bluuebunny/crossref_metadata_2025 huggingface dataset:
Complex photonic response reveals three-dimensional self-organization of structural coloured bacterial colonies
Authors: Schertel Lukas , van de Kerkhof Gea T. , Jacucci Gianni , Catón Laura , Ogawa Yu , Wilts Bodo D. , Ingham Colin J. , Vignolini Silvia , Johansen Villads E.
Published: May 2020

Vivid colours found in living organisms are often the result of scattering from hierarchical nanostructures, where the interplay between order and disorder in their packing defines visual appearance. In the case ofFlavobacteriumIR1, the complex arrangement of the cells in polycrystalline three-dimensional lattices is found to be a distinctive fingerprint of colony organization. By combining analytical analysis of the angle-resolved scattering response ofin vivobacterial colonies with numerical modelling, we show that we can assess the inter-cell distance and cell diameter with a resolution below 10 nm, far better than what can be achieved with conventional electron microscopy, suffering from preparation artefacts. Retrieving the role of disorder at different length scales from the salient features in the scattering response enables a precise understanding of the structural organization of the bacteria.
Coordinated changes across the O2transport pathway underlie adaptive increases in thermogenic capacity in high-altitude deer mice
Authors: Tate Kevin B. , Wearing Oliver H. , Ivy Catherine M. , Cheviron Zachary A. , Storz Jay F. , McClelland Grant B. , Scott Graham R.
Published: May 2020

Animals native to the hypoxic and cold environment at high altitude provide an excellent opportunity to elucidate the integrative mechanisms underlying the adaptive evolution and plasticity of complex traits. The capacity for aerobic thermogenesis can be a critical determinant of survival for small mammals at high altitude, but the physiological mechanisms underlying the evolution of this performance trait remain unresolved. We examined this issue by comparing high-altitude deer mice (Peromyscus maniculatus) with low-altitude deer mice and white-footed mice (P. leucopus). Mice were bred in captivity and adults were acclimated to each of four treatments: warm (25°C) normoxia, warm hypoxia (12 kPa O2), cold (5°C) normoxia or cold hypoxia. Acclimation to hypoxia and/or cold increased thermogenic capacity in deer mice, but hypoxia acclimation led to much greater increases in thermogenic capacity in highlanders than in lowlanders. The high thermogenic capacity of highlanders was associated with increases in pulmonary O2extraction, arterial O2saturation, cardiac output and arterial–venous O2difference. Mechanisms underlying the evolution of enhanced thermogenic capacity in highlanders were partially distinct from those underlying the ancestral acclimation responses of lowlanders. Environmental adaptation has thus enhanced phenotypic plasticity and expanded the physiological toolkit for coping with the challenges at high altitude.
DNA methylation mediates the effect of cocaine use on HIV severity
Authors: Shu Chang , Justice Amy C. , Zhang Xinyu , Wang Zuoheng , Hancock Dana B. , Johnson Eric O. , Xu Ke
Published: May 2020

Background

Cocaine use accelerates human immunodeficiency virus (HIV) progression and worsens HIV outcomes. We assessed whether DNA methylation in blood mediates the association between cocaine use and HIV severity in a veteran population.

Methods

We analyzed 1,435 HIV-positive participants from the Veterans Aging Cohort Study Biomarker Cohort (VACS-BC). HIV severity was measured by the Veteran Aging Cohort Study (VACS) index. We assessed the effect of cocaine use on VACS index and mortality among the HIV-positive participants. We selected candidate mediators that were associated with both persistent cocaine use and VACS index by epigenome-wide association (EWA) scans at a liberal p-value cutoff of 0.001. Mediation analysis of the candidate CpG sites between cocaine’s effect and the VACS index was conducted, and the joint mediation effect of multiple CpGs was estimated. A two-step epigenetic Mendelian randomization (MR) analysis was conducted as validation.

Results

More frequent cocaine use was significantly associated with a higher VACS index (β=1.00, p=2.7E-04), and cocaine use increased the risk of 10-year mortality (hazard ratio=1.10, p=0.011) with adjustment for confounding factors. Fifteen candidate mediator CpGs were selected from the EWA scan. Twelve of these CpGs showed significant mediation effects, with each explaining 11.3%-29.5% of the variation. The mediation effects for 3 of the 12 CpGs were validated by the two-step epigenetic MR analysis. The joint mediation effect of the 12 CpGs accounted for 47.2% of cocaine’s effect on HIV severity. Genes harboring these 12 CpGs are involved in the antiviral response(IFIT3, IFITM1, NLRC5, PLSCR1, PARP9)and HIV progression(CX3CR1, MX1).

Conclusions

We identified 12 DNA methylation CpG sites that appear to play a mediation role in the association between cocaine use and HIV severity.
Problems of Deploying CNN Transfer Learning to Detect COVID-19 from Chest X-rays
Authors: Majeed Taban , Rashid Rasber , Ali Dashti , Asaad Aras
Published: May 2020

The Covid-19 first occurs in Wuhan, China in December 2019. After that the virus spread all around the world and at the time of writing this paper the total number of confirmed cases are above 4.7 million with over 315000 deaths. Machine learning algorithms built on radiography images can be used as a decision support mechanism to aid radiologists to speed up the diagnostic process. The aim of this work is to conduct a critical analysis to investigate the applicability of convolutional neural networks (CNNs) for the purpose of COVID-19 detection in chest X-ray images and highlight the issues of using CNN directly on the whole image. To achieve this task, we first use 12-off-the-shelf CNN architectures in transfer learning mode on 3 publicly available chest X-ray databases together with proposing a shallow CNN architecture in which we train it from scratch. Chest X-ray images fed into CNN models without any preprocessing to follow the many of researches using chest X-rays in this manner. Next, a qualitative investigation performed to inspect the decisions made by CNNs using a technique known as class activation maps (CAM). Using CAMs, one can map the activations contributed most to the decision of CNNs back to the original image to visualize the most discriminating regions on the input image.

