bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid SARS-CoV-2 Inactivation in a Simulated Hospital Room Using a Mobile and Autonomous Robot Emitting Ultraviolet-C Light
Authors: Lorca-Oró Cristina , Vila Jordi , Pleguezuelos Patricia , Vergara-Alert Júlia , Rodon Jordi , Majó Natàlia , López Sergio , Segalés Joaquim , Saldaña-Buesa Francesc , Visa-Boladeras Maria , Veà-Baró Andreu , Campistol Josep Maria , Abad Xavier 
Published: November 2021

Abstract
The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) since 2019 has made mask-wearing, physical distancing, hygiene, and disinfection complementary measures to control virus transmission. Especially for health facilities, we evaluated the efficacy of an UV-C autonomous robot to inactivate SARS-CoV-2 desiccated on potentially contaminated surfaces. ASSUM (autonomous sanitary sterilization ultraviolet machine) robot was used in an experimental box simulating a hospital intensive care unit room. Desiccated SARS-CoV-2 samples were exposed to UV-C in 2 independent runs of 5, 12, and 20 minutes. Residual virus was eluted from surfaces and viral titration was carried out in Vero E6 cells. ASSUM inactivated SARS-CoV-2 by ≥ 99.91% to ≥ 99.99% titer reduction with 12 minutes or longer of UV-C exposure and onwards and a minimum distance of 100cm between the device and the SARS-CoV-2 desiccated samples. This study demonstrates that ASSUM UV-C device is able to inactivate SARS-CoV-2 within a few minutes.
Environmental Thermal Stress Induces Neuronal Cell Death and Developmental Malformations in Reptiles
Authors: Sanger Thomas J , Harding Laura , Kyrkos Judith , Turnquist Alexandrea J , Epperlein Lilian , Nunez Sylvia A , Lachance Dryden , Dhindsa Seerat , Stroud James T , Diaz Raul E , Czesny Beata 
Published: November 2021

SynopsisEvery stage of organismal life history is being challenged by global warming. Many species are already experiencing temperatures approaching their physiological limits; this is particularly true for ectothermic species, such as lizards. Embryos are markedly sensitive to thermal insult. Here, we demonstrate that temperatures currently experienced in natural nesting areas can modify gene expression levels and induce neural and craniofacial malformations in embryos of the lizard Anolis sagrei. Developmental abnormalities ranged from minor changes in facial structure to significant disruption of anterior face and forebrain. The first several days of postoviposition development are particularly sensitive to this thermal insult. These results raise new concern over the viability of ectothermic species under contemporary climate change. Herein, we propose and test a novel developmental hypothesis that describes the cellular and developmental origins of those malformations: cell death in the developing forebrain and abnormal facial induction due to disrupted Hedgehog signaling. Based on similarities in the embryonic response to thermal stress among distantly related species, we propose that this developmental hypothesis represents a common embryonic response to thermal insult among amniote embryos. Our results emphasize the importance of adopting a broad, multidisciplinary approach that includes both lab and field perspectives when trying to understand the future impacts of anthropogenic change on animal development.
Key requirements of a video-call system in a critical care department as discovered during the rapid development of a solution to address COVID-19 visitor restrictions
Authors: Conroy Irial , Murray Aoife , Kirrane Frank , Cullen Leonie , Anglim Paul , O’Keeffe Derek 
Published: November 2021

Abstract
The COVID-19 pandemic necessitated stringent visitor restrictions in critical care departments worldwide, creating challenges in keeping family members connected to patients and clinical staff. Previous studies have examined how hospitals addressed this challenge by repurposing existing tele-ICU systems or by using personal smartphones as a workaround and have analyzed clinical and family feedback. This case report addresses the experience of rapidly implementing a video-call system in the critical care department of a tertiary referral hospital that had no prior video-call system in place, detailing the key requirements in that setting. The 24 requirements were identified via interviews and surveys to both clinical and technical professionals. The top requirements identified were sound and video quality, usability for clinical staff, call control by staff, and patient privacy. From tailoring a video-call solution for this setting, we learned that video-endpoint selection is a key design decision. The initial proposal was to use wireless tablets, but the selection of a large wired video-endpoint allowed us to better address the requirements in the critical care setting. This was based on several characteristics of the large wired video-endpoint, including: high-fidelity video and sound, with directional noise-cancelling; large touch-screen setup for minimal-click navigation; wired as well as wireless connectivity.
Evaluation of reticulorumen temperature boluses for the diagnosis of subclinical cases of bovine respiratory disease in feedlot cattle
Authors: Flattot Emilie A-L , Batterham Tony R , Timsit Edouard , White Brad J , McMeniman Joe P , Ward Michael P , González Luciano A 
Published: November 2021

