bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterizing the Chemical Profile of Incidental Ultrafine Particles for Toxicity Assessment Using an Aerosol Concentrator
Authors: Viana M , Salmatonidis A , Bezantakos S , Ribalta C , Moreno N , Córdoba P , Cassee F R , Boere J , Fraga S , Teixeira J P , Bessa M J , Monfort E 
Published: January 2021

AbstractIncidental ultrafine particles (UFPs) constitute a key pollutant in industrial workplaces. However, characterizing their chemical properties for exposure and toxicity assessments still remains a challenge. In this work, the performance of an aerosol concentrator (Versatile Aerosol Concentration Enrichment System, VACES) was assessed to simultaneously sample UFPs on filter substrates (for chemical analysis) and as liquid suspensions (for toxicity assessment), in a high UFP concentration scenario. An industrial case study was selected where metal-containing UFPs were emitted during thermal spraying of ceramic coatings. Results evidenced the comparability of the VACES system with online monitors in terms of UFP particle mass (for concentrations up to 95 µg UFP/m3) and between filters and liquid suspensions, in terms of particle composition (for concentrations up to 1000 µg/m3). This supports the applicability of this tool for UFP collection in view of chemical and toxicological characterization for incidental UFPs. In the industrial setting evaluated, results showed that the spraying temperature was a driver of fractionation of metals between UF (&lt;0.2 µm) and fine (0.2–2.5 µm) particles. Potentially health hazardous metals (Ni, Cr) were enriched in UFPs and depleted in the fine particle fraction. Metals vaporized at high temperatures and concentrated in the UF fraction through nucleation processes. Results evidenced the need to understand incidental particle formation mechanisms due to their direct implications on particle composition and, thus, exposure. It is advisable that personal exposure and subsequent risk assessments in occupational settings should include dedicated metrics to monitor UFPs (especially, incidental).
Intraspecific trait variation in plants: a renewed focus on its role in ecological processes
Authors: Westerband A C , Funk J L , Barton K E 
Published: January 2021

AbstractBackgroundInvestigating the causes and consequences of intraspecific trait variation (ITV) in plants is not novel, as it has long been recognized that such variation shapes biotic and abiotic interactions. While evolutionary and population biology have extensively investigated ITV, only in the last 10 years has interest in ITV surged within community and comparative ecology.ScopeDespite this recent interest, still lacking are thorough descriptions of ITV’s extent, the spatial and temporal structure of ITV, and stronger connections between ITV and community and ecosystem properties. Our primary aim in this review is to synthesize the recent literature and ask: (1) How extensive is intraspecific variation in traits across scales, and what underlying mechanisms drive this variation? (2) How does this variation impact higher-order ecological processes (e.g. population dynamics, community assembly, invasion, ecosystem productivity)? (3) What are the consequences of ignoring ITV and how can these be mitigated? and (4) What are the most pressing research questions, and how can current practices be modified to suit our research needs? Our secondary aim is to target diverse and underrepresented traits and plant organs, including anatomy, wood, roots, hydraulics, reproduction and secondary chemistry. In addressing these aims, we showcase papers from the Special Issue.ConclusionsPlant ITV plays a key role in determining individual and population performance, species interactions, community structure and assembly, and ecosystem properties. Its extent varies widely across species, traits and environments, and it remains difficult to develop a predictive model for ITV that is broadly applicable. Systematically characterizing the sources (e.g. ontogeny, population differences) of ITV will be a vital step forward towards identifying generalities and the underlying mechanisms that shape ITV. While the use of species means to link traits to higher-order processes may be appropriate in many cases, such approaches can obscure potentially meaningful variation. We urge the reporting of individual replicates and population means in online data repositories, a greater consideration of the mechanisms that enhance and constrain ITV’s extent, and studies that span sub-disciplines.
Laser and Light-Based Device Education in a Plastic Surgery Residency Program: A Continuing Medical Education Overview
Authors: Wamsley Christine E , Hoopman John , Kenkel Jeffrey M 
Published: January 2021