We conclude that CNN decisions should not be taken into consideration, despite their high classification accuracy, until clinicians can visually inspect, and approve, the region(s) of the input image used by CNNs that lead to its prediction.
Dynamic liver function indexes monitoring and clinical characteristics in three types of COVID-19 patients
Authors: Chen Cheng , Jiang Jie , Xu Xiaoxiao , Hu Yiyang , Hu Yi , Zhao Yu
Published: May 2020

Background and Aims: The abnormal liver function and even liver failure related death were reported in the COVID-19 patients, but less of studies focus on the dynamic liver function changes. We analysed the liver function indexes of COVID-19 patients to explore the characteristics of liver function changes in patients with different severity. Methods: This study included 54 moderate, 50 severe, and 31 death nucleic acid-confirmed COVID-19 patients hospitalized at the central hospital of Wuhan, China. Epidemiological histories, clinical features, imaging materials, medications and especially major liver function laboratory tests were collected for analysis. Results: The clinical symptoms did not present any significant difference in the patients at admission, but the older male patients had pronounced mortality risk. The normal ratio of ALT, TB, and DBIL of moderate patients was 96.3%, 94.44%, and 98.15% separately at the first test, but 59.26% of patients showed declined ALB levels. The normal ratio of all liver function indexes declined after admission, but most abnormalities were mild (1-2 times of upper limit unit) and went back normal before discharge. In severe patients, the normal ratio of ALB dropped down to 30.61% at admission along with the dramatic impaired normal ratio of bilirubin at the second test. The severe patients liver function dysfunction was worse than the moderate patients but without a significant difference. The dead patients showed a significantly higher level of DBIL, AST, GGT and CRP than other groups patients in the final test, along with the hypoalbuminemia. What is worse, 16.13% of non-survivors were diagnosed with liver failure. No medication was found to be related to ALT, AST, and GGT abnormality in our study. Conclusion: In moderate and severe patients, liver dysfunction was mild. Patients widely presented lower level of ALB. The higher level of bilirubin, AST, and GGT was likely to indicate the worse outcome. Dynamic monitoring of liver function indexes could be considered and liver failure related death should be noticed and prevented in the early stage.
Who is lonely in lockdown? Cross-cohort analyses of predictors of loneliness before and during the COVID-19 pandemic
Authors: Bu Feifei , Steptoe Andrew , Fancourt Daisy
Published: May 2020

Background

There are concerns internationally that lockdown measures taken during the COVID-19 pandemic could lead to a rise in loneliness. As loneliness is recognised as a major public health concern, it is therefore vital that research considers the impact of the current COVID-19 pandemic on loneliness in order to provide necessary support. But it remains unclear who is lonely in lockdown?

Methods

This study compared socio-demographic predictors of loneliness before and during the COVID-19 pandemic using cross-cohort analyses of data from UK adults captured before the pandemic (UK Household Longitudinal Study, n=31,064) and during the pandemic (UCL COVID-19 Social Study, n=60,341).

Results

Risk factors for loneliness were near identical prior to and during the pandemic. Young adults, women, people with lower education or income, the economically inactive, people living alone, and urban residents had a higher risk of being lonely. Some people who were already at risk for being lonely (e.g. young adults aged 18-30, people with low household income, and adults living alone) experienced a heightened risk during the COVID-19 pandemic compared to prior to COVID-19 emerging. Further, being a student emerged as a higher risk factor during lockdown than usual.

Conclusions

Findings suggest that interventions to reduce or prevent loneliness during COVID-19 should be targeted at those socio-demographic groups already identified as high-risk in previous research. These groups are likely not just to experience loneliness during the pandemic but to have an even higher risk than normal of experiencing loneliness relative to low-risk groups.
Modeling the Effects of Non-Pharmaceutical Interventions on COVID-19 Spread in Kenya
Authors: Gathungu Duncan K. , Ojiambo Viona N. , Kimathi Mark E. M. , Mwalili Samuel M.
Published: May 2020

Mathematical modeling of non-pharmaceutical interventions (NPIs) of COVID-19 in Kenya is presented. An SEIR compartment model is considered with additional compartments of hospitalized population whose condition is severe or critical and also the fatalities compartment. The basic reproduction number (R_0) is computed by next generation matrix approach and later expressed as a time-dependent function so as to incorporate the NPIs into the model. The resulting system of ordinary differential equations (ODEs) are solved using fourth-order and fifth-order Runge-Kutta methods. Different intervention scenarios are considered and results show that, implementation of closure of education insitutions, curfew and partial lockdown yield predicted delayed peaks of the overall infections, severe cases and fatalities and subsequently containement of the pandemic in the country.
COVID-19; Systematic and literature review of transmission, case definitions, clinical management and clinical trials.
Authors: McArthur Laura , Sakthivel DhanaSekaran , Ataide Ricardo , Chan Felicia , Richards Jack S , Narh Charles A
Published: May 2020

