bluuebunny/crossref_metadata_2025 huggingface dataset:
Ahmed Versus Baerveldt Glaucoma Drainage Device in Uveitic Glaucoma: A Retrospective Comparative Study
Authors: Sinha Sapna , Ganjei Allen Y. , McWatters Zoe , Lee Daniel , Moster Marlene R. , Myers Jonathan S. , Kolomeyer Natasha , Mantravadi Anand V. , Pro Michael J. , Razeghinejad Reza
Published: June 2020

Precis:

Baerveldt glaucoma drainage device demonstrated a greater reduction in intraocular pressure (IOP) than Ahmed in patients with uveitic glaucoma. The most common cause of failure was uncontrolled IOP in Ahmed and hypotony in the Baerveldt group.

Purpose:

To compare the efficacy and safety of Ahmed and Baerveldt glaucoma drainage devices in uveitic glaucoma.

Materials and Methods:

The retrospective comparative study included patients with uveitic glaucoma who underwent Ahmed or Baerveldt glaucoma drainage device implantation with a minimum follow-up of 3 months. Success was defined as IOP ≥6 and ≤21 mm Hg and >20% reduction on 2 consecutive visits after the third month with (qualified success) or without (complete success) medications and no further glaucoma surgery or loss of vision. IOP, number of medications, visual acuity, complications, and interventions were compared between groups.

Results:

In total, 137 eyes of 122 patients (67 Ahmed, 70 Baerveldt) were included. The preoperative IOP and number of medications in the Ahmed group (32.7±10.3 mm Hg; 4.1±1.3) were similar to Baerveldt (32.1±10.2 mm Hg; 4.3±1.3; P=0.73, 0.35). These at the last follow-up were (18.1±9.8 mm Hg; 2.1±1) in Ahmed and (12.7±6.9 mm Hg; 1.3±1.3) in Baerveldt groups (P=0.04, 0.01). The Baerveldt had greater IOP reduction (60.3% vs. 44.5%) and complete success rate (30% vs. 9%) with higher complication rate (51.4% vs. 20.9%) (all P≤0.05). The de novo glaucoma reoperation rate was 19% in the Ahmed group and 4% in the Baerveldt group (P=0.006). Hypotony resulted in failure in 7 eyes (10%) in the Baerveldt group and none in the Ahmed group (P=0.013).

Conclusions:

Higher complete success rate and significantly greater reduction in mean IOP and number of medications were observed in the Baerveldt group, but with a higher rate of complications including hypotony.
Tissue-Resident Macrophages in the Control of Infection and Resolution of Inflammation
Authors: Mu Xingjiang , Li Yutian , Fan Guo-Chang
Published: June 2020

Macrophage, as an integral component of the immune system and the first responder to local damage, is on the front line of defense against infection. Over the past century, the prevailing view of macrophage origin states that all macrophage populations resided in tissues are terminally differentiated and replenished by monocytes from bone-marrow progenitors. Nonetheless, this theory has been reformed by ground-breaking discoveries from the past decades. It is now believed that tissue-resident macrophages (TRMs) are originated from the embryonic precursors and seeded in tissue prenatally. They can replenish via self-renewal throughout the lifespan. Indeed, recent studies have demonstrated that tissue-resident macrophages should not be classified by the over-simplified macrophage polarization (M1/M2) dogma during inflammation. Moreover, multiple lines of evidence have indicated that tissue-resident macrophages play critical roles in maintaining tissue homeostasis and facilitating tissue repair through controlling infection and resolving inflammation. In this review, we summarize the properties of resident macrophages in the lung, spleen, and heart, and further highlight the impact of TRM populations on inflammation control and tissue repair. We also discuss the potential role of local proliferation in maintaining a physiologically stable TRM pool in response to acute inflammation.
Prospective multi-center evaluation on risk factors, clinical characteristics and outcomes due to carbapenem resistance in Acinetobacter baumannii complex bacteraemia: experience from the Chinese Antimicrobial Resistance Surveillance of Nosocomial Infections (CARES) Network
Authors: Liu Yudong , Wang Qi , Zhao Chunjiang , Chen Hongbin , Li Henan , Wang Hui , CARES Network on behalf of the
Published: June 2020

Introduction. Increasing evidence demonstrates unfavourable outcomes in bloodstream infections (BSI) due to the carbapenem-resistant

Acinetobacter baumannii

complex (CRAB).

Aim. To investigate the differences in risk factors, clinical characteristics and outcomes in patients with

A. baumannii

complex BSI stratified by carbapenem resistance, a prospective multi-center study was conducted.

Methodology. Information was collected in a predefined form. A total of 317 cases was included for comparison between CRAB BSI vs. carbapenem-susceptible

A. baumannii

complex (CSAB) BSI. Among these cases, 229 cases were defined as CRAB BSI and 88 cases as CSAB BSI.

Results. Univariable analysis showed that male gender, underlying neurologic disease, prior carbapenems exposure, intensive care unit (ICU) stay, presence of central venous catheter, endotracheal intubation, tracheotomy, Foley catheter, nasogastric intubation, lower respiratory tract infections and catheter-related infections were more prevalent in CRAB BSI. Only male gender, prior carbapenems exposure and presence of endotracheal intubation persisted as independent risk factors for acquiring CRAB BSI. Patients with CRAB BSI displayed unfavourable outcomes characterized by failure of pathogen clearance, continuous fever, disease aggravation and higher incidence of 30-day all-cause mortality. Multivariate analysis demonstrated carbapenem resistance as an independent risk factor for 30-day all-cause mortality.

Conclusion. Our findings reveal the epidemiological differences between CRAB BSI and CSAB BSI in a Chinese cohort. Our data suggest that carbapenem resistance has a significant impact on mortality for patients with

A. baumannii

complex BSI, further strengthening the importance of active prevention and control strategies for the spread of CRAB in Chinese hospitals.
Impact of public health interventions on the COVID-19 epidemic: a stochastic model based on data from an African island
Authors: Nuckchady D. C.
Published: June 2020

A stochastic model was created to simulate the impact of various healthcare measures on the COVID-19 epidemic. Travel restrictions and point of entry or exit screening help to delay the onset of the outbreak by a few weeks. Population surveillance is critical to detect the start of community transmission early and to avoid a surge in cases. Contact reduction and contact tracing are key interventions that can help to control the outbreak. To promptly curb the number of new cases, countries should diagnose patients using a highly sensitive test.
Timeline from receipt to online publication of COVID-19 original research articles
Authors: Barakat Amr F. , Shokr Mohamed , Ibrahim Joseph , Mandrola John , Elgendy Islam Y.
Published: June 2020

Objective

To examine the timeline from submission of Coronavirus Disease 2019 (COVID)-related original articles compared with non-COVID-related original articles.

Background

There have been growing concerns about the speed and rigor of the review process for COVID-related articles by journals.

Methods

Using Dimensions, an online searchable platform, we identified PubMed-indexed journals that published >50 COVID-related articles (regardless of article type) between 1/1/2020 and 5/16/2020 and had available data on the date of article receipt. For the control group, we included consecutive full-length original investigations with available receipt date (regardless of topic) published in these journals starting from 3/1/2019 until a 1:2 ratio of COVID to non-COVID-related articles per journal was achieved.

Results

The final number included 294 COVID-related full-length original investigations with available article receipt dates published in 16 journals with corresponding 588 control articles from the same journals. The median time from article receipt to online publication was 20 (11-32) days for COVID-articles vs. 119 (62-182) days for controls (P<0.001). The median time to final acceptance (available for 97% of the articles) was 13 (5-23) days for COVID vs. 102 (55-161) days for controls (P<0.001). These observations were seen across all the included journals in the analysis.

Conclusions

In this analysis of full-length original investigations published in 16 medical journals, the median time from receipt to final acceptance of COVID-related articles was 8 times faster compared to non-COVID-related articles published in a similar time frame in the previous year. Online publication was 6 times faster for COVID-related articles compared to controls.
Treatment of ARDS and hyperinflammation in COVID-19 with IL-6 antagonist Tocilizumab: a tertiary care experience from Pakistan
Authors: Nasir Nosheen , Mahmood Syed Faisal , Habib Kiren , Khanum Iffat , Jamil Bushra
Published: June 2020

Cytokine release syndrome in COVID-19 is characterized by hyperinflammation which manifests as ARDS, multi-organ failure, and high inflammatory parameters. Tocilizumab, an IL-6 antagonist has been used in COVID-19 acute respiratory distress syndrome (ARDS) with conflicting results from different parts of the world. We conducted a retrospective descriptive study from Feb 2020 to May 2020 on COVID-19 patients with ARDS and hyperinflammation characterized by raised CRP and/or ferritin. A total of 244 patients with COVID-19 were admitted out of which 107 had ARDS. Thirty patients had both ARDS and hyperinflammation and received tocilizumab. The mean age was 62.5 years (SD: 13.5) and the majority were male (83%). The mean CRP pre-treatment was 217.5 mg/L and post 48 to 72 hours of tocilizumab treatment was 98.5 mg/L. Twenty-one patients (70%) also received concomitant intravenous methylprednisolone. Of the 30 patients, 7 died and 20 recovered. Ten patients required intensive care unit admission and nine developed nosocomial infections. COVID-19 associated aspergillosis was diagnosed in three patients post tocilizumab treatment. Mortality was significantly higher in patients who developed a nosocomial infection and who required intermittent positive pressure ventilation (IPPV). Our study is the first to describe the treatment outcomes with tocilizumab from a low-middle income country. The availability and cost of tocilizumab in our region which makes it imperative to understand its potential for use in our setting. Our study supports the use of tocilizumab in a select patient population with COVID-19 and recommends monitoring of nosocomial infections and opportunistic infections.
Intense bitterness of molecules: machine learning for expediting drug discovery
Authors: Margulis Eitan , Dagan-Wiener Ayana , Ives Robert S. , Jaffari Sara , Siems Karsten , Niv Masha Y.
Published: June 2020

Drug development is a long, expensive and multistage process geared to achieving safe drugs with high efficacy. A crucial prerequisite for completing the medication regimen for oral drugs, particularly for pediatric and geriatric populations, is achieving taste that does not hinder compliance. Currently, the aversive taste of drugs is tested in late stages of clinical trials. This can result in the need to reformulate, potentially resulting in the use of more animals for additional toxicity trials, increased financial costs and a delay in release to the market. Here we present BitterIntense, a machine learning tool that classifies molecules into “very bitter” or “not very bitter”, based on their chemical structure. The model, trained on chemically diverse compounds, has above 80% accuracy on several test sets. BitterIntense suggests that intense bitterness does not correlate with toxicity and hepatotoxicity of drugs and that the prevalence of very bitter compounds among drugs is lower than among microbial compounds. BitterIntense allows quick and easy prediction of strong bitterness of compounds of interest for food and pharma industries. We estimate that implementation of BitterIntense or similar tools early in drug discovery and development process may lead to reduction in delays, in animal use and in overall financial burden.

Significance Statement

Drug development integrates increasingly sophisticated technologies, but extreme bitterness of drugs remains a poorly addressed cause of medicine regimen incompletion. Reformulating the drug can result in delays in the development of a potential medicine, increasing the lead time to the patients. It might also require the use of extra animals in toxicity trials and lead to increased costs for pharma companies. We have developed a computational predictor for intense bitterness, that has above 80% accuracy. Applying the classifier to annotated datasets suggests that intense bitterness does not correlate with toxicity and hepatotoxicity of drugs. BitterIntense can be used in the early stages of drug development to identify drug candidates that require bitterness masking, and thus reduce animal use, time and monetary loss.
Learning feedback loops in transcriptome network during cell fate transition
Authors: Xiong Lingyun , Schoenberg William A. , Swartz Jeremy D.
Published: June 2020

Embryonic development is characterized by series of cell fate transitions, during which non-linear feedback of signaling events and network dynamics in the transcriptome are instrumental to determine differentiation outcomes. Changes in selected genes or pathways have been described extensively, but a system-level understanding of gene regulatory network regulation is still lacking. Leveraging time-series data from single-cell transcriptome profiling of developing mouse embryos, we collapsed dynamic gene expressions into changes in 14 core biological processes, and constructed an ordinary differential equation-based machine learning model of the transcriptomic network to capture its feedback structure. We evaluated the polarity and magnitude of direct pairwise causal relationships between biological processes and identified higher-order feedback loops that dominate system behavior. Despite heterogeneous expressions at the gene level, we find that the transcriptome at the macroscale level has a feedback structure that is intrinsically stable and robust. We show the pivotal role of intracellular signaling in driving systemic changes and uncover the importance of homeostatic process and establishment of localization in regulating network dynamics. Local regulatory structures represent domain-specific regulations that are essential to cell fate transition, especially lipid metabolic process. Together, this study provides a holistic picture of transcriptomic network dynamics during mouse organogenesis, offering insight into key aspects of information flow in the transcriptome that control cell fate transition.

Conflict of interest statement

The authors declare no potential conflicts of interest.

Funding

The authors received no funding for this study.

Author contributions

Conceptualization: LX; Methodology: LX, WAS, and JDS; Data Curation: LX; Investigation: LX and WAS; Formal Analysis: LX and WAS; Visualization: WAS and LX;

Writing – review & editing: LX and WAS.
Adaptation of STARR-seq method to be used with 3rdgeneration integrase-deficient promoterless lentiviral vectors
Authors: Matjusaitis Mantas , Tedesco Donato , Ciukas Azuolas
Published: June 2020

Ability to functionally screen gene regulatory sequences, such as promoters and enhancers, in high throughput manner is an important prerequisite for many basic and translational research programs. One of the methods that allow such screening is STARR-seq, or self-transcribing active regulatory region sequencing. It allows to quickly screen millions of candidate sequences in the cell type of interest. However, it does rely on transfection as a delivery method which can be a limiting-step for some hard-to-transfect cells such as senescent cells. Here we show that integration-deficient and integration-competent promoterless lentiviral particles can be used to deliver STARR-seq constructs into cells. These constructs reported CMV enhancer activity both at protein and mRNA level. While further validations are necessary, ability to deliver STARR-seq libraries using lentiviral particles will significantly improve the versatility and usability of such a method.
Systematic evaluation of parameters for genome-scale metabolic models of cultured mammalian cells
Authors: Schinn Song-Min , Morrison Carly , Wei Wei , Zhang Lin , Lewis Nathan E.
Published: June 2020

Genome-scale metabolic models describe cellular metabolism with mechanistic detail. Given their high complexity, such models need to be parameterized correctly to yield accurate predictions and avoid overfitting. Effective parameterization has been well-studied for microbial models, but it remains unclear for higher eukaryotes, including mammalian cells. To address this, we enumerated model parameters that describe key features of cultured mammalian cells – including cellular composition, bioprocess performance metrics, mammalian-specific pathways, and biological assumptions behind model formulation approaches. We tested these parameters by building thousands of metabolic models and evaluating their ability to predict the growth rates of a panel of phenotypically diverse Chinese Hamster Ovary cell clones. We found the following considerations to be most critical for accurate parameterization: (1) cells limit metabolic activity to maintain homeostasis, (2) cell morphology and viability change dynamically during a growth curve, and (3) cellular biomass has a particular macromolecular composition. Depending on parameterization, models predicted different metabolic phenotypes, including contrasting mechanisms of nutrient utilization and energy generation, leading to varying accuracies of growth rate predictions. Notably, accurate parameter values broadly agreed with experimental measurements. These insights will guide future investigations of mammalian metabolism.
Development of a novel medical physics patient consult program
Authors: Schuller Bradley W , Baldwin Jonathan A , Ceilley Elizabeth A , Markovic Alexander , Albert Jeffrey M
Published: June 2020

Purpose

To develop a new patient consult program, where patients are invited to meet directly with a clinical medical physicist to learn and ask questions about the technical aspects of their care.

