bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Distinct Phylogenetic Cluster of Indian Severe Acute Respiratory Syndrome Coronavirus 2 Isolates
Authors: Banu Sofia , Jolly Bani , Mukherjee Payel , Singh Priya , Khan Shagufta , Zaveri Lamuk , Shambhavi Sakshi , Gaur Namami , Reddy Shashikala , Kaveri K , Srinivasan Sivasubramanian , Gopal Dhinakar Raj , Siva Archana Bharadwaj , Thangaraj Kumarasamy , Tallapaka Karthik Bharadwaj , Mishra Rakesh K , Scaria Vinod , Sowpati Divya Tej 
Published: September 2020

Abstract

Background
From an isolated epidemic, coronavirus disease 2019 has now emerged as a global pandemic. The availability of genomes in the public domain after the epidemic provides a unique opportunity to understand the evolution and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus across the globe.

Methods
We performed whole-genome sequencing of 303 Indian isolates, and we analyzed them in the context of publicly available data from India.

Results
We describe a distinct phylogenetic cluster (Clade I/A3i) of SARS-CoV-2 genomes from India, which encompasses 22% of all genomes deposited in the public domain from India. Globally, approximately 2% of genomes, which to date could not be mapped to any distinct known cluster, fall within this clade.

Conclusions
The cluster is characterized by a core set of 4 genetic variants and has a nucleotide substitution rate of 1.1 × 10–3 variants per site per year, which is lower than the prevalent A2a cluster. Epidemiological assessments suggest that the common ancestor emerged at the end of January 2020 and possibly resulted in an outbreak followed by countrywide spread. To the best of our knowledge, this is the first comprehensive study characterizing this cluster of SARS-CoV-2 in India.
Crystallization and Segregation of Syenite in Shallow Mafic Sills: Insights from the San Rafael Subvolcanic Field, Utah
Authors: Germa Aurelie , Koebli Danielle , Wetmore Paul , Atlas Zachary , Arias Austin , Savov Ivan P , Diez Mikel , Greaves Vanessa , Gallant Elisabeth 
Published: September 2020

AbstractExposed plumbing systems provide important insight into crystallization and differentiation in shallow sills beneath volcanic fields. We use whole rock major element, trace element and radiogenic isotopic compositions, along with mineral geochemical data on 125 samples to examine the conditions of melt differentiation in shallow sills from the exposed 4-Ma-old San Rafael subvolcanic field (SRVF), Utah. The field consists of ∼2000 dikes, 12 sills and 63 well preserved volcanic conduits. Intrusive rocks consist of mainly fine-grained trachybasalts and coarse-grained syenites, which are alkaline, comagmatic and enriched in Ba, Sr and LREE. Within sills, syenite is found as veins, lenses, and sheets totally enveloped by the basalt. The SRVF intrusions have geochemical signatures of both enriched sub-continental lithospheric and asthenospheric mantle sources. We estimate partial melting occurred between 1·2 and 1·9 GPa (50–70 km), with mantle potential temperatures in the range 1260–1326 ± 25°C, consistent with those estimated for volcanic rocks erupted on the Colorado Plateau. Geobarometry results based on clinopyroxene chemistry indicate that (1) basalt crystallized during ascent from at least 40 km deep with limited lithospheric storage, and (2) syenites crystallized only in the sills, ∼1 km below the surface. San Rafael mafic magma was emplaced in sills and started to crystallize inward from the sill margins. Densities of basalt and syenite at solidus temperatures are 2·6 and 2·4 g/cc, respectively, with similar viscosities of ∼150 Pa s. Petrographic observations and physical properties suggest that syenite can be physically separated from basalt by crystal compaction and segregation of the tephrophonolitic residual liquid out of the basaltic crystal mush after reaching 30–45% of crystallization. Each individual sill is 10–50 m thick and would have solidified fairly rapidly (1–30 years), the same order of magnitude as the duration of common monogenetic eruptions. Our estimates imply that differentiation in individual shallow sills may occur during the course of an eruption whose style may vary from effusive to explosive by tapping different magma compositions. Our study shows that basaltic magmas have the potential to differentiate to volatile-rich magma in shallow intrusive systems, which may increase explosivity.
Knowledge, attitudes and practices associated with the COVID-19 among slum dwellers resided in Dhaka City: a Bangladeshi interview-based survey
Authors: Islam Saiful , Emran Galib Ishraq , Rahman Estiar , Banik Rajon , Sikder Tajuddin , Smith Lee , Hossain Sahadat 
Published: September 2020

Abstract

Background
The emergent COVID-19 has impacted unprecedentedly to all classes of people. Slum-dwellers’ knowledge, attitudes and practices (KAP) toward COVID-19 are currently poorly understood. The present study aimed to investigate the KAP toward COVID-19 among slum dwellers resided in Dhaka City, Bangladesh.