Abstract
The increasing prevalence of laser use, particularly in plastic surgery, demands education of both practitioners and trainees to ensure efficacy and patient safety. The purpose of this continuing medical education module is to provide the learner with a detailed outline for laser training education for plastic surgery trainees. In this overview, a discussion of the characteristics of light, an introduction to fundamental laser principles, a comparison of lasers and pulsed light systems, and examples of several therapeutic applications for light-based devices in the clinical setting will be presented. Additionally, the 5 parameters necessary for operation of light-based devices, as well as the importance of laser safety education, will be reviewed. We hope this continuing medical education will provide both practicing plastic surgeons and trainees with the proper education on the lasers and pulsed light devices they will use in their clinical practices.
Generating property-matched decoy molecules using deep learning
Authors: Imrie Fergus , Bradley Anthony R , Deane Charlotte M 
Published: January 2021

AbstractMotivationAn essential step in the development of virtual screening methods is the use of established sets of actives and decoys for benchmarking and training. However, the decoy molecules in commonly used sets are biased meaning that methods often exploit these biases to separate actives and decoys, and do not necessarily learn to perform molecular recognition. This fundamental issue prevents generalization and hinders virtual screening method development.ResultsWe have developed a deep learning method (DeepCoy) that generates decoys to a user’s preferred specification in order to remove such biases or construct sets with a defined bias. We validated DeepCoy using two established benchmarks, DUD-E and DEKOIS 2.0. For all 102 DUD-E targets and 80 of the 81 DEKOIS 2.0 targets, our generated decoy molecules more closely matched the active molecules’ physicochemical properties while introducing no discernible additional risk of false negatives. The DeepCoy decoys improved the Deviation from Optimal Embedding (DOE) score by an average of 81% and 66%, respectively, decreasing from 0.166 to 0.032 for DUD-E and from 0.109 to 0.038 for DEKOIS 2.0. Further, the generated decoys are harder to distinguish than the original decoy molecules via docking with Autodock Vina, with virtual screening performance falling from an AUC ROC of 0.70 to 0.63.Availability and implementationThe code is available at https://github.com/oxpig/DeepCoy. Generated molecules can be downloaded from http://opig.stats.ox.ac.uk/resources.Supplementary informationSupplementary data are available at Bioinformatics online.
Coronavirus Disease 2019 Symptoms and Severe Acute Respiratory Syndrome Coronavirus 2 Antibody Positivity in a Large Survey of First Responders and Healthcare Personnel, May–July 2020
Authors: Akinbami Lara J , Petersen Lyle R , Sami Samira , Vuong Nga , Lukacs Susan L , Mackey Lisa , Atas Jenny , LaFleur Bonnie J 
Published: January 2021

Abstract
A severe acute respiratory syndrome coronavirus 2 serosurvey among first responder/healthcare personnel showed that loss of taste/smell was most predictive of seropositivity; percent seropositivity increased with number of coronavirus disease 2019 symptoms. However, 22.9% with 9 symptoms were seronegative, and 8.3% with no symptoms were seropositive. These findings demonstrate limitations of symptom-based surveillance and importance of testing.
Immunodeficiency and Cancer in 3.5 Million People Living With Human Immunodeficiency Virus (HIV): The South African HIV Cancer Match Study
Authors: Ruffieux Yann , Muchengeti Mazvita , Egger Matthias , Efthimiou Orestis , Bartels Lina , Olago Victor , Davidović Maša , Dhokotera Tafadzwa , Bohlius Julia , Singh Elvira , Rohner Eliane 
Published: January 2021

Abstract

Background
We analyzed associations between immunodeficiency and cancer incidence in a nationwide cohort of people living with human immunodeficiency virus (HIV; PLWH) in South Africa.

Methods
We used data from the South African HIV Cancer Match Study built on HIV-related laboratory measurements from the National Health Laboratory Services and cancer records from the National Cancer Registry. We evaluated associations between time-updated CD4 cell count and cancer incidence rates using Cox proportional hazards models. We reported adjusted hazard ratios (aHRs) over a grid of CD4 values and estimated the aHR per 100 CD4 cells/µL decrease.