Methods

Patients are invited to meet voluntarily with a clinical medical physicist directly after the treatment planning CT appointment, and then again after treatment starts. Each consult starts with an overview of the clinical medical physicist’s role in patient care. This is followed by a detailed explanation of the treatment planning CT, treatment planning, and treatment delivery processes. Data are collected after each patient encounter, including: age, gender, treatment intent, treatment site, consult duration, discussion points, overall impression, and a summary of the questions asked. Qualitative data analysis focused on understanding the number and types of questions asked during the physics consults. Additional analyses focused on evaluating the encounter notes for interesting insights regarding meeting tone, number of meeting attendees, and other non-clinical discussion points.

Results

Sixty three patients were seen between August 2016 and December 2017, accounting for 29% of the total department patient load. The average physics consult duration was 24 minutes. When evaluating the patient encounter notes for overall tone, 55 patients (87%) had positive descriptors such as “pleasant conversation”. Thirty three patients (52%) brought at least one other person into the consult, and 27 patients (43%) contributed personal stories or professional background information to the conversation. When the collection of patient questions was grouped into question types, the data show that the majority of the consult discussion addresses questions related to treatment delivery, treatment planning, and other technical questions.

Conclusions

Incorporation of a medical physics patient consult program into clinical practice requires modest time commitment, and has the benefits of increasing medical physics engagement with patient care and improving patient satisfaction through better education.
Seroprevalence of SARS-CoV-2 IgG Specific Antibodies among Healthcare Workers in the Northern Metropolitan Area of Barcelona, Spain, after the first pandemic wave
Authors: Barallat J , Fernández-Rivas G , Quirant-Sánchez B , González V , Doladé M , Martinez-Caceres E , Piña M , Matllo J , Estrada O , Blanco I
Published: June 2020

Background

The rapid spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) around the world has caused a global pandemic, infecting millions of individuals worldwide, with an unprecedented impact in health care systems worldwide. Healthcare workers are one of the risk groups that need to be well characterized due to their strategic role in the management of patients, presently and in prevention of healthcare needs for future outbreaks. This study presents the results of the first SARS-CoV-2 seroprevalence study in the Northern Metropolitan Area of Barcelona, Spain.

Methods

IgG SARS-CoV2 antibodies were analyzed in serum samples from 7563 healthcare workers of the Northern Metropolitan Area of Barcelona taken during the pandemia (from May 4th to May 22nd, 2020) by chemiluminescence assays.

Results

A total of 779 of 7563 (10.3%) healthcare workers had detectable anti-SARS-CoV-2 IgG (specific for either S1/S2 or N antigens). No significant differences were observed between those working at primary care or at the reference hospital.

Interestingly, in 29 (8.53%) of the previously confirmed positive reverse-transcriptase polymerase chain reaction (rRT-PCR) patients SARS-CoV-2 IgG (S1/S2 or recombinant N antigen) were negative.

Conclusion

Seroprevalence of anti-SARS-CoV-2 IgG in the healthcare workers of the Nord Metropolitan Area of Barcelona was significantly increased in comparison with the general population in the same geographical area. These results give us an important insight for a better understanding of SARS-CoV-2 epidemiology, in a collective that is essential for the response against this pandemic.
Stimulus-induced Gamma rhythms are weaker in human elderly with Mild Cognitive Impairment and Alzheimer’s Disease
Authors: Murty Dinavahi V. P. S. , Manikandan Keerthana , Ramesh Ranjini Garani , Purokayastha Simran , Nagendra Bhargavi , Abhishek M. L. , Balakrishnan Aditi , Javali Mahendra , Rao Naren Prahalada , Ray Supratim
Published: June 2020

Alzheimer’s Disease (AD) in elderly adds substantially to socio-economic burden necessitating early diagnosis. While recent studies in rodent models of AD have suggested diagnostic and therapeutic value for gamma rhythms in brain, the same has not been rigorously tested in humans. We recruited a large population (N=247; 106 females) of elderly (>49 years) individuals from the community, who viewed large gratings that induced strong gamma oscillations in their electroencephalogram (EEG). These individuals were classified as healthy (N=227), mild-cognitively-impaired (MCI; 14) or AD (6) based on clinical history and Clinical Dementia Rating scores. Surprisingly, stimulus-induced gamma rhythms, but not alpha or steady-state-visually-evoked-responses, were significantly lower in both MCI and AD patients compared to their age and gender matched controls. This reduction was not due to differences in eye movements or baseline power. Our results suggest that gamma could be used as potential diagnostic tool for MCI/AD in humans.