Abstract
Bovine respiratory disease (BRD) is the most important and costly health issue of the feedlot industry worldwide. Remote monitoring of reticulorumen temperature has been suggested as a potential tool to improve the diagnostic accuracy of BRD. The present study aimed to evaluate 1) the difference and degree of reticulorumen hyperthermia episodes between healthy and subclinical BRD feedlot steers, and 2) determine the correlation between reticulorumen hyperthermia and lung pathology, performance, and carcass traits. Mixed-breed feedlot steers (n = 148) with a mean arrival weight of 321 ± 3.34 kg were administered a reticulorumen bolus at feedlot entry and monitored for visual and audible signs of BRD until slaughter when lungs were examined and scored for lesions indicative of BRD. Post-slaughter animals with no record of BRD treatment were assigned to one of three case definitions. Healthy steers had no visual or audible signs of BRD (i.e., CIS=1), and total lung consolidation score &lt; 5% or pleurisy score &lt; 3 at slaughter. Subclinical BRD cases had a CIS of 1, and a lung consolidation score ≥ 5% or a pleurisy score of 3 at slaughter. Mild CIS cases had at least one CIS of 2, and a lung consolidation score &lt; 5% and a pleurisy score &lt; 3 at slaughter. Subclinical BRD and mild CIS cases had longer total duration of reticulorumen hyperthermia, more episodes and longer average episode duration above 40.0 °C compared to healthy steers (P &lt; 0.05). A moderate positive correlation was found between lung consolidation and total duration (r = 0.27, P &lt; 0.001), episode duration (r = 0.29, P &lt; 0.001), and number of episodes (r = 0.20, P &lt; 0.05). Pleurisy score was also found to be moderately and positively correlated with total duration (r = 0.23, P &lt; 0.01), episode duration (r = 0.37, P &lt; 0.001), and number of episodes (r = 0.26, P &lt; 0.01). Moderate negative correlations were found between reticulorumen hyperthermia and carcass traits including hot standard carcass weight (HSCW) (−0.22 ≤ r ≤ −0.23, P &lt; 0.05) and P8-fat depth (−0.18 ≤ r ≤ −0.32, P &lt; 0.05). Subclinical BRD reduced carcass weight by 22 kg and average daily gain (ADG) by 0.44 kg/day compared to healthy steers (P &lt; 0.05), but mild CIS cases had no effect on performance (P &gt; 0.05). The reticulorumen bolus technology appears promising for detection of subclinical BRD cases in feedlot cattle as defined by lung pathology at slaughter.
Technical note: overcoming host contamination in bovine vaginal metagenomic samples with nanopore adaptive sequencing
Authors: Ong Chian Teng , Ross Elizabeth M , Boe-Hansen Gry B , Turni Conny , Hayes Ben J , Tabor Ala E 
Published: November 2021

