bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gaps in Emergency General Surgery Coverage in the United States
Authors: Ingraham Angela M. , Chaffee Scott M. , Ayturk M. Didem , Heh Victor K. , Kiefe Catarina I. , Santry Heena P. 
Published: February 2021

Introduction:
Despite 3 million adults in the United States being admitted annually for emergency general surgery (EGS) conditions, which disproportionately affect vulnerable populations, we lack an understanding of the barriers to round-the-clock EGS care. Our objective was to measure gaps in round-the-clock EGS care.

Methods:
From August 2015 to December 2015, we surveyed all US-based adult acute care general hospitals that have an emergency room and ≥1 operating room and provided EGS care, utilizing paper and electronic methods. Surgeons or chief medical officers were queried regarding EGS practices.

Results:
Of 2811 hospitals, 1634 (58.1%) responded; 279 (17.1%) were unable to always provide round-the-clock EGS care. Rural location, smaller bed size, and nonteaching status were associated with lack of round-the-clock care. Inconsistent surgeon coverage was the primary reason for lacking round-the-clock EGS care (n = 162; 58.1%). However, lack of a tiered system for booking emergency cases, no anesthesia availability overnight, and no stipend for EGS call were also associated with the inability to provide round-the-clock EGS care.

Discussion:
We found significant gaps in access to EGS care, often attributable to workforce deficiencies.
d-dimer and Death in Critically Ill Patients With Coronavirus Disease 2019
Authors: Short Samuel A. P. , Gupta Shruti , Brenner Samantha K. , Hayek Salim S. , Srivastava Anand , Shaefi Shahzad , Singh Harkarandeep , Wu Benjamin , Bagchi Aranya , Al-Samkari Hanny , Dy Rajany , Wilkinson Katherine , Zakai Neil A. , Leaf David E. 
Published: February 2021

OBJECTIVES:
Hypercoagulability may be a key mechanism for acute organ injury and death in patients with severe coronavirus disease 2019, but the relationship between elevated plasma levels of d-dimer, a biomarker of coagulation activation, and mortality has not been rigorously studied. We examined the independent association between d-dimer and death in critically ill patients with coronavirus disease 2019.

DESIGN:
Multicenter cohort study.

SETTING:
ICUs at 68 hospitals across the United States.

PATIENTS:
Critically ill adults with coronavirus disease 2019 admitted to ICUs between March 4, 2020, and May 25, 2020, with a measured d-dimer concentration on ICU day 1 or 2.

INTERVENTIONS:
None.

MEASUREMENTS AND MAIN RESULTS:
The primary exposure was the highest normalized d-dimer level (assessed in four categories: < 2×, 2–3.9×, 4–7.9×, and ≥ 8× the upper limit of normal) on ICU day 1 or 2. The primary endpoint was 28-day mortality. Multivariable logistic regression was used to adjust for confounders. Among 3,418 patients (63.1% male; median age 62 yr [interquartile range, 52–71 yr]), 3,352 (93.6%) had a d-dimer concentration above the upper limit of normal. A total of 1,180 patients (34.5%) died within 28 days. Patients in the highest compared with lowest d-dimer category had a 3.11-fold higher odds of death (95% CI, 2.56–3.77) in univariate analyses, decreasing to a 1.81-fold increased odds of death (95% CI, 1.43–2.28) after multivariable adjustment for demographics, comorbidities, and illness severity. Further adjustment for therapeutic anticoagulation did not meaningfully attenuate this relationship (odds ratio, 1.73; 95% CI, 1.36–2.19).

CONCLUSIONS:
In a large multicenter cohort study of critically ill patients with coronavirus disease 2019, higher d-dimer levels were independently associated with a greater risk of death.
Exposure to metal mixtures in relation to blood pressure among children 5–7 years old
Authors: Shih Yu-Hsuan , Howe Caitlin G. , Scannell Bryan Molly , Shahriar Mohammad , Kibriya Muhammad G. , Jasmine Farzana , Sarwar Golam , Graziano Joseph H. , Persky Victoria W. , Jackson Brian , Ahsan Habibul , Farzan Shohreh F. , Argos Maria 
Published: February 2021

Background:
Hypertension in later life, a significant risk factor for cardiovascular disease, has been linked to elevated blood pressure in early life. Exposure to metals may influence childhood blood pressure; however, previous research is limited and has mainly focused on evaluating the toxicity of single metal exposures. This study evaluates the associations between exposure to metal mixtures and blood pressure among Bangladeshi children age 5–7 years.

