bluuebunny/crossref_metadata_2025_split huggingface dataset:
Is the age of diagnosis of esophageal adenocarcinoma getting younger? Analysis at a tertiary care center
Authors: Strauss Alexandra , Min Eun Jeong , Long Qi , Gabriel Peter , Yang Yu-Xiao , Falk Gary W 
Published: February 2020

Summary
There are emerging data that patients &lt;50 years are diagnosed with esophageal adenocarcinoma (EAC) more frequently, suggesting that the age threshold for screening should be revisited. This study aimed to determine the age distribution, outcomes, and clinical features of EAC over time. The pathology database at the Hospital of the University of Pennsylvania was reviewed from 1991 to 2018. The electronic health records and pathology were reviewed for age of diagnosis, pathology grade, race, and gender for a cohort of 630 patients with biopsy proven EAC. For the patients diagnosed from 2009 to 2018, the Penn Abramson Cancer Center Registry was reviewed for survival and TNM stage. Of the 630 patients, 10.3% (65 patients) were &lt;50 years old [median 43 years, range 16–49]. There was no increase in the number of patients &lt;50 years diagnosed with EAC (R = 0.133, P = 0.05). Characteristics of those &lt;50 years versus &gt;50 years showed no difference in tumor grade. Among the 179 eligible patients in the cancer registry, there was no significant difference in clinical or pathological stage for patients &lt;50 years (P value = 0.18). There was no association between diagnosis age and survival (P = 0.24). A substantial subset of patients with EAC is diagnosed at &lt;50 years. There was no increasing trend of EAC in younger cohorts from 1991 to 2018. We could not identify more advanced stage tumors in the younger cohort. There was no significant association between diagnosis age and survival.
Short-term single-centre experience with the HeartMate 3 left ventricular assist device for advanced heart failure
Authors: Nowacka Anna , Hullin Roger , Tