brain and heart-blood) increased significantly at the last few time points. PMR of tramadol was therefore confirmed. The process of PMR of tramadol could be slowed or stopped at lower storage temperatures (−20 or 4°C), which is significant in cases of suspected tramadol poisoning.
Dynamic localization of αB-crystallin at the microtubule cytoskeleton network in beating heart cells
Authors: Ohto-Fujita Eri , Hayasaki Saaya , Atomi Aya , Fujiki Soichiro , Watanabe Toshiyuki , Boelens Wilbert C , Shimizu Miho , Atomi Yoriko
Published: May 2020

αB-crystallin is highly expressed in the heart and slow skeletal muscle; however, the roles of αB-crystallin in the muscle are obscure. Previously, we showed that αB-crystallin localizes at the sarcomere Z-bands, corresponding to the focal adhesions of cultured cells. In myoblast cells, αB-crystallin completely colocalizes with microtubules and maintains cell shape and adhesion. In this study, we show that in beating cardiomyocytes α-tubulin and αB-crystallin colocalize at the I- and Z-bands of the myocardium, where it may function as a molecular chaperone for tubulin/microtubules. Fluorescence recovery after photobleaching (FRAP) analysis revealed that the striated patterns of GFP-αB-crystallin fluorescence recovered quickly at 37°C. FRAP mobility assay also showed αB-crystallin to be associated with nocodazole-treated free tubulin dimers but not with taxol-treated microtubules. The interaction of αB-crystallin and free tubulin was further confirmed by immunoprecipitation and microtubule sedimentation assay in the presence of 1–100 μM calcium, which destabilizes microtubules. Förster resonance energy transfer analysis showed that αB-crystallin and tubulin were at 1–10 nm apart from each other in the presence of colchicine. These results suggested that αB-crystallin may play an essential role in microtubule dynamics by maintaining free tubulin in striated muscles, such as the soleus or cardiac muscles.
Clinical Utility of Buccal Swabs for Severe Acute Respiratory Syndrome Coronavirus 2 Detection in Coronavirus Disease 2019–Infected Children
Authors: Kam Kai-qian , Yung Chee Fu , Maiwald Matthias , Chong Chia Yin , Soong Han Yang , Loo Liat Hui , Tan Natalie Woon Hui , Li Jiahui , Nadua Karen Donceras , Thoon Koh Cheng
Published: May 2020

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was detected from at least 1 buccal specimen in 9 of 11 coronavirus disease 2019 (COVID-19)–infected children (81.8%). Viral loads in buccal specimens were substantially lower than those in nasopharyngeal specimens. Buccal swabs are not good as COVID-19 screening specimens in children.
Oxford Nanopore sequencing: new opportunities for plant genomics?
Authors: Dumschott Kathryn , Schmidt Maximilian H-W , Chawla Harmeet Singh , Snowdon Rod , Usadel Björn
Published: May 2020

DNA sequencing was dominated by Sanger’s chain termination method until the mid-2000s, when it was progressively supplanted by new sequencing technologies that can generate much larger quantities of data in a shorter time. At the forefront of these developments, long-read sequencing technologies (third-generation sequencing) can produce reads that are several kilobases in length. This greatly improves the accuracy of genome assemblies by spanning the highly repetitive segments that cause difficulty for second-generation short-read technologies. Third-generation sequencing is especially appealing for plant genomes, which can be extremely large with long stretches of highly repetitive DNA. Until recently, the low basecalling accuracy of third-generation technologies meant that accurate genome assembly required expensive, high-coverage sequencing followed by computational analysis to correct for errors. However, today’s long-read technologies are more accurate and less expensive, making them the method of choice for the assembly of complex genomes. Oxford Nanopore Technologies (ONT), a third-generation platform for the sequencing of native DNA strands, is particularly suitable for the generation of high-quality assemblies of highly repetitive plant genomes. Here we discuss the benefits of ONT, especially for the plant science community, and describe the issues that remain to be addressed when using ONT for plant genome sequencing.
Dental Calculus as a Tool to Study the Evolution of the Mammalian Oral Microbiome
Authors: Brealey Jaelle C , Leitão Henrique G , van der Valk Tom , Xu Wenbo , Bougiouri Katia , Dalén Love , Guschanski Katerina
Published: May 2020

Dental calculus, the calcified form of the mammalian oral microbial plaque biofilm, is a rich source of oral microbiome, host, and dietary biomolecules and is well preserved in museum and archaeological specimens. Despite its wide presence in mammals, to date, dental calculus has primarily been used to study primate microbiome evolution. We establish dental calculus as a valuable tool for the study of nonhuman host microbiome evolution, by using shotgun metagenomics to characterize the taxonomic and functional composition of the oral microbiome in species as diverse as gorillas, bears, and reindeer. We detect oral pathogens in individuals with evidence of oral disease, assemble near-complete bacterial genomes from historical specimens, characterize antibiotic resistance genes, reconstruct components of the host diet, and recover host genetic profiles. Our work demonstrates that metagenomic analyses of dental calculus can be performed on a diverse range of mammalian species, which will allow the study of oral microbiome and pathogen evolution from a comparative perspective. As dental calculus is readily preserved through time, it can also facilitate the quantification of the impact of anthropogenic changes on wildlife and the environment.
Benchmarking of long-read correction methods
Authors: Dohm Juliane C , Peters Philipp , Stralis-Pavese Nancy , Himmelbauer Heinz
Published: May 2020

Third-generation sequencing technologies provided by Pacific Biosciences and Oxford Nanopore Technologies generate read lengths in the scale of kilobasepairs. However, these reads display high error rates, and correction steps are necessary to realize their great potential in genomics and transcriptomics. Here, we compare properties of PacBio and Nanopore data and assess correction methods by Canu, MARVEL and proovread in various combinations. We found total error rates of around 13% in the raw datasets. PacBio reads showed a high rate of insertions (around 8%) whereas Nanopore reads showed similar rates for substitutions, insertions and deletions of around 4% each. In data from both technologies the errors were uniformly distributed along reads apart from noisy 5′ ends, and homopolymers appeared among the most over-represented kmers relative to a reference. Consensus correction using read overlaps reduced error rates to about 1% when using Canu or MARVEL after patching. The lowest error rate in Nanopore data (0.45%) was achieved by applying proovread on MARVEL-patched data including Illumina short-reads, and the lowest error rate in PacBio data (0.42%) was the result of Canu correction with minimap2 alignment after patching. Our study provides valuable insights and benchmarks regarding long-read data and correction methods.
Characteristics of Nontuberculous Mycobacterial Infections at a Midwestern Tertiary Hospital: A Retrospective Study of 365 Patients
Authors: Hannah Claire E , Ford Bradley A , Chung Jina , Ince Dilek , Wanat Karolyn A
Published: May 2020

Background

The prevalence of infections due to nontuberculous mycobacteria (NTM) is increasing worldwide, yet little is known about the epidemiology and pathophysiology of these ubiquitous environmental organisms. Pulmonary disease due to Mycobacterium avium complex is most prevalent, but many other NTM species can cause disease in virtually any organ system. As NTM becomes an increasingly common cause of morbidity and mortality, more information is needed about the epidemiology of NTM disease.

Methods

We conducted a retrospective chart review of all patients with cultures that grew NTM at a Midwestern tertiary hospital from 1996 to 2017. Information on demographics, medical history, clinical findings, treatment, and outcome was obtained from medical records of all NTM isolates. American Thoracic Society/Infectious Diseases Society of America criteria were used to define pulmonary NTM infections.

