bluuebunny/crossref_metadata_2025 huggingface dataset:
Experience with Social Distancing Early in the COVID-19 Pandemic in the United States: Implications for Public Health Messaging
Authors: Moore Ryan C. , Lee Angela , Hancock Jeffrey T. , Halley Meghan , Linos Eleni
Published: April 2020

Our goal is to inform ongoing public health policy on the design and communication of COVID-19 social distancing measures to maximize compliance. We assessed the US public’s early experience with the COVID-19 crisis during the period when shelter-in-place orders were widely implemented to understand non-compliance with those orders, sentiment about the crisis, and to compare across age categories associated with different levels of risk. We posted our survey on Twitter, Facebook, and NextDoor on March 14th to March 23rd that included 21 questions including demographics, impact on daily life, actions taken, and difficulties faced.1 We analyzed the free-text responses to the impact question using LIWC, a computational natural language processing tool2, and performed a thematic content analysis of the reasons people gave for non-compliance with social distancing orders. Stanford University’s IRB approved the study.

In 9 days, we collected a total of 20,734 responses. 6,573 individuals provided a response (≥30 words) to the question, “Tell us how the coronavirus crisis is impacting your life.” Our data (Figure 1) show that younger people (18-31) are more emotionally negative, self-centered, and less concerned with family, while middle-aged people are group-oriented (32-44) and focused on family (32-64) (all p values < .05 corrected for multiple comparisons). Unsurprisingly, the oldest and most at-risk group (65+) are more focused on biological terms (e.g., health-related topics), but were surprisingly low in anxiety and high in emotionally positive terms relative to those at lower risk.

We also content-analyzed 7,355 responses (kappa’s > .75) to the question, “What are the reasons you are not self-isolating more?” Of these participants, 39.8% reported not being compliant, with the youngest group (18-31) having the lowest compliance rate (52.4%) compared to the other age groups (all > 60%; all p values < .01). Table 1 describes the seven primary themes for non-compliance. Non-essential work requirements, concerns about mental and physical health, and the belief that other precautions were sufficient were the most common reasons, although other rationales included wanting to continue everyday activities and beliefs that society is over-reacting. Childcare was an important concern for a subset of respondents.

Overall, our findings suggest that public health messages should focus on young people and 1) address their negative affect, 2) refocus their self-orientation by emphasizing the importance of individual behavior to group-level health outcomes, and 3) target the specific rationales that different people have regarding the pandemic to maximize compliance with social distancing.
On the corona infection model with contact restriction
Authors: Mimkes Juergen , Janssen Rainer
Published: April 2020

This article presents a mathematical infection model that is designed to estimate the course of coronavirus infection in Germany for several days in advance: How many people become ill or die, what is the temporal development? If the contact restriction is perfect, then the model predicts the development of the virus infection after the initial subsidence of the infection. However, since this restriction cannot always be strictly adhered to, the model is dynamically adapted to the development. This makes it possible to estimate the number of infected people, the number of new infections and deaths in Germany about a week in advance.
COVID-19 Epidemic Analysis using Machine Learning and Deep Learning Algorithms
Authors: Punn Narinder Singh , Sonbhadra Sanjay Kumar , Agarwal Sonali
Published: April 2020

The catastrophic outbreak of Severe Acute Respiratory Syndrome - Coronavirus (SARS-CoV-2) also known as COVID-2019 has brought the worldwide threat to the living society. The whole world is putting incredible efforts to fight against the spread of this deadly disease in terms of infrastructure, finance, data sources, protective gears, life-risk treatments and several other resources. The artificial intelligence researchers are focusing their expertise knowledge to develop mathematical models for analyzing this epidemic situation using nationwide shared data. To contribute towards the well-being of living society, this article proposes to utilize the machine learning and deep learning models with the aim for understanding its everyday exponential behaviour along with the prediction of future reachability of the COVID-2019 across the nations by utilizing the real-time information from the Johns Hopkins dashboard.
Assessing the risks of “infodemics” in response to COVID-19 epidemics
Authors: Gallotti Riccardo , Valle Francesco , Castaldo Nicola , Sacco Pierluigi , De Domenico Manlio
Published: April 2020

Our society is built on a complex web of interdependencies whose effects become manifest during extraordinary events such as the COVID-19 pandemic, with shocks in one system propagating to the others to an exceptional extent. We analyzed more than 100 millions Twitter messages posted worldwide in 64 languages during the epidemic emergency due to SARS-CoV-2 and classified the reliability of news diffused. We found that waves of unreliable and low-quality information anticipate the epidemic ones, exposing entire countries to irrational social behavior and serious threats for public health. When the epidemics hit the same area, reliable information is quickly inoculated, like antibodies, and the system shifts focus towards certified informational sources. Contrary to mainstream beliefs, we show that human response to falsehood exhibits early-warning signals that might be mitigated with adequate communication strategies.
Assessing the Hospital Surge Capacity of the Kenyan Health System in the Face of the COVID-19 Pandemic
Authors: Barasa Edwine , Ouma Paul , Okiro Emelda
Published: April 2020

Introduction

The COVID-19 pandemic will test the capacity of health systems worldwide. Health systems will need surge capacity to absorb acute increases in caseload due to the pandemic. We assessed the capacity of the Kenyan health system to absorb surges in the number of people that will need hospitalization and critical care because of the COVID-19.