Background: SARS-CoV-2, the viral agent responsible for coronavirus disease 2019 (COVID-19) was identified in Wuhan, China at the end of December 2019. It rapidly spread to the rest of the world, and was declared a Public Health Emergency of International Concern on the 30th of January 2020. Our understanding of the virus, it is clinical manifestations and treatment options continues to evolve at an unparalleled pace.
Objective: This review sought to summarise the key literature regarding transmission, case definitions, clinical management and trials, and performed a systematic review of reported clinical data on COVID-19.
Synthesis methods: Two reviewers selected all the literature independently, and extracted information according to pre-defined topics.
Results: COVID-19 is pandemic with ~4 million cases and 270,000 deaths in 210 countries as of 8 May 2020. Our review of reports showed that SARS-CoV-2 was mainly transmitted via inhalation of respiratory droplets containing the virus and had an incubation period of four to six days. The commonly reported symptoms were fever (80%) and cough (60%) across the spectrum of clinical disease - mild, moderate, severe and critical. Categorization of these cases for home care or hospital management need to be well defined considering the age of the patient and the presence of underlying co-morbidities. The case definitions we reviewed varied among affected countries, which could have contributed to the differences observed in the mean case fatality rates among continents: Oceania (1%), Asia (3%), Africa (4%), South America (5%), North America (6%) and Europe (10%). Asymptomatic cases, which constituted an estimated 80% of COVID-19 cases are a huge threat to control efforts.
Conclusion: The presence of fever and cough may be sufficient to warrant a COVID-19 testing but using these symptoms in isolation will miss a proportion of cases. A clear definition of a COVID-19 case is important for managing, treating and tracking clinical illness. While several treatments are in development or in clinical trials for COVID-19, home care of mild/moderate cases and hospital care for severe and critical cases remain the recommended management for the disease. Quarantine measures and social distancing can help control the spread of SARS-CoV-2.
Serological prevalence of antibodies to SARS CoV-2 amongst cancer centre staff
Authors: Sikora Karol , Barwick Ian , Hamilton Ceri
Published: May 2020

Objectives

the aim of this study was to test Rutherford Health (RH) staff for the presence of SARS CoV-2 antibodies to reduce the risk of infection to cancer patients.

Setting

Between 14 and 24 April 2020 we tested 161 staff at four locations: our cancer centres in Reading - Berkshire, Newport - S Wales, Liverpool - Merseyside, and Bedlington in Northumberland.

Participants

Testing was available to all staff who were on site at the four locations named above at the time the study was carried out. 161 staff (80 men, 81 women) gave voluntary consent to have the tests and all testing gave rise to valid results.

Interventions

We used the South Korean test for antibodies to SARS CoV-2: Sugentech SGTi-flex COVID-19 IgM/IgG1. For each test, blood was collected and added to the sample well of the test cassette and buffer solution added. The test result was legible after 15 minutes. Outcome measures: The number of tests positive for the presence of antibodies was the primary outcome measure. The ratio of tests positive for the presence of IgM antibodies versus IgG antibodies was the secondary outcome measure.

Results

Between 14 and 24 April 2020, 161 staff (age m = 43) were tested at four Rutherford Cancer Care centres that offer proton beam therapy, radiotherapy and chemotherapy. Out of 161, 12 samples (7.50%) tested positive of which 7 samples (4.35%) detected IgM only, 2 samples (1.24%) detected IgG only and 3 samples (1.86%) detected both IgM and IgG.

Conclusions

The low seroconversion rate in the sample population limits the current utility of the test as a way of reducing risk to vulnerable patient populations but longitudinal retesting will provide further data.

Strengths and limitations of the study

This is the first UK study on SARS CoV-2 antibody testing using the Sugentech SGTi-flex COVID-19 IgM/IgG in the workplace;

This is the first UK study testing a population of cancer centre staff for SARS CoV-2 antibodies;

This study builds on similar studies in other countries3-4, albeit with a smaller sample;

Data on previous clinical symptoms is not included. We are in the process of revising consent paperwork for the test to include a question about previous symptoms like temperature, dry/persistent cough;

Patient data is not included. We will consider testing patients once the pilot test with staff has reached conclusions about the efficacy and value of the test.
Time series forecasting of COVID-19 confirmed cases with ARIMA model in the South East Asian countries of India and Thailand: a comparative case study
Authors: Chandu Viswa Chaitanya
Published: May 2020

Background

As economic burden makes it increasingly difficult for countries to continue imposing control measures, it is vital for countries to make predictions using time series forecasting before making decisions on lifting the restrictions.

Aim

Since apparent differences were noted in the disease transmission between the two South East Asian countries of India and Thailand, the study aims to draw comparative account of the progression of COVID 19 in near future between these two countries.

Methods

The study used data of COVID 19 confirmed cases in India and Thailand from WHO COVID 19 situation reports during the time period between 25th March, 2020 and 14th May, 2020. After determination of stationarity in the data and differencing, observation of autocorrelation function (ACF) and partial autocorrelation function (PACF), Auto Regressive Integrated Moving Average (ARIMA) (2,2,1) model was used to forecast the COVID 19 confirmed cases in both these countries for two weeks (i.e. 28th May, 2020). IBM SPSS version 20.0 software was used for data analysis.