One Sentence Summary

A large double-blinded EEG study suggests that narrow-band visual gamma rhythms are weaker in MCI/AD patients compared to cognitively healthy controls.
Weeding Through the Haze: A Survey on Cannabis Use Among People Living with Parkinson’s Disease in the US
Authors: Feeney Megan P. , Bega Danny , Kluger Benzi M. , Stoessl A. Jon , Evers Christiana M. , Leon Rebeca De , Beck James C.
Published: June 2020

Symptomatic management of Parkinson’s disease (PD) is complex and many symptoms, especially non-motor symptoms, are not effectively addressed with current medications. In the US, cannabis has become more widely available for medical and recreational use, permitting those in the PD community to try alternative means of symptom control. However, little is known about the attitudes towards, and experiences with, cannabis use among those living with PD. To address this shortcoming, we distributed an anonymous survey to 7,607 people with PD in January 2020 and received 1,339 responses (17.6%). 1,064 complete responses were available for analysis. Respondents represented 49 states with a mean age of 71.2 years (± 8.3) and mean PD duration of 7.4 years (± 6.2). About a quarter of respondents (24.5%) reported cannabis use within the previous six months. Age and gender were found to be predictors of cannabis use in this sample (Age OR = 0.95, 95% CI 0.93 to 0.97; Male OR = 1.44, 95% CI 1.03 to 2.03). Users reported learning about cannabis use from the internet/news (30.5%) and friends or other people with PD (26.0%). Cannabis users were more likely to report insufficient control of their non-motor symptoms with prescription medications than non-users (p = 0.03). Cannabis was primarily used for PD (63.6%) and was most often used to treat nonmotor symptoms of anxiety (45.5%), pain (44.0%), and sleep disorders (44.0%). However, nearly a quarter of users (23.0%) also reported they had stopped cannabis use in the previous six months, primarily due to a lack of symptom improvement (35.5%). Three quarters of respondents (75.5%) did not use cannabis, primarily because there was a lack of scientific evidence supporting efficacy (59.9%). Our results suggest that the lack of formal guidance or research evidence about cannabis for PD may in part underlie inconsistencies in both use and reported effectiveness.
Regional Association of Disability and SARS-CoV-2 Infection in 369 Counties of the United States
Authors: Olulana Oluwaseyi , Abedi Vida , Avula Venkatesh , Chaudhary Durgesh , Khan Ayesha , Shahjouei Shima , Li Jiang , Zand Ramin
Published: June 2020

Background

There have been outbreaks of SARS-CoV-2 in long term care facilities and recent reports of disproportionate death rates among the vulnerable population. The goal of this study was to better understand the impact of SARS-CoV-2 infection on the non-institutionalized disabled population in the United States using data from the most affected states as of April 9th, 2020.

Methods

This was an ecological study of county-level factors associated with the infection and mortality rate of SARS-CoV-2 in the non-institutionalized disabled population. We analyzed data from 369 counties from the most affected states (Michigan, New York, New Jersey, Pennsylvania, California, Louisiana, Massachusetts) in the United States using data available by April 9th, 2020. The variables include changes in mobility reported by Google, race/ethnicity, median income, education level, health insurance, and disability information from the United States Census Bureau. Bivariate regression analysis adjusted for state and median income was used to analyze the association between death rate and infection rate.

Results

The independent sample t-test of two groups (group 1: Death rate≥3.4% [median] and group 2: Death rate < 3.4%) indicates that counties with a higher total population, a lower percentage of Black males and females, higher median income, higher education, and lower percentage of disabled population have a lower rate (< 3.4%) of SARS-CoV-2 related mortality (all p-values<4.3E-02). The results of the bivariate regression when controlled for median income and state show counties with a higher White disabled population (est: 0.19, 95% CI: 0.01-0.37; p-value:3.7E-02), and higher population with independent living difficulty (est: 0.15, 95% CI: −0.01-0.30; p-value: 6.0E-02) have a higher rate of SARS-CoV-2 related mortality. Also, the regression analysis indicates that counties with higher White disabled population (est: - 0.22, 95% CI: −0.43-(-0.02); p-value: 3.3E-02), higher population with hearing disability (est: −0.26, 95% CI: - 0.42- (-0.11); p-value:1.2E-03), and higher population with disability in the 18-34 years age group (est: −0.25, 95% CI: −0.41-(-0.09); p-value:2.4E-03) show a lower rate of SARS-CoV-2 infection.

Conclusion

Our results indicate that while counties with a higher percentage of non-institutionalized disabled population, especially White disabled population, show a lower infection rate, they have a higher rate of SARS-CoV-2 related mortality.
Absolute quantification and degradation evaluation of SARS-CoV-2 RNA by droplet digital PCR
Authors: Mello Curtis J. , Kamitaki Nolan , Rivera Heather de , McCarroll Steven A.
Published: June 2020

Quantifying SARS-CoV-2 infectivity, formulating well-calibrated public-health policy, and managing the safety of workplaces would all be facilitated by precise measurement of the extent to which SARS-CoV-2 RNA is present in an intact form in biological specimens and human environments. We describe assays that use digital PCR in nanoliter droplets (droplet digital PCR) to measure these properties. Such assays could be broadly deployed to inform COVID-19 epidemiology, measure symptomatic and asymptomatic infectivity, and help manage the safety of environments in which people live, move, and work.
Simple cloning of large natural product biosynthetic gene clusters from Streptomyces by an engineered CRISPR/Cas12a system
Authors: Liang Mindong , Liu Leshi , Wang Weishan , Zeng Xiaoqian , Liu Jiakun , Karthik Loganathan , Zhu Guoliang , Bai Linquan , Hou Chengjian , Chen Xiangyin , Ouyang Liming , Liu Xueting , Hu Bin , Xia Xuekui , Tong Yaojun , Lou Chunbo , Alterovitz Gil , Tan Gao-Yi , Zhang Li-Xin
Published: June 2020