Methods

We assumed that 2% of the Kenyan population get symptomatic infection by SARS-Cov-2 based on modelled estimates for Kenya and determined the health system surge capacity for COVID-19 under three transmission curve scenarios, 6, 12, and 18 months. We estimated four measures of hospital surge capacity namely: 1) hospital bed surge capacity 2) ICU bed surge capacity 3) Hospital bed tipping point, and 5) ICU bed tipping point. We computed this nationally and for all the 47 county governments.

Results

The capacity of Kenyan hospitals to absorb increases in caseload due to COVID-19 is constrained by the availability of oxygen, with only 58% of hospital beds in hospitals with oxygen supply. There is substantial variation in hospital bed surge capacity across counties. For example, under the 6 months transmission scenario, the percentage of available general hospital beds that would be taken up by COVID-19 cases varied from 12% Tharaka Nithi county, to 145% in Trans Nzoia county. Kenya faces substantial gaps in ICU beds and ventilator capacity. Only 22 out of the 47 counties have at least 1 ICU unit. Kenya will need an additional 1,511 ICU beds and 1,609 ventilators (6 months transmission curve) to 374 ICU beds and 472 ventilators (18 months transmission curve) to absorb caseloads due to COVID-19.

Conclusion

Significant gaps exist in Kenya’s capacity for hospitals to accommodate a potential surge in caseload due to COVID-19. Alongside efforts to slow and supress the transmission of the infection, the Kenyan government will need to implement adaptive measures and additional investments to expand the hospital surge capacity for COVID-19. Additional investments will however need to be strategically prioritized to focus on strengthening essential services first, such as oxygen availability before higher cost investments such as ICU beds and ventilators.
Prevalence of anxiety disorder among workers with cancer in Amman, Jordan
Authors: Abu Shreea Abdel Rahman Aref Ali , Khuan Lee , Syed Ismail Sharifah Norkhadijah , Subhi Nasrudin , Abu-Shanab Sobuh (Moh’d Sobhi) Ahmad , Mashrqi Zaher Juma’ Raja , Rasdi Irniza
Published: April 2020

Introduction

Cancer is now being recognised as a long term conditions due to advances in treatments that increase the survival rate of patients with cancer to as long as 10 years from the time of the disease. Anxiety is among the commonly discovered psychiatric illness in patients with cancer and is often neglected. Approximately 10% of patients with cancer are affected with anxiety worldwide. Hence, this study was aimed to determine the prevalence of anxiety disorder and its associated factors among workers with cancer in Jordanian population.

Methods

A cross-sectional study was conducted at the King Husain Cancer Centre (KHCC) in Amman, Jordan. Proportional sampling technique was used to obtain the sample population of 355 workers with cancer. Data were collected through self-administered Generalized Anxiety Disorder (GAD-7) questionnaire and analyses were carried out using SPSS version 25.

Results

Response rate of 100% were obtained from the participants. Prevalence of anxiety disorder among workers with cancer was recorded at 20.8% with male (23.1%) having the higher prevalence rate than female (17.3%) workers with cancers. A significant difference in anxiety between marital status (p=0.025), types of cancer (p=0.001), treatment types (p=0.024) were observed. A multiple regression was run to predict anxiety disorder from marital status, type of cancer and treatment types. These variables statistically significantly predicted anxiety disorder [F(3, 351) = 8.117, p < .001, R2 = 0.225].

Conclusion

There is high prevalent of anxiety disorder among workers with cancer in Jordan. Predictors of anxiety among workers with cancer were also identified in this report.
Long-term predictions for COVID-19 pandemic dynamics in Ukraine, Austria and Italy
Authors: Nesteruk Igor
Published: April 2020

The SIR (susceptible-infected-removed) model, statistical approach to the parameter identification and the official WHO daily data about the confirmed cumulative number of cases were used to make some estimations for the dynamics of the coronavirus pandemic dynamics in Ukraine, Italy and Austria. The volume of the data sets and the influence of the information about the initial stages of the epidemics were discussed in order to have reliable long-time predictions. The final sizes and durations for the pandemic in these countries are estimated.
Is the spread of COVID-19 across countries influenced by environmental, economic and social factors?
Authors: Hossain Mohammad Alamgir
Published: April 2020

The SARS-CoV-2 virus, emerged from Wuhan, China is spreading all over the world in an unprecedented manner, causing millions of infections and thousands of deaths. However, the spread of the disease across countries and regions are not even. Why some countries and regions are more affected than some other countries and regions? We employ simple statistical methods to investigate any linkage between the severity of the disease and the environmental, economic and social factors of countries. The estimation results indicate that the number of confirmed cases of Coronavirus infection is higher in countries with lower yearly average temperatures, higher economic openness and stronger political democracy. However, findings of this analysis should be interpreted carefully keeping in mind the fact that statistical relations do not necessarily imply causation. Only clinical experiments with medical expertise can confirm how the virus behaves in the environment.
U.S. county-level characteristics to inform equitable COVID-19 response
Authors: Chin Taylor , Kahn Rebecca , Li Ruoran , Chen Jarvis T. , Krieger Nancy , Buckee Caroline O. , Balsari Satchit , Kiang Mathew V.
Published: April 2020

Background

The spread of Coronavirus Disease 2019 (COVID-19) across the United States confirms that not all Americans are equally at risk of infection, severe disease, or mortality. A range of intersecting biological, demographic, and socioeconomic factors are likely to determine an individual’s susceptibility to COVID-19. These factors vary significantly across counties in the United States, and often reflect the structural inequities in our society. Recognizing this vast inter-county variation in risks will be critical to mounting an adequate response strategy.