Abstract
Animal metagenomic studies, in which host-associated microbiomes are profiled, are an increasingly important contribution to our understanding of the physiological functions, health and susceptibility to diseases of livestock. One of the major challenges in these studies is host DNA contamination, which limits the sequencing capacity for metagenomic content and reduces the accuracy of metagenomic profiling. This is the first study comparing the effectiveness of different sequencing methods for profiling bovine vaginal metagenomic samples. We compared the new method of Oxford Nanopore Technologies (ONT) adaptive sequencing, which can be used to target or eliminate defined genetic sequences, to standard ONT sequencing, Illumina 16S rDNA amplicon sequencing, and Illumina shotgun sequencing. The efficiency of each method in recovering the metagenomic data and recalling the metagenomic profiles was assessed. ONT adaptive sequencing yielded a higher amount of metagenomic data than the other methods per 1 Gb of sequence data. The increased sequencing efficiency of ONT adaptive sequencing consequently reduced the amount of raw data needed to provide sufficient coverage for the metagenomic samples with high host-to-microbe DNA ratio. Additionally, the long reads generated by ONT adaptive sequencing retained the continuity of read information, which benefited the in-depth annotations for both taxonomical and functional profiles of the metagenome. The different methods resulted in the identification of different taxa. Genera Clostridium, which was identified at low abundances and categorized under Order “Unclassified Clostridiales” when using the 16S rDNA amplicon sequencing method, was identified to be the dominant genera in the sample when sequenced with the three other methods. Additionally, higher numbers of annotated genes were identified with ONT adaptive sequencing, which also produced high coverage on most of the commonly annotated genes. This study illustrates the advantages of ONT adaptive sequencing in improving the amount of metagenomic data derived from microbiome samples with high host-to-microbe DNA ratio and the advantage of long reads in preserving intact information for accurate annotations.
Smoking Cessation Prevalence and Inequalities in the United States: 2014-2019
Authors: Leventhal Adam M , Dai Hongying , Higgins Stephen T 
Published: November 2021

AbstractBackgroundSmoking is a leading cause of premature death and health inequities in the United States.MethodsWe estimated cross-sectional prevalence of smoking cessation indicators among US adult recent smokers (n = 43 602) overall and by sociodemographic subgroups in the Current Population Survey Tobacco Use Supplement 2014-2015 and 2018-2019 timepoints. Respondents reported past-year quit smoking interest, attempts, sustained (successful) cessation for 6 or more months and use of e-cigarettes or behavioral or pharmacological cessation treatments to quit smoking.ResultsPast-year quit smoking attempts declined slightly from 2014-2015 (52.9%) to 2018-2019 (51.3%) overall. Quit interest (pooled = 77.1%) and sustained cessation (pooled = 7.5%) did not change across timepoints. Among smokers making past-year quit attempts, 34.4% reported using cessation treatments in 2018-2019, and using e-cigarettes to quit smoking declined from 2014-2015 (33.3%) to 2018-2019 (25.0%). Several non-White (vs White) racial and ethnic groups had higher prevalence of quit interest and attempts but lower prevalence of sustained cessation or using e-cigarettes or treatments to quit. Income, education, employment, and metropolitan residence were positively associated with sustained cessation. Sociodemographic inequalities in sustained cessation and most other outcomes did not change across timepoints.ConclusionsAlthough about half of US adult smokers made past-year quit attempts from 2014 to 2019, only 7.5% reported sustained cessation, and most who made quit attempts did not report using cessation treatments. Sociodemographic inequalities in cessation were pervasive and not entirely correspondent with sociodemographic variation in motivation to quit. Smoking cessation prevalence and inequalities did not improve from 2014 to 2019. Encouraging quit attempts and equitable access to smoking cessation aids are public health priorities.
Cancer Microbiology
Authors: DiMaio Daniel , Emu Brinda , Goodman Andrew L , Mothes Walther , Justice Amy 
Published: November 2021

Abstract
Microbes play important roles in cancer from direct carcinogenic effects to their use in treatment. Cancers caused by microorganisms account for approximately 15% of cancers, primarily in low- and middle-income countries. Unique features of infectious carcinogens include their transmissibility, mutability, and specific immune interactions, which provide challenges and opportunities for cancer prevention and treatment. For these agents, infection control through exposure reduction, antivirals, antibiotics, and vaccines is cancer control. In addition, developing evidence suggests that microorganisms including the human microbiome can indirectly modulate cancer formation and influence the effectiveness and toxicity of cancer treatments. Finally, microorganisms themselves can be used to prevent or treat cancer. The convergence of these factors signals the emergence of a new field, cancer microbiology. Recognition of cancer microbiology will spur research, stimulate cross-disciplinary training, inform drug development, and improve public health.
Crouching TIGER, hidden structure: Exploring the nature of linguistic data using TIGER values
Authors: Syrjänen Kaj , Maurits Luke , Leino Unni , Honkola Terhi , Rota Jadranka , Vesakoski Outi 
Published: November 2021

