bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interactions between host genetics and gut microbiota determine susceptibility to CNS autoimmunity
Authors: Montgomery Theresa L. , Künstner Axel , Kennedy Josephine J. , Fang Qian , Asarian Lori , Culp-Hill Rachel , D’Alessandro Angelo , Teuscher Cory , Busch Hauke , Krementsov Dimitry N. 
Published: October 2020

SignificanceIncreasing evidence suggests a role for the gut microbiome in autoimmune diseases, including multiple sclerosis. However, the impact of natural genetic variation in the mammalian host and other underlying mechanisms has been largely overlooked. We used a mouse model of natural genetic diversity to explore interactions between the host and the microbiome. Our results demonstrate a complex interplay between host genotype and gut microbiota in autoimmune disease, and identify a single commensal species capable of modifying disease susceptibility in a genetically susceptible host. Our studies underscore the need to consider host genetics and baseline gut microbiota composition in autoimmunity.
Nucleosome Positioning Regulates the Establishment, Stability, and Inheritance of Heterochromatin in
Saccharomyces cerevisiae
Authors: Saxton Daniel S. , Rine Jasper 
Published: October 2020

Significance
Cells control which genes are actively providing instructions to the cell, and which genes are silenced. This regulation requires DNA to be wrapped around molecular scaffolds to form repeating units called nucleosomes. The organization of nucleosomes varies across the genome, with regular placement being a feature of regions adjacent to nucleosome-depleted regions (NDRs) and irregular positions more common elsewhere. To test whether regular positioning of nucleosomes is especially important in gene silencing, we altered the distance between NDRs within heterochromatin. These changes to NDR positioning revealed an oscillatory correlation between inter-NDR distance and poor nucleosome positioning. These defects in nucleosome positioning correlated with defects in silencing efficiency, indicating that regular placement of nucleosomes helps cells achieve gene silencing.
Acceleration of plague outbreaks in the second pandemic
Authors: Earn David J. D. , Ma Junling , Poinar Hendrik , Dushoff Jonathan , Bolker Benjamin M. 
Published: October 2020

SignificanceEpidemics of plague devastated Europe’s population throughout the Medieval and Renaissance periods. Genetic studies of modest numbers of skeletal remains indicate that the causative agent of all these epidemics was the bacteriumYersinia pestis, but such analyses cannot identify overall patterns of transmission dynamics. Analysis of thousands of archival records from London, United Kingdom, reveals that plague epidemics spread much faster in the 17th century than in the 14th century.
Prenatal and early-life exposure to the Great Chinese Famine increased the risk of tuberculosis in adulthood across two generations
Authors: Cheng Qu , Trangucci Robert , Nelson Kristin N. , Fu Wenjiang , Collender Philip A. , Head Jennifer R. , Hoover Christopher M. , Skaff Nicholas K. , Li Ting , Li Xintong , You Yue , Fang Liqun , Liang Song , Yang Changhong , He Jin’ge , Zelner Jonathan L. , Remais Justin V. 
Published: October 2020

Significance
Food system collapse incurs major societal costs that may extend across generations. The Great Chinese Famine—widely acknowledged as the largest famine in human history—was associated with tremendous short-term adverse health consequences, yet its long-term effect on infectious disease incidence has not been estimated. We conducted a cohort analysis of >1 million pulmonary tuberculosis (PTB) cases in a major center of ongoing transmission that experienced high famine mortality, finding a substantial burden of active PTB potentially attributable to the famine in the birth cohort that experienced prenatal and early-life exposure to famine, as well in their putative offspring. The Great Chinese Famine occurred >60 y ago, yet continues to contribute to the high PTB burden in China.
Chaos in a simple model of a delta network
Authors: Salter Gerard , Voller Vaughan R. , Paola Chris 
Published: October 2020

Significance
River deltas are threatened with rapid change due to human activity, highlighting the importance of predicting their dynamics. Based on a model of a simple delta network, we find that delta dynamics can be chaotic, implying a fundamental constraint on detailed long-term predictions of deltas. However, our estimates of the fundamental predictability horizon suggest substantial room for improvement in delta modeling. We test our model by using it to generate stratigraphy, translating our measure of predictability from time to vertical distance, and identifying the time scale required for long-term averages to become predictable. Although chaos precludes long-term prediction of deltas, the statistical behavior of deltas and their response to external changes such as human activity are predictable.
Initial economic damage from the COVID-19 pandemic in the United States is more widespread across ages and geographies than initial mortality impacts
Authors: Polyakova Maria , Kocks Geoffrey , Udalova Victoria , Finkelstein Amy 
Published: October 2020

