bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessment of the Impact of COVID-19 pandemic on population level interest in Skincare: Evidence from a google trends-based Infodemiology study
Authors: Symum Hasan , Islam Md. F. , Hiya Habsa K. , Ali Sagor Kh M.
Published: November 2020

Background

COVID-19 pandemic created an unprecedented disruption of daily life including the pattern of skin related treatments in healthcare settings by issuing stay-at-home orders and newly coronaphobia around the world.

Objective

This study aimed to evaluate whether there are any significant changes in population interest for skincare during the COVID-19 pandemic.

Methods

For the skincare, weekly RSV data were extracted for worldwide and 23 counties between August 1, 2016, and August 31, 2020. Interrupted time-series analysis was conducted as the quasi-experimental approach to evaluate the longitudinal effects of COVID-19 skincare related search queries. For each country, autoregressive integrated moving average (ARIMA) model relative search volume (RSV) time series and then testing multiple periods simultaneously to examine the magnitude of the interruption. Multivariate linear regression was used to estimate the correlation between countries’ relative changes in RSV with COVID-19 confirmed cases/ per 10000 patients and lockdown measures.

Results

Out of 23 included countries in our study, 17 showed significantly increased (p<0.01) RSVs during the lockdown period compared with the ARIMA forecasted data. The highest percentage of increments occurs in May and June 2020 in most countries. There was also a significant correlation between lockdown measures and the number of COVID-19 cases with relatives changes in population interests for skincare.

Conclusion

Understanding the trend and changes in skincare public interest during COVID-19 may assist health authorities to promote accessible educational information and preventive initiatives regarding skin problems.
Comparative efficacy and safety of current drugs against COVID-19: A systematic review and network meta-analysis
Authors: Li Yi , He Wei
Published: November 2020

The rapid spread of coronavirus disease (COVID-19) has greatly disrupted the livelihood of many people around the world. To date, more than 35.16 million COVID-19 cases with 1.037million total deaths have been reported worldwide. Compared with China, where the disease was first reported, cases of COVID-19, the number of confirmed cases for the disease in the rest of the world have been incredibly high. Even though several dugs have been suggested to be used against the disease, the said interventions should be backed by empirical clinical evidence. Therefore, this paper provides a systematic review and a meta-analysis of efficacy and safety of different COVID-19 drugs.

Research in context

Evidence before this study

Currently, Covid-19 is one of the most urgent and significant health challenge, globally. However, so far there is no specific and effective treatment strategy against the disease. Nonetheless, there are numerous debates over the effectiveness and potential adverse effects of different COVID-19 antivirals. In general, there is invaluable need to continually report on new advances and successes against COVID-19, apparently to aid in managing the pandemic.

Added value of this study

This study provides a comprehensive, evidence-based guide on the management of multiple COVID-19 symptoms. In particular, we provide a review of 14 drugs, placebos and standard treatments against COVID 19. Meanwhile, we also performed a meta-analysis based on four clinical outcome indicators, to measure and compare the efficacy and safety of current interventions.

Implications of all the available evidence

Findings of this research will guide clinical decision in COVID-19 patients. It will also provide a basis for predicting clinical outcomes such as efficacy, mortality and safety of interventions against the disease.
WEVar: a novel statistical learning framework for predicting noncoding regulatory variants
Authors: Wang Ye , Jiang Yuchao , Yao Bing , Huang Kun , Liu Yunlong , Wang Yue , Qin Xiao , Saykin Andrew J. , Chen Li
Published: November 2020

Understanding the functional consequence of noncoding variants is of great interest. Though genome-wide association studies (GWAS) or quantitative trait locus (QTL) analyses have identified variants associated with traits or molecular phenotypes, most of them are located in the noncoding regions, making the identification of causal variants a particular challenge. Existing computational approaches developed for for prioritizing non-coding variants produce inconsistent and even conflicting results. To address these challenges, we propose a novel statistical learning framework, which directly integrates the precomputed functional scores from representative scoring methods. It will maximize the usage of integrated methods by automatically learning the relative contribution of each method and produce an ensemble score as the final prediction. The framework consists of two modes. The first “context-free” mode is trained using curated causal regulatory variants from a wide range of context and is applicable to predict noncoding variants of unknown and diverse context. The second “context-dependent” mode further improves the prediction when the training and testing variants are from the same context. By evaluating the framework via both simulation and empirical studies, we demonstrate that it outperforms integrated scoring methods and the ensemble score successfully prioritizes experimentally validated regulatory variants in multiple risk loci.
Using A Socio-Ecological System (SES) Framework to Explain Factors Influencing Countries’ Success Level in Curbing COVID-19
Authors: Suhud Nur Amiera , Ling Gabriel Hoh Teck , Leng Pau Chung , Matusin AK Muhamad Rafiq AK
Published: November 2020