Results

We identified 1064 NTM isolates, 365 of which met criteria for NTM infection. Pulmonary cases predominated (185 of 365; 50.7%), followed by skin/soft tissue (56 of 365; 15.3%), disseminated (40 of 365; 11%), and lymphatic (28 of 365; 7.7%) disease. Mycobacterium avium complex was the most common species (184 of 365; 50.4%). Individuals aged >50 years were most affected (207 of 365; 56.7%). Common comorbidities included structural lung disease (116 of 365; 31.8%), use of immunosuppressive medications (78 of 365; 21.4%), malignancy (59 of 365; 16.2%), and human immunodeficiency virus (42 of 365; 11.5%).

Conclusions

This large cohort provides information on the demographics, risk factors, and disease course of patients with pulmonary and extrapulmonary NTM infections. Most patients had medical comorbidities that resulted in anatomic, genetic, or immunologic risk factors for NTM infection. Further population-based studies and increased disease surveillance are warranted to further characterize NTM infection prevalence and trends.
The IGNITE Trial: Participant Recruitment Lessons Prior to SARS-CoV-2
Authors: Vidoni Eric D. , Szabo-Reed Amanda , Kang Chaeryon , Perales-Puchalt Jaime , Shaw Ashley R. , Grove George , Hamill Morgan , Henry Donovan , Burns Jeffrey M. , Hillman Charles , Kramer Arthur F. , McAuley Edward , Erickson Kirk I.
Published: May 2020

Full and diverse participant enrollment is critical to the success and generalizability of all large-scale Phase III trials. Recruitment of sufficient participants is among the most significant challenges for many studies. The novel SARS-CoV-2 coronavirus pandemic has further changed and challenged the landscape for clinical trial execution, including screening and randomization. The Investigating Gains in Neurocognition in an Intervention Trial of Exercise (IGNITE) study has been designed as the most comprehensive test of aerobic exercise effects on cognition and brain health. Here we assess recruitment into IGNITE prior to the increased infection rates in the United States, and examine new challenges and opportunities for recruitment with a goal of informing the remaining required recruitment as infection containment procedures are lifted. The results may assist the design and implementation of recruitment for future exercise studies, and outline opportunities for study design that are flexible in the face of emerging threats.
Model-based prediction of spatial gene expression via generative linear mapping
Authors: Okochi Yasushi , Sakaguchi Shunta , Nakae Ken , Kondo Takefumi , Naoki Honda
Published: May 2020

Decoding spatial transcriptomes from single-cell RNA sequencing (scRNA-seq) data has become a fundamental technique for understanding multicellular systems; however, existing computational methods lack both accuracy and biological interpretability due to their model-free frameworks. Here, we introduced Perler, a model-based method to integrate scRNA-seq data with referencein situhybridization (ISH) data. To calibrate differences between these datasets, we developed a biologically interpretable model that uses generative linear mapping based on a Gaussian-mixture model using the Expectation-Maximization algorithm. Perler accurately predicted the spatial gene expression ofDrosophilaembryos, zebrafish embryos, mammalian liver, and mouse visual cortex from scRNA-seq data. Furthermore, the reconstructed transcriptomes did not over-fit the ISH data and preserved the timing information of the scRNA-seq data. These results demonstrated the generalizability of Perler for dataset integration, thereby providing a biologically interpretable framework for accurate reconstruction of spatial transcriptomes in any multicellular system.
Avoiding COVID-19: Aerosol Guidelines
Authors: Evans Matthew J.
Published: May 2020

Abstract

The COVID-19 pandemic has brought into sharp focus the need to understand respiratory virus transmission mechanisms. In preparation for an anticipated influenza pandemic, a substantial body of literature has developed over the last few decades showing that the short-range aerosol route is an important, though often neglected transmission path. We develop a simple mathematical model for COVID-19 transmission via aerosols, apply it to known outbreaks, and present quantitative guidelines for ventilation and occupancy in the workplace.
Flattening the COVID 19 curve in susceptible forest indigenous tribes using SIR model
Authors: Adwibowo Andrio
Published: May 2020