Methods:
We investigated the associations of 17 toenail metal concentrations with blood pressure using linear regression models. Principal component analysis (PCA), weighted quantile sum (WQS) regression, and Bayesian kernel machine regression (BKMR) were conducted as secondary analyses.

Results:
Associations were observed for selenium with diastolic blood pressure (per doubling of exposure β = 2.91, 95% confidence interval [CI] = 1.08, 4.75), molybdenum with systolic (β = 0.33, 95% CI = 0.05, 0.61) and diastolic blood pressure (β = 0.39, 95% CI = 0.12, 0.66), tin with systolic blood pressure (β = –0.33, 95% CI = –0.60, –0.06), and mercury with systolic (β = –0.83, 95% CI = –1.49, –0.17) and diastolic blood pressure (β = –0.89, 95% CI = –1.53, –0.26). Chromium was associated with diastolic blood pressure among boys only (β = 1.10, 95% CI = 0.28, 1.92, P for interaction = 0.02), and copper was associated with diastolic blood pressure among girls only (β = –1.97, 95% CI = –3.63, –0.32, P for interaction = 0.01). These findings were largely robust to the secondary analyses that utilized mixture modeling approaches (PCA, WQS, and BKMR).

Conclusions:
Future prospective studies are needed to investigate further the impact of early life exposure to metal mixtures on children’s blood pressure trajectories and cardiovascular disease risk later in life.
Rapid SARS-CoV-2 variants spread detected in France using specific RT-PCR testing
Authors: Haim-Boukobza Stéphanie , Roquebert Benedicte , Trombert-Paolantoni Sabine , Lecorche Emmanuel , Verdurme Laura , Foulongne Vincent , Selinger Christian , Michalakis Yannis , Sofonea Mircea T. , Alizon Samuel 
Published: February 2021

AbstractSARS-CoV-2 variants raise major concerns regarding the control of COVID-19 epidemics. We analyse 40,000 specific RT-PCR tests performed on SARS-CoV-2-positive samples collected between Jan 26 and Feb 16, 2021. We find a high transmission advantage of variants and show that their spread in the country is more advanced than anticipated.
Associations Between Google Search Trends for Symptoms and COVID-19 Confirmed and Death Cases in the United States
Authors: Abbas Mostafa , Morland Thomas B. , Hall Eric S. , EL-Manzalawy Yasser 
Published: February 2021

ABSTRACTWe utilize functional data analysis techniques to investigate patterns of COVID-19 positivity and mortality in the US and their associations with Google search trends for COVID-19 related symptoms. Specifically, we represent state-level time series data for COVID-19 and Google search trends for symptoms as smoothed functional curves. Given these functional data, we explore the modes of variation in the data using functional principal component analysis (FPCA). We also apply functional clustering analysis to identify patterns of COVID-19 confirmed case and death trajectories across the US. Moreover, we quantify the associations between Google COVID-19 search trends for symptoms and COVID-19 confirmed case and death trajectories using dynamic correlation. Finally, we examine the dynamics of correlations for the top nine Google search trends of symptoms commonly associated with COVID-19 confirmed case and death trajectories. Our results reveal and characterize distinct patterns for COVID-19 spread and mortality across the US. The dynamics of these correlations suggest the feasibility of using Google queries to forecast COVID-19 cases and mortality for up to three weeks in advance. Our results and analysis framework set the stage for the development of predictive models for forecasting COVID-19 confirmed cases and deaths using historical data and Google search trends for nine symptoms associated with both outcomes.
Lactic Acid Production byClostridium acetobutylicumandClostridium beijerinckiiUnder Anaerobic Conditions Using a Complex Substrate
Authors: L. Mattiello-Franisco , F.M. Vieira , G. Peixoto , G. Mockaitis 
Published: February 2021