Little attention has been paid to interactions between institutional-human-environment dimensions, which are believed to impact the outcome of COVID-19 abatement. Thus, through the diagnostic SES framework analysis, this paper aims to investigate what and how the multifaceted social, physical, and governance factors affect the success level of 7 selected Asia-Pacific countries (namely South Korea, Japan, Malaysia, Singapore, Vietnam, Indonesia, and New Zealand) in combatting the COVID-19 pandemic. Drawing on secondary data from February 2020 to June 2020, the success or severity level of a country was measured by cumulative positive cases, average daily increase, and the mortality rate. A qualitative content analysis, covering code assignation, i.e., Present (P), Partially Present (PP), Absent (A) for each SES attribute, as well as rank ordering (from 1stto 7th) and score calculation (from 3 to 21) for the success level between the countries, was undertaken. Attributes (design principles) of SES factors, such as past experiences facing similar diseases, facilities mobility, lockdown measures, penalty, and standard of procedures in public spaces are deemed significant in determining the abatement outcome or severity of a country. The findings show that Vietnam (1st) and New Zealand (2nd) adopting most of the design principles of governance (with the scores of 15 and above) had successfully eliminated the virus, while Indonesia (7th) and Japan (6th) were deemed least successful (scoring between 3-9), likely due to the low presence frequency of design principles. Not only does the study validate SES framework adaptability in a health-related (non-commons) setting, where some design principles used in resource/commons governance are also relevant in explaining the COVID-19 outcome, the critical attributes of institutional-social-ecological factors are highlighted, ultimately helping policymakers devise more strategic measures to address the crisis.
Delayed Stroke Treatment during COVID-19 Pandemic in China
Authors: Gu Shiyuan , Dai Zhengze , Shen Huachao , Bai Yongjie , Zhang Xiaohao , Liu Xinfeng , Xu Gelin
Published: November 2020

Background

Social distance, quarantine, pathogen testing and other preventive strategies implemented during COVID-19 pandemic may negatively influence the management of acute stroke.

Objective

The current study aimed to evaluate the impacts of COVID-19 pandemic on treatment delay of acute stroke in China.

Methods

This study included patients with acute stroke admitted in two hospitals in Jiangsu, China. Patients admitted before and after the COVID-19 epidemic outbreak (January 31, 2020, as officially announced by Chinese government) were compared for pre- (measured as onset-to-door time) and post-hospital delay (measured as door-to-needle time). The influence factors for delayed treatment (indicated as onset-to-needle time >4.5 hours) were analyzed with multivariate logistic regression analysis.

Results

Onset-to-door time increased from 202 min (IQR 65-492) before to 317 min (IQR 75-790) after the COVID-19 pandemic (P=0.001). Door-to-needle time increased from 50min (IQR 40-75) before to 65 min (IQR 48-84) after the COVID-19 pandemic (P=0.048). The proportion of patients with intravenous thrombolysis in those with acute ischemic stroke was decreased significantly after the pandemic (15.4% vs 20.1%; P=0.030). Multivariate logistic regression analysis indicated that patients after COVID-19 pandemic, lower educational level, rural residency, mild symptoms and transported by other means than ambulance were associated with delayed treatment.

Conclusions

COVID-19 pandemic has remarkable impacts on the management of acute ischemic stroke. Both pre- and post-hospital delays were prolonged significantly, and proportion of patient arrived within the 4.5-hour time window for intravenous thrombolysis treatment was decreased. Given that anti-COVID-19 measures are becoming medical routines, efforts are warranted to shorten the delay so that the outcomes of stroke could be improved.
Meta-analysis of the SARS-CoV-2 serial interval and the impact of parameter uncertainty on the COVID-19 reproduction number
Authors: Challen Robert , Brooks-Pollock Ellen , Tsaneva-Atanasova Krasimira , Danon Leon
Published: November 2020

The serial interval of an infectious disease, commonly interpreted as the time between onset of symptoms in sequentially infected individuals within a chain of transmission, is a key epidemiological quantity involved in estimating the reproduction number. The serial interval is closely related to other key quantities, including the incubation period, the generation interval (the time between sequential infections) and time delays between infection and the observations associated with monitoring an outbreak such as confirmed cases, hospital admissions and deaths. Estimates of these quantities are often based on small data sets from early contact tracing and are subject to considerable uncertainty, which is especially true for early COVID-19 data. In this paper we estimate these key quantities in the context of COVID-19 for the UK, including a meta-analysis of early estimates of the serial interval. We estimate distributions for the serial interval with a mean 5.6 (95% CrI 5.1–6.2) and SD 4.2 (95% CrI 3.9–4.6) days (empirical distribution), the generation interval with a mean 4.8 (95% CrI 4.3–5.41) and SD 1.7 (95% CrI 1.0–2.6) days (fitted gamma distribution), and the incubation period with a mean 5.5 (95% CrI 5.1–5.8) and SD 4.9 (95% CrI 4.5–5.3) days (fitted log normal distribution). We quantify the impact of the uncertainty surrounding the serial interval, generation interval, incubation period and time delays, on the subsequent estimation of the reproduction number, when pragmatic and more formal approaches are taken. These estimates place empirical bounds on the estimates of most relevant model parameters and are expected to contribute to modelling COVID-19 transmission.
Interaction of intestinal bacteria with human rotavirus during infection in children
Authors: Gozalbo-Rovira Roberto , Rubio-del-Campo Antonio , Santiso-Bellón Cristina , Vila-Vicent Susana , Buesa Javier , Delgado Susana , Molinero Natalia , Margolles Abelardo , Yebra María Jesús , Collado María Carmen , Monedero Vicente , Rodríguez-Díaz Jesús
Published: November 2020

The gut microbiota has emerged as a key factor in the pathogenesis of intestinal viruses, including enteroviruses, noroviruses and rotaviruses (RV), where stimulatory and inhibitory effects on infectivity have been reported. With the aim of determining whether members of the microbiota interact with RV during infection, a combination of anti-RV antibody labelling, fluorescence-activated cell sorting and 16S rRNA amplicon sequencing was used to characterize the interaction between specific bacteria and RV in stool samples of children suffering diarrhea produced by G1P[8] RV. The genera Ruminococcus and Oxalobacter were identified as RV binders in stools, displaying enrichments between 4.8 to 5.4-fold compared to samples non-labelled with anti-RV antibodies. In vitro binding of the G1P[8] Wa human RV strain to two Ruminococcus gauvreauii human isolates was confirmed by fluorescence microscopy. Analysis in R. gauvreauii with antibodies directed to several histo-blood group antigens (HBGA) indicated that these bacteria express HBGA-like substances at their surfaces that can be the target for RV binding. Furthermore, in vitro infection of Wa strain in differentiated Caco-2 cells was significantly reduced by incubation with R. gauvreauii. These data, together with previous findings that had shown a negative correlation between Ruminococcus levels and antibody titers to RV in healthy individuals, suggest a pivotal interaction between this bacterial group and human RV. These results reveal likely mechanisms on how specific bacterial taxa of the intestinal microbiota could negatively affect RV infection and open new possibilities for anti-viral strategies.
A comparison of clinical outcomes, service satisfaction, and well-being in people using Acute Day Units and Crisis Resolution Teams: a cohort study in England
Authors: Lamb Danielle , Steare Thomas , Marston Louise , Canaway Alastair , Johnson Sonia , Kirkbride James B. , Lloyd-Evans Brynmor , Morant Nicola , Pinfold Vanessa , Smith Deb , Weich Scott , Osborn David
Published: November 2020

Background

For people in mental health crisis, Acute Day Units (ADUs) provide daily structured sessions and peer support in non-residential settings, often as an addition or alternative to Crisis Resolution Teams (CRTs). There is little recent evidence about outcomes for those using ADUs, particularly in comparison to those receiving CRT care alone.

Aims

To investigate readmission rates, satisfaction, and wellbeing outcomes for ADU and CRT service users.

Methods

A cohort study comparing readmission to acute mental health care during a six-month period for ADU and CRT participants. Secondary outcomes included satisfaction (CSQ), wellbeing (SWEMWBS), and depression (CES-D).

Results

We recruited 744 participants (ADU: 431, 58%; CRT 312, 42%) across 4 NHS Trusts/health regions. There was no statistically significant overall difference in readmissions; 21% of ADU participants (versus 23% CRT) were readmitted over 6 months (adjusted HR 0.78, 95%CI 0.54, 1.14). However, readmission results varied substantially by setting. At follow-up, ADU participants had significantly higher Client Satisfaction Questionnaire (CSQ) scores (2.5, 95% CI 1.4 to 3.5, p<0.001) and wellbeing scores (1.3, 95%CI 0.4 to 2.1, p=0.004), and lower depression scores (−1.7, 95%CI −2.7 to −0.8, p<0.001) than CRT participants.

Conclusions

Service users who accessed ADUs demonstrated better outcomes for satisfaction, wellbeing, and depression, and no significant differences in risk of readmission compared to those who only used CRTs. Given the positive outcomes for service users, and the fact that ADUs are inconsistently provided across the country, their value and place in the acute care pathway needs further consideration and research.
Glutathione as a molecular marker of functional impairment in patients with at-risk mental state: 7-Tesla 1H-MRS study
Authors: Jeon Peter , Limongi Roberto , Ford Sabrina D. , Branco Cassandra , Mackinley Michael , Gupta Maya , Powe Laura , Théberge Jean , Palaniyappan Lena
Published: November 2020

A substantial number of individuals with clinical high-risk (CHR) mental state do not transition to psychosis. However, regardless of future diagnostic trajectories, many of these individuals develop poor social and occupational functional outcomes. The levels of glutathione, a crucial cortical antioxidant, may track variations in functional outcomes in early psychosis and prodromal states.

Thirteen clinical high-risk and 30 healthy control volunteers were recruited for a 7-Tesla magnetic resonance spectroscopy scan with voxel positioned within the dorsal anterior cingulate cortex (ACC). Clinical assessment scores were collected to determine if any association was observable with glutathione levels.

Bayesian Spearman test revealed a positive association between the Social and Occupational Functioning Assessment Scale (SOFAS) and the glutathione concentration in the clinical high-risk group but not in the healthy control group. After accounting for variations in SOFAS, CHR group had higher GSH levels than the healthy subjects.

