bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Vibrio cholerae master regulator for the activation of biofilm biogenesis genes, VpsR, senses both cyclic di-GMP and phosphate
Authors: Hsieh Meng-Lun , Kiel Niklas , Jenkins Lisa M Miller , Ng Wai-Leung , Knipling Leslie , Waters Christopher M , Hinton Deborah M 
Published: April 2022

Abstract
Vibrio cholerae biofilm formation/maintenance is controlled by myriad factors; chief among these are the regulator VpsR and cyclic di-guanosine monophosphate (c-di-GMP). VpsR has strong sequence similarity to enhancer binding proteins (EBPs) that activate RNA polymerase containing sigma factor σ54. However, we have previously shown that transcription from promoters within the biofilm biogenesis/maintenance pathways uses VpsR, c-di-GMP and RNA polymerase containing the primary sigma factor (σ70). Previous work suggested that phosphorylation of VpsR at a highly conserved aspartate, which is phosphorylated in other EBPs, might also contribute to activation. Using the biofilm biogenesis promoter PvpsL, we show that in the presence of c-di-GMP, either wild type or the phospho-mimic VpsR D59E activates PvpsL transcription, while the phospho-defective D59A variant does not. Furthermore, when c-di-GMP levels are low, acetyl phosphate (Ac∼P) is required for significant VpsR activity in vivo and in vitro. Although these findings argue that VpsR phosphorylation is needed for activation, we show that VpsR is not phosphorylated or acetylated by Ac∼P and either sodium phosphate or potassium phosphate, which are not phosphate donors, fully substitutes for Ac∼P. We conclude that VpsR is an unusual regulator that senses phosphate directly, rather than through phosphorylation, to aid in the decision to form/maintain biofilm.
Rational guide RNA engineering for small-molecule control of CRISPR/Cas9 and gene editing
Authors: Liu Xingyu , Xiong Wei , Qi Qianqian , Zhang Yutong , Ji Huimin , Cui Shuangyu , An Jing , Sun Xiaoming , Yin Hao , Tian Tian , Zhou Xiang 
Published: April 2022

Abstract
It is important to control CRISPR/Cas9 when sufficient editing is obtained. In the current study, rational engineering of guide RNAs (gRNAs) is performed to develop small-molecule-responsive CRISPR/Cas9. For our purpose, the sequence of gRNAs are modified to introduce ligand binding sites based on the rational design of ligand–RNA pairs. Using short target sequences, we demonstrate that the engineered RNA provides an excellent scaffold for binding small molecule ligands. Although the ‘stem–loop 1’ variants of gRNA induced variable cleavage activity for different target sequences, all ‘stem–loop 3’ variants are well tolerated for CRISPR/Cas9. We further demonstrate that this specific ligand–RNA interaction can be utilized for functional control of CRISPR/Cas9 in vitro and in human cells. Moreover, chemogenetic control of gene editing in human cells transfected with all-in-one plasmids encoding Cas9 and designer gRNAs is demonstrated. The strategy may become a general approach for generating switchable RNA or DNA for controlling other biological processes.
TeachOpenCADD 2022: open source and FAIR Python pipelines to assist in structural bioinformatics and cheminformatics research
Authors: Sydow Dominique , Rodríguez-Guerra Jaime , Kimber Talia B , Schaller David , Taylor Corey J , Chen Yonghui , Leja Mareike , Misra Sakshi , Wichmann Michele , Ariamajd Armin , Volkamer Andrea 
Published: April 2022

AbstractComputational pipelines have become a crucial part of modern drug discovery campaigns. Setting up and maintaining such pipelines, however, can be challenging and time-consuming—especially for novice scientists in this domain. TeachOpenCADD is a platform that aims to teach domain-specific skills and to provide pipeline templates as starting points for research projects. We offer Python-based solutions for common tasks in cheminformatics and structural bioinformatics in the form of Jupyter notebooks, based on open source resources only. Including the 12 newly released additions, TeachOpenCADD now contains 22 notebooks that cover both theoretical background as well as hands-on programming. To promote reproducible and reusable research, we apply software best practices to our notebooks such as testing with automated continuous integration and adhering to the idiomatic Python style. The new TeachOpenCADD website is available at https://projects.volkamerlab.org/teachopencadd and all code is deposited on GitHub.
DNA tension-modulated translocation and loop extrusion by SMC complexes revealed by molecular dynamics simulations
Authors: Nomidis Stefanos K , Carlon Enrico , Gruber Stephan , Marko John F 
Published: April 2022

Abstract
Structural Maintenance of Chromosomes (SMC) complexes play essential roles in genome organization across all domains of life. To determine how the activities of these large (≈50 nm) complexes are controlled by ATP binding and hydrolysis, we developed a molecular dynamics model that accounts for conformational motions of the SMC and DNA. The model combines DNA loop capture with an ATP-induced ‘power stroke’ to translocate the SMC complex along DNA. This process is sensitive to DNA tension: at low tension (0.1 pN), the model makes loop-capture steps of average 60 nm and up to 200 nm along DNA (larger than the complex itself), while at higher tension, a distinct inchworm-like translocation mode appears. By tethering DNA to an experimentally-observed additional binding site (‘safety belt’), the model SMC complex can perform loop extrusion (LE). The dependence of LE on DNA tension is distinct for fixed DNA tension vs. fixed DNA end points: LE reversal occurs above 0.5 pN for fixed tension, while LE stalling without reversal occurs at about 2 pN for fixed end points. Our model matches recent experimental results for condensin and cohesin, and makes testable predictions for how specific structural variations affect SMC function.
How clear is our current view on microbial dark matter? (Re-)assessing public MAG & SAG datasets with MDMcleaner
Authors: Vollmers John , Wiegand Sandra , Lenk Florian , Kaster Anne-Kristin 
Published: April 2022

AbstractAs of today, the majority of environmental microorganisms remain uncultured and is therefore referred to as ‘microbial dark matter’ (MDM). Hence, genomic insights into these organisms are limited to cultivation-independent approaches such as single-cell- and metagenomics. However, without access to cultured representatives for verifying correct taxon-assignments, MDM genomes may cause potentially misleading conclusions based on misclassified or contaminant contigs, thereby obfuscating our view on the uncultured microbial majority. Moreover, gradual database contaminations by past genome submissions can cause error propagations which affect present as well as future comparative genome analyses. Consequently, strict contamination detection and filtering need to be applied, especially in the case of uncultured MDM genomes. Current genome reporting standards, however, emphasize completeness over purity and the de facto gold standard genome assessment tool, checkM, discriminates against uncultured taxa and fragmented genomes. To tackle these issues, we present a novel contig classification, screening, and filtering workflow and corresponding open-source python implementation called MDMcleaner, which was tested and compared to other tools on mock and real datasets. MDMcleaner revealed substantial contaminations overlooked by current screening approaches and sensitively detects misattributed contigs in both novel genomes and the underlying reference databases, thereby greatly improving our view on ‘microbial dark matter’.
Efficient golden gate assembly of DNA constructs for single molecule force spectroscopy and imaging
Authors: Bell Nicholas A W , Molloy Justin E 
Published: April 2022

Abstract
Single-molecule techniques such as optical tweezers and fluorescence imaging are powerful tools for probing the biophysics of DNA and DNA-protein interactions. The application of these methods requires efficient approaches for creating designed DNA structures with labels for binding to a surface or microscopic beads. In this paper, we develop a simple and fast technique for making a diverse range of such DNA constructs by combining PCR amplicons and synthetic oligonucleotides using golden gate assembly rules. We demonstrate high yield fabrication of torsionally-constrained duplex DNA up to 10 kbp in length and a variety of DNA hairpin structures. We also show how tethering to a cross-linked antibody substrate significantly enhances measurement lifetime under high force. This rapid and adaptable fabrication method streamlines the assembly of DNA constructs for single molecule biophysics.
Individual Health Determinants That Predict Low Risk of Transitioning to Tobacco Use During Young Adulthood: An In-Depth Examination of Race and Ethnicity
Authors: Horn Kimberly , Crandell Ian , Patel Minal , Rose Shyanika W , Schillo Barbara , Folger Shanell , Bernat Debra , Branstetter Steve 
Published: April 2022

AbstractIntroductionThe present study examines the contributions of individual-level health determinants on young adult tobacco use initiation to improve understanding of racial and ethnic distinctions and to inform effective tobacco prevention strategies.MethodsUsing time-to-event analyses, the 10–wave (2011–2016) Truth Initiative Young Adult Cohort, a probability-based, nationally representative sample of the US young adults aged 18–34 years (N = 7 665), provides data to examine differences in variables that influence tobacco uptake, by race and ethnicity.ResultsAmong Non–Hispanic White young adults, having fewer peers who smoke cigarettes is protective against any tobacco initiation, whereas hazard of tobacco initiation increases for males, having low confidence to resist smoking, and having higher proclivity for sensation seeking. Depressive and anxiety symptoms increase uptake hazard most in the Non–Hispanic All Other Races group and least among Non–Hispanic Black individuals. Among Hispanic young adults, being female and perceiving tobacco as harmful are notably protective while being male is a notable uptake hazard. Unlike other groups, higher income levels do not lower hazards among Hispanic individuals. Cannabis use and overestimating the smoking rate among peers increase hazard least among Hispanic individuals. In the Non–Hispanic All Other Races group, aging is least protective; hazard increases notably if individuals engage in regular alcohol or cannabis use.ConclusionsTobacco prevention efforts are critical during young adulthood. Specific tobacco uptake hazard and protective factors exist by race and ethnicity and should be considered when developing selective young adult prevention, particularly among groups with the highest risk for tobacco initiation during this life stage.ImplicationsRising rates of tobacco initiation among the US young adults necessitate expanded efforts to prevent tobacco use initiation and progression beyond youth. Results highlight nuanced and differential tobacco uptake hazards by race and ethnicity for late initiation and sustained non–tobacco use among young adults. The study confirms existing evidence on tobacco use patterns and contributes to new knowledge on risk and protective factors. Tobacco prevention and control interventions, including policies, tailored in more meaningful ways could reduce tobacco use disparities among those most disproportionately affected.
Rethinking the “Pan-Culture”: Clinical Impact of Respiratory Culturing in Patients With Low Pretest Probability of Ventilator-Associated Pneumonia
Authors: Albin Owen R , Saravolatz Louis , Petrie Joshua , Henig Oryan , Kaye Keith S 
Published: April 2022

AbstractBackgroundRespiratory cultures are often obtained as part of a “pan-culture” in mechanically ventilated patients in response to new fevers or leukocytosis, despite an absence of clinical or radiographic evidence suggestive of pneumonia.MethodsThis was a propensity score–stratified cohort study of hospitalized mechanically ventilated adult patients between 2014 and 2019, with a new abnormal temperature or serum white blood cell count (NATW), but without radiographic evidence of pneumonia, change in ventilator requirements, or documentation of purulent secretions. Two patient groups were compared: those with respiratory cultures performed within 36 hours after NATW and those without respiratory cultures performed. The co-primary outcomes were the proportion of patients receiving &gt;2 days of total antibiotic therapy and &gt;2 days of broad-spectrum antibiotic therapy within 1 week after NATW.ResultsOf 534 included patients, 113 (21.2%) had respiratory cultures obtained and 421 (78.8%) did not. Patients with respiratory cultures performed were significantly more likely to receive antibiotics for &gt;2 days within 1 week after NATW than those without respiratory cultures performed (total antibiotic: adjusted odds ratio [OR], 2.57; 95% CI, 1.39–4.75; broad-spectrum antibiotic: adjusted OR, 2.47, 95% CI, 1.46–4.20).ConclusionsPerformance of respiratory cultures for fever/leukocytosis in mechanically ventilated patients without increasing ventilator requirements, secretion burden, or radiographic evidence of pneumonia was associated with increased antibiotic use within 1 week after incident abnormal temperature and/or white blood cell count. Diagnostic stewardship interventions targeting performance of unnecessary respiratory cultures in mechanically ventilated patients may reduce antibiotic overuse within intensive care units.
An Anatomy-Informed, Novel Technique for S1 Dorsal Root Ganglion Stimulation Lead Placement
Authors: Chapman Kenneth B , van Helmond Noud , Kallewaard Jan Willem , Vissers Kris C , Patel Kiran V , Motivala Soriaya , Hagedorn Jonathan M , Deer Timothy R , Dickerson David M 
Published: April 2022

Abstract

Objective
A heightened and organized understanding of sacral anatomy could potentially lead to a more effective and safe method of dorsal root ganglion stimulation (DRG-S) lead placement. The aim of this technical note is to describe a standardized access method for S1 DRG-S lead placement.

Design
Technical note.

Methods
The described approach utilizes alignment of the lumbosacral prominence and is measurement-based, allowing for standardized sacral access, even when visualization is suboptimal. The medial-to-lateral needle trajectory is designed to limit interaction with the sensitive neural structures and allows for a more parallel orientation of the lead to the DRG and nerve root.

Conclusions
The described technique potentially improves the safety of S1 DRG-S lead placement. The parallel lead orientation to the DRG may also increase efficacy while lowering energy requirements.
Optimizing COVID-19 surveillance using historical electronic health records of influenza infections
Authors: Du Zhanwei , Bai Yuan , Wang Lin , Herrera-Diestra Jose L , Yuan Zhilu , Guo Renzhong , Cowling Benjamin J , Meyers Lauren A , Holme Petter 
Published: April 2022

Abstract
Targeting surveillance resources toward individuals at high risk of early infection can accelerate the detection of emerging outbreaks. However, it is unclear which individuals are at high risk without detailed data on interpersonal and physical contacts. We propose a data-driven COVID-19 surveillance strategy using Electronic Health Record (EHR) data that identifies the most vulnerable individuals who acquired the earliest infections during historical influenza seasons. Our simulations for all three networks demonstrate that the EHR-based strategy performs as well as the most-connected strategy. Compared to the random acquaintance surveillance, our EHR-based strategy detects the early warning signal and peak timing much earlier. On average, the EHR-based strategy has 9.8 days of early warning and 13.5 days of peak timings, respectively, before the whole population. For the urban network, the expected values of our method are better than the random acquaintance strategy (24% for early warning and 14% in-advance for peak time). For a scale-free network, the average performance of the EHR-based method is 75% of the early warning and 109% in-advance when compared with the random acquaintance strategy. If the contact structure is persistent enough, it will be reflected by their history of infection. Our proposed approach suggests that seasonal influenza infection records could be used to monitor new outbreaks of emerging epidemics, including COVID-19. This is a method that exploits the effect of contact structure without considering it explicitly.
Interspecific mating bias may drive Aedes albopictus displacement of Aedes aegypti during its range expansion
Authors: Zhou Jiayong , Liu Shuang , Liu Hongkai , Xie Zhensheng , Liu Liping , Lin Lifeng , Jiang Jinyong , Yang Mingdong , Zhou Guofa , Gu Jinbao , Zhou Xiaohong , Yan Guiyun , James Anthony A , Chen Xiao-Guang 
Published: April 2022

Abstract
Aedes albopictus is the most invasive mosquito in the world and often displaces Ae. aegypti in regions where their populations overlap. Interspecific mating has been proposed as a possible cause for this displacement, but whether this applies across the range of their sympatry remains unclear. Aedes albopictus and Ae. aegypti collected from allopatric and sympatric areas in China were allowed to interact in cage experiments with different crosses and sex-choices. The results confirm that asymmetric interspecific mating occurs in these populations with matings between allopatric Ae. albopictus males and Ae. aegypti females being significantly higher (55.2%) than those between Ae. aegypti males and Ae. albopictus females (27.0%), and sympatric mosquitoes showed a similar but lower frequency bias, 25.7% versus 6.2%, respectively. The cross-mated females can mate second time (remate) with the respective conspecific males and the 66.7% remating success of female Ae. albopictus was significantly higher than the 9.3% of Ae. aegypti females. Furthermore, 17.8% of the matings of Ae. albopictus males exposed to mixed pools of Ae. albopictus and Ae. aegypti females and 9.3% of the matings of Ae. aegypti males with mixed Ae. aegypti and Ae. albopictus females were interspecific. The difference in the length of clasper between male Ae. albopictus (0.524 mm) and Ae. aegypti (0.409 mm) may be correlated with corresponding mates. We conclude that stronger Ae. albopictus male interspecific mating and more avid female intraspecific remating result in a satyr effect and contribute to competitive displacement of Ae. aegypti as allopatric Ae. albopictus invade during range expansion.
Short-range contributions of local sources to ambient air
Authors: Gusareva Elena S , Gaultier Nicolas E , Uchida Akira , Premkrishnan Balakrishnan N V , Heinle Cassie E , Phung Wen J , Wong Anthony , Lau Kenny J X , Yap Zhei H , Koh Yanqing , Ang Poh N , Putra Alexander , Panicker Deepa , Lee Jessica G H , Neves Luis C , Drautz-Moses Daniela I , Schuster Stephan C 
Published: April 2022

Abstract
Recent developments in aerobiology have enabled the investigation of airborne biomass with high temporal and taxonomic resolution. In this study, we assess the contributions of local sources to ambient air within a 160,000 m2 tropical avian park (AP). We sequenced and analyzed 120 air samples from seven locations situated 160 to 400 m apart, representing distinct microhabitats. Each microhabitat contained a characteristic air microbiome, defined by the abundance and richness of its airborne microbial community members, supported by both, PCoA and Random Forest analysis. Each outdoor microhabitat contained 1% to 18.6% location-specific taxa, while a core microbiome of 27.1% of the total taxa was shared. To identify and assess local sources, we compared the AP dataset with a DVE reference dataset from a location 2 km away, collected during a year-round sampling campaign. Intersection of data from the two sites demonstrated 61.6% of airborne species originated from local sources of the AP, 34.5% from ambient air background, and only 3.9% of species were specific to the DVE reference site. In-depth taxonomic analysis demonstrated association of bacteria-dominated air microbiomes with indoor spaces, while fungi-dominated airborne microbial biomass was predominant in outdoor settings with ample vegetation. The approach presented here demonstrates an ability to identify local source contributions against an ambient air background, despite the prevailing mixing of air masses caused by atmospheric turbulences.
The Impact of the COVID-19 Pandemic on Election Administration, Voting Options, and Turnout in the 2020 US Election
Authors: Herrnson Paul S , Hanmer Michael J , Weil Matthew , Orey Rachel 
Published: April 2022

Abstract
COVID-19 had a major impact on how some states administered the 2020 election and little effect on others. Using a new dataset, we identify the options states introduced to make voting safer, the measures they took to encourage voters to use these options, and the options’ effects on voter turnout. We show that most states introduced few, if any, significant changes in voting policies. We identify relationships between the states’ responses and preexisting election policies, party control of government, and other state characteristics. We also demonstrate the introduction of safe voting options had an effect on aggregate voter turnout. The results give insights into factors that influence election policymaking and the prospects for future election reforms.
Grotesque transparency and public health communication: the aesthetics and the ethics of ill bodies in the era of digital networks
Authors: Nahon-Serfaty Isaac 
Published: April 2022

Abstract

Background
We discuss the aesthetics of grotesque transparency in public health communication campaigns and health-related social marketing initiatives, and its strategic and ethical implications.

Methods
Some emblematic cases are discussed illustrating the relevance of the grotesque transparency strategy.

Results
These case studies show aesthetical and emotional considerations that public health scholars and professionals should carefully consider in the context of an expansive visual culture driven by digital communications. They also indicate that with the advent of technologies that expand the capabilities of manipulating and diffusing images the role of the transparently grotesque is more prevalent in public health and social marketing initiatives.

Discussion
The study of grotesque transparency is particularly important when facing emerging global public health challenges, such as pandemics and climate change-related health issues, in a disruptive communication ecosystem.
Socio-economics beyond the Global North
Authors: Jackson Gregory 
Published: April 2022

AbstractThis editorial argues for understanding socio-economics as an interdisciplinary space. While economic sociology and political economy are largely grounded in disciplines, the scope of socio-economics extends beyond any disciplinary subfields. But rather than a grand integration, a realistic aspiration behind this project is establishing a space of dialogue and engagement between them. Here scholarly innovation can take place in a more phenomenon-driven form and via eclectic borrowing and blending of discipline-based theories and methods. The next challenge facing socio-economics is to expand this interdisciplinary space from encompassing the Global North to engage with scholarship on and scholars from the Global South. This long-term challenge reflects very deep economic and social inequalities. The editorial offers several modest observations regarding the practices of writing and publication, while calling for a wider conversation about these issues. Specifically, the editorial highlights the potential of leveraging cross-context engagement with concepts to further new theoretical development.