Methods and Findings

Using publicly available county-specific data we identified key biological, demographic, and socioeconomic factors influencing susceptibility to COVID-19, guided by international experiences and consideration of epidemiological parameters of importance. We created bivariate county-level maps to summarize examples of key relationships across these categories, grouping age and poverty; comorbidities and lack of health insurance; proximity, density and bed capacity; and race and ethnicity, and premature death. We have also made available an interactive online tool that allows public health officials to query risk factors most relevant to their local context.

Our data demonstrate significant inter-county variation in key epidemiological risk factors, with a clustering of counties in certain states, which will result in an increased demand on their public health system. While the East and West coast cities are particularly vulnerable owing to their densities (and travel routes), a large number of counties in the Southeastern states have a high proportion of at-risk populations, with high levels of poverty, comorbidities, and premature death at baseline, and low levels of health insurance coverage.

The list of variables we have examined is by no means comprehensive, and several of them are interrelated and magnify underlying vulnerabilities. The online tool allows readers to explore additional combinations of risk factors, set categorical thresholds for each covariate, and filter counties above different population thresholds.

Conclusion

COVID-19 responses and decision making in the United States remain decentralized. Both the federal and state governments will benefit from recognizing high intra-state, inter-county variation in population risks and response capacity. Many of the factors that are likely to exacerbate the burden of COVID-19 and the demand on healthcare systems are the compounded result of long-standing structural inequalities in US society. Strategies to protect those in the most vulnerable counties will require urgent measures to better support communities’ attempts at social distancing and to accelerate cooperation across jurisdictions to supply personnel and equipment to counties that will experience high demand.
Work-related Covid-19 transmission
Authors: Lan Fan-Yun , Wei Chih-Fu , Hsu Yu-Tien , Christiani David C. , Kales Stefanos N.
Published: April 2020

Importance

Our study helps fill the knowledge gap related to work-related transmission in the emerging coronaviral pandemic.

Objective

To demonstrate high-risk occupations for early coronavirus disease 2019 (Covid-19) local transmission.

Methods

In this observational study, we extracted confirmed Covid-19 cases from governmental investigation reports in Hong Kong, Japan, Singapore, Taiwan, Thailand, and Vietnam. We followed each country/area for 40 days after its first locally transmitted case, and excluded all imported cases. We defined a possible work-related case as a worker with evidence of close contact with another confirmed case due to work, or an unknown contact history but likely to be infected in the working environment (e.g. an airport taxi driver). We calculated the case number for each occupation, and illustrated the temporal distribution of all possible work-related cases and healthcare worker (HCW) cases. The temporal distribution was further defined as early outbreak (the earliest 10 days of the following period) and late outbreak (11th to 40th days of the following period).

Results

We identified 103 possible work-related cases (14.9%) among a total of 690 local transmissions. The five occupation groups with the most cases were healthcare workers (HCWs) (22%), drivers and transport workers (18%), services and sales workers (18%), cleaning and domestic workers (9%) and public safety workers (7%). Possible work-related transmission played a substantial role in early outbreak (47.7% of early cases).

Occupations at risk varied from early outbreak (predominantly services and sales workers, drivers, construction laborers, and religious professionals) to late outbreak (predominantly HCWs, drivers, cleaning and domestic workers, police officers, and religious professionals).

Conclusions

Work-related transmission is considerable in early Covid-19 outbreaks, and the elevated risk of infection was not limited to HCW. Implementing preventive/surveillance strategies for high-risk working populations is warranted.
A Comprehensive Analysis of COVID-19 Outbreak situation in India
Authors: Gupta Rajan , Pal Saibal K. , Pandey Gaurav
Published: April 2020

The outbreak of COVID-19 in different parts of the world is a major concern for all the administrative units of respective countries. India is also facing this very tough task for controlling the virus outbreak and has managed its growth rate through some strict measures. This study presents the current situation of coronavirus spread in India along with the impact of various measures taken for it. With the help of data sources (till 7th-8th April 2020) from various state units of India and Ministry of Health and Family Welfare, Government of India, this study presents various trends and patterns. This study answers six different research questions in a comprehensive manner. It has been reported that growth rate of infected cases has been controlled with the help of National Lockdown, however some uncontrolled mass level events had a negative impact on the infected cases. With the help of exponential and polynomial regression modelling, the predictions of up to 75000 cases have been done by the end of April 2020. It has also been seen that there are some prominent clusters and patient nodes in the network of patients which are the major influencers for COVID-19 spread. Also, death rate case predictions have been done through two-class classification models with an accuracy of 60%. At the end, strategies for continuation for lockdown has been discussed and presented. It appears that only essential services should be open for the citizens of India and the national lockdown should be carried on for next 2-4 weeks. This study will be useful for the Government of India and various states of India, Administrative Units of India, Frontline health workforce of India, researchers and scientists. This study will also be favorable for the administrative units of other countries to consider various aspects related to the control of COVID-19 outspread in their respective regions.
Through the Eyes of a Patient: Visuospatial Perspective Taking and Empathy in Medical Students
Authors: Bukowski Henryk , Ahmad Kamal Nor Faizaah , Bennett Deirdre , Rizzo Gabriella , O’Tuathaigh Colm M.P.
Published: April 2020