SUMMARY/ ABSTRACTHigh societies consumption, elevated residues generation and environmental awareness strengthen alternatives solutions for bioprocess’ residues. This study investigated the production of volatile acids from a complex substrate, which intends to be replaceable in the future by vinasse of sugar cane, in anaerobic reactors operated in triplicates at 35 °C. Two different inoculum were studied:Clostridium acetobutylicumATCC 824 andClostridium beijerinckiiATCC 25752. The nutrient medium had as carbon source a complex substrate containing sucrose without addition of vitamins, buffer solution and micronutrients. The experiment was conducted in the variation of F/M-ratio (food-to-microorganisms) by increasing substrate concentration.The concentration of sucrose in the complex substrate were 5.2 g·L-1(conditions of 10,000 mg O2· L-1in terms of COD) and 10.5 g· L-1(conditions of 20,000 mg O2·L-1in terms of COD), keeping the initial concentration of inoculum in 500 mg SVT·L-1. CulturesC. acetobutylicumandC. beijerinckiiresulted in high lactic acid production. Concentrations of COD of 10,000 mg O2· L-1produced optimum lactic acid of 3,331 mg·L-1and 5,709 mg·L-1with respectively C.acetobutylicumandC. beijerinckii.Moreover, cultures C.acetobutylicumandC. beijerinckiiwith 20,000 mg O2· L-1concentrations in terms of COD produced optimum lactic acid of 6,417 mg· L-1and 7.136 mg·L-1respectively. There was repeatability in the reactors when considering level of significance of 0.05, independent of the concentration and inoculum used.
Genomics-based deconvolution of multiplexed transcriptional responses to wood smoke particles defines rapid AHR signaling dynamics
Authors: Gupta Arnav , Sasse Sarah K , Gruca Margaret A. , Sanford Lynn , Dowell Robin D. , Gerber Anthony N. 
Published: February 2021

AbstractHeterogeneity of respirable particulates and compounds complicates understanding transcriptional responses to air pollution. Here, we address this problem through applying precision nuclear run-on sequencing (PRO-seq) to measure nascent transcription and the assay for transposase-accessible chromatin using sequencing (ATAC-seq) to airway epithelial cells after wood smoke particle (WSP) exposure. We used transcription factor enrichment analysis to agnostically identify temporally distinct roles for the TCF/SRF family, the aryl hydrocarbon receptor (AHR), and NFkB in regulating transcriptional changes induced by WSP. Transcription of canonical targets of the AHR, such asCYP1A1andAHRR, was robustly increased after just 30 minutes of WSP exposure, and we discovered novel AHR-regulated pathways and targets including the DNA methyltransferase,DNMT3L. Transcription of these genes and associated enhancers rapidly returned to near baseline by 120 minutes. The kinetics of AHR- and NFkB-regulated responses to WSP were distinguishable based on the timing of both transcriptional responses and chromatin remodeling, with induction of several cytokines implicated in maintaining NFkB responses through 120 minutes of exposure. In aggregate, our data establish a direct and primary role for AHR in mediating airway epithelial responses to WSP and identify crosstalk between AHR and NFkB signaling in controlling pro-inflammatory gene expression. This work also defines an integrated genomics-based strategy for deconvoluting multiplexed transcriptional responses to heterogeneous environmental exposures.
Emergence of variation between groups through time in fish shoal collective motion
Authors: MacGregor Hannah E. A. , Ioannou Christos C. 
Published: February 2021

AbstractDespite extensive interest in the dynamic interactions between individuals that drive collective motion in animal groups, the dynamics of collective motion over longer time frames are understudied. Using three-spined sticklebacks,Gasterosteus aculateus, randomly assigned to twelve shoals of eight fish, we tested how six key traits of collective motion changed over shorter (within trials) and longer (between days) timescales under controlled laboratory conditions. Over both timescales, groups became less social with reduced cohesion, polarisation, group speed and information transfer. There was consistent inter-group variation (i.e. collective personality variation) for all collective motion parameters, but groups also differed in how their collective motion changed over days in their cohesion, polarisation, group speed and information transfer. This magnified differences between groups, suggesting that over time the ‘typical’ collective motion cannot be easily characterised. The minimal sample size of independent groups and their divergence over time need to be considered in future studies.
Comprehensive evaluation ofACE2expression in female ovary by single-cell RNA-seq analysis
Authors: Kong Siming , Yan Zhiqiang , Yuan Peng , Liu Xixi , Chen Yidong , Yang Ming , Chen Wei , Song Shi , Yan Jie , Yan Liying , Qiao Jie 
Published: February 2021

AbstractPneumonia induced by severe acute respiratory coronavirus 2 (SARS-CoV-2) via ACE2 receptor may affect many organ systems like lung, heart and kidney. An autopsy report revealed positive SARS-Cov-2 detection results in ovary, however, the developmental-stage-specific and cell-type-specific risk in fetal primordial germ cells (PGCs) and adult women ovary remained unclear. In this study, we used single-cell RNA-sequencing (scRNA-seq) datasets spanning several developmental stages of ovary including PGCs and cumulus-oocyte complex (COC) to investigate the potential risk of SARS-CoV-2 infection. We found that PGCs and COC exhibited highACE2expression. More importantly, the ratio ofACE2-positive cells was sharply up-regulated in primary stage andACE2was expressed in all oocytes and cumulus cells in preovulatory stage, suggesting the possible risk of SARS-CoV-2 infection in follicular development. CatB/L, not TMPRSS2, was identified to prime for SARS-CoV-2 entry in follicle. Our findings provided insights into the potential risk of SARS-CoV-2 infection during folliculogenesis in adulthood and the possible risk in fetal PGCs.
IFNγ and iNOS-mediated alterations in the bone marrow and thymus and its impact onMycobacterium avium-induced thymic atrophy
Authors: Barreira-Silva Palmira , Melo-Miranda Rita , Nobrega Claudia , Roque Susana , Serre-Miranda Cláudia , Borges Margarida , de Sá Calçada Daniela , Behar Samuel M. , Appelberg Rui , Correia-Neves Margarida 
Published: February 2021