This study is the first to use 7-Tesla magnetic resonance spectroscopy to test whether ACC glutathione levels related to social and occupational functioning in a clinically high-risk group and offers preliminary support for glutathione levels as a clinically actionable marker of prognosis in emerging adults presenting with risk features for various severe mental illnesses.
An assessment of efficacy of Iodine complex (Renessans) against SARS-CoV-2 in non-human primates (Rhesus macaque)
Authors: Nawaz Muhammad , Ali Muhammad Asad , Ashraf Muhammad Adnan , Shabbir Muhammad Zubair , Shabbir Muhammad Abu Bakr , Altaf Imran , Raza Sohail , Rafique Saira , Hassan Sohail , Sardar Nageen , Mehmood Adnan , Aziz Muhammad Waqar , Fazal Sehar , Khan Muhammad Tahir , Attique Muhammad Moavia , Asif Ali , Ullah Zia , Iqbal Mubashir , Imtiaz Talha , Anwar Muhammad , Mukhtar Nadia , Yaqub Tahir
Published: November 2020

Renessans is an iodine complex which has provenin vitroantiviral activity including Anti-SARS-CoV-2 activity. The present study was designed to determine its efficacy against SARS-CoV-2 in monkeys (Rhesus macaque). A total of 14 monkeys were divided into four groups: A) Prophylactic group (n=03), (B) Treatment group (n=03), (C) infection control group (n=04) and (D) negative control group (n=04) and were housed in BSL-3 Animal facility while group D was housed at another animal house. Group A was administered with Renessans @ 2.85 mg/7 kg from 5 days prior to the infection to 08 days post infections (DPI). Group B was administered with Renessans from 03-08 DPI @ 2.85 mg/7 kg. Group C was administered with WIF only. The infection @ 2 × 106TCID of SARS-CoV-2 was given to all group monkeys through intranasal and oral route under anesthesia. Nasal swab samples (at different times) and fecal matter on daily basis were collected for the detection of SARS-CoV-2 through real-time quantitative PCR. Three monkeys (one from each of group A, B and C) were euthanized at 07 DPI to determine the gross pathological lesions and SARS-CoV-2 detection from internal tissues. Nasal swabs from all the monkeys from group A, B and C were positive for SARS-CoV-2 at 02 and 07 DPI (Day 05 of treatment). At 14 DPI, all (100%) nasal swabs from group A were negative for SARS-CoV-2 while 50% and 100% were positive from group B and C, respectively. At 21 DPI, monkeys from group B were negative and all in group C were still positive for SARS-CoV-2. Similarly, fecal matter of monkeys in group A and B was returned negative in significantly lesser time as compared to monkeys from infection control group. Based on these research findings it is concluded that the Renessans hasin-vivoSARS-CoV-2 activity and may result in early clearance of SARS-CoV-2. Therefore, a clinical trial of the drug in COVID-19 patients may reveal its anti-COVID-19 potential.
A comprehensive map of genetic interactions in childhood cancer reveals multiple underlying biological mechanisms
Authors: Daub Josephine T. , Amini Saman , Kersjes Denise J.E. , Ma Xiaotu , Jäger Natalie , Zhang Jinghui , Pfister Stefan M. , Holstege Frank C.P. , Kemmeren Patrick
Published: November 2020

Childhood cancer is a major cause of child death in developed countries. Genetic interactions between mutated genes play an important role in cancer development. They can be detected by searching for pairs of mutated genes that co-occur more (or less) often than expected. Co-occurrence suggests a cooperative role in cancer development, while mutual exclusivity points to synthetic lethality, a phenomenon of interest in cancer treatment research. Little is known about genetic interactions in childhood cancer. We apply a statistical pipeline to detect genetic interactions in a combined dataset comprising over 2,500 tumors from 23 cancer types. The resulting genetic interaction map of childhood cancers comprises 15 co-occurring and 27 mutually exclusive candidates. The biological mechanisms underlying most candidates are either tumor subtype, pathway epistasis or cooperation while synthetic lethality plays a much smaller role. Thus, other explanations beyond synthetic lethality should be considered when interpreting results of genetic interaction tests.
Genome-wide maps of nucleolus interactions reveal distinct layers of repressive chromatin domains
Authors: Bersaglieri Cristiana , Kresoja-Rakic Jelena , Gupta Shivani , Bär Dominik , Kuzyakiv Rostyslav , Santoro Raffaella
Published: November 2020

Eukaryotic chromosomes are folded into hierarchical domains, enabling the organization of the genome into functional compartments. Nuclear periphery and nucleolus are two nuclear landmarks thought to contribute to repressive chromosome architecture. However, while the role of nuclear lamina (NL) in genome organization has been well documented, the function of the nucleolus remains under-investigated due to the lack of methods for genome-wide maps of nucleolar associated domains (NADs). Here we established a method based on a Dam-fused engineered nucleolar histone H2B that marks DNA contacting the nucleolus. NAD-maps of ESCs and neural progenitors revealed layers of genome compartmentalization with distinct, repressive chromatin states based on the interaction with the nucleolus, NL, or both. NADs showed higher H3K9me2 and lower H3K27me3 content than regions exclusively interacting with NL. Upon ESC differentiation, chromosomes around the nucleolus acquire a more compact, rigid architecture whereas NADs specific for ESCs decrease their interaction strength within the repressive B-compartment strength, unlocking neural genes from repressive nuclear environment. The methodologies here developed will make possible to include the contribution of the nucleolus in future studies investigating the relationship between nuclear space and genome function.
Consensus molecular subtyping of colorectal cancers is influenced by goblet cell content
Authors: Miller Samuel A. , Ghobashi Ahmed , O’Hagan Heather M.
Published: November 2020