AbstractIn recent years, techniques such as Bayesian inference of phylogeny have become a standard part of the quantitative linguistic toolkit. While these tools successfully model the tree-like component of a linguistic dataset, real-world datasets generally include a combination of tree-like and nontree-like signals. Alongside developing techniques for modeling nontree-like data, an important requirement for future quantitative work is to build a principled understanding of this structural complexity of linguistic datasets. Some techniques exist for exploring the general structure of a linguistic dataset, such as NeighborNets, δ scores, and Q-residuals; however, these methods are not without limitations or drawbacks. In general, the question of what kinds of historical structure a linguistic dataset can contain and how these might be detected or measured remains critically underexplored from an objective, quantitative perspective. In this article, we propose TIGER values, a metric that estimates the internal consistency of a genetic dataset, as an additional metric for assessing how tree-like a linguistic dataset is. We use TIGER values to explore simulated language data ranging from very tree-like to completely unstructured, and also use them to analyze a cognate-coded basic vocabulary dataset of Uralic languages. As a point of comparison for the TIGER values, we also explore the same data using δ scores, Q-residuals, and NeighborNets. Our results suggest that TIGER values are capable of both ranking tree-like datasets according to their degree of treelikeness, as well as distinguishing datasets with tree-like structure from datasets with a nontree-like structure. Consequently, we argue that TIGER values serve as a useful metric for measuring the historical heterogeneity of datasets. Our results also highlight the complexities in measuring treelikeness from linguistic data, and how the metrics approach this question from different perspectives.
Roles of the wound hormone jasmonate in plant regeneration
Authors: Zhang Guifang , Liu Wu , Gu Zewei , Wu Shasha , E Yilan , Zhou Wenkun , Lin Jinxing , Xu Lin 
Published: November 2021

AbstractPlants have remarkable abilities to regenerate in response to wounding. How wounding triggers rapid signal transduction to induce a cellular response is a key topic for understanding the molecular mechanism of plant regeneration. An increasing body of evidence indicates that jasmonate, a hormone that is produced rapidly in response to wounding, plays multiple roles in different plant regeneration processes. In this review, we summarize recent advances on the roles of jasmonate in tissue repair, the formation of wound-induced callus, de novo organ regeneration, and somatic embryogenesis. Physiological and molecular analyses indicate that jasmonate can regulate stem cell activities, cell proliferation, cell fate transition, and auxin production, thereby contributing to plant regeneration. In addition, jasmonate is strictly controlled in plant cells via restriction of the jasmonate concentration and its signalling pathway in a spatial and temporal manner during regeneration. Overall, jasmonate acts as the hormone linking wounding to distinct types of regeneration in plants.
Regulatory mechanisms underlying cuticular wax biosynthesis
Authors: Lee Saet Buyl , Suh Mi Chung 
Published: November 2021

AbstractPlants are sessile organisms that have developed hydrophobic cuticles that cover their aerial epidermal cells to protect them from terrestrial stresses. The cuticle layer is mainly composed of cutin, a polyester of hydroxy and epoxy fatty acids, and cuticular wax, a mixture of very-long-chain fatty acids (&gt;20 carbon atoms) and their derivatives, aldehydes, alkanes, ketones, alcohols, and wax esters. During the last 30 years, forward and reverse genetic, transcriptomic, and biochemical approaches have enabled the identification of key enzymes, transporters, and regulators involved in the biosynthesis of cutin and cuticular waxes. In particular, cuticular wax biosynthesis is significantly influenced in an organ-specific manner or by environmental conditions, and is controlled using a variety of regulators. Recent studies on the regulatory mechanisms underlying cuticular wax biosynthesis have enabled us to understand how plants finely control carbon metabolic pathways to balance between optimal growth and development and defense against abiotic and biotic stresses. In this review, we summarize the regulatory mechanisms underlying cuticular wax biosynthesis at the transcriptional, post-transcriptional, post-translational, and epigenetic levels.
Optimizing the Impact of Pragmatic Clinical Trials for Veteran and Military Populations: Lessons From the Pain Management Collaboratory
Authors: Ali Joseph , Antonelli Margaret , Bastian Lori , Becker William , Brandt Cynthia A , Burgess Diana J , Burns Amy , Cohen Steven P , Davis Alison F , Dearth Christopher L , Dziura Jim , Edwards Rob , Erdos Joe , Farrokhi Shawn , Fritz Julie , Geda Mary , George Steven Z , Goertz Christine , Goodie Jeffrey , Hastings Susan N , Heapy Alicia , Ilfeld Brian M , Katsovich Lily , Kerns Robert D , Kyriakides Tassos C , Lee Allison , Long Cynthia R , Luther Stephen L , Martino Steve , Matheny Michael E , McGeary Don , Midboe Amanda , Pasquina Paul , Peduzzi Peter , Raffanello Michael , Rhon Daniel , Rosen Marc , Esposito Elizabeth Russell , Scarton Dylan , Hastings Susan N , Seal Karen , Silliker Norman , Taylor Sakasha , Taylor Stephanie L , Tsui Megan , Wright Fred S , Zeliadt Steven 
Published: November 2021