Results
Of 3 532 266 PLWH, 15 078 developed cancer. The most common cancers were cervical cancer (4150 cases), Kaposi sarcoma (2262 cases), and non-Hodgkin lymphoma (1060 cases). The association between lower CD4 cell count and higher cancer incidence rates was strongest for conjunctival cancer (aHR per 100 CD4 cells/µL decrease: 1.46; 95% confidence interval [CI], 1.38–1.54), Kaposi sarcoma (aHR, 1.23; 95% CI, 1.20–1.26), and non-Hodgkin lymphoma (aHR, 1.18; 95% CI, 1.14–1.22). Among infection-unrelated cancers, lower CD4 cell counts were associated with higher incidence rates of esophageal cancer (aHR, 1.06; 95% CI, 1.00–1.11) but not breast, lung, or prostate cancer.

Conclusions
Lower CD4 cell counts were associated with an increased risk of developing various infection-related cancers among PLWH. Reducing HIV-induced immunodeficiency may be a potent cancer-prevention strategy among PLWH in sub-Saharan Africa, a region heavily burdened by cancers attributable to infections.
Exercise training in patients after kidney transplantation
Authors: De Smet Stefan , Van Craenenbroeck Amaryllis H. 
Published: January 2021

AbstractKidney transplantation is the treatment of choice for patients with end-stage renal disease. Next to the risk of allograft failure, major obstacles for disease-free survival after kidney transplantation include a higher incidence of cancer, infection and cardiovascular events. Risk factors for adverse clinical outcomes include pre-existent comorbidities, the introduction of an immunodeficient status and (lack of) lifestyle changes after transplantation. Indeed, physical inactivity and poor physical fitness are important targets to address in order to improve clinical outcomes after kidney transplantation. This review summarizes the current evidence on exercise training after kidney transplantation, derived from randomized controlled trials. As much as possible, results are discussed in the perspective of the Standardized Outcomes in Nephrology-Transplantation core outcomes, which were recently described as critically important outcome domains for trials in kidney transplant recipients.
bc-GenExMiner 4.5: new mining module computes breast cancer differential gene expression analyses
Authors: Jézéquel Pascal , Gouraud Wilfried , Ben Azzouz Fadoua , Guérin-Charbonnel Catherine , Juin Philippe P , Lasla Hamza , Campone Mario 
Published: January 2021

Abstract
‘Breast cancer gene-expression miner’ (bc-GenExMiner) is a breast cancer–associated web portal (http://bcgenex.ico.unicancer.fr). Here, we describe the development of a new statistical mining module, which permits several differential gene expression analyses, i.e. ‘Expression’ module. Sixty-two breast cancer cohorts and one healthy breast cohort with their corresponding clinicopathological information are included in bc-GenExMiner v4.5 version. Analyses are based on microarray or RNAseq transcriptomic data. Thirty-nine differential gene expression analyses, grouped into 13 categories, according to clinicopathological and molecular characteristics (‘Targeted’ and ‘Exhaustive’) and gene expression (‘Customized’), have been developed. Output results are visualized in four forms of plots. This new statistical mining module offers, among other things, the possibility to compare gene expression in healthy (cancer-free), tumour-adjacent and tumour tissues at once and in three triple-negative breast cancer subtypes (i.e. C1: molecular apocrine tumours; C2: basal-like tumours infiltrated by immune suppressive cells and C3: basal-like tumours triggering an ineffective immune response). Several validation tests showed that bioinformatics process did not alter the pathobiological information contained in the source data. In this work, we developed and demonstrated that bc-GenExMiner ‘Expression’ module can be used for exploratory and validation purposes.
Database URL: http://bcgenex.ico.unicancer.fr
Diversity of putative ericoid mycorrhizal fungi increases with soil age and progressive phosphorus limitation across a 4.1-million-year chronosequence
Authors: Leopold Devin R , Peay Kabir G , Vitousek Peter M , Fukami Tadashi 
Published: January 2021