A critical obstacle in the field of colorectal cancer (CRC) is the establishment of precise tumor subtypes to facilitate the development of targeted therapeutic regimens. While dysregulated mucin production is a histopathological feature of multiple CRC subtypes, it is not clear how well these pathologies are associated with the proportion of goblet cells in the tumor, or whether or not this proportion is variable across all CRC. This study demonstrates that consensus molecular subtype 3 (CMS3) CRC tumors and cell lines are enriched for the expression of goblet cell marker genes. Further, the proportion of goblet cells in the tumor is associated with the probability of CMS3 subtype assignment and these CMS3 subtype tumors are mutually exclusive from mucinous adenocarcinoma pathologies. This study provides proof of principle for the use of machine learning classification systems to subtype tumors based on cellular content, and provides further context regarding the features weighing CMS3 subtype assignment.
The polarity specific nature of single session high-definition transcranial direct current stimulation to the cerebellum and prefrontal cortex on motor and non-motor task performance
Authors: Maldonado Ted , Bernard Jessica A.
Published: November 2020

The cerebellum has an increasingly recognized role in higher order cognition. Advancements in noninvasive neuromodulation techniques allows one to focally create functional alterations in the cerebellum to investigate its role in cognitive functions. To this point, work in this area has been mixed, in part due to varying methodologies for stimulation, and it is unclear whether or not transcranial direct current stimulation (tDCS) effects on the cerebellum are task or load dependent. Here, we employed a between-subjects design using a high definition tDCS system to apply anodal, cathodal, or sham stimulation to the cerebellum or prefrontal cortex (PFC) to examine the role the cerebellum plays in verbal working memory, inhibition, motor learning, and balance performance, and how this interaction might interact with the cortex (i.e. PFC). We predicted performance decrements following anodal stimulation and performance increases following cathodal stimulation, compared to sham. Broadly, our work provides evidence for cerebellar contributions to cognitive processing, particularly in verbal working memory and sequence learning. Additionally, we found the effect of stimulation might be load specific, particularly when applied to the cerebellum. Critically, anodal simulation negatively impacted performance during effortful processing, but was helpful during less effortful processing. Cathodal stimulation hindered task performance, regardless of simulation region. The current results suggest an effect of stimulation on cognition, perhaps suggesting that the cerebellum is more critical when processing is less effortful but becomes less involved under higher load when processing is more prefrontally-dependent.
Replicating bacterium-vectored vaccine expressing SARS-CoV-2 Membrane and Nucleocapsid proteins protects against severe COVID-19 disease in hamsters
Authors: Jia Qingmei , Bielefeldt-Ohmann Helle , Maison Rachel , Masleša-Galić Saša , Bowen Richard , Horwitz Marcus A.
Published: November 2020

An inexpensive readily manufactured COVID-19 vaccine that protects against severe disease is needed to combat the pandemic. We have employed the LVS ΔcapBvector platform, previously used successfully to generate potent vaccines against the Select Agents of tularemia, anthrax, plague, and melioidosis, to generate a COVID-19 vaccine. The LVS ΔcapBvector, a replicating intracellular bacterium, is a highly attenuated derivative of a tularemia vaccine (LVS) previously administered to millions of people. We generated vaccines expressing SARS-CoV-2 structural proteins and evaluated them for efficacy in the golden Syrian hamster, which develops severe COVID-19 disease. Hamsters immunized intradermally or intranasally with a vaccine co-expressing the Membrane (M) and Nucleocapsid (N) proteins, then challenged 5-weeks later with a high dose of SARS-CoV-2, were protected against severe weight loss and lung pathology and had reduced viral loads in the oropharynx and lungs. Protection by the vaccine, which induces murine N-specific interferon-gamma secreting T cells, was highly correlated with pre-challenge serum anti-N TH1-biased IgG. This potent vaccine against severe COVID-19 should be safe and easily manufactured, stored, and distributed, and given the high homology between MN proteins of SARS-CoV and SARS-CoV-2, has potential as a universal vaccine against the SARS subset of pandemic causing β-coronaviruses.
Evolved increases in hemoglobin-oxygen affinity and Bohr effect coincided with the aquatic specialization of penguins
Authors: Signore Anthony V. , Tift Michael S. , Hoffmann Federico G. , Schmitt Todd. L. , Moriyama Hideaki , Storz Jay F.
Published: November 2020

Dive capacities of air-breathing vertebrates are dictated by onboard O2stores, suggesting that physiological specializations of diving birds like penguins may have involved adaptive changes in convective O2transport. It has been hypothesized that increased hemoglobin (Hb)-O2affinity improves pulmonary O2extraction and enhance capacities for breath-hold diving. To investigate evolved changes in Hb function associated with the aquatic specialization of penguins, we integrated comparative measurements of whole-blood and purified native Hbs with protein engineering experiments based on site-directed mutagenesis. We reconstructed and resurrected ancestral Hbs representing the common ancestor of penguins and the more ancient ancestor shared by penguins and their closest nondiving relatives (order Procellariiformes, which includes albatrosses, shearwaters, petrels, and storm petrels). These two ancestors bracket the phylogenetic interval in which penguin-specific changes in Hb function would have evolved. The experiments revealed that penguins evolved a derived increase in Hb-O2affinity and a greatly augmented Bohr effect (reduced Hb-O2affinity at low pH). Although an increased Hb-O2affinity reduces the gradient for O2diffusion from systemic capillaries to metabolizing cells, this can be compensated by a concomitant enhancement of the Bohr effect, thereby promoting O2unloading in acidified tissues. We suggest that the evolved increase in Hb-O2affinity in combination with the augmented Bohr effect maximizes both O2extraction from the lungs and O2unloading from the blood, allowing penguins to fully utilize their onboard O2stores and maximize underwater foraging time.
Optimized detection of acute MHV68 infection with a reporter system identifies large peritoneal macrophages as a dominant target of primary infection
Authors: Riggs Julianne B. , Medina Eva M. , Perrenoud Loni J. , Bonilla Diana L. , Clambey Eric T. , van Dyk Linda F. , Berg Leslie J.
Published: November 2020