Significance
A full picture of the COVID-19 pandemic requires information on how its impact on lives and on livelihoods relates across different groups. We therefore estimate excess all-cause mortality and employment displacement in April 2020 nationally and separately by state and by age group. Initial economic damages from the pandemic are more widespread across groups than deaths, which were primarily concentrated in a few states and among the oldest old. While the two states with the largest mortality increase account for about half of national excess mortality, the two most economically affected states account for only 7% of national economic damages. These findings suggest that policy responses to contain the pandemic involve trade-offs across different demographic and geographic groups.
Liquid-liquid phase separation promotes animal desiccation tolerance
Authors: Belott Clinton , Janis Brett , Menze Michael A. 
Published: October 2020

SignificanceRecent research has shown that intracellular proteinaceous condensates (membraneless organelles [MLOs]) are involved in various processes, ranging from Alzheimer’s disease to RNA processing, and here we demonstrate that this phenomenon governs a mechanism of anhydrobiosis. The proteinAfrLEA6 is found in the desiccation-tolerant life stage of the animal extremophileArtemia franciscana,and the protein engages in two distinct molecular mechanisms to confer protection during water loss.AfrLEA6 forms MLOs that may act as protective nodes for desiccation-sensitive proteins, while a cytosolic fraction of the protein promotes structural integrity of cells during anhydrobiosis. These findings significantly advance our understanding of “life without water” and promote transformative advancements in various fields, ranging from cell preservation technology to improvement of crop desiccation tolerance.
Scanning digital oil immersion lithography providing high-speed large area patterning with diffraction limited sub-micron resolution
Authors: Jakkinapalli Aravind , Bhaskar Arun , Wen Sy-Bor 
Published: October 2020

Abstract
A high numerical aperture (NA) scanning digital oil immersion lithography scheme is proposed and demonstrated in this study. To successfully conduct the scanning digital oil immersion lithography, immersion oil should be removed from the photoresist layer before the development process. Also, uniformity of the projected light patterns becomes crucial in the quality of this high NA photolithography. To solve these issues, we developed a cleaning procedure for the immersion oil and an intensity calibration scheme to achieve a highly uniform intensity distribution of the projected patterns. With these preparations, we were able to achieve 400 nm resolution large area patterning with the developed scanning digital oil immersion lithography system and a better than 200 nm resolution in the single line patterning. Also, with a double layered photoresist scheme and our lab-prepared photoresist, we successfully achieved large area lift-off patterns of 400 nm metallic dot arrays through the scanning digital oil immersion lithography system.
Entanglement and correlation in two-nucleon systems
Authors: Kruppa A T , Kovács J , Salamon P , Legeza Ö 
Published: October 2020

Abstract
We examine mode entanglement and correlation of two fermionic particles analytically and numerically. We study the one- and two-mode entropies and a global characteristic, the one-body entanglement entropy considering angular momentum coupled state with a single configuration. We show that with rearrangement of the single-particle orbitals the Slater decomposition can be obtained which can also be applied for configuration mixing subject to special restriction. With the help of the Slater decomposition, we derive analytical expressions for the entanglement measures, which becomes very simple for zero total angular momentum. The Slater decomposition allows us to define associated modes, and it turns out that they have identical one- and two-mode entropies. Furthermore, we show that specific single configurations describe maximally entangled states when the total angular momentum is zero. The numerical shell model study of two valence neutrons in the sd shell is revealed that the one-body entanglement entropy of the ground state is close to the maximal value, and the associated modes have the largest mutual information.
Magneto-transport phenomena of type-I multi-Weyl semimetals in co-planar setups
Authors: Nag Tanay , Nandy Snehasish 
Published: October 2020