ABSTRACTEricaceous plants rely on ericoid mycorrhizal fungi for nutrient acquisition. However, the factors that affect the composition and structure of fungal communities associated with the roots of ericaceous plants remain largely unknown. Here, we use a 4.1-million-year (myr) soil chronosequence in Hawaii to test the hypothesis that changes in nutrient availability with soil age determine the diversity and species composition of fungi associated with ericoid roots. We sampled roots of a native Hawaiian plant, Vaccinium calycinum, and used DNA metabarcoding to quantify changes in fungal diversity and community composition. We also used a fertilization experiment at the youngest and oldest sites to assess the importance of nutrient limitation. We found an increase in diversity and a clear pattern of species turnover across the chronosequence, driven largely by putative ericoid mycorrhizal fungi. Fertilization with nitrogen at the youngest site and phosphorus at the oldest site reduced fungal diversity, suggesting a direct role of nutrient limitation. Our results also reveal the presence of novel fungal species associated with Hawaiian Ericaceae and suggest a greater importance of phosphorus availability for communities of ericoid mycorrhizal fungi than is generally assumed.
Genome assemblies for two Neotropical trees: Jacaranda copaia and Handroanthus guayacan
Authors: Burley John T , Kellner James R , Hubbell Stephen P , Faircloth Brant C 
Published: January 2021

Abstract
The lack of genomic resources for tropical canopy trees is impeding several research avenues in tropical forest biology. We present genome assemblies for two Neotropical hardwood species, Jacaranda copaia and Handroanthus (formerly Tabebuia) guayacan, that are model systems for research on tropical tree demography and flowering phenology. For each species, we combined Illumina short-read data with in vitro proximity-ligation (Chicago) libraries to generate an assembly. For Jacaranda copaia, we obtained 104X physical coverage and produced an assembly with N50/N90 scaffold lengths of 1.020/0.277 Mbp. For H. guayacan, we obtained 129X coverage and produced an assembly with N50/N90 scaffold lengths of 0.795/0.165 Mbp. J. copaia and H. guayacan assemblies contained 95.8% and 87.9% of benchmarking orthologs, although they constituted only 77.1% and 66.7% of the estimated genome sizes of 799 and 512 Mbp, respectively. These differences were potentially due to high repetitive sequence content (&gt;59.31% and 45.59%) and high heterozygosity (0.5% and 0.8%) in each species. Finally, we compared each new assembly to a previously sequenced genome for Handroanthus impetiginosus using whole-genome alignment. This analysis indicated extensive gene duplication in H. impetiginosus since its divergence from H. guayacan.
Assessing the effects of genotype-by-environment interaction on epigenetic, transcriptomic, and phenotypic response in a Pacific salmon
Authors: Christensen Kris A , Le Luyer Jérémy , Chan Michelle T T , Rondeau Eric B , Koop Ben F , Bernatchez Louis , Devlin Robert H 
Published: January 2021

AbstractGenotype-by-environment (GxE) interactions are non-parallel reaction norms among individuals with different genotypes in response to different environmental conditions. GxE interactions are an extension of phenotypic plasticity and consequently studying such interactions improves our ability to predict effects of different environments on phenotype as well as the fitness of genetically distinct organisms and their capacity to interact with ecosystems. Growth hormone transgenic coho salmon grow much faster than non-transgenics when raised in tank environments, but show little difference in growth when reared in nature-like streams. We used this model system to evaluate potential mechanisms underlying this growth rate GxE interaction, performing RNA-seq to measure gene transcription and whole-genome bisulfite sequencing to measure gene methylation in liver tissue. Gene ontology (GO) term analysis revealed stress as an important biological process potentially influencing growth rate GxE interactions. While few genes with transcription differences also had methylation differences, in promoter or gene regions, many genes were differentially methylated between tank and stream environments. A GO term analysis of differentially methylated genes between tank and stream environments revealed increased methylation in the stream environment of more than 95% of the differentially methylated genes, many with biological processes unrelated to liver function. The lower nutritional condition of the stream environment may cause increased negative regulation of genes less vital for liver tissue function than when fish are reared in tanks with unlimited food availability. These data show a large effect of rearing environment both on gene expression and methylation, but it is less clear that the detected epigenetic marks are responsible for the observed altered growth and physiological responses.
Continental-Scale Gene Flow Prevents Allopatric Divergence of Pelagic Freshwater Bacteria
Authors: Hoetzinger Matthias , Pitt Alexandra , Huemer Andrea , Hahn Martin W 
Published: January 2021