COVID 19 is a global threat and globally spreading. The international cooperation involving indigenous peoples and local communities is urgently required in joint prevention to control the epidemic. Currently, many indigenous populations are continuing to face COVID 19. This study is concerned about the dynamic of COVID 19 pandemic among indigenous populations living in the remote Amazon rainforest enclaves. Using the Susceptible Infectious Recovered (SIR) model, the spread of the COVID 19 under 3 intervention scenarios (low, moderate, high) is simulated and predicted in indigenous tribe populations. The SIR model forecasts that without intervention, the epidemic peak may reach within 1020 days. Nonetheless the peak can be reduced with strict interventions. Under low intervention, the COVID 19 cases are reduced to 73% and 56% of the total populations. While, in the scenario of high intervention, the COVID 19 peaks can be reduced to values ranging from 53% to 15%. To conclude, the simulated interventions tested by SIR model have reduced the pandemic peak and flattened the COVID 19 curve in indigenous populations. Nonetheless, it is mandatory to strengthen all mitigation efforts, reduce exposures, and decrease transmission rate as possible for COVID 19 containment.
Effects of Government Mandated Social Distancing Measures on Cumulative Incidence of COVID-19 in the United States and its Most Populated Cities
Authors: Krishnamachari Bhuma , Morris Alexander , Zastrow Diane , Dsida Andrew , Harper Brian , Santella Anthony J.
Published: May 2020

COVID-19, caused by the SARS-CoV-2 virus, has quickly spread throughout the world, necessitating assessment of the most effective containment methods. Very little research exists on the effects of social distancing measures on this pandemic. The purpose of this study was to examine the effects of government implemented social distancing measures on the cumulative incidence rates of COVID-19 in the United States on a state level, and in the 25 most populated cities, while adjusting for socio-demographic risk factors. The social distancing variables assessed in this study were: days to closing of non-essential business; days to stay home orders; days to restrictions on gathering, days to restaurant closings and days to school closing. Using negative binomial regression, adjusted rate ratios and 95% confidence intervals were calculated comparing two levels of a binary variable: “above median value,” and “median value and below” for days to implementing a social distancing measure. For city level data, the effects of these social distancing variables were also assessed in high (above median value) vs low (median value and below) population density cities. For the state level analysis, days to school closing was associated with cumulative incidence, with an adjusted rate ratio of 1.59 (95% CI:1.03,2.44), p=0.04 at 35 days. Some results were counterintuitive, including inverse associations between cumulative incidence and days to closure of non-essential business and restrictions on gatherings. This finding is likely due to reverse causality, where locations with slower growth rates initially chose not to implement measures, and later implemented measures when they absolutely needed to respond to increasing rates of infection. Effects of social distancing measures seemed to vary by population density in cities. Our results suggest that the effect of social distancing measures may differ between states and cities and between locations with different population densities. States and cities need individual approaches to containment of an epidemic, with an awareness of their own structure in terms of crowding and socio-economic variables. In an effort to reduce infection rates, cities may want to implement social distancing in advance of state mandates.
Rate Estimation and Identification of COVID-19 Infections: Towards Rational Policy Making During Early and Late Stages of Epidemics
Authors: Beigel Richard , Kasif Simon
Published: May 2020

Pandemics have a profound impact on our world, causing loss of life, affecting our culture and historically shaping our genetics. The response to a pandemic requires both resilience and imagination. It has been clearly documented that obtaining an accurate estimate and trends of the actual infection rate and mortality risk are very important for policy makers and medical professionals. One cannot estimate mortality rates without an accurate assessment of the number of infected individuals in the population. This need is also aligned with identifying the infected individuals so they can be properly treated, monitored and tracked. However, accurate estimation of the infection rate, locally, geographically and nationally is important independently. These infection rate estimates can guide policy makers at both state, national or world level to achieve a better management of risk to society. The decisions facing policy makers are very different during early stages of an emerging epidemic where the infection rate is low, middle stages where the rate is rapidly climbing, and later stages where the epidemic curve has flattened to a low and relatively sustainable rate. In this paper we provide relatively efficient pooling methods to both estimate infection rates and identify infected individuals for populations with low infection rates. These estimates may provide significant cost reductions for testing in rural communities, third world countries and other situations where the cost of testing is expensive or testing is not widely available. As we prepare for the second wave of the pandemic this line of work may provide new solutions for both the biomedical community and policy makers at all levels.
An intriguing characteristic of enhancer-promoter interactions
Authors: Talukder Amlan , Hu Haiyan , Li Xiaoman
Published: May 2020