Methods
A cross-sectional offline survey was carried out enrolling 406 slum dwellers (53.2% male; mean age = 44.9 years [SD = 12.1]; age range = 18–85 years) between August and September, 2020. The face to face interview was conducted to collect data from six selected slum areas in Dhaka City using convenience sampling. The questionnaire consisted of informed consent along with questions concerning observational checklists, socio-demographics and KAP.

Results
A sizeable minority were observed without wearing face masks during the survey periods (18.2%) and a vast portion (97.5%) without any hand protection. The mean scores of KAP were 6.1 ± 2.6 (out of 17), 12.3 ± 1.7 (out of 14) and 9.8 ± 1.6 (out of 12), respectively. Moreover, the KAP were strongly and positively correlated with each other.

Conclusions
The findings revealed that the majority of slum dwellers in Bangladesh have limited knowledge of COVID-19. Poor practices (i.e. face mask and hand protection) were directly observed during the survey. The findings suggest the immediate implementation of health education programs and adequate interventions.
Responses of functional traits to seven-year nitrogen addition in two tree species: coordination of hydraulics, gas exchange and carbon reserves
Authors: Zhang Hongxia , Yuan Fenghui , Wu Jiabing , Jin Changjie , Pivovaroff Alexandria L , Tian Jinyuan , Li Weibin , Guan Dexin , Wang Anzhi , McDowell Nate G 
Published: September 2020

Abstract
Atmospheric nitrogen (N) deposition has been observed to impact plant structure and functional traits in terrestrial ecosystems. Although the effect of N deposition on plant water use has been well-evaluated in laboratories and in experimental forests, the linkages between water and carbon relations under N deposition are unclear. Here, we report on hydraulics, gas exchange and carbon reserves of two broad-leaved tree species (Quercus mongolica and Fraxinus mandshurica) in mature temperate forests after a seven-year experiment with different levels of N addition (control (CK), low (23 kg N ha−1 yr−1), medium (46 kg N ha−1 yr−1) and high (69 kg N ha−1 yr−1)). We investigated variation in hydraulic traits (xylem-specific hydraulic conductivity (Ks), native percentage loss of conductivity (PLC) and leaf water potential), xylem anatomy (vessel diameter and density), gas exchange (maximum net photosynthesis rate and stomatal conductance) and carbon reserves (soluble sugars, starch and total nonstructural carbohydrates (NSC)) with different N addition levels. We found that medium N addition significantly increased Ks and vessel diameter compared to control, but accompanied increasing PLC and decreasing leaf water potential, suggesting that N addition results in a greater hydraulic efficiency and higher risk of embolism. N addition promoted photosynthetic capacity via increasing foliar N concentration but did not change stomatal conductance. In addition, we found increase in foliar soluble sugar concentration and decrease in starch concentration with N addition, and positive correlations between hydraulic traits (vessel diameter and PLC) and soluble sugars. These coupled responses of tree hydraulics and carbon metabolism are consistent with a regulatory role of carbohydrates in maintaining hydraulic integrity. Our study provides an important insight into the relationship of plant water transport and carbon dynamics under increasing N deposition.
Chlorophyll fluorescence parameters, leaf traits and foliar chemistry of white oak and red maple trees in urban forest patches
Authors: Sonti Nancy F , Hallett Richard A , Griffin Kevin L , Trammell Tara L E , Sullivan Joe H 
Published: September 2020