Abstract
Having the chiral anomaly (CA) induced magneto-transport phenomena extensively studied in single Weyl semimetal as characterized by topological charge n = 1, we here address the transport properties in the context of multi-Weyl semimetals (m-WSMs) where n > 1. Using semiclassical Boltzmann transport formalism with the relaxation time approximation, we investigate several intriguing transport properties such as longitudinal magneto-conductivity (LMC), planar Hall conductivity (PHC), thermo-electric coefficients (TECs) and planar Nernst coefficient (PNC) for m-WSMs in the co-planar setups with external magnetic field, electric field and temperature gradient. Starting from the low-energy model, we show analytically that at zero temperature both LMC and PHC vary cubically with topological charge as n
3 while the finite temperature (T ≠ 0) correction is proportional to (n + n
2)T
2. Interestingly, we find that both the longitudinal and transverse TECs vary quadratically with topological charge as n
2 and the PNC is found to vary non-monotonically as a function of n. Our study hence clearly suggests that the inherent properties of m-WSMs indeed show up distinctly through the CA and the chiral magnetic effect induced transport coefficients in two different setups. Moreover, in order to obtain an experimentally realizable picture, we simultaneously verify our analytical findings through the numerical calculations using the lattice model of m-WSMs.
Combination therapy of biogenic C-dots and lysozyme for enhanced antibacterial and antibiofilm activity
Authors: Singh Anirudh , Verma Arushi , Singh Ruhar , Sahoo Amaresh Kumar , Samanta Sintu Kumar 
Published: October 2020

Abstract
Nearly 80% of human chronic infections are caused due to bacterial biofilm formation. The increased resistance against the conventional antimicrobial agents makes it difficult to treat the biofilm-related infections. The antibiotics resistance developed by planktonic cells has also become a major threat for human. Therefore, we have attempted here to develop an effective alternative strategy to overcome the issues of antibiotics resistance of bacteria. Upon synthesis, biogenic C-dots were combined with lysozymes which were further encapsulated into chitosan nanocarrier to form C-dots carrier (CDC). The as-synthesized C-dots were found irregular shaped and the average size of C-dots and CDC were 8 ± 2 nm and 450 ± 50 nm, respectively. To ensure secure and targeted delivery of C-dots and lysozyme we have employed chitosan, a biodegradable and natural biopolymer, as a delivery system. The study of time-dependent bacterial growth and flow cytometry analysis demonstrated that CDC can exhibit a synergistic bactericidal activity against the antibiotics resistant recombinant E. coli cells. Further, we have shown that the CDC could be a potent agent for both prevention of biofilm formation and eradication of preformed biofilm. In addition, we have observed that our drug delivery system is hemocompatible in nature making it suitable for in vivo applications. Therefore, we believe that the combination therapy of C-dots and lysozyme may be used as an excellent antibacterial and antibiofilm strategy.
Propagating Dirac plasmon polaritons in topological insulators
Authors: Wang Yong , Law Stephanie 
Published: October 2020

Abstract
We investigate the excitation of propagating Dirac plasmon polaritons (DPPs) in topological insulator (TI) thin films. A series of TI thin films were grown by molecular beam epitaxy. Periodic gold grating couplers with different periodicity were fabricated on the TI films to excite the propagating DPPs. A series of absorption peaks that shift with the grating periodicity were observed in Fourier transform infrared spectroscopy transmission scans. We have ruled out any source other than the excitation of propagating DPPs that could have caused the peaks to appear. The peak dispersion is consistent with theoretical predictions for coupled DPPs in TI thin films.
Effect of Ag nanoparticles on wafer-scale quasi-free-standing graphene characterization by surface enhanced Raman spectroscopy
Authors: Sun Li , Jiang Chao , Chen Xiufang , Yu Fapeng , Zhao Xian , Xu Xiangang , Xu Shicai 
Published: October 2020

Abstract
Quasi-free-standing graphene (QFSG) obtained by H intercalation on SiC (0001) substrate paves a new way for widening the applications in microelectronics field. In this work, the direct and efficient characterization of wafer-scale quasi-free-standing graphene on SiC was presented by Ag-assisting Raman spectroscopy. The Si-H peak existing at the interface between graphene and substrate was tested unambiguously. The effects of Ag distribution and particle size on Raman enhancement were clarified both theoretically and experimentally. It was found that relative larger Ag particles at aggregation area were accompanied with the better enhancement. Moreover, Raman mapping with Ag assisting was executed on QFSG obtained under different growth conditions and the corresponding QFSG coverages were evaluated effectively. The optimum H intercalation temperature was determined to be around 1000 °C with the coverage being 73%. This study would supply a new approach for uniform and wafer-scale QFSG fabrication.
Cyclosporin A and FGF signaling support the proliferation/survival of mouse primordial germ cell-like cells in vitro†
Authors: Ohta Hiroshi , Yabuta Yukihiro , Kurimoto Kazuki , Nakamura Tomonori , Murase Yusuke , Yamamoto Takuya , Saitou Mitinori 
Published: October 2020