Investigating the dynamics of virus-host interactions in vivo remains an important challenge, often limited by the ability to directly identify virally-infected cells. Here, we combine detection of a beta-lactamase activated fluorescent substrate with full spectrum flow cytometry to identify primary targets of murine gammaherpesvirus 68 (MHV68) infection in the peritoneal cavity. By optimizing substrate and detection conditions, we were able to achieve multiparameter characterization of infected cells and the ensuing host response. MHV68 infection leads to a pronounced increase in immune cells, with CD8+ T cells increasing by 3 days, and total infiltrate peaking around 8 days post-infection. MHV68 infection results in near elimination of large peritoneal macrophages by 8 days post-infection, and a concordant increase in small peritoneal macrophages and monocytes. Infection is associated with prolonged changes to myeloid cells, with a distinct population of MHC IIhighlarge peritoneal macrophages emerging by 14 days. Targets of MHV68 infection could be readily detected. Between 1 to 3 days post-infection, MHV68 infects ~5-10% of peritoneal cells, with >75% being large peritoneal macrophages. By 8 days post-infection, the frequency of MHV68 infection is reduced at least 10-fold, with infection primarily in small peritoneal macrophages, with few infected dendritic cells and B cells. MHV68 infection at 3 days post-infection contains both lytic and latent infection, consistent with the identification of cells with active reporter gene expression. Our findings demonstrate the utility of the beta-lactamase MHV68 reporter system for high throughput single-cell analysis and identify dynamic changes during primary gammaherpesvirus infection.

Importance

Identifying virally-infected cells in vivo is key to tracking viral infection and understanding host-pathogen interactions. The ability to further characterize and phenotype virally-infected cells is technically challenging. We use a mouse gammaherpesvirus, MHV68, expressing a reporter gene to identify infected cells during primary infection via flow cytometry. Optimization using this reporter system allowed us to further characterize infected cells via multiparameter full spectrum flow cytometry. Our study provides a technical model for high throughput single-cell immunophenotyping methods in the context of gammaherpesvirus infection. Furthermore, we show that acute MHV68 infection in the peritoneal cavity dramatically changes the immune landscape of this tissue, results in a high number of infected macrophages at early times, and is characterized by both lytic and latent infection within immune cells.
A sense of being needed: an interpretative phenomenological analysis of hospital-based allied health professionals’ experiences during the COVID-19 pandemic
Authors: Oorsouw Roel van , Oerlemans Anke , Klooster Emily , Berg Manon van den , Kalf Johanna , Vermeulen Hester , Graff Maud , Wees Philip van der , Koenders Niek
Published: November 2020

Background

The outbreak of COVID-19 has led to many hospitalizations in the Netherlands and worldwide. As a result, the work of hospital-based allied health professionals changed rapidly. In such a healthcare crisis, professionals may not be able to fulfill their own professional values regarding good care, resulting in ethical issues and moral distress. The aim of this study was to explore the lived experiences of allied health professionals working in hospitals during the COVID-19 pandemic, including the ethical issues and moral distress these professionals might have encountered.

Methods and findings

Lived experiences were collected in semi-structured interviews with 39 allied health professionals including dieticians, occupational therapists, physical therapists, and speech-language therapists, working in four different hospitals in the Netherlands. Interviews were held in June and July 2020, after waning of the first wave of COVID-19 spreading. Interpretative phenomenological analysis revealed four themes: ‘a disease with great impact’, ‘personal health and safety’, ‘staying human in chaotic times’ and ‘solidarity and changing roles’. Participant experiences show that the virus and COVID-19 measures had a significant impact on the in-hospital working environment due to the massive downscaling of regular care, infection prevention measures and unknown risks to allied health professionals’ personal health. At the same time, participants experienced a certain freedom, which made room for authentic motives, connection and solidarity. Participants felt welcomed and appreciated at the COVID-19 wards and intensive care units, and were proud that they were able to fulfill their roles. The themes and accompanying ethical issues reflect a wide range of situations that were morally complex and led to moral distress.

Conclusions

To diminish long-lasting negative impact of the COVID-19 pandemic and moral distress, employers should empathize with experiences of allied health professionals and create conditions for ethical reflection. Our data show that allied health professionals value professional autonomy. Creating room for professional autonomy makes them feel needed, connected and energized. However, the needs of allied health professionals may conflict with organizational rules and structures.
Early impact of school closure and social distancing for COVID-19 on the number of inpatients with childhood non-COVID-19 acute infections in Japan
Authors: Kishimoto Kenji , Bun Seiko , Shin Jung-ho , Takada Daisuke , Morishita Tetsuji , Kunisawa Susumu , Imanaka Yuichi
Published: November 2020

Many countries have implemented school closures as part of social distancing measures intended to control the spread of coronavirus disease 2019 (COVID-19). The aim of this study was to assess the early impact of nationwide school closure (March-May 2020) and social distancing for COVID-19 on the number of inpatients with major childhood infectious diseases in Japan. Using data from the Diagnosis Procedure Combination system in Japan, we identified patients aged 15 years or younger with admissions for a diagnosis of upper respiratory tract infection (URTI), lower respiratory tract infection (LRTI), influenza, gastrointestinal infection (GII), appendicitis, urinary tract infection (UTI), or skin and soft tissue infection (SSTI) between July 2018 and June 2020. Two periods were considered in the analysis: a pre- and a post-school-closure period. Changes in the trend of the weekly number of inpatients between the two periods were assessed using interrupted time-series analysis. A total of 75,053 patients in 210 hospitals were included. We found a marked reduction in the number of inpatients in the post-school-closure period, with an estimated reduction of 581 (standard error 42.9) inpatients per week (p < 0.001). The main part of the reduction was for pre-school children. Remarkable decreases in the number of inpatients with URI, LRTI, and GII were observed, while there were relatively mild changes in the influenza, appendicitis, UTI, and SSTI groups. We confirmed a marked reduction in the number of inpatients with childhood non-COVID-19 acute infections in the post-school-closure period.
Isolation of nuclei and downstream processing of cell-type-specific nuclei from micro-dissected mouse brain regions – techniques and caveats
Authors: Chongtham M.C , Todorov H , Wettschereck J.E. , Gerber S. , Winter J.
Published: November 2020

The mammalian brain consists of several structurally and functionally distinct regions equipped with an equally complex cell-type system. Due to its relevance in uncovering disease mechanisms, the study of cell-type-specific molecular signatures of different brain regions has increased. The rapid evolution of newer and cheaper sequencing techniques has also boosted the interest in cell-type-specific epigenetic studies. In fact, the nucleus holds most of the cell’s epigenetic information and is quite resistant to tissue dissociation processes as compared to cells. As such, nuclei are continually preferred over cells for epigenetic studies. However, the isolation of nuclei from cells is still a biochemically complex process, with every step affecting downstream results. Therefore, it is necessary to use protocols that fit the experimental design to yield nuclei of high quality and quantity. However, the current protocols are not suitable for nuclei isolation of small volumes of micro-dissected brain regions from individual mouse brains.

Additionally, the caveats associated with centrifugation steps of nuclei extraction and the effects of different buffers have not been thoroughly investigated. Therefore, in this study, we describe an iodixanol based density gradient ultracentrifugation protocol suitable for micro-dissected brain regions from individual mice using ArccreERT2 (TG/WT).R26CAG-Sun1-sfGFP-Myc (M/WT or M/M). This mouse model shows sfGFP expression (sfGFP+) in the nuclear membrane of specific stimulus activated cells, thereby providing a good basis for the study - nuclei isolation and separation of cell-type-specific nuclei. The study also introduces new tools for rapid visualization and assessment of quality and quantity of nascent extracted nuclei. These tools were then used to examine critical morphological features of nuclei derived from different centrifugation methods and the use of different buffers to uncover underlying effects. Finally, to obtain cell-type-specific nuclei (sfGFP+nuclei) from the isolated nuclei pool of high viscosity, an optimized protocol for fluorescence activated nuclei sorting (FANS) was established to speed up sorting. Additionally, we present a 1% PFA protocol for fixation of isolated nuclei for long term microscopic visualization.
The early endosomal protein Rab21 is critical for enterocyte functions and intestinal homeostasis
Authors: Nassari Sonya , Lévesque Dominique , Boisvert François-Michel , Jean Steve
Published: November 2020

Membrane trafficking is defined as the vesicular transport of molecules into, out of, and throughout the cell. In intestinal enterocytes, defects in endocytic/recycling pathways result in impaired function and are linked to genetic diseases. However, how these trafficking pathways regulate intestinal tissue homeostasis is poorly understood. Using theDrosophilaintestine as anin vivomodel system, we investigated enterocyte-specific functions for the early endosomal trafficking machinery in gut homeostasis. We focused on the small GTPase Rab21, which regulates specific steps in early endosomal trafficking. Rab21-depleted guts showed severe abnormalities in intestinal morphology, with deregulated homeostasis associated with a gain in mitotic cells and increased cell death. Increases in both apoptosis and yorkie signaling were responsible for compensatory proliferation and tissue inflammation. Using a RNA interference screen, we identified specific regulators of autophagy and membrane trafficking that phenocopied Rab21 loss. We further showed that Rab21-induced hyperplasia was rescued by inhibition of epidermal growth factor receptor signaling, and identified improperly trafficked cargoes in Rab21-depleted enterocytes. Our data shed light on an important role for early endosomal trafficking, and particularly Rab21, in enterocyte-mediated intestinal homeostasis.
A wide-rangingPseudomonas aeruginosaPeptideAtlas build: a useful proteomic resource for a versatile pathogen
Authors: Reales-Calderón J.A. , Sun Z. , Mascaraque V. , Pérez-Navarro E. , Vialás V. , Deutsch E.W. , Moritz RL , Gil C. , Martínez JL , Molero G.
Published: November 2020