Results

The study demonstrated a possible increasing trend in number of COVID 19 cases in India in the coming two weeks with an estimated point forecast of 1,28,772 (95% CI 115023–142520) by 28th May, 2020. A stationary phase was forecasted for Thailand with a difference of only 43 cases between 14th May (the last case of input data) and 28th May.

Conclusion

The time series forecasting employed in the present study warrants thorough preparation on part of the Indian health care system and authorities and calls for caution with regard to decisions made on lifting the control measures. The difference in the time series forecasting between these two South East Asian countries also highlights the need for strengthening of public health systems.
Pitfalls and solutions in case fatality risk estimation – A multi-country analysis on the role of demographics, surveillance, time lags between reporting and death and healthcare system capacity on COVID-19
Authors: Vanella Patrizio , Wiessner Christian , Holz Anja , Krause Gérard , Möhl Annika , Wiegel Sarah , Lange Berit , Becher Heiko
Published: May 2020

European countries report large differences in COVID-19 case fatality risk (CFR) and high variation over the year. CFR estimates may both depend on the method used for estimation and of country-specific characteristics. While crude methods simply use cumulative total numbers of cases and deaths, the CFR can be influenced by the demographic characteristics of the cases, case detection rates, time lags between reporting of infections and deaths and infrastructural characteristics, such as healthcare capacities.

We used publicly available weekly data from the national health authorities of Germany, Italy, France and Spain on case and death numbers by age group connected to COVID-19 for the year 2020. We propose to use smoothed data of national weekly test rates for case adjustment and investigated the impact of different time lags from case reporting to death on the estimation of the CFR. Finally, we described the association between case fatality and the demand for hospital beds for COVID-19, taking into account national hospital bed capacities.

Crude CFR estimates differ considerably between the four study countries with end-of-year values of approximately 1.9%, 3.5%, 2.5% and 2.7% for Germany, Italy, France and Spain, respectively. Age-adjustment reduces the differences considerably, resulting in values of 1.61%, 2.4% and 2% for Germany, Italy and Spain, respectively. France’s age-specific data was restricted to hospitalised cases only and is therefore not comparable in that regard. International crude International CFR time series show smaller differences when adjusting for demographics of the cases or the test rates. Curves adjusted for age structure, testing or time lags show smaller variance over the year and a smaller degree of non-stationarity. The data does not suggest any connection of CFRs to hospital capacities for the four countries under study.
Extended Storage of SARS-CoV2 Nasopharyngeal Swabs Does Not Negatively Impact Results of Molecular-Based Testing
Authors: Skalina Karin A , Goldstein D. Yitzchak , Sulail Jaffar , Hahm Eunkyu , Narlieva Momka , Szymczak Wendy , Fox Amy S.
Published: May 2020

With the global outbreak of the novel coronavirus disease 2019, the demand for testing rapidly increased and quickly exceeded the testing capacities for many laboratories. Clinical tests which receive CE and FDA authorizations cannot always be tested thoroughly in a real-world environment. Here we demonstrate the long-term stability of nasopharyngeal swab specimens for SARS-CoV-2 molecular testing across three assays recently approved by the U.S. FDA under Emergency Use Authorization. This study demonstrates that nasopharyngeal swab specimens can be stored under refrigeration or even ambient conditions for 21 days without clinically impacting the results of the real-time RT-PCR testing.
Local propagation dynamics of MEG interictal spikes: source reconstruction with traveling wave priors
Authors: Kuznetsova Aleksandra , Lebedev Mikhail , Ossadtchi Alexei
Published: May 2020

Abstract

Epilepsy is one of the most common neurological disorders, with about 30% of cases being drug-resistant and requiring surgical intervention. To localize the epileptogenic zone (EZ), the pathological area that has to be surgically removed, brain regions are inspected for the presence of spikes during the interictal periods. This procedure maps irritative zones where spikes are present, but it is still challenging to determine which of the irritative zones generate seizures. To localize the source of seizures more precisely, a large-scale approach could be applied where the causal relationship is assessed between the signals recorded in a finite number of irritative zones [27]. This method however, does not reveal the fine-grained spatiotemporal patterns of spikes, which could provide valuable information regarding EZ location and increase the likelihood of surgery success [33].

Here we present a framework to noninvasively investigate the fine patterns of interictal spikes present in magnetoencephalographic (MEG) data. We use a traveling wave model, previously employed in the analysis of cortical alpha oscillations [16], to regularize the MEG inverse problem and to determine the cortical paths of spike traveling waves. Our algorithm represents spike propagation patterns as a superposition of local waves traveling along radial paths stemming from a single origin. With the help of the positively constrained LASSO technique we scan over wave onset moment and propagation velocity parameters to determine their combination that yields the best fit to the MEG sensor data of each spike.