Physicians’ cognitive empathy is associated with improved diagnosis and better patient outcomes. The relationship between self-reported and performance-based measures of cognitive empathic processes is unclear. This study examined the association between medical students’ empathy scale scores and their empathic performance in a perspective-taking task and communication skills assessment. Undergraduate medical students (N=91) completed the following: Jefferson Scale of Physician Empathy (JSPE); Empathy Quotient (EQ); a Level-1 visual perspective-taking task (VPT). Clinical communication skills were measured in a simulation-enhanced ‘breaking bad news’ assessment. Pearson’s or Spearman’s correlation coefficients and t-tests were used to determine correlation and group differences, respectively. Higher scores on the “Standing in Patients’ Shoes” sub-scale of the JSPE were associated with lower egocentric bias (r = -0.299, p < 0.05) in the VPT, which relates to capacity to adopt someone else’s perspective without being erroneously influenced by our own point of view. Additionally, a lower self-perspective advantage in the VPT, reflecting less attentional priority given to the self-perspective, was associated with higher scores on the the “Cognitive Empathy” (r = -0.283, p < 0.05) and “Emotional Empathy” (r = -0.342, p < 0.01) sub-scales of the EQ. Improved communication skills performance was associated with higher scores on the “Social Skills” EQ sub-scale (r = 0.298, p < 0.005). We show that self-assessment scores are moderately associated with performance-based measures of perspective-taking and communication skills. These results are expected to lead to improved experimental designs and a better understanding of empathy in medical education.
Biological aging measures based on blood DNA methylation and risk of cancer: a prospective study
Authors: Dugué Pierre-Antoine , Bassett Julie K , Wong Ee Ming , Joo JiHoon E , Li Shuai , Yu Chenglong , Schmidt Daniel F , Makalic Enes , Doo Nicole Wong , Buchanan Daniel D , Hodge Allison M , English Dallas R , Hopper John L , Giles Graham G , Southey Melissa C , Milne Roger L
Published: April 2020

We previously investigated the association between five ‘first-generation’ measures of epigenetic aging and cancer risk in the Melbourne Collaborative Cohort Study. The present study assesses cancer risk associations for three recently developed methylation-based measures of aging:PhenoAge, GrimAge, and predicted telomere length. We estimated rate ratios (RRs) for risk of colorectal (N=814), gastric (N=166), kidney (N=139), lung (N=327), mature B-cell (N=426), prostate (N=847) and urothelial (N=404) cancer, using conditional logistic regression models. We observed relatively strong associations ofPhenoAgewith risk of colorectal, kidney, lung, mature B-cell, and urothelial cancers (RR per standard deviation ∼ 1.2-1.3). Similar findings were obtained forGrimAge, but the association with lung cancer risk was remarkably stronger (RR ∼ 1.8 after adjustment for smoking status, pack-years, starting age, time since quitting and other cancer risk factors). The methylation-based measuresPhenoAgeandGrimAgemay provide insights into the relationship between biological aging and cancer.
Deep learning discerns cancer mutation exclusivity
Authors: Gupta Prashant , Jindal Aashi , Jayadeva  , Sengupta Debarka
Published: April 2020

The exclusivity of a vast majority of cancer mutations remains poorly understood, despite the availability of large amounts of whole genome and exome sequencing data. In clinical settings, this markedly hinders the identification of the previously uncharacterized deleterious mutations due to the unavailability of matched normal samples. We employed state of the art deep learning algorithms for cross-exome learning of mutational embeddings and demonstrated their utility in sequence based detection of cancer-specific Single Nucleotide Variants (SNVs).
Maternal exposure to the cannabinoid agonist WIN 55,12,2 during lactation induces lasting behavioral and synaptic alterations in the rat adult offspring of both sexes
Authors: Scheyer Andrew F , Borsoi Milene , Pelissier-Alicot Anne-Laure , Manzoni Olivier JJ
Published: April 2020

Consumption of cannabis during pregnancy and the lactation period is a rising public health concern (Scheyer et al., 2019). We have previously shown that exposure to synthetic or plant-derived cannabinoids via lactation disrupts perinatal programming of the gamma-aminobutyric acid trajectory in the prefrontal cortex and early-life behaviors (Scheyer et al., 2020b). Recently, we described lasting behavioral and neuronal consequences of Δ9-tetrahydrocannabinol (THC) perinatal exposure via lactation (Scheyer et al., 2020a).

Here, we extend upon these findings by testing the effects in offspring of maternal exposure to the synthetic cannabinoid agonist WIN 55,12,2 (WIN). The data demonstrate that rats exposed during lactation to WIN display social, cognitive and motivational deficits at adulthood. These behavioral changes were paralleled by a specific loss of endocannabinoid-mediated long-term depression in the prefrontal cortex and nucleus accumbens, while other forms of synaptic plasticity remained intact. Thus, similarly to THC, perinatal WIN exposure via lactation induces behavioral and synaptic abnormalities lasting into adulthood.
Furin controls β cell function via mTORC1 signaling
Authors: Brouwers Bas , Coppola Ilaria , Vints Katlijn , Dislich Bastian , Jouvet Nathalie , Van Lommel Leentje , Gounko Natalia V. , Thorrez Lieven , Schuit Frans , Lichtenthaler Stefan F. , Estall Jennifer L. , Declercq Jeroen , Ramos-Molina Bruno , Creemers John W.M.
Published: April 2020