Abstract
Primordial germ cells (PGCs) are the founding population of the germ cell lineage that undergo a multistep process to generate spermatozoa or oocytes. Establishing an appropriate culture system for PGCs is a key challenge in reproductive biology. By a chemical screening using mouse PGC-like cells (mPGCLCs), which were induced from mouse embryonic stem cells, we reported previously that forskolin and rolipram synergistically enhanced the proliferation/survival of mPGCLCs with an average expansion rate of ~20-fold. In the present study, we evaluated other chemicals or cytokines to see whether they would improve the current mPGCLC culture system. Among the chemicals and cytokines examined, in the presence of forskolin and rolipram, cyclosporin A (CsA) and fibroblast growth factors (FGFs: FGF2 and FGF10) effectively enhanced the expansion of mPGCLCs in vitro (~50-fold on average). During the expansion by CsA or FGFs, mPGCLCs comprehensively erased their DNA methylation to acquire a profile equivalent to that of gonadal germ cells in vivo, while maintaining their highly motile phenotype as well as their transcriptional properties as sexually uncommitted PGCs. Importantly, these mPGCLCs robustly contributed to spermatogenesis and produced fertile offspring. Furthermore, mouse PGCs (mPGCs) cultured with CsA ex vivo showed transcriptomes and DNA methylomes similar to those of cultured mPGCLCs. The improved culture system for mPGCLCs/mPGCs would be instructive for addressing key questions in PGC biology, including the mechanisms for germ cell migration, epigenetic reprogramming, and sex determination of the germline.
Componentwise approximate Bayesian computation via Gibbs-like steps
Authors: Clarté Grégoire , Robert Christian P , Ryder Robin J , Stoehr Julien 
Published: October 2020

SummaryApproximate Bayesian computation methods are useful for generative models with intractable likelihoods. These methods are, however, sensitive to the dimension of the parameter space, requiring exponentially increasing resources as this dimension grows. To tackle this difficulty we explore a Gibbs version of the approximate Bayesian computation approach that runs component-wise approximate Bayesian computation steps aimed at the corresponding conditional posterior distributions, and based on summary statistics of reduced dimensions. While lacking the standard justifications for the Gibbs sampler, the resulting Markov chain is shown to converge in distribution under some partial independence conditions. The associated stationary distribution can further be shown to be close to the true posterior distribution, and some hierarchical versions of the proposed mechanism enjoy a closed-form limiting distribution. Experiments also demonstrate the gain in efficiency brought by the Gibbs version over the standard solution.
A Research Agenda for Urban Biodiversity in the Global Extinction Crisis
Authors: Knapp Sonja , Aronson Myla F J , Carpenter Ela , Herrera-Montes Adriana , Jung Kirsten , Kotze D Johan , La Sorte Frank A , Lepczyk Christopher A , MacGregor-Fors Ian , MacIvor J Scott , Moretti Marco , Nilon Charles H , Piana Max R , Rega-Brodsky Christine C , Salisbury Allyson , Threlfall Caragh G , Trisos Christopher , Williams Nicholas S G , Hahs Amy K 
Published: October 2020

AbstractRapid urbanization and the global loss of biodiversity necessitate the development of a research agenda that addresses knowledge gaps in urban ecology that will inform policy, management, and conservation. To advance this goal, we present six topics to pursue in urban biodiversity research: the socioeconomic and social–ecological drivers of biodiversity loss versus gain of biodiversity; the response of biodiversity to technological change; biodiversity–ecosystem service relationships; urban areas as refugia for biodiversity; spatiotemporal dynamics of species, community changes, and underlying processes; and ecological networks. We discuss overarching considerations and offer a set of questions to inspire and support urban biodiversity research. In parallel, we advocate for communication and collaboration across many fields and disciplines in order to build capacity for urban biodiversity research, education, and practice. Taken together we note that urban areas will play an important role in addressing the global extinction crisis.
Productivity divergence: state policy, corporate capture and labour power in the USA
Authors: Warner Mildred E , Xu Yuanshuo 
Published: October 2020