We first used realistically simulated MEG data to validate the algorithm ability to successfully track interictal activity on a millimeter-millisecond scale. Next, we examined MEG data from three patients with drug-resistant epilepsy. Wave-like spike patterns with clear propagation dynamics were found in a fraction of spikes, whereas the other fraction could not be explained by the wave propagation model with a small number of propagation directions. Moreover, in agreement with the previous work [33], the spike waves with clear propagation dynamics exhibited spatial segregation and matched the clinical records on seizure onset zones (SOZs) available for two patients out of three.
COVID-19 death rates by age and sex and the resulting mortality vulnerability of countries and regions in the world
Authors: Guilmoto Christophe Z Z
Published: May 2020

The growing number of series on COVID-19 deaths classified by age and sex, released by national health authorities, has allowed us to compute age and sex patterns of its mortality, based on 183,619 deaths from Western Europe and the USA. We highlight the specific age schedule of COVID-19 mortality and its pronounced excess male mortality and we then apply these COVID-19 death rates to world populations, in 2020. Our results underscore that considerable variations exist between world regions, as concerns the potential impact of COVID-19 mortality, because of their demographic structures. When compared to younger countries in Sub-Saharan Africa, the vulnerability to COVID-19 mortality is shown to be 17 times higher in several industrialized countries of East Asia and Europe. There is a high correlation (r2= .44) between demographic vulnerability to COVID-19 mortality and current COVID-19 death rates.
Dynamic meta-analysis: a method of using global evidence for local decision making
Authors: Shackelford Gorm E. , Martin Philip A. , Hood Amelia S. C. , Christie Alec P. , Kulinskaya Elena , Sutherland William J.
Published: May 2020

Meta-analysis is often used to make generalizations across all available evidence at the global scale. But how can these global generalizations be used for evidence-based decision making at the local scale, if only the local evidence is perceived to be relevant to a local decision? We show how an interactive method of meta-analysis — dynamic meta-analysis — can be used to assess the local relevance of global evidence. We developed Metadataset (www.metadataset.com) as an example of dynamic meta-analysis. Using Metadataset, we show how evidence can be filtered and weighted, and results can be recalculated, using dynamic methods of subgroup analysis, meta-regression, and recalibration. With an example from agroecology, we show how dynamic meta-analysis could lead to different conclusions for different subsets of the global evidence. Dynamic meta-analysis could also lead to a rebalancing of power and responsibility in evidence synthesis, since evidence users would be able to make decisions that are typically made by systematic reviewers — decisions about which studies to include (e.g., critical appraisal) and how to handle missing or poorly reported data (e.g., sensitivity analysis). We suggest that dynamic meta-analysis could be scaled up and used for subject-wide evidence synthesis in several scientific disciplines (e.g., agroecology and conservation biology). However, the metadata that are used to filter and weight the evidence would need to be standardized within disciplines.
Investigation of biological activities ofColocasia giganteaHook.f. leaves and PASS prediction, in silico molecular docking with ADME/T analysis of its isolated bioactive compounds
Authors: Alam Safaet , Emon Nazim Uddin , Rashid Mohammad A. , Arman Mohammad , Haque Mohammad Rashedul
Published: May 2020

Background

Colocasia giganteais locally named as kochu and also better known due to its various healing power. This research is to investigate the antidiarrheal, antimicrobial, and antioxidant possibilities of the methanol soluble extract ofColocasia gigantea.

Methods

Antidiarrheal investigation was performed by usingin vivocastor oil induced diarrheal method where asin vitroantimicrobial and antioxidant investigation have been implemented by disc diffusion and DPPH scavenging method respectively. Moreover,in silicostudies were followed by molecular docking analysis of several secondary metabolites were appraised with Schrödinger-Maestro v 11.1.

Results

The induction of plant extract (200 and 400 mg/kg, b.w, p.o), the castor oil mediated diarrhea has been minimized 19.05 % (p < 0.05) and 42.86 % (p < 0.001) respectively. The methanolic extract ofC. giganteashowed mild sensitivity against almost all the tested strains but it shows high consistency of phenolic content and furthermore yielded 67.68 μg/mL of IC50value in the DPPH test. The higher and lower binding affinity was shown in beta-amyrin and monoglyceryl stearic acid against the kappa-opioid receptor (PDB ID: 4DJH) with a docking score of -3.28 kcal/mol and -6.64 kcal/mol respectively. In the antimicrobial investigation, Penduletin and Beta-Amyrin showed the highest and lowest binding affinity against the selected receptors with the docking score of -8.27 kcal/mol and -1.66 kcal/mol respectively.

Conclusion

The results of our scientific research reflect that the methanol soluble extract ofC. giganteais safe which may provide possibilities of alleviation of diarrhea and as a potential wellspring of antioxidants which can be considered as an alternate source for exploration of new medicinal products.
Kinship, acquired and inherited status, and population structure at the Early Bronze Age Mokrin necropolis in northern Serbia
Authors: Žegarac Aleksandra , Winkelbach Laura , Blöcher Jens , Diekmann Yoan , Gavrilović Marija Krečković , Porčić Marko , Stojković Biljana , Milašinović Lidija , Schreiber Mona , Wegmann Daniel , Veeramah Krishna R. , Stefanović Sofija , Burger Joachim
Published: May 2020