ABSTRACT
Pragmatic clinical trials (PCTs) are well-suited to address unmet healthcare needs, such as those arising from the dual public health crises of chronic pain and opioid misuse, recently exacerbated by the COVID-19 pandemic. These overlapping epidemics have complex, multifactorial etiologies, and PCTs can be used to investigate the effectiveness of integrated therapies that are currently available but underused. Yet individual pragmatic studies can be limited in their reach because of existing structural and cultural barriers to dissemination and implementation. The National Institutes of Health, Department of Defense, and Department of Veterans Affairs formed an interagency research partnership, the Pain Management Collaboratory. The partnership combines pragmatic trial design with collaborative tools and relationship building within a large network to advance the science and impact of nonpharmacological approaches and integrated models of care for the management of pain and common co-occurring conditions. The Pain Management Collaboratory team supports 11 large-scale, multisite PCTs in veteran and military health systems with a focus on team science with the shared aim that the “whole is greater than the sum of the parts.” Herein, we describe this integrated approach and lessons learned, including incentivizing all parties; proactively offering frequent opportunities for problem-solving; engaging stakeholders during all stages of research; and navigating competing research priorities. We also articulate several specific strategies and their practical implications for advancing pain management in active clinical, “real-world,” settings.
Implementation of a clinical decision rule for selecting empiric treatment for invasive aspergillosis in a setting with high triazole resistance
Authors: van de Peppel Robert J , van Grootveld Rebecca , Hendriks Bart J C , van Paassen Judith , Bernards Sandra , Jolink Hetty , Koopmans Julia G , von dem Borne Peter A , van der Beek Martha T , de Boer Mark G J 
Published: November 2021

Abstract

World-wide, emerging triazole resistance increasingly complicates treatment of invasive aspergillosis (IA). In settings with substantial (&gt;10%) prevalence of triazole resistance, empiric combination therapy with both a triazole and liposomal amphotericin B (LAmB) can be considered because of the low yields of susceptibility testing. To avoid toxicity while optimizing outcome, a strategy with monotherapy would be preferable. A newly designed treatment algorithm based on literature and expert consensus provided guidance for empiric monotherapy with either voriconazole or LAmB. Over a four and a half year period, all adult patients in our hospital treated for IA were included and patient data were collected. An independent committee reviewed the attributability of death to IA for each patient. Primary outcomes were 30- and 100-day crude mortality and attributable mortality. In total, 110 patients were treated according to the treatment algorithm. Fifty-six patients (51%) were initially treated with voriconazole and 54 patients (49%) with LAmB. Combined attributable and contributable mortality was 13% within 30 days and 20% within 100 days. Treatment switch to LAmB was made in 24/56 (43%) of patients who were initially treated with voriconazole. Combined contributable and attributable 100-day mortality in this subgroup was 21% and was not increased when compared with patients initially treated with LAmB (P = 0.38). By applying a comprehensive clinical decision algorithm, an antifungal-sparing regime was successfully introduced. Further research is warranted to explore antifungal treatment strategies that account for triazole-resistance.

Lay summary
Due to resistance of Aspergillus against triazoles, combination therapy with liposomal amphotericin B (LAmB) is applied more often as primary therapy against invasive aspergillosis. This study presents the results of a decision tool which differentiated between triazole or LAmB monotherapy.