Abstract
The provisioning of critical ecosystem services to cities of the eastern USA depends on the health and physiological function of trees in urban areas. Although we know that the urban environment may be stressful for trees planted in highly developed areas, it is not clear that trees in urban forest patches experience the same stressful environmental impacts. In this study, we examine chlorophyll fluorescence parameters, leaf traits, foliar nutrients and stable isotope signatures of urban forest patch trees compared with trees growing at reference forest sites, in order to characterize physiological response of these native tree species to the urban environment of three major cities arranged along a latitudinal gradient (New York, NY; Philadelphia, PA; Baltimore, MD). Overall, white oaks (Quercus alba L.) show more differences in chlorophyll fluorescence parameters and leaf traits by city and site type (urban vs reference) than red maples (Acer rubrum L.). The exceptions were δ13C and δ15N, which did not vary in white oak foliage but were significantly depleted (δ13C) and enriched (δ15N) in urban red maple foliage. Across all sites, red maples had higher thermal tolerance of photosynthesis (Tcrit) than white oaks, suggesting a greater ability to withstand temperature stress from the urban heat island effect and climate change. However, the highest average values of Tcrit were found in the Baltimore urban white oaks, suggesting that species suitability and response to the urban environment varies across a latitudinal gradient. Stomatal pore index (SPI) showed inter-specific differences, with red maple SPI being higher in urban trees, whereas white oak SPI was lower in urban trees. These results demonstrate that differences in native tree physiology occur between urban and reference forest patches, but they are site- and species-specific. Data on local site characteristics and tree species performance over time remain necessary to gain insight about urban woodland ecosystem function.
The cold truth about postcardiac arrest targeted temperature management
Authors: Knippa Sara , Butler Jana , Johnson Lauren , Perman Sarah M. 
Published: September 2020

Abstract:
This article provides nurses with up-to-date evidence to empower them in contributing to the 33°C versus 36°C discussion in postcardiac arrest targeted temperature management (TTM). Presented in debate format, this article addresses the pros and cons of various target temperatures, examines the evidence around TTM, and applies it to clinical scenarios.
Fractures in Patients With COVID-19 Infection: Early Prognosis and Management. A Case Series of 20 Patients in a Single Institution in Lombardy, Northern Italy
Authors: Jannelli Eugenio , Castelli Alberto , Ferranti Calderoni Enrico , Annunziata Salvatore , Maccario Gaia , Ivone Alessandro , Pasta Gianluigi , Mosconi Mario 
Published: September 2020

Summary:
Fifty-eight percent of the total infections in Italy of COVID-19 were found in northern Italy, in particular, Lombardy. From February 21, 2020, to March 23, 2020, 20 patients with a fracture and a diagnosis of COVID-19 were hospitalized. Demographic data, COVID-19 symptoms, laboratory and radiographic examinations, and treatment methods were recorded. At 1-month follow-up, patients were assessed with the SF-36 score. This case series includes 20 patients (16 women and 4 men), with an average age of 82.35 years (range 59–95). Eleven patients (55%) had a femur fracture. Fourteen patients (70%) had 3 or more comorbidities or previous pathologies. Three patients with severe comorbidities died during the hospitalization. Thirteen patients (65%) had fever, 18 patients (90%) asthenia, and 17 patients (85%) dyspnea. All patients (100%) were given antibiotic therapy, whereas 16 patients (80%) underwent hydroxychloroquine therapy and 8 (40%) were treated with corticosteroids. Eighteen patients (90%) underwent antithromboembolic prophylaxis. Eighteen patients (90%) had lymphopenia. All 20 patients (100%) required noninvasive mechanical ventilation. High D-dimer and polymerase chain reaction values were found in all patients (100%), whereas lactate dehydrogenase was increased in 18 patients (90%). Patients with fractures, especially in the lower limbs, frequently require hospitalization, making these patients more subjected to the risk of COVID-19 infection. COVID-19 infection therefore does not seem to influence the fracture pattern in the elderly population but can lead to health deterioration with increased mortality. The typical symptoms of COVID-19 disease have not changed when associated with a fracture or trauma. Laboratory data are in line with what is reported in recent studies, whereas a more invasive assisted ventilation is associated with a poor prognosis. Finally, analyzing the data obtained from the SF-36 score, significantly lower values emerged when compared with those reported in the literature.