Twenty-four ancient genomes with an average sequencing coverage of 0.85±0.25 X were produced from the Mokrin necropolis, an Early Bronze Age (2,100-1,800 BC) Maros culture site in Serbia, to provide unambiguous identification of biological sex, population structure, and genetic kinship between individuals. Of the 24 investigated individuals, 15 were involved in kinship relationships of varying degrees, including 3 parent-offspring relationships. All observed parent-offspring pairs were mother and son. In addition to the absence of biological daughters, we observed a number of young women and girls with no biological relatives in our sample. These observations, together with the high mitochondrial diversity in our sample, are consistent with the practice of female exogamy in the population served by Mokrin. However, moderate-to-high Y-chromosomal diversity suggests a degree of male mobility greater than that expected under strict patrilocality. Individual status differences at Mokrin, as indicated by grave goods, support the inference that females could inherit status, but could not transmit status to all their sons. The case of a son whose grave good richness outstrips that of his biological mother suggests that sons had the possibility to acquire status during their lifetimes. The Mokrin sample resembles a genetically unstructured population, suggesting that the community’s social hierarchies were not accompanied by strict marriage barriers.
An ex vivo model ofToxoplasmarecrudescence
Authors: Goerner Amber L. , Vizcarra Edward A. , Hong David D. , Bergersen Kristina V. , Alvarez Carmelo A. , Talavera Michael A. , Wilson Emma H. , White Michael W.
Published: May 2020

Toxoplasmahas been a useful parasite model for decades because it is relatively easy to genetically modify and culture, however, attempts to generate and study the recrudescence of tissue cysts have come up short with lab-adapted strains generating low numbers of tissue cysts in vivo. Here we have established a new model ofToxoplasmarecrudescence using bradyzoites from an unadapted Type II ME49 strain (ME49EW) isolated from murine brain tissue. Ex vivo bradyzoite infection of fibroblasts and astrocytes produced sequential tachyzoite growth stages; a fast-growing stage was followed by formation of a slower-growing stage. In astrocytes, but not in fibroblasts, bradyzoites also initiated a second recrudescent pathway involving bradyzoite to bradyzoite replication. Intraperitoneal infections of mice with either bradyzoites or the fast-growing tachyzoite stage efficiently disseminated to brain tissue leading to high numbers of tissue cysts, while infections with the slow-growing tachyzoite stage were largely retained in the peritoneum. Poor infection and cyst formation of slow-growing tachyzoites was reversible by serial tissue cyst passage, while the poor tissue cyst formation of lab-adapted tachyzoites was not reversible by these approaches. To distinguish strain developmental competency, we identifiedToxoplasmagenes highly expressed in ME49EW in vivo tissue cysts and developed a qPCR approach that differentiates immature from mature bradyzoites. In summary, the results presented describe a new ex vivo bradyzoite recrudescence model that fully captures the growth and developmental processes during toxoplasmosis reactivation in vivo opening the door to the further study of these important features of theToxoplasmaintermediate life cycle.
Dissemination of Carbapenem-resistance and Plasmids-encoding Carbapenemases in Gram-negative Bacteria Isolated from India
Authors: Manohar Prasanth , Leptihn Sebastian , Lopes Bruno S. , Ramesh Nachimuthu
Published: May 2020

Carbapenem resistance in Gram-negative bacteria is an ongoing public-health problem of global dimensions leaving very few treatment options for severely infected patients. This study focuses on the dissemination of plasmid-borne carbapenemase genes in Gram-negative bacteria in Tamil Nadu, India. A total of 151 non-repetitive isolates belonging to 11 genera were collected from a diagnostic center in Tamil Nadu.E. coli(n=57) isolates were classified as, Enteropathogenic (n=12), Enteroaggregative (n=9), Enterohemorrhagic (n=8), Enterotoxigenic (n=3), Enteroinvasive (n=1) and unclassifiedE. coli(n=24). Of the 45Klebsiellaspecies, 14 were K1 whereas 11 were K2 serotype and in 20Klebsiellaserotype could not be determined. Other isolates (n=49) consisted ofP. aeruginosa,S. typhi,E. cloacae,A. baumannii,S. marcescens,A. xylosoxidans,P. mirabilisandE. meningoseptica. Of the 151 isolates, 71% (n=107) and 68% (n=103) were found to be resistant to meropenem and imipenem respectively. The most prevalent beta-lactamase gene wasblaNDM-1(21%, 12/57) followed byblaOXA-181(16%, 9/57),blaGES-9(n=8),blaOXA-23(n=7),blaIMP-1(n=3),blaGES-1(n=11) andblaOXA-51(n=9). The unusual presence ofblaOXA-23was seen inE. coli(n=4), andblaOXA-23andblaOXA-51(IncA/C) inK. pneumoniae(n=3). Plasmid incompatibility (inc/rep) typing results showed that the plasmids carrying resistance genes (n=11) belonged to IncX, IncA/C, IncFIA-FIB and IncFIIA groups.E. coliandK. pneumoniaewere able to transfer plasmid-borne carbapenemase via conjugation. This study highlights the prevalence of carbapenem resistance and the acquisition of plasmid-borne carbapenemase genes in Gram-negative bacteria highlighting the role of plasmid transfer in disseminating resistance.
Phytoplankton trigger the production of cryptic metabolites in the marine actinobacteriaSalinispora tropica
Authors: Chhun Audam , Sousoni Despoina , del Mar Aguiló-Ferretjans Maria , Song Lijiang , Corre Christophe , Christie-Oleza Joseph A.
Published: May 2020