It is still challenging to predict interacting enhancer-promoter pairs (IEPs), partially because of our limited understanding of their characteristics. To understand IEPs better, here we studied the IEPs in nine cell lines and nine primary cell types. We observed that one enhancer is likely to interact with either none or all of the target genes of another enhancer. This observation implies that enhancers form clusters, and every enhancer in the same cluster synchronously interact with almost every member of a set of genes and only this set of genes. We perceived that an enhancer can be up to two mega base pairs away from other enhancers in the same cluster. We also noticed that although a fraction of these clusters of enhancers do overlap with super-enhancers, the majority of the enhancer clusters are different from the known super-enhancers. Our study showed a new characteristic of IEPs, which may shed new light on distal gene regulation and the identification of IEPs.
Coupling between slow-waves and sharp-wave ripples organizes distributed neural activity during sleep in humans
Authors: Skelin Ivan , Zhang Haoxin , Zheng Jie , Ma Shiting , Mander Bryce A. , Mcmanus Olivia Kim , Vadera Sumeet , Knight Robert T. , McNaughton Bruce L. , Lin Jack J.
Published: May 2020

Hippocampal-dependent memory consolidation during sleep is hypothesized to depend on the synchronization of distributed neuronal ensembles, organized by the hippocampal sharp-wave ripples (SWRs, 80-150 Hz) and subcortical/cortical slow-waves (0.5-4 Hz). However, the precise role of SWR-slow-wave interactions in synchronizing subcortical/cortical neuronal activity is unclear. Here, we leverage intracranial electrophysiological recordings from the human hippocampus, amygdala, temporal and frontal cortices, to examine activity modulation and cross-regional coordination during SWRs. Hippocampal SWRs are associated with widespread modulation of high frequency activity (HFA; 70-200 Hz) a measure of local neuronal activation. This peri-SWR HFA modulation is predicted by the coupling between hippocampal SWRs and local subcortical/cortical slow-waves. Finally, local cortical slow-wave phase offsets during SWRs predicted functional connectivity between the frontal and temporal cortex. These findings suggest a selection mechanism wherein hippocampal SWR and cortical slow-wave synchronization governs the transient engagement of distributed neuronal populations supporting hippocampal-dependent memory consolidation.
Joint (Ad)ventures—Family firms' international entry mode choices for emerging markets
Authors: Loehde Ann Sophie K. , Calabrò Andrea , Torchia Mariateresa , Kraus Sascha
Published: May 2020

Purpose

The aim of this study is to advance knowledge on family firms' entry mode choices by examining the linkage between target market context, especially in the emerging economies of China and India, and the dominant family firm logic of keeping ownership and control in the family.

Design/methodology/approach

We use an exploratory multiple case study analysis approach based on nine German family firms' internationalization endeavors. We use both primary and secondary data.

Findings

Traditionally, extant research concludes that family principals prefer foreign direct investments (FDIs) in order to exert maximum control when entering international markets. In contrast, our study finds a clear preference for international joint ventures (IJVs) as an initial entry mode of choice into unfamiliar markets. Our findings propose this decision to be rooted in cultural unfamiliarity and the complexity of the target markets' legal environment. The effect of these two factors is amplified by prior IJVs experiences.