Level of Evidence:
Prognostic Level IV. See Instructions for Authors for a complete description of levels of evidence.
Early Orthopaedic Trauma Outcomes in COVID-19 Infected Patients: A Case Series
Authors: Edwards Diep N. , Arguello Alexandra M. , Ponce Brent A. , Spitler Clay A. , Quade Jonathan H. 
Published: September 2020

Summary:
Orthopaedic trauma presents a unique and complex challenge in the initial phase of the coronavirus 2019 (COVID-19) global crisis. Little is currently known about the surgical practices in orthopaedic emergencies in the early days of the COVID-19 outbreak (1). This is a retrospective case series of 10 orthopaedic trauma patients who underwent fracture fixation in March 2020. Of the 10 patients testing COVID-19 positive, there were a total of 16 long bone fractures, 5 pelvic ring fractures, and 1 lumbar burst fracture. There were 7 (70%) males in this cohort. Two (20%) of the COVID-positive patients did not develop fever, leukocytosis, respiratory insufficiency, or positive imaging findings and were younger (average age 25.5 years) with fewer comorbidities (average 0.5) compared with the 8 symptomatic COVID-19–positive patients (56.6 years with 1.88 comorbidities). Advancement of COVID-19 pathogenesis with lung opacities and prolonged intubation occurred in all 5 patients who remained on ventilation postoperatively (range 9 hours–11 days). At the time of most recent follow-up, all patients survived, 1 continues to require ventilation support, 1 remains admitted without ventilation support, and 8 (80%) were discharged to home.

Level of Evidence:
Prognostic Level II. See Instructions for Authors for a complete description of levels of evidence.
The Association of Inflammatory Cytokines in the Pulmonary Pathophysiology of Respiratory Failure in Critically Ill Patients With Coronavirus Disease 2019
Authors: Stukas Sophie , Hoiland Ryan L. , Cooper Jennifer , Thiara Sonny , Griesdale Donald E. , Thomas Adam D. , Orde Matthew M. , English John C. , Chen Luke Y. C. , Foster Denise , Mitra Anish R. , Romano Kali , Sweet David D. , Ronco Juan J. , Kanji Hussein D. , Chen Yu-Wei R. , Wong Sophia L. , Wellington Cheryl L. , Sekhon Mypinder S. 
Published: September 2020

Objectives:
The majority of coronavirus disease 2019 mortality and morbidity is attributable to respiratory failure from severe acute respiratory syndrome coronavirus 2 infection. The pathogenesis underpinning coronavirus disease 2019-induced respiratory failure may be attributable to a dysregulated host immune response. Our objective was to investigate the pathophysiological relationship between proinflammatory cytokines and respiratory failure in severe coronavirus disease 2019.

Design:
Multicenter prospective observational study.

Setting:
ICU.

Patients:
Critically ill patients with coronavirus disease 2019 and noncoronavirus disease 2019 critically ill patients with respiratory failure (ICU control group).

Interventions:
Daily measurement of serum inflammatory cytokines.

Measurements and Main Results:
Demographics, comorbidities, clinical, physiologic, and laboratory data were collected daily. Daily serum samples were drawn for measurements of interleukin-1β, interleukin-6, interleukin-10, and tumor necrosis factor-α. Pulmonary outcomes were the ratio of Pao
2/Fio
2 and static lung compliance. Twenty-six patients with coronavirus disease 2019 and 22 ICU controls were enrolled. Of the patients with coronavirus disease 2019, 58% developed acute respiratory distress syndrome, 62% required mechanical ventilation, 12% underwent extracorporeal membrane oxygenation, and 23% died. A negative correlation between interleukin-6 and Pao
2/Fio
2 (rho, –0.531; p = 0.0052) and static lung compliance (rho, –0.579; p = 0.033) was found selectively in the coronavirus disease 2019 group. Diagnosis of acute respiratory distress syndrome was associated with significantly elevated serum interleukin-6 and interleukin-1β on the day of diagnosis.

Conclusions:
The inverse relationship between serum interleukin-6 and Pao
2/Fio
2 and static lung compliance is specific to severe acute respiratory syndrome coronavirus 2 infection in critically ill patients with respiratory failure. Similar observations were not found with interleukin-β or tumor necrosis factor-α.
Clinical Practice Guidelines for Early Mobilization in the ICU: A Systematic Review
Authors: Lang Jenna K. , Paykel Melanie S. , Haines Kimberley J. , Hodgson Carol L. 
Published: September 2020

Objectives:
To evaluate the methodological quality and thematic completeness of existing clinical practice guidelines, addressing early mobilization of adults in the ICU.

Data Sources:
Systematic review of Medline, Embase, CINAHL, Cochrane, and grey literature from January 2008 to February 2020.

Study Selection:
Two reviewers independently screened titles and abstracts and then full texts for eligibility. Ten publications were included.