Bacteria from the Actinomycete family are a remarkable source of natural products with pharmaceutical potential. The discovery of novel molecules from these organisms is, however, hindered because most of the biosynthetic gene clusters (BGCs) encoding these secondary metabolites are cryptic or silent and are referred to as orphan BGCs. While co-culture has proven to be a promising approach to unlock the biosynthetic potential of many microorganisms by activating the expression of these orphan BGCs, it still remains an underexplored technique. The marine actinobacteriaSalinispora tropica, for instance, produces valuable compounds such as the anti-cancer molecule salinosporamide A but half of its putative BGCs are still orphan. Although previous studies have looked into using marine heterotrophs to induce orphan BGCs inSalinispora, the potential impact of co-culturing marine phototrophs withSalinisporahas yet to be investigated. Following the observation of clear antimicrobial phenotype of the actinobacterium on a range of phytoplanktonic organisms, we here report the discovery of novel cryptic secondary metabolites produced byS. tropicain response to its co-culture with photosynthetic primary producers. An approach combining metabolomics and proteomics revealed that the photosynthate released by phytoplankton influences the biosynthetic capacities ofS. tropicawith both production of new molecules and the activation of orphan BGCs. Our work pioneers the use of phototrophs as a promising strategy to accelerate the discovery of novel natural products from actinobacteria.

Importance

The alarming increase of antimicrobial resistance has generated an enormous interest in the discovery of novel active compounds. The isolation of new microbes to untap novel natural products is currently hampered because most biosynthetic gene clusters (BGC) encoded by these microorganisms are not expressed under standard laboratory conditions,i.e.mono-cultures. Here we show that co-culturing can be an easy way for triggering silent BGC. By combining state-of-the-art metabolomics and high-throughput proteomics, we characterized the activation of cryptic metabolites and silent biosynthetic gene clusters in the marine actinobacteriaSalinispora tropicaby the presence of phytoplankton photosynthate. We further suggest a mechanistic understanding of the antimicrobial effect this actinobacterium has on a broad range of prokaryotic and eukaryotic phytoplankton species and reveal a promising candidate for antibiotic production.
Early assessment of knowledge, attitudes, anxiety and behavioral adaptations of Connecticut residents to COVID-19
Authors: Ha Toan , Schensul Stephen , Lewis Judy , Brown Stacey
Published: May 2020

Objectives. To assess knowledge, attitudes, anxiety and behavioral adaptations to COVID-19.

Methods. A cross-sectional study was conducted among non-healthcare-related participants after a stringent stay-at-home directive was implemented. Multivariate logistic regression analysis was conducted to identify factors associated with anxiety, perceived seriousness of COVID-19 and loneliness.

Results. A total of 464 participants responded to the survey. Most participants recognized cough, shortness of breath and fever as primary symptoms of COVID-19. Nearly 50% reported high levels of anxiety to COVID-19 and 48% reported being loneliness during the social isolation. Those with higher level of COVID-19 knowledge had 1.20 times higher levels with anxiety. Being married had 1.79 times higher levels of anxiety about COVID-19. Older age was associated with loneliness during the social isolation. Older age was also associated with taking the pandemic seriously. Females were less likely to report loneliness than males.

Conclusions. It is crucial for the public health authorities not only provide accurate and scientific information about the COVID-19 promoting protective behavior changes but also to minimize anxiety through supportive messages and recommendations for positive coping strategies and timely offering of counseling services for those in need.
Normalization of single-cell RNA-seq counts by log(x+1)* or log(1+x)*
Authors: Booeshaghi A. Sina , Pachter Lior
Published: May 2020

Single-cell RNA-seq technologies have been successfully employed over the past decade to generate many high resolution cell atlases. These have proved invaluable in recent efforts aimed at understanding the cell type specificity of host genes involved in SARS-CoV-2 infections. While single-cell atlases are based on well-sampled highly-expressed genes, many of the genes of interest for understanding SARS-CoV-2 can be expressed at very low levels. Common assumptions underlying standard single-cell analyses don’t hold when examining low-expressed genes, with the result that standard workflows can produce misleading results.

Key Points

Lowly expressed genes in single-cell RNA-seq can be easliy misanalyzed.

log(1+x) count normalization introduces errors for lowly expressed genes

The average log(1+x) expression differs considerably from log(x) when x is small

An alternative approach is to use the fraction of cells with non-zero expression
Ribo-Pop: Simple, cost-effective, and widely applicable ribosomal RNA depletion
Authors: Thompson Mary Kay , Kiourlappou Maria , Davis Ilan
Published: May 2020

The measurement of RNA abundance derived from massively parallel sequencing experiments is an essential technique. Methods that reduce ribosomal RNA levels are usually required prior to sequencing library construction because ribosomal RNA typically comprises the vast majority of a total RNA sample. For some experiments, ribosomal RNA depletion is favored over poly(A) selection because it offers a more inclusive representation of the transcriptome. However, methods to deplete ribosomal RNA are generally proprietary, complex, inefficient, applicable to only specific species, or compatible with only a narrow range of RNA input levels. Here, we describe Ribo-Pop (ribosomal RNA depletion for popular use), a simple workflow and antisense oligo design strategy that we demonstrate works over a wide input range and can be easily adapted to any organism with a sequenced genome. We provide a computational pipeline for probe selection, a streamlined 20-minute protocol, and ready-to-use oligo sequences for several organisms. We anticipate that our simple and generalizable “open source” design strategy would enable virtually any lab to pursue full transcriptome sequencing in their organism of interest with minimal time and resource investment.
Using targeted genome integration for virus-free genome-wide mammalian CRISPR screen
Authors: Xiong Kai , Karottki Karen Julie la Cour , Hefzi Hooman , Li Songyuan , Grav Lise Marie , Li Shangzhong , Spahn Philipp , Lee Jae Seong , Lee Gyun Min , Kildegaard Helene Faustrup , Lewis Nathan E. , Pedersen Lasse Ebdrup
Published: May 2020