ABSTRACTDisseminated infection with the high virulence strain ofMycobacterium avium25291 lead to progressive thymic atrophy. We previously uncovered thatM. avium-induced thymic atrophy is due to increased levels of glucocorticoids synergizing with nitric oxide (NO) produced by interferon gamma (IFNγ) activated macrophages. Where and how these mediators are playing, was yet to be understood. We hypothesized that IFNγ and NO might be affecting bone marrow (BM) T cell precursors and/or T cell differentiation in the thymus. We show thatM. aviuminfection causes a reduction on the percentage of lymphoid-primed multipotent progenitors (LMPP) and common lymphoid progenitors (CLP). Additionally, BM precursors from infected mice are unable to reconstitute thymi of RAGKO mice in an IFNγ-dependent way. Thymi from infected mice presents a NO-dependent inflammation. When transplanted under the kidney capsule of non-infected mice, thymic stroma from infected mice is unable to sustain T cell differentiation. Finally, we observed increased thymocyte death via apoptosis after infection, independent of both IFNγ and iNOS, and a decrease on activated caspase-3 positive thymocytes, that was not observed in the absence of iNOS expression. Together our data suggests thatM. avium-induced thymic atrophy results from a combination of impairments, mediated by IFNγ and NO, affecting different steps of T cell differentiation from T cell precursor cells in the BM to the thymic stroma and thymocytes.
Adaptive introgression and standing genetic variation, two facilitators of adaptation to high latitudes in European aspen (Populus tremulaL.)
Authors: Rendón-Anaya Martha , Wilson Jonathan , Sveinsson Sæmundur , Fedorkov Aleksey , Cottrell Joan , Bailey Mark E.S. , Ruņģis Dainis , Lexer Christian , Jansson Stefan , Robinson Kathryn M. , Street Nathaniel R. , Ingvarsson Pär K. 
Published: February 2021

AbstractUnderstanding local adaptation in plants from a genomic perspective has become a key research area given the ongoing climate challenge and the concomitant requirement to conserve genetic resources. Perennial plants, such as forest trees, are good models to study local adaptation given their wide geographic distribution, largely outcrossing mating systems and demographic histories. We evaluated signatures of local adaptation in European aspen (Populus tremula) across Europe by means of whole genome re-sequencing of a collection of 411 individual trees. We dissected admixture patterns between aspen lineages and observed a strong genomic mosaicism in Scandinavian trees, evidencing different colonization trajectories into the peninsula from Russia, Central and Western Europe. As a consequence of the secondary contacts between populations after the last glacial maximum (LGM), we detected an adaptive introgression event in a genome region of ∼500kb in chromosome 10, harboring a large-effect locus that has previously been shown to contribute to adaptation to the short growing seasons characteristic of northern Scandinavia. Demographic simulations and ancestry inference suggest an Eastern origin - probably Russian - of the adaptive Nordic allele which nowadays is present in a homozygous state at the north of Scandinavia. The strength of introgression and positive selection signatures in this region is a unique feature in the genome. Furthermore, we detected signals of balancing selection, shared across regional populations, that highlight the importance of standing variation as a primary source of alleles that facilitate local adaptation. Our results therefore emphasize the importance of migration-selection balance underlying the genetic architecture of key adaptive quantitative traits.
A framework for selectively breeding corals for assisted evolution
Authors: Humanes Adriana , Bythell John , Beauchamp Elizabeth , Carl Mitch , Craggs Jamie , Edwards Alasdair , Golbuu Yimnang , Lachs Liam , Randle Janna Leigh , Martinez Helios , Palmowski Pawel , Paysinger Faith , van der Steeg Eveline , Sweet Michael , Treumann Achim , Guest James 
Published: February 2021