Pseudomonas aeruginosais an important opportunistic pathogen with high prevalence in nosocomial infections. This microorganism is a good model for understanding biological processes such as the quorum-sensing response, the metabolic integration of virulence, the mechanisms of global regulation of bacterial physiology, and the evolution of antibiotic resistance. Till now,P. aeruginosaproteomic data, although available in several on-line repositories, were dispersed and difficult to access. In the present work, proteomes of the PAO1 strain grown under very different conditions and from diverse cellular compartments have been analyzed and joined to build thePseudomonasPeptideAtlas. This resource is a comprehensive mass spectrometry-derived peptide and inferred protein database with 71.3% coverage of the total predicted proteome ofP. aeruginosaPAO1. This is the highest published coverage among the eight bacterial PeptideAtlas datasets currently available. The proteins in thePseudomonasPeptideAtlas cover 84% of metabolic proteins, 71% of proteins involved in genetic information processing, 72% of proteins responsible for environmental information processing, more than 80% of proteins related to quorum sensing and biofilm formation, and 81% of proteins responsible for antimicrobial resistance. It exemplifies a necessary tool for targeted proteomics studies, system-wide observations, and cross-species observational studies. Here we describe how this resource was built and some of the physiologically important proteins of this pathogen.

Significance

Pseudomonas aeruginosais among the most versatile bacterial pathogens. Studies of its proteome are very important as they can reveal virulence factors and mechanisms of antibiotic resistance. The construction of a proteomic resource such as the PeptideAtlas enables targeted proteomics studies, system-wide observations, and cross-species observational studies.
The human cytomegalovirus UL116 glycoprotein is a chaperone to control gH-based complexes levels on virions
Authors: Vezzani Giacomo , Amendola Diego , Yu Dong , Chandramuli Sumana , Frigimelica Elisabetta , Maione Domenico , Merola Marcello
Published: November 2020

Human cytomegalovirus (HCMV) relies in large part upon the viral membrane fusion glycoprotein B (gB) and two alternative gH/gL complexes, gH/gL/gO (Trimer) and the gH/gL/UL128/UL130/UL131A (Pentamer) to enter into cells. The relative amounts of the Trimer and Pentamer vary among HCMV strains and contribute to differences in cell tropism. Although the viral ER resident protein UL148 has been shown to interact with gH to facilitate gO incorporation, the mechanisms that favor the assembly and maturation of one complex over another remain poorly understood. HCMV virions also contain an alternative non-disulfide bound heterodimer comprised of gH and UL116 whose function remains unknown. Here, we show that disruption of HCMV geneUL116causes infectivity defects of ~10-fold relative to wild-type virus and leads to reduced expression of both gH/gL complexes in virions. Furthermore, gH that is not covalently bound to other viral glycoproteins, which are readily detected in wild-type HCMV virions, become undetectable in the absence ofUL116suggesting that the gH/UL116 complex is abundant in virions. We find evidence that UL116 and UL148 interact during infection indicating that the two proteins might cooperate to regulate the abundance of HCMV gH complexes. Altogether, these results are consistent with a role of UL116 as a chaperone for gH during the assembly and maturation of gH complexes in infected cells.
Modeling Versatile and Dynamic Anaerobic Metabolism for PAOs/GAOs Competition Using Agent-based Model and Verification via Single Cell Raman Micro-spectroscopy
Authors: Li Guangyu , Tooker Nicholas B. , Wang Dongqi , Srinivasan Varun , Barnard James L. , Russell Andrew , Stinson Beverley , McQuarrie Jim , Schauer Peter , Menniti Adrienne , Varga Erika , Hauduc Hélène , Takács Imre , Bott Charles , Dombrowski Paul , Onnis-Hayden Annalisa , Gu April Z.
Published: November 2020

Side-stream enhanced biological phosphorus removal process (S2EBPR) has been demonstrated to improve performance stability and offer a suite of advantages compared to conventional EBPR design. Design and optimization of S2EBPR require modification of the current EBPR models that were not able to fully reflect the metabolic functions of and competition between the polyphosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs) under extended anaerobic conditions as in the S2EBPR conditions. In this study, we proposed and validated an improved model (iEBPR) for simulating PAO and GAO competition that incorporated heterogeneity and versatility in PAO sequential polymer usage, staged maintenance-decay, and glycolysis-TCA pathway shifts. The iEBPR model was first calibrated against bulk batch testing experiment data, being proved to perform better than the previous EBPR model for predicting the soluble orthoP, ammonia, biomass glycogen, and PHA temporal profiles in a batch starvation testing under prolonged anaerobic conditions. We further validated the model with another independent set of batch anaerobic batch testing data that included high-resolution single-cell and specific population level intracellular polymer measurements enabled by the single-cell Raman micro-spectroscopy technique. The model accurately predicted the temporal changes in the intracellular polymers at cellular and population levels within PAOs and GAOs, and further confirmed the proposed mechanism of sequential polymer utilization, and polymer availability-dependent and staged maintenance-decay in PAOs. These results indicate that under extended anaerobic phases as in S2EBPR, the PAOs may gain competitive advantages over GAOs due to the possession of multiple intracellular polymers and the adaptive switching of the anaerobic metabolic pathways that consequently lead to the later and slower decay in PAOs than GAOs. The iEBPR model can be applied to facilitate and optimize the design and operations of S2EBPR for more reliable nutrient removal and recovery from wastewater.