Originality/value

This article offers several original insights. First, we identify the triggers of the paradoxical IJVs’ entry mode choice among family firms and thus explain the motivation for breaking with the dominant family firm logic of maximizing control. Second, we account for factors in China's and India's particular emerging market environments. In the light of family control, the unfamiliarity with these markets triggers the decision to compensate for the high level of uncertainty by engaging in an IJV partnership. Third, our study shows that family firms are indeed willing to share control if it serves the long-term survival of the firm.
Maintenance downtime evaluation in a process bottling plant
Authors: Inyiama Gerald Kenechukwu , Oke Sunday Ayoola
Published: May 2020

Purpose

Downtime is a process parameter that substantially impacts on the operating hours and results in production losses, thus motivating maintenance engineers to control process plants. Notwithstanding, the impacting nature of process equipment failure on the operating hours in bottling plants remains inadequately examined. In this paper, the cause-and-effect analysis was used to establish the root cause of the downtime problem and Pareto analysis employed to justify the greatest opportunities for improvement in reducing downtime and increasing reliability levels. Weibull analysis is then conducted on the industrial setting. Novel aspect ratios are proposed.

Design/methodology/approach

Using the Weibull failure function of machines as a principal facilitator to produce failure predictions, the downtime behaviour of a process plant was modelled and tested with practical data from a bottling process plant. This research was conducted in a Nigerian process bottling plant where historical data were examined.

Findings

The analysis of the results shows the following principal outcome: First, the machines with the highest and least downtime values are 2 and 5, respectively, with correspondingly mean values of 22.83 and 4.39 h monthly. Second, the total downtime 92.05 and 142.14 h for the observed and target downtime, with a coefficient of determination of 0.5848 was recorded. Third, as month 1 was taken as the base period (target), all the machines, except M5 had accepted performance, indicating proper preventive maintenance plan execution for the bottling process plant. Availability shows a direct relationship between the failure and uptime of the machines and the downtime impacts on production. Two machines had random failure pattern and five machines exhibited a wear-out failure pattern and probably due to old age and wear of components in the machines.

Originality/value

The major contribution of the paper is the Weibull modelling in a unique application to a bottling plant to avoid current practices that use reliability software that is not easily accessible.
Longevity, body dimension and reproductive mode drive differences in aquatic versus terrestrial life‐history strategies
Authors: Capdevila Pol , Beger Maria , Blomberg Simone P. , Hereu Bernat , Linares Cristina , Salguero‐Gómez Roberto
Published: May 2020

Aquatic and terrestrial environments display stark differences in key environmental factors and phylogenetic composition but their consequences for the evolution of species' life‐history strategies remain poorly understood.

Here, we examine whether and how life‐history strategies vary between terrestrial and aquatic species. We use demographic information for 685 terrestrial and 122 aquatic animal and plant species to estimate key life‐history traits. We then use phylogenetically corrected least squares regression to explore potential differences in trade‐offs between life‐history traits between both environments. We contrast life‐history strategies of aquatic versus terrestrial species in a principal component analysis while accounting for body dimensions and phylogenetic relationships.

Our results show that the same trade‐offs structure terrestrial and aquatic life histories, resulting in two dominant axes of variation that describe species' pace of life and reproductive strategies. Terrestrial plants display a large diversity of strategies, including the longest‐lived species in this study. Aquatic animals exhibit higher reproductive frequency than terrestrial animals. When correcting for body size, mobile and sessile terrestrial organisms show slower paces of life than aquatic ones.

Aquatic and terrestrial species are ruled by the same life‐history trade‐offs, but have evolved different strategies, likely due to distinct environmental selective pressures. Such contrasting life‐history strategies have important consequences for the conservation and management of aquatic and terrestrial species.

A free Plain Language Summary can be found within the Supporting Information of this article.
Benedicto Kiwanuka and Catholic Democracy in Uganda
Authors: Carney J. J.
Published: May 2020