AbstractCoral cover on tropical reefs has declined during the last three decades due to the combined effects of climate change, destructive fishing, pollution, and land use change. Drastic reductions in greenhouse gas emissions combined with effective coastal management and conservation strategies are essential to slow this decline. Innovative approaches, such as selective breeding for adaptive traits combined with large-scale sexual propagation, are being developed with the aim of pre-adapting reefs to increased ocean warming. However, there are still major gaps in our understanding of the technical and methodological constraints to producing corals for such restoration interventions. Here we propose a framework for selectively breeding corals and rearing them from eggs to 2.5-year old colonies using the coralAcropora digitiferaas a model species. We present methods for choosing colonies for selective crossing, enhancing early survivorship inex situandin situnurseries, and outplanting and monitoring colonies on natal reefs. We used a short-term (7-day) temperature stress assay to select parental colonies based on heat tolerance of excised branches. From six parental colonies, we produced 12 distinct crosses, and compared survivorship and growth of colonies transferred toin situnurseries or outplanted to the reef at different ages. We demonstrate that selectively breeding and rearing coral colonies is technically feasible at small scales and could be upscaled as part of restorative assisted evolution initiatives. Nonetheless, there are still challenges to overcome before selective breeding can be implemented as a viable conservation tool, especially at the post-settlement and outplanting phases. Although interdisciplinary approaches will be needed to overcome many of the challenges identified in this study, selective breeding has the potential to be a viable tool within reef managers’ toolbox to support the persistence of selected reefs in the face of climate change.
Longitudinal preclinical imaging characterization of drug delivery potential after radiotherapy in the healthy and leukemic bone marrow vascular microenvironment
Authors: Brooks Jamison , Zuro Darren , Song Joo Y. , Sargur Madabushi Srideshikan , Sanchez James F , Kortylewski Marcin , Chen Bihong T. , Gupta Kalpna , Storme Guy , Froelich Jerry , Hui Susanta K 
Published: February 2021

AbstractObjectivesRadiotherapy improves blood perfusion and cellular chemotherapy uptake in mice with acute lymphoblastic leukemia (ALL). However, its ability to influence drug delivery and permeation through the bone marrow vasculature (BMV) is unknown, due in part to a lack of methodology. This study developed longitudinal quantitative multiphoton (L-QMPM) imaging and used it to characterize drug delivery potential and the BMV before and after radiotherapy in mice bearing leukemia.MethodsWe developed a longitudinal window implant for L-QMPM imaging of the calvarium BMV before, 2 days after, and 5 days after radiotherapy. Live time-lapsed images of a fluorescent drug surrogate were used to obtain measurements including tissue wash-in slope (WIStissue) to measure drug delivery potential. We performed L-QMPM imaging using 2 Gy and 10 Gy total body irradiation (TBI) on C57/B6 (WT) mice, mice bearing ALL, and acute myeloid leukemia (AML).ResultsImplants had no effects on calvarium dose, and parameters for WT untreated mice were stable during imaging. We observed increased angiogenesis, decreased single-vessel blood flow, and decreased WIStissuewith the onset of AML and ALL. 2Gy and 10Gy TBI increased WIStissue2 days after radiotherapy in all 3 groups of mice and increased single-vessel blood flow in mice bearing ALL and AML. Significant increases in WIStissuewere observed 2 days after 2Gy TBI compared to 5 days. Morphological and functional alterations in the BMV were sustained for a significantly longer time period after 10Gy TBI (5 days post-treatment) compared to 2Gy TBI (2 days post-treatment).ConclusionL-QMPM provides stable functional assessments of the BMV. TBI increases the drug delivery potential of the leukemic BMV 2-5 days post-treatment, likely through improved blood perfusion and drug exchange from the BMV to the extravascular tissue. Our data show that neo-adjuvant 2Gy and 10Gy TBI condition the BMV for increased drug delivery.
Potassium isomerized linoleate satisfies EPA MB-35-00 for surface disinfection ofCandida auris(AR-0381)
Authors: Changaris David , Carenbauer Anne 
Published: February 2021

AbstractFour distinct lots of Potassium Isomerized Linoleate, 442 mM or 141 mg/ml (within the cosmetic-cleanser and commercial-soap acceptable concentration ranges but much greater than physiologic conditions), showed greater than 5 log kill rates (total) forCandida auris(AR-0381) for all carriers during 5 separate procedural runs of EPA MB-35-00. After exposing the inoculated stainless-steel carriers to the plant-oil soap for 1, 2, or 10 minute(s), we recovered noCandida aurison these tested carriers. Control carriers with phosphate-buffered saline applied, recovered 5.0-6.8 Log of colony-forming units per carrier.