Directly cloning of biosynthetic gene clusters (BGCs) from microbial genomes has been revolutionizing the natural product-based drug discovery. However, it is still very challenging to efficiently clone, for example, large (> 80kb) and GC-rich (> 70%), streptomycete originating BGCs. In this study, we developed a simple, fast yet efficient and low-costin vitroplatform for direct cloning large BGCs from streptomycete genomic DNA, named as CAT-FISHING (CRISPR/Cas12a- andAgarose plug-based sysTem forFast bIoSyntHetIc geNe cluster cloninG), by combining the advantages of CRISPR/Cas12a cleavage and bacterial artificial chromosome (BAC) library construction. CAT-FISHING was demonstrated by directly cloning large DNA fragments ranging from 47 to 139 kb with GC content of > 70% from theS. albusJ1074 genome in a relatively efficient manner. Moreover, surugamides, encoded by a captured 87-kb BGC with GC content of 76%, was heterologously expressed in aStreptomyceschassis. These results indicate that CAT-FISHING is a powerful platform for BGCs batch cloning, which would be greatly beneficial to the natural products-based drug discovery. We believe that this system will lead a renaissance of interest in microorganisms as a source for drug development.
Optimization of cerebrospinal fluid microbial metagenomic sequencing diagnostics
Authors: Olausson Josefin , Brunet Sofia , Vracar Diana , Tian Yarong , Abrahamsson Sanna , Meghadri Sri Harsha , Sikora Per , Karlberg Maria Lind , Jakobsson Hedvig Engström , Tang Ka-Wei
Published: June 2020

Background

Infection in the central nervous system is a severe condition associated with high morbidity and mortality. Despite ample testing, the majority of encephalitis and meningitis cases remain undiagnosed. Metagenomic sequencing of cerebrospinal fluid has emerged as an unbiased approach to identify rare microbes and novel pathogens. However, several major hurdles remains, including establishment of individual limits of detection, removal of false positives and implementation of universal controls.

Results

Twenty-one cerebrospinal fluid samples, in which a known pathogen had been positively identified by available clinical techniques, were subjected to metagenomic DNA sequencing using massive parallel sequencing. Fourteen samples contained minute levels of Epstein-Barr virus. Calculation of the detection threshold for each sample was made using total leukocyte content in the sample and environmental contaminants found in bioinformatic classifiers. Virus sequences were detected in all ten samples, in which more than one read was expected according to calculations. Conversely, no viral reads were detected in seven out of eight samples, in which less than one read was expected according to calculations. False positive pathogens of computational or environmental origin were readily identified, by using a commonly available cell control. For bacteria additional filters including a comparison between classifiers removed the remaining false positives and alleviated pathogen identification.

Conclusions

Here we show a generalizable method for detection and identification of pathogen species using metagenomic sequencing. The sensitivity for each sample can be calculated using the leukocyte count and environmental contamination. The choice of bioinformatic method mainly affected the efficiency of pathogen identification, but not the sensitivity of detection. Identification of pathogens require multiple filtering steps including read distribution, sequence diversity and complementary verification of pathogen reads.
Biodegradation of polyester polyurethane byAspergillus flavusG10
Authors: Khan Sehroon , Nadir Sadia , Dong Yang , Schaefer Douglas A. , Mortimer Peter E. , Gui Heng , Khan Afsar , Yu Mingming , Iqbal Shahid , Sheng Jun , Xu Jianchu
Published: June 2020

Polyurethanes (PU) are integral to many aspects of our daily lives. Due to the extensive use of and difficulties in recycling or reusing PU, it mostly accumulates as waste. Various bacteria and fungi have been reported to degrade PU. We examined the fungusAspergillus flavus G10in that regard, after isolating it from the guts ofGryllus bimaculatus, a common cricket species. We observed surficial and chemical changes of PU with atomic force microscopy, scanning electron microscopy, and attenuated total reflectance Fourier-transform infrared spectroscopy. We measured physical changes as loss in tensile stress, stretching force, and weight of PU after incubations. Fungal hydrolysis of urethane bonds in the polymer backbone was demonstrated by detecting the formation of methylene di-aniline during incubations. Trapped CO2during incubations equaled 52.6% of PU carbon. Biodegradation of PU was maximal by fungi cultured on a malt extract medium at 25 °C, pH 12, and 14:10 hrs light to dark ratio. Pretreating PU films with UV light or 1% FeSO4or NaCl solutions further enhanced the rate of biodegradation. A range of techniques are needed to fully characterize the degradation of PU or other plastic polymers and to optimize conditions for their microbial degradation.
The Prevalence of RT-PCR Positivity of SARS-CoV-2 on 10,000 Patients from Three Cities Located on the Eastern of Turkey
Authors: Murat Karamese , Didem Ozgur , Ceyda Tarhan , Susamber Dik Altintas , Okan Caliskan , Aysegul Tuna , Saliha Kazci , Mursel Karadavut , Abdullah Gumus , Gozde Apaydin , Necati Mumcu , Onur Coruh , Ediz Tutuncu Emin
Published: June 2020

COVID-19, is caused by SARS-CoV-2, has been started on December/2019 in Wuhan/China and spread all over the world. We analyzed RT-PCR results of 10,000 cases from April-2 to May-30, 2020 in three neighbor cities located on the Eastern of Turkey. The final study population was 7853 cases after excluded screening tests. RT-PCR were performed to detect the SARS-CoV-2-specific RdRp (RNA-dependent-RNA-polymerase) gene fragment. The number of total positive samples out of 7853 were 487; however, the number of non-repeating positive patient was 373 (4.8%). The cough and fever were the most common symptoms in positive cases. The epidemiologic studies should be performed about the prevalence of SARS-CoV-2 infection to better understand the effect of the virus all over the world.
Crystal structure of posnjakite formed in the first crystal water-cooling line of the ANSTO Melbourne Australian Synchrotron MX1 Double Crystal Monochromator
Authors: Mills Stuart , Aishima Jun , Aragao David , Caradoc-Davies Tom Tudor , Cowieson Nathan , Gee Christine L. , Ericsson Daniel , Harrop Stephen , Panjikar Santosh , Smith Kate Mary Louise , Riboldi-Tunnicliffe Alan , Williamson Rachel , Price Jason Roy
Published: June 2020

Exceptionally large crystals of posnjakite, Cu4SO4(OH)6(H2O), formed during corrosion of a Swagelock(tm) Snubber copper gasket within the MX1 beamline at the ANSTO-Melbourne, Australian Synchrotron. The crystal structure was solved using synchrotron radiation toR1= 0.029 and revealed a structure based upon [Cu4(OH)6(H2O)O] sheets, which contain Jahn–Teller-distorted Cu octahedra. The sulfate tetrahedra are bonded to one side of the sheetviacorner sharing and linked to successive sheetsviaextensive hydrogen bonds. The sulfate tetrahedra are split and rotated, which enables additional hydrogen bonds.
COVID-19, supply chain disruption and China’s hog market: a dynamic analysis
Authors: Wang Yubin , Wang Jingjing , Wang Xiaoyang
Published: June 2020

Purpose

The authors explicitly evaluate the dynamic impact of five most concerned supply chain disruption scenarios, including: (1) a short-term shortage and price jump of corn supply in hog farms; (2) a shortage of market hogs to packing facilities; (3) disruption in breeding stock adjustments; (4) disruption in pork import; and (5) a combination of scenario (1)–(4).

Design/methodology/approach

The agricultural supply chain experienced tremendous disruptions from the COVID-19 pandemic. To evaluate the impact of disruptions, the authors employ a system dynamics model of hog market to simulate and project the impact of COVID-19 on China hog production and pork consumption. In the model the authors explicitly characterize the cyclical pattern of hog market. The hog cycle model is calibrated using market data from 2018–2019 to represent the market situation during an ongoing African swine fever.

Findings

The authors find that the impacts of supply chain disruption are generally short-lived. Market hog transportation disruption has immediate impact on price and consumption. But the impact is smoothed out in six months. Delay in import shipment temporarily reduces consumption and raises hog price. A temporary increase of corn price or delay in breeding stock acquisition does not produce significant impact on national hog market as a whole, despite mass media coverage on certain severely affected regions.

Originality/value

This is the first evaluation of short-term supply chain disruption on China hog market from COVID-19. The authors employ a system dynamics model of hog markets with an international trade component. The model allows for monthly time step analysis and projection of the COVID-19 impact over a five-year period. The results and discussion have far-reaching implications for agricultural markets around the world.
Critical factors influencing the bid or no-bid decision of the indigenous small building contractors in Tanzania
Authors: Chileshe Nicholas , Kavishe Neema , Edwards David John
Published: June 2020

Purpose

This study aims to investigate and ranks the critical factors influencing the bid or no-bid decision and their importance for the indigenous small building contractors within the Tanzanian construction industry.

Design/methodology/approach

An interpretivist epistemological design was adopted to extensively manually review and search extant literature on bid or no-bid decision-making criteria. A total of 30 most common bid or no-bid decision-making criteria were identified. These were included in a questionnaire survey data collection instrument. The survey was distributed to 40 small indigenous (local) building contractors in Dar es Salaam, Tanzania. In total, 33 responses were received. Response data was subjected to both descriptive and inferential statistics.

Findings

The results show a disparity of ranking of the 30 bid/no-bid criteria factors among the two grades of small contractors, with 11 factors having statistically significant differences (p = < 0.05). Based on the overall sample, the most highly ranked seven factors in ascending order were: availability of capital; financial capacity of the client; project size; profitability; project type; need of work; and current workload. The following were the least ranked: tax liability; the degree of safety; availability of other projects; availability of labor; bidding document price; and uncertainty because of weather conditions. Availability of capital and financial capacity of the client were jointly ranked as the most important by Class VI contractors. In comparison, availability of capital and need of study were rated highly for Class VII contractors.

Research limitations/implications

The sample consisted of indigenous small building contractors in one industry operating in Tanzania only and did not include the perceptions of the foreign contractors based in Dar es Salaam. Future studies are required to expand the current research and investigate this specific aspect further.