Abstract
What factors explain the divergence between returns to labour and overall productivity across US counties? We model the role of power at the subnational state level: Republican partisan control, corporate lobbying (measured by ALEC-sponsored bills) and labour power (unionisation). We find where state policy is captured by corporate interests, this undermines inclusive growth. Our hierarchical models use 2012 data for county areas in the continental USA and find labour returns are higher in states with more unionisation, but lower in states with Republican control and more corporate penetration of state legislatures. Labour and local government power have limited effect.
Rapid and Extraction-Free Detection of SARS-CoV-2 from Saliva by Colorimetric Reverse-Transcription Loop-Mediated Isothermal Amplification
Authors: Lalli Matthew A , Langmade Joshua S , Chen Xuhua , Fronick Catrina C , Sawyer Christopher S , Burcea Lauren C , Wilkinson Michael N , Fulton Robert S , Heinz Michael , Buchser William J , Head Richard D , Mitra Robi D , Milbrandt Jeffrey 
Published: October 2020

Abstract

Background
Rapid, reliable, and widespread testing is required to curtail the ongoing COVID-19 pandemic. Current gold-standard nucleic acid tests are hampered by supply shortages in critical reagents including nasal swabs, RNA extraction kits, personal protective equipment, instrumentation, and labor.

Methods
To overcome these challenges, we developed a rapid colorimetric assay using reverse-transcription loop-mediated isothermal amplification (RT-LAMP) optimized on human saliva samples without an RNA purification step. We describe the optimization of saliva pretreatment protocols to enable analytically sensitive viral detection by RT-LAMP. We optimized the RT-LAMP reaction conditions and implemented high-throughput unbiased methods for assay interpretation. We tested whether saliva pretreatment could also enable viral detection by conventional reverse-transcription quantitative polymerase chain reaction (RT-qPCR). Finally, we validated these assays on clinical samples.

Results
The optimized saliva pretreatment protocol enabled analytically sensitive extraction-free detection of SARS-CoV-2 from saliva by colorimetric RT-LAMP or RT-qPCR. In simulated samples, the optimized RT-LAMP assay had a limit of detection of 59 (95% confidence interval: 44–104) particle copies per reaction. We highlighted the flexibility of LAMP assay implementation using 3 readouts: naked-eye colorimetry, spectrophotometry, and real-time fluorescence. In a set of 30 clinical saliva samples, colorimetric RT-LAMP and RT-qPCR assays performed directly on pretreated saliva samples without RNA extraction had accuracies greater than 90%.

Conclusions
Rapid and extraction-free detection of SARS-CoV-2 from saliva by colorimetric RT-LAMP is a simple, sensitive, and cost-effective approach with broad potential to expand diagnostic testing for the virus causing COVID-19.
Sleep pattern in the US and 16 European countries during the COVID-19 outbreak using crowdsourced smartphone data
Authors: Lee Paul H , Marek Jan , Nálevka Petr 
Published: October 2020

Abstract

Background
To stop the spread of the new coronavirus disease in 2019 (COVID-19), many countries had completely locked down. This lockdown restricted the everyday life of the affected residents and changed their mobility pattern, but its effects on sleep pattern were largely unknown.

Methods
Here, utilizing one of the largest crowdsourced database (Sleep as Android), we analyzed the sleep pattern of 25 217 users with 1 352 513 sleep records between 1 January and 29 April 2020 in the US and 16 European countries (Germany, UK, Spain, France, Italy, The Netherlands, Belgium, Hungary, Denmark, Finland, Norway, Czech, Sweden, Austria, Poland and Switzerland) with more than 100 records in all days of 2020.

Results
During the COVID-19 pandemic, the sleeping pattern before and after the country-level lockdown largely differed. The subjects increased their sleep duration by an average of 11.3 to 18.6 min on weekday nights, except Denmark (4.9 min) and Finland (7.1 min). In addition, subjects form all 16 European countries delayed their sleep onset from 10.7 min (Sweden) to 29.6 min (Austria).

Conclusion
During the COVID-19 pandemic, residents in the US and 16 European countries delayed their bedtime and slept longer than usual.