In this article, I introduce Benedicto Kiwanuka (1922–72), Uganda’s first prime minister and most prominent modern Catholic politician, and explore how his religious and political sensibilities — especially his vision of democracy — intersected with Catholic thought and historical experience in Buganda and Uganda. Far from turning him into a “Catholic tribalist” looking to empower Catholics vis à vis other religious groups, Kiwanuka’s Catholic identity was a core component of his political commitment to non‐sectarian democracy, the common good, and pan‐ethnic nation‐building. He saw in Catholicism the possibility of envisioning political solidarity during a moment of social rupture, and he and his Democratic Party used Catholic and biblical discourse and theology to help undergird a broader political commitment to liberal democratic nationalism during Uganda’s transition to independence (1958–62). At the same time, Kiwanuka’s prophetic commitment to principle — an uncompromising dogmatism often expressed in religious and theological language — also helped cost him the opportunity to lead Uganda into and beyond independence.
An improved recombinase polymerase amplification assay for visual detection of Vibrio parahaemolyticus with lateral flow strips
Authors: Yang Xiaohan , Zhao Panpan , Dong Yu , Shen Xin , Shen Hui , Li Juan , Jiang Ge , Wang Weiling , Dai Hong , Dong Jingquan , Gao Song , Si Xinxin
Published: May 2020

Vibrio parahaemolyticus is an important pathogenic bacterium in both food safety management and mariculture. Rapid and accurate detection technologies are critical for effective control of its outbreak and spreading. Conventional technologies and polymerase chain reaction (PCR)‐based approaches have limited usage because of the requirement of laboratory instruments and trained personnel. Using the isothermal recombinase polymerase amplification (RPA) technology, several detection assays have been developed with added convenience. Combining the lateral flow strip (LFS) test with RPA can further simplify the detection. In this study, an improved RPA assay using LFS for visual detection of V. parahaemolyticus was developed. Primers were designed targeting the virulence genes and screened for amplification efficiency, nonspecific amplification, and primer–dimer formation. Probes were designed for the best primer pairs, and the weakness of LFS tests, being easily affected by primer‐dependent artifacts, was overcome by sequence modifications on primers and probe. The RPA–LFS assay took 25 min at 35 to 45 °C, and showed excellent specificity. It detected as low as one colony forming unit (CFU) of V. parahaemolyticus per reaction without DNA purification, or 10 CFU/10 g spiked food samples with 2 hr of enrichment. The detection limit was better than the currently available RPA‐based detection methods. Application of the RPA–LFS assay for simulated samples or real clinical samples showed accurate and consistent detection results compared to bioassay and quantitative PCR. The RPA–LFS assay provided a rapid, accurate, and convenient V. parahaemolyticus detection method suitable for on‐site detection in resource‐limited conditions.

Practical Application

This research developed a rapid and visual detection technology for Vibrio parahaemolyticus that is not dependent on complicated equipment. The detection process takes 25 min and the result is read with the naked eye. A detection kit can be developed based on this technology for on‐site detection of V. parahaemolyticus in resource‐limited regions for food safety management and mariculture.
Effect on the ensilage performance and microbial community of adding Neolamarckia cadamba leaves to corn stalks
Authors: Wang Yi , Zhou Wei , Wang Cheng , Yang Fuyu , Chen Xiaoyang , Zhang Qing
Published: May 2020

To comprehensively evaluate the fermentation performance and microbial community of corn stalks (CS) silage mixed with Neolamarckia cadamba leaves (NCL), CS were ensiled with four levels (0%, 10%, 30% and 50% of fresh weight) of NCL for 1, 7, 14, 30, 60 days in two trials. The results showed that all silages were well preserved with low pH (3.60–3.88) and ammonia nitrogen content (0.08–0.19% DM). The silage samples with NCL displayed lower (P < 0.05) acetic acid, propionic acid and ammonia nitrogen contents and lactic acid bacteria population during ensiling than control silages (100% CS). The addition of NCL also influenced the distribution of bacterial and fungal communities. Fungal diversity (Shannon’s indices were 5.15–5.48 and 2.85–4.27 in trial 1 and trial 2 respectively) increased while the relative abundances of Lactobacillus, Leuconostocs, Acetobacter and two moulds (Aspergillus and Fusarium) decreased after added NCL. In summary, mixing NCL is a promising effective approach to preserve protein of CS silage and inhibit the growth of undesirable bacteria and mould, thus to improve the forage quality to some extent.