Furin is a proprotein convertase (PC) responsible for proteolytic activation of a wide array of precursor proteins within the secretory pathway. It maps to the PRC1 locus, a type 2 diabetes susceptibility locus, yet its specific role in pancreatic β cells is largely unknown. The aim of this study was to determine the role of furin in glucose homeostasis. We show that furin is highly expressed in human islets, while PCs that potentially could provide redundancy are expressed at considerably lower levels. β cell-specific furin knockout (βfurKO) mice are glucose intolerant, due to smaller islets with lower insulin content and abnormal dense core secretory granule morphology. RNA expression analysis and differential proteomics on βfurKO islets revealed activation of Activating Transcription Factor 4 (ATF4), which was mediated by mammalian target of rapamycin C1 (mTORC1). βfurKO cells show impaired cleavage of the essential V-ATPase subunit Ac45, and by blocking this pump in β cells the mTORC1 pathway is activated. Furthermore, βfurKO cells show lack of insulin receptor cleavage and impaired response to insulin. Taken together, these results suggest a model of mTORC1-ATF4 hyperactivation in β cells lacking furin, which causes β cell dysfunction.
MYB5a/NEGANactivates petal anthocyanin pigmentation and shapes the MBW regulatory network inMimulus luteusvar.variegatus
Authors: Zheng Xingyu , Om Kuenzang , Stanton Kimmy A. , Thomas Daniel , Cheng Philip A. , Eggert Allison , Yuan Yao-Wu , Puzey Joshua R. , Cooley Arielle M.
Published: April 2020

Much of the visual diversity of angiosperms is due to the frequent evolution of novel pigmentation patterns in flowers. The gene network responsible for anthocyanin pigmentation, in particular, has become a model for investigating how genetic changes give rise to phenotypic innovation. In the monkeyflower genusMimulus, an evolutionarily recent gain of petal lobe anthocyanin pigmentation inM. luteusvar.variegatuswas previously mapped to genomic regionpla2. Here, we use DNA sequence analysis and spatiotemporal patterns of gene expression to identifyMYB5a- homologous to theNEGANtranscriptional activator fromM. lewisii- as a likely candidate gene within thepla2region. Transgenic manipulation of gene expression confirms thatMYB5ais both necessary and sufficient for petal lobe anthocyanin pigmentation. The deployment ofMYB5a/NEGANto the petal lobe stands in contrast to its more restricted role as a nectar guide anthocyanin activator in otherMimulusspecies. Transcriptome sequencing of aMYB5aRNAi line reveals the degree to which other regulators of the anthocyanin pathway - including R3 MYB repressors and bHLH and WD40 co-activators - are responsive to the level of expression ofMYB5a. Overall, this work reveals that a genetically simple change, which we hypothesize to be a regulatory mutation incistoMYB5a, has cascading effects on gene expression, not only on the genes downstream ofMYB5abut also on all of its known partners in the anthocyanin regulatory network.

Graphical abstract.

Solid black arrows indicate the direction (though not magnitude) of gene expression change, following RNAi knockdown ofMYB5a/NEGANinM. l. variegatus. The number of black arrows corresponds to the number of gene copies identified in the transcriptome. Grey symbols denote positive and negative regulatory interactions. RTO is an R3 MYB protein that inhibits anthocyanin biosynthesis by sequestering bHLH proteins away from the MBW complex.
Systems Biology under heat stress in Indian Cattle
Authors: Khan Raja Ishaq Nabi , Sahu Amit Ranjan , Malla Waseem Akram , Praharaj Manas Ranjan , Hosamani Neelima , Kumar Shakti , Gupta Smita , Sharma Shweta , Saxena Archana , Varshney Anshul , Singh Pragya , Verma Vinay , Kumar Puneet , Singh Gyanendra , Pandey Aruna , Saxena Shikha , Gandham Ravi Kumar , Tiwari Ashok Kumar
Published: April 2020

Transcriptome profiling of Vrindavani and Tharparkar cattle revealed that more numbers of genes dysregulated in Vrindavani than in Tharparkar. A contrast in gene expression was observed with 18.5 % of upregulated genes in Vrindavani were downregulated in Tharparkar and 17.5% upregulated genes in Tharparkar were downregulated in Vrindavani. Functional annotation of genes differentially expressed in Tharparkar and Vrindavani revealed that the systems biology in Tharparkar is moving towards counteracting the effects due to heat stress. Unlike Vrindavani, Tharparkar is not only endowed with higher expression of the scavengers (UBE2G1, UBE2S, andUBE2H) of misfolded proteins but also with protectors (VCP, Serp1, andCALR) of naïve unfolded proteins. Further, higher expression of the antioxidants in Tharparkar enables it to cope up with higher levels of free radicals generated as a result of heat stress. In this study we found relevant genes dysregulated in Tharparkar in the direction that can counter heat stress.
Assessing the Performance of qpAdm: A Statistical Tool for Studying Population Admixture
Authors: Harney Éadaoin , Patterson Nick , Reich David , Wakeley John
Published: April 2020

qpAdm is a statistical tool for studying the ancestry of populations with histories that involve admixture between two or more source populations. Using qpAdm, it is possible to identify plausible models of admixture that fit the population history of a group of interest and to calculate the relative proportion of ancestry that can be ascribed to each source population in the model. Although qpAdm is widely used in studies of population history of human (and non-human) groups, relatively little has been done to assess its performance. We performed a simulation study to assess the behavior of qpAdm under various scenarios in order to identify areas of potential weakness and establish recommended best practices for use. We find that qpAdm is a robust tool that yields accurate results in many cases, including when data coverage is low, there are high rates of missing data or ancient DNA damage, or when diploid calls cannot be made. However, we caution against co-analyzing ancient and present-day data, the inclusion of an extremely large number of reference populations in a single model, and analyzing population histories involving extended periods of gene flow. We provide a user guide suggesting best practices for the use of qpAdm.
The eccDNA Replicon: A heritable, extra-nuclear vehicle that enables gene amplification and glyphosate resistance inAmaranthus palmeri
Authors: Molin William T. , Yaguchi Allison , Blenner Mark , Saski Christopher A.
Published: April 2020

Gene copy number variation is a predominant mechanism by which organisms respond to selective pressures in nature, which often results in unbalanced structural variations that perpetuate as adaptations to sustain life. However, the underlying mechanisms that give rise to gene proliferation are poorly understood. Here, we show a unique result of genomic plasticity inAmaranthus palmeri, a massive, ∼400kb extrachromosomal circular DNA (eccDNA), that harbors the 5-enoylpyruvylshikimate-3-phosphate synthase (EPSPS) gene and 58 other encoded genes whose functions traverse detoxification, replication, recombination, transposition, tethering, and transport. Gene expression analysis under glyphosate stress showed transcription of 41 of the 59 genes, with high expression ofEPSPS, aminotransferase, zinc-finger, and several uncharacterized proteins. The genomic architecture of the eccDNA replicon is comprised of a complex arrangement of repeat sequences and mobile genetic elements interspersed among arrays of clustered palindromes that may be crucial for stability, DNA duplication and tethering, and/or a means of nuclear integration of the adjacent and intervening sequences. Comparative analysis of orthologous genes in grain amaranth (Amaranthus hypochondriacus) and water-hemp (Amaranthus tuberculatus) suggest higher order chromatin interactions contribute to the genomic origins of theAmaranthus palmerieccDNA replicon structure.

One-sentence summary

The eccDNA replicon is a large extra-nuclear circular DNA that is composed of a sophisticated repetitive structure, harbors theEPSPSand several other genes that are transcribed during glyphosate stress.
Whales and Men: genetic inferences uncover a detailed history of hunting in bowhead whale
Authors: Hoareau TB
Published: April 2020

After millennia of hunting and a population collapse, it is still challenging to understand the genetic consequences of whaling on the circumarctic bowhead whale. Here I use published modern mtDNA sequences from the Bering-Chukchi-Beaufort population and a new time calibration to show that late–glacial climate changes and whaling have been the major drivers of population change. Cultures that hunted in the Arctic Seas from as early as 5000 years ago appear to be responsible for successive declines of the population growth, bringing the effective size down to 38% of its pristine population size. The Thules and the Basques (year 1000–1730) who only hunted in the North Atlantic had a major impact on this North Pacific population, indicating that bowhead whale stocks respond to harvesting as a single population unit. Recent positive growth is inferred only after the end of commercial whaling in 1915, and for levels of harvesting that are close to the current annual quota of 67 whales. By unfolding the population history of the bowhead whale, I provide compelling evidence that mtDNA yields critical yet undervalued information for management and conservation of natural populations.
A framework for detecting and quantifying relationship alterations in microbial community: Quantifying microbial relationship alteration
Authors: Liu Zhi , Mi Kai , Xu Zhenjiang Zech , Zhang Qiangkun , Liu Xingyin
Published: April 2020

Dysbiosis of gut microbiota is associated with the pathogenesis of human disease. Observing shifts in the microbe abundance cannot fully reveal underlying perturbations. Examining the relationship alteration (RA) in microbiome between different healthy status provides additional hints about the pathogenesis of human disease. However, no methods were designed to directly detect and quantify the RA between different conditions. Here, we present PM2RA (Profile Monitoring for Microbial Relationship Alteration), an analysis framework to identify and quantify the microbial RAs. The performance of PM2RA were evaluated in synthetic data, and found to show higher specificity and sensitivity than the co-occurrence-based methods. Analyses of real microbial dataset show that PM2RA is robust for quantifying microbial RA across different datasets in several diseases. By applying PM2RA, we identified both previously reported and novel microbes implicated in multiple diseases. The PM2RA is implemented as a web-based application available athttp://www.pm2ra-xingyinliulab.cn/.
FORK-seq: replication landscape of theSaccharomyces cerevisiaegenome by nanopore sequencing
Authors: Hennion Magali , Arbona Jean-Michel , Lacroix Laurent , Cruaud Corinne , Theulot Bertrand , Tallec Benoît Le , Proux Florence , Wu Xia , Novikova Elizaveta , Engelen Stefan , Lemainque Arnaud , Audit Benjamin , Hyrien Olivier
Published: April 2020

Genome replication mapping methods profile cell populations, masking cell-to-cell heterogeneity. Here, we describe FORK-seq, a nanopore sequencing method to map replication of single DNA molecules at 200 nucleotide resolution. By quantifying BrdU incorporation along pulse-chased replication intermediates fromSaccharomyces cerevisiae, we orient 58,651 replication tracks reproducing population-based replication directionality profiles and map 4,964 and 4,485 individual initiation and termination events, respectively. Although most events cluster at known origins and fork merging zones, 9% and 18% of initiation and termination events, respectively, occur at many locations previously missed. Thus, FORK-seq reveals the full extent of cell-to-cell heterogeneity in DNA replication.
Strand-specific cDNA library-based RNA sequencing dataset of un-infected andAscosphaera apis-infected larval guts ofApis cerana cerana
Authors: Chen Huazhi , Zhu Zhiwei , Wang Jie , Fan Yuanchan , Jiang Haibin , Zheng Yanzhen , Xiong Cuiling , Chen Dafu , Guo Rui
Published: April 2020

Apis cerana ceranais a subspecies of eastern honeybee,Apis cerana.Ascosphaera apisis a widespread fungal pathogen of honeybee, leading to chalkbrood, which results in heavy losses for beekeeping industry. In this article, 4-, 5-, and 6-day-old larval guts of un-infected (AcCK1, AcCK2, and AcCK3) andA. apis-infectedA. c. cerana(AcT1, AcT2, and AcT3) were sequenced by next generation sequencing. Totally, 73830148, 96586212, 94552744, 76672564, 90954858, and 83418832 raw reads were respectively produced from AcCK1, AcCK2, AcCK3, AcT1, AcT2, and AcT3. The sequencing depth was enough to detect all expressed genes. After strict quality control, 73775592, 96513798, 94495000, 76593924, 90870608 and 83339288 clean reads were obtained, with a mean GC content of 48.54%. Additionally, average Q20 and Q30 for aforementioned six groups were 98.10% and 94.36%, respectively. Moreover, 45302685, 65872823, 52709987, 49947838, 56476339, and 42657156 clean reads from above-mentioned six groups were mapped to the reference genome ofApis cerana, respectively. In addition, exons were the most abundant regions in reference genome mapped by clean reads, followed by intergenic regions and introns. Our data presented here can be used to identify long non-coding RNAs (lncRNAs), circlular RNAs (circRNAs), mRNAs and their regulatory networks engaged in response of eastern honeybee larvae toA. apisinfection, and decipher molecular mechanisms underlying host-pathogen interaction.

Value of the Data

The current data can be used for exploration of mRNAs, lncRNAs, circRNAs and their competing endogenous RNA (ceRNA) networks engaged in response ofA. c. ceranalarvae toA. apisinfection.

This data provides a valuable genetic resource for better understanding non-coding RNA-mediated cross-kingdom regulation of eastern honey larvae toA. apis.

The accessible data offers novel insights into understanding the molecular mechanism underlying interaction between eastern honeybee larvae andA. apis.
Spontaneous alpha and theta oscillations are related to complementary aspects of cognitive control in younger and older adults
Authors: Clements Grace M. , Bowie Daniel C. , Gyurkovics Mate , Low Kathy A. , Fabiani Monica , Gratton Gabriele
Published: April 2020

The resting-state human EEG power spectrum is dominated by alpha (8-12 Hz) and theta (4-8Hz) oscillations, and also includes non-oscillatory broadband activity inversely related to frequency (1/factivity). Gratton (2018) proposed that alpha and theta oscillations are both related to cognitive control function, though in a complementary manner. Alpha activity is hypothesized to facilitate themaintenanceof representations, such as task sets in preparation forexpectedtask conditions. In contrast, theta activity would facilitatechangesin representations, such as theupdatingof task sets in response tounpredictedtask demands. Therefore, theta should be related to reactive control (which may prompt changes in task representations), while alpha may be more relevant to proactive control (which implies the maintenance of current task representations). Less is known about the possible relationship between 1/factivity and cognitive control, which was analyzed here in an exploratory fashion. To investigate these hypothesized relationships, we recorded eyes-open and eyes-closed resting-state EEG from younger and older adults and subsequently tested their performance on a cued flanker task, expected to elicit both proactive and reactive control processes. Results showed that alpha power and 1/fslope were smaller in older than younger adults, whereas theta power did not show age-related reductions. Resting alpha power and 1/fslope were predictive of proactive control processes, whereas theta power was related to reactive control as measured by the cued flanker task. All predictive associations were present over and above the effect of age, suggesting that these resting-state EEG correlates could be indicative of trait-like individual differences in cognitive control performance, which may be already evident in younger adults, and are still similarly present in healthy older adults.
LipidLynxX: a data transfer hub to support integration of large scale lipidomics datasets
Authors: Ni Zhixu , Fedorova Maria
Published: April 2020

Modern high throughput lipidomics provides large-scale datasets reporting hundreds of lipid molecular species. However, cross-laboratory comparison, meta-analysis, and systems biology integration of in-house generated and published datasets remain challenging due to a high diversity of used lipid annotation systems, different levels of reported structural information, and shortage in links to data integration resources. To support lipidomics data integration and interoperability of experimental lipidomics with data integration tools, we developed LipidLynxX serving as a hub facilitating data flow from high-throughput lipidomics analysis to systems biology data integration. LipidLynxX provides the possibility to convert, cross-match, and link various lipid annotations to the tools supporting lipid ontology, pathway, and network analysis aiming systems-wide integration and functional annotation of lipidome dynamics in health and disease. LipidLynxX is a flexible, customizable open-access tool freely available for download athttps://github.com/SysMedOs/LipidLynxX.
High-throughput AFM analysis reveals unwrapping pathways of H3 and CENP-A nucleosomes
Authors: Konrad Sebastian F. , Vanderlinden Willem , Frederickx Wout , Brouns Tine , Menze Björn , De Feyter Steven , Lipfert Jan
Published: April 2020

Nucleosomes, the fundamental units of chromatin, regulate readout and expression of eukaryotic genomes. Single-molecule experiments have revealed force-induced transient nucleosome accessibility, but a high-resolution unwrapping landscape in the absence of external forces is currently lacking. Here, we introduce a high-throughput pipeline for the analysis of nucleosome conformations based on atomic force microscopy and automated, multi-parameter image analysis. Our data set of ~10,000 nucleosomes reveals multiple unwrapping states corresponding to steps of 5 bp DNA. For canonical H3 nucleosomes, we observe that dissociation from one side impedes unwrapping from the other side, but unlike to force-induced unwrapping, we find only a weak sequence-dependent asymmetry. Centromeric CENP-A nucleosomes do not unwrap anti-cooperatively, in stark contrast to H3 nucleosomes, likely due to their shorter N-terminal α-helix. Finally, our results reconcile previously conflicting findings about the differences in height between H3 and CENP-A nucleosomes. We expect our approach to enable critical insights into epigenetic regulation of nucleosome structure and stability.
A Systematic Analysis of Mosquito-Microbiome Biosynthetic Gene Clusters Reveals Antimalarial Siderophores that Reduce Mosquito Reproduction Capacity
Authors: Ganley Jack G. , Pandey Ashmita , Sylvester Kayla , Lu Kuan-Yi , Toro-Moreno Maria , Rütschlin Sina , Bradford James M. , Champion Cody J. , Böttcher Thomas , Xu Jiannong , Derbyshire Emily R.
Published: April 2020

Advances in infectious disease control strategies through genetic manipulation of insect microbiomes have heightened interest in microbially produced small molecules within mosquitoes. Herein, 33 mosquito-associated bacterial genomes were mined and over 700 putative biosynthetic gene clusters (BGCs) were identified, 135 of which belong to known classes of BGCs. After an in-depth analysis of the 135 BGCs, iron-binding siderophores were chosen for further investigation due to their high abundance and well-characterized bioactivities. Through various metabolomic strategies, eight siderophore scaffolds were identified in six strains of mosquito-associated bacteria. Among these, serratiochelin A and pyochelin were found to reduce femaleAnopheles gambiaeoverall fecundity likely by lowering their blood feeding rate. Serratiochelin A and pyochelin were further found to inhibit thePlasmodiumparasite asexual blood and liver stagesin vitro. Our work supplies a bioinformatic resource for future mosquito microbiome studies and highlights an understudied source of bioactive small molecules.
Type 2 and interferon inflammation strongly regulate SARS-CoV-2 related gene expression in the airway epithelium
Authors: Sajuthi Satria P. , DeFord Peter , Jackson Nathan D. , Montgomery Michael T. , Everman Jamie L. , Rios Cydney L. , Pruesse Elmar , Nolin James D. , Plender Elizabeth G. , Wechsler Michael E. , Mak Angel CY , Eng Celeste , Salazar Sandra , Medina Vivian , Wohlford Eric M. , Huntsman Scott , Nickerson Deborah A. , Germer Soren , Zody Michael C. , Abecasis Gonçalo , Kang Hyun Min , Rice Kenneth M. , Kumar Rajesh , Oh Sam , Rodriguez-Santana Jose , Burchard Esteban G. , Seibold Max A.
Published: April 2020

Coronavirus disease 2019 (COVID-19) outcomes vary from asymptomatic infection to death. This disparity may reflect different airway levels of the SARS-CoV-2 receptor, ACE2, and the spike protein activator, TMPRSS2. Here we explore the role of genetics and co-expression networks in regulating these genes in the airway, through the analysis of nasal airway transcriptome data from 695 children. We identify expression quantitative trait loci (eQTL) for bothACE2andTMPRSS2, that vary in frequency across world populations. Importantly, we findTMPRSS2is part of a mucus secretory network, highly upregulated by T2 inflammation through the action of interleukin-13, and that interferon response to respiratory viruses highly upregulatesACE2expression. Finally, we define airway responses to coronavirus infections in children, finding that these infections upregulateIL6while also stimulating a more pronounced cytotoxic immune response relative to other respiratory viruses. Our results reveal mechanisms likely influencing SARS-CoV-2 infectivity and COVID-19 clinical outcomes.
Polymorphic centromere locations in the pathogenic yeastCandida parapsilosis
Authors: Ola Mihaela , O’Brien Caoimhe E. , Coughlan Aisling Y. , Ma Qinxi , Donovan Paul D. , Wolfe Kenneth H. , Butler Geraldine
Published: April 2020

Centromeres pose an evolutionary paradox: strongly conserved in function, but rapidly changing in sequence and structure. However, in the absence of damage, centromere locations are usually conserved within a species. We report here that isolates of the pathogenic yeast speciesCandida parapsilosisexhibit within-species polymorphism for the location of centromeres on two of its eight chromosomes. Its old centromeres have an inverted-repeat (IR) structure, whereas its new centromeres have no obvious structural features, but are located within 30 kb of the old site. Centromeres can therefore move naturally from one chromosomal site to another, apparently spontaneously and in the absence of any significant changes in DNA sequence. Our observations are consistent with a model where all centromeres are genetically determined, such as by the presence of short or long IRs, or the ability to form cruciforms. We also find that centromeres have been hotspots for genomic rearrangements in theC. parapsilosisclade.