Practical implications

The identified “bid/no-bid criteria” information will allow indigenous small building contractors to enhance the efficiency and effectiveness of their bidding decision-making process. Emergent findings will enable said contractors to: better fit into the competitive construction business environment; increase their awareness of existing decision-making practices; and develop appropriate strategies for evaluation of opportunities encountered. Cumulatively, these findings benefit small indigenous building contractors by increasing their understanding of the factors influencing bid decision.

Originality/value

The study represents the first empirical study in Tanzania on the critical factors influencing the bid or no-bid decision among the indigenous small building contractors, which face fierce competition from foreign contractors.
Business model designs, big data analytics capabilities and new product development performance: evidence from China
Authors: Sun Biao , Liu Yu
Published: June 2020

Purpose

Although the business model (BM) has become a top priority in management research, existing literature still offers a confusing and partial picture about how to leverage BM designs for new product development (NPD) because of two limitations. First, research has paid little attention to different BM designs' effects on NPD performance. Second, few empirical studies have examined the moderating roles of firms' learning capabilities, such as big data analytics capabilities (BDA capabilities). This study aims to investigate the effects of BM novelty design and BM efficiency design on NPD performance and the ways in which BDA capabilities moderate these effects.

Design/methodology/approach

A literature review provides the model and hypotheses. Using a sample of 208 Chinese firms, the authors conducted an empirical test following multiple regression analysis.

Findings

The results demonstrate that BM novelty design has a positive effect on NPD performance while BM efficiency design takes the form of an inverted U-shape. Moreover, BDA capabilities (i.e. BDA technology capability and BDA management capability) have complicated moderating effects on BM novelty design- and BM efficiency design-NPD performance relationships.

Research limitations/implications

The results may be affected by both the context (solely in China) and type (cross-sectional) of the data set. This study has explored the moderating effects of BDA capabilities, further studies considering other significant practices such as social media usage, could yield richer insights that would help validate the results of this study.

Practical implications

First, we suggest that managers should be explicitly aware of the different impacts of BM novelty design and BM efficiency design on NPD performance. Second, this study encourages managers to build relevant BDA capabilities to work with BM designs to improve NPD performance.

Originality/value

This is one of the first studies to investigate BM designs' complicated influences on NPD success and explore BDA capabilities' moderating effects on the BM design-NPD performance linkage.
Madrasah Education Program implementation in the Philippines: an exploratory case study
Authors: Sali Abdul Haiy Abdul , Marasigan Arlyne Canales
Published: June 2020

Purpose

The purpose of the paper is to explore the implementation of Madrasah Education Program (MEP) in selected Arabic Language and Islamic Values Education (ALIVE) schools in Quezon City, Philippines and identify some challenges faced in their implementation practice.

Design/methodology/approach

This study utilized qualitative method of research using exploratory study, employing in-depth interviews, document analysis, and observation. The authors used purposive sampling with eight research participants: one Administrator, three ALIVE Coordinators, and four Madrasah Teachers or Asatidz.

Findings

The main findings in the MEP implementation, generally, the schools delivered some program goals through institutional support, pedagogical and instructional development, and enrichment of cultural diversity in the school community. However, the study identified some major challenges affecting the program implementation in selected ALIVE schools such as: lack of permanent infrastructure, limited instructional resources, learners' absenteeism, low and delayed Asatidz allowances, and cultural variances among Muslim Filipinos.

Research limitations/implications

The results of the study provide a general overview of MEP implementation and the major challenges experienced by program implementers. However, the study is limited to three selected ALIVE schools in the Philippines.

Practical implications

These results are useful in guiding education stakeholders in evidence-based policymaking to further improve the implementation of Madrasah Education.

Originality/value

This study provides enrichment of evidence-based research especially on the lived experiences of grassroots implementers. Fewer studies on Madrasah Education were conducted outside the Bangsamoro Autonomous Region (BARMM) particularly in the context of a non-Muslim dominated locale.
Inequalities in common mental disorders between advantaged and disadvantaged groups: an Oaxaca – Blinder decomposition analysis on socio-economic factors
Authors: Veisani Yousef , Rezaeian Shahab , Mohamadian Fathola , Delpisheh Ali
Published: June 2020

Purpose

This paper aims to evaluate the socio-economic factors of inequalities in common mental disorders (MDs) between advantaged and disadvantaged groups and also to determine the main contributors of inequality.

Design/methodology/approach

This cross-sectional study was conducted in 2016–2017. The authors included 763 persons by stratified cluster sampling; clusters were cities, geographical area and households. Blinder-Oaxaca decomposition technique was used to estimate of main inequalities determinant between advantaged and disadvantaged groups.

Findings

Overall prevalence of MDs was 22.6 and 35.6% in the advantage and disadvantaged groups, respectively. The concentration index was −0.013 [95% Confidence Interval (95% CI): −0.022, −0.004]; therefore, MDs were more concentrated in the deprived group. The risk of MDs in deprived group and females was 81 and 60% higher than advantaged group (OR: 1.81; 95% CI: 1.28, 2.57) and males (OR: 1.60; 95% CI: 1.21, 2.24), respectively. Educational status [−0.06 (95% CI: −0.10, −0.01)] was the highest level of contribution in inequality in gaps between groups.

Originality/value

The socio-demographic inequality in MDs among adult population was more explained by lower educational level, married persons and unemployment variables.