Pooled CRISPR screens have been widely applied in mammalian cells to discover genes regulating various phenotypes of interest. In such screens, CRISPR components are generally delivered with a lentivirus. However, lentiviral CRISPR screens are limited by unpredictable genome insertion, the requirement of biosafety level II lab facilities and personnel trained to work with viruses. Here we established a virus-free (VF) genome-wide CRISPR screening platform for Chinese hamster ovary (CHO) cells with 74,617 gRNAs targeting 18,353 genes. Each gRNA expression cassette in the library is precisely integrated into a genomic landing pad thus reducing the clonal variation. Using this VF CRISPR screening platform, 338 genes are identified as essential for CHO cell growth and 76 genes were found to be involved in the unfolded protein response (UPR) induced endoplasmic reticulum (ER) stress. Extensive validation of the candidate genes further demonstrated the robustness of this novel non-viral CRISPR screen method.
Cryptic prophages within aStreptococcus pyogenesgenotypeemm4 lineage
Authors: Remmington Alex , Haywood Samuel , Edgar Julia , Turner Claire E.
Published: May 2020

The major human pathogenStreptococcus pyogenesshares an intimate evolutionary history with mobile genetic elements, which in many cases, carry genes encoding bacterial virulence factors. During recent whole genome sequencing of a longitudinal sample ofS. pyogenesisolates in the United Kingdom, we identified a lineage withinemm4 that clustered with the reference genome MEW427. Like MEW427, this lineage was characterised by substantial gene loss within all three prophage regions, compared to MGAS10750 and isolates outside of the MEW427-like lineage. Gene loss primarily affected lysogeny, replicatory and regulatory modules, and to a lesser and more variable extent, structural genes. Importantly, prophage-encoded superantigen and DNase genes were retained in all isolates. In isolates where the prophage elements were complete, like MGAS10750, they could be induced experimentally, but not in MEW427-like isolates with degraded prophages. We also found gene loss within the chromosomal island SpyCIM4 of MEW427-like isolates, although surprisingly, the SpyCIM4 element could not be experimentally induced in either MGAS10750-like or MEW427-like isolates. This did not, however, appear to abolish expression of the mismatch repair operon, within which this element resides. The inclusion of furtheremm4 genomes in our analyses ratified our observations and revealed an internationalemm4 lineage characterised by prophage degradation. Intriguingly, the USA population ofemm4S. pyogenesappeared to constitute predominantly MEW427-like isolates, whereas the UK comprised both MEW427-like and MGAS10750-like strains. The degradation and cryptic nature of these elements may have important phenotypic ramifications foremm4S. pyogenesand the geographical distribution of this lineage raises interesting questions on the population dynamics of the genotype.

Data summary

All raw sequence data used in this study has been previously published and was obtained from NCBI short read archive. Accession numbers and citations for the genome data for each individual isolate is provided in Supplementary Table 1.
Structure and Evolution of Constitutive Bacterial Promoters
Authors: Lagator Mato , Sarikas Srdjan , Steinrück Magdalena , Toledo-Aparicio David , Bollback Jonathan P. , Tkacik Gasper , Guet Calin C.
Published: May 2020

Predicting gene expression levels from any DNA sequence is a major challenge in biology. Using libraries with >25,000 random mutants, we developed a biophysical model that accounts for major features of σ70-binding bacterial promoters to accurately predict constitutive gene expression levels of any sequence. We experimentally and theoretically estimated that 10-20% of random sequences lead to expression and 82% of non-expressing sequences are one point mutation away from a functional promoter. Generating expression from random sequences is pervasive, such that selection acts against σ70-RNA polymerase binding sites even within inter-genic, promoter-containing regions. The pervasiveness of σ70– binding sites, which arises from the structural features of promoters captured by our biophysical model, implies that their emergence is unlikely the limiting step in gene regulatory evolution.
The autophagy adaptor NDP52 and the FIP200 coiled-coil allosterically activate ULK1 complex membrane recruitment
Authors: Shi Xiaoshan , Chang Chunmei , Yokom Adam L. , Hurley James H.
Published: May 2020

The selective autophagy pathways of xenophagy and mitophagy are initiated when the adaptor NDP52 recruits the ULK1 complex to autophagic cargo. Hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS) was used to map the membrane and NDP52 binding sites of the ULK1 complex to unique regions of the coiled coil of the FIP200 subunit. Electron microscopy of the full-length ULK1 complex shows that the FIP200 coiled coil projects away from the crescent-shaped FIP200 N-terminal domain dimer. NDP52 allosterically stimulates membrane-binding by FIP200 and the ULK1 complex by promoting a more dynamic conformation of the membrane-binding portion of the FIP200 coiled coil. Giant unilamellar vesicle (GUV) reconstitution confirmed that membrane recruitment by the ULK1 complex is triggered by NDP52 engagement. These data reveal how the allosteric linkage between NDP52 and the ULK1 complex could drive the first membrane recruitment event of phagophore biogenesis in xenophagy and mitophagy.