Data Extraction:
A single reviewer extracted data from the included publications and a second reviewer completed cross-checking. Qualitative data were extracted in five categories relating to the key factors influencing delivery of early mobilization to critically ill patients.

Data Synthesis:
Methodological quality was appraised using the Appraisal of Guidelines for Research and Evaluation II tool. Appraisal of Guidelines for Research and Evaluation II scores for applicability were low. Median quality scores for editorial independence, rigor of development, and stakeholder engagement were also poor. Narrative synthesis of publication content was undertaken. All publications supported implementation of early mobilization. Most documents agreed upon seven topics: 1) early mobilization is safe and may reduce healthcare costs, 2) safety criteria should be provided, 3) a protocolized or structured approach should be used, 4) collaborative teamwork is required, 5) staff require specific skills or experience, 6) patient and family engagement is important, and 7) program evaluation and outcome measurement are a key component of implementation. There was no consensus on dosage and patient selection. The areas of team culture and leadership were poorly addressed.

Conclusions:
Despite significant variation in the methodological quality of clinical practice guidelines for early mobilization, there were important consistencies in recommendations internationally. Future research should address gaps related to patient selection, dosage, team culture, and expertise. Future clinical practice guidelines in this area should focus on engagement of patients and families in the development process and provision of resources to support implementation based on the consideration of known barriers and facilitators.
High-Flow Nasal Cannula Compared With Conventional Oxygen Therapy or Noninvasive Ventilation Immediately Postextubation: A Systematic Review and Meta-Analysis
Authors: Granton David , Chaudhuri Dipayan , Wang Dominic , Einav Sharon , Helviz Yigal , Mauri Tommaso , Mancebo Jordi , Frat Jean-Pierre , Jog Sameer , Hernandez Gonzalo , Maggiore Salvatore M. , Hodgson Carol L. , Jaber Samir , Brochard Laurent , Trivedi Vatsal , Ricard Jean-Damien , Goligher Ewan C. , Burns Karen E. A. , Rochwerg Bram 
Published: September 2020

Objectives:
Reintubation after failed extubation is associated with increased mortality and longer hospital length of stay. Noninvasive oxygenation modalities may prevent reintubation. We conducted a systematic review and meta-analysis to determine the safety and efficacy of high-flow nasal cannula after extubation in critically ill adults.

Data Sources:
We searched MEDLINE, EMBASE, and Web of Science.

Study Selection:
We included randomized controlled trials comparing high-flow nasal cannula to other noninvasive methods of oxygen delivery after extubation in critically ill adults.

Data Extraction:
We included the following outcomes: reintubation, postextubation respiratory failure, mortality, use of noninvasive ventilation, ICU and hospital length of stay, complications, and comfort.

Data Synthesis:
We included eight randomized controlled trials (n = 1,594 patients). Compared with conventional oxygen therapy, high-flow nasal cannula decreased reintubation (relative risk, 0.46; 95% CI, 0.30–0.70; moderate certainty) and postextubation respiratory failure (relative risk, 0.52; 95% CI, 0.30–0.91; very low certainty), but had no effect on mortality (relative risk, 0.93; 95% CI, 0.57–1.52; moderate certainty), or ICU length of stay (mean difference, 0.05 d fewer; 95% CI, 0.83 d fewer to 0.73 d more; high certainty). High-flow nasal cannula may decrease use of noninvasive ventilation (relative risk, 0.64; 95% CI, 0.34–1.22; moderate certainty) and hospital length of stay (mean difference, 0.98 d fewer; 95% CI, 2.16 d fewer to 0.21 d more; moderate certainty) compared with conventional oxygen therapy, however, certainty was limited by imprecision. Compared with noninvasive ventilation, high-flow nasal cannula had no effect on reintubation (relative risk, 1.16; 95% CI, 0.86–1.57; low certainty), mortality (relative risk, 1.12; 95% CI, 0.82–1.53; moderate certainty), or postextubation respiratory failure (relative risk, 0.82; 95% CI, 0.48–1.41; very low certainty). High-flow nasal cannula may reduce ICU length of stay (moderate certainty) and hospital length of stay (moderate certainty) compared with noninvasive ventilation.

Conclusions:
High-flow nasal cannula reduces reintubation compared with conventional oxygen therapy, but not compared with noninvasive ventilation after extubation.