Abstract
Allopatric divergence is one of the principal mechanisms for speciation of macro-organisms. Microbes by comparison are assumed to disperse more freely and to be less limited by dispersal barriers. However, thermophilic prokaryotes restricted to geothermal springs have shown clear signals of geographic isolation, but robust studies on this topic for microbes with less strict habitat requirements are scarce. Furthermore, it has only recently been recognized that homologous recombination among conspecific individuals provides species coherence in a wide range of prokaryotes. Recombination barriers thus may define prokaryotic species boundaries, yet, the extent to which geographic distance between populations gives rise to such barriers is an open question. Here, we investigated gene flow and population structure in a widespread species of pelagic freshwater bacteria, Polynucleobacter paneuropaeus. Through comparative genomics of 113 conspecific strains isolated from freshwater lakes and ponds located across a North–South range of more than 3,000 km, we were able to reconstruct past gene flow events. The species turned out to be highly recombinogenic as indicated by significant signs of gene transfer and extensive genome mosaicism. Although genomic differences increased with spatial distance on a regional scale (&lt;170 km), such correlations were mostly absent on larger scales up to 3,400 km. We conclude that allopatric divergence in European P. paneuropaeus is minor, and that effective gene flow across the sampled geographic range in combination with a high recombination efficacy maintains species coherence.
Multi-scale assessment of distribution and density of procellariiform seabirds within the Northern Antarctic Peninsula marine ecosystem
Authors: Warwick-Evans V , A Santora J , Waggitt J J , Trathan P N 
Published: January 2021

AbstractThe Antarctic Peninsula is one of the most rapidly warming regions on earth, and it is likely that the abundance and distribution of marine predators will change as a result.Procellariiform seabirds are highly mobile predators, which target specific habitat characteristics associated with underlying distributions of prey and areas of increased prey availability. We use ship surveys and hurdle models, to estimate the summer distribution and relative density of 11 seabird species within the northern Antarctic Peninsula marine ecosystem. Models differed among species; however, sea surface temperature and depth were frequently associated with seabird occurrence and had the greatest explanatory power across many species. Null models based on observation data were better at predicting seabird density than models that included environmental covariates. This suggests that the main driver of distribution patterns is the broad-scale habitat features, and fine-scale aggregations within these ranges are harder to predict. Our seabird distribution models reflect known habitat associations, species hotspots, and community organization relative to oceanic and coastal marine processes. Application of species distribution models will benefit the assessments of critical habitat and potential responses to climate change and anthropogenic disturbance, which will provide insight into how species may change in polar ecosystems.
Human Monoclonal Antibody Cocktail for the Treatment or Prophylaxis of Middle East Respiratory Syndrome Coronavirus
Authors: Sivapalasingam Sumathi , Saviolakis George A , Kulcsar Kirsten , Nakamura Aya , Conrad Thomas , Hassanein Mohamed , Sumner Giane , Elango Chinnasamy , Kamal Mohamed A , Eng Simon , Kyratsous Christos A , Musser Bret J , Frieman Matthew , Kantrowitz Joel , Weinreich David M , Yancopoulos George , Stahl Neil , Lipsich Leah 
Published: January 2021

Abstract

Background
REGN3048 and REGN3051 are human monoclonal antibodies (mAb) targeting the spike glycoprotein on the Middle East respiratory syndrome coronavirus (MERS-CoV), which binds to the receptor dipeptidyl peptidase-4 (DPP4) and is necessary for infection of susceptible cells.

Methods
Preclinical study: REGN3048, REGN3051 and isotype immunoglobulin G (IgG) were administered to humanized DPP4 (huDPP4) mice 1 day prior to and 1 day after infection with MERS-CoV (Jordan strain). Virus titers and lung pathology were assessed. Phase 1 study: healthy adults received the combined mAb (n = 36) or placebo (n = 12) and followed for 121 days. Six dose levels were studied. Strict safety criteria were met prior to dose escalation.

Results
Preclinical study: REGN3048 plus REGN3051, prophylactically or therapeutically, was substantially more effective for reducing viral titer, lung inflammation, and pathology in huDPP4 mice compared with control antibodies and to each antibody monotherapy. Phase 1 study: REGN3048 plus REGN3051 was well tolerated with no dose-limiting adverse events, deaths, serious adverse events, or infusion reactions. Each mAb displayed pharmacokinetics expected of human IgG1 antibodies; it was not immunogenic.

Conclusions
REGN3048 and REGN3051 in combination were well tolerated. The clinical and preclinical data support further development for the treatment or prophylaxis of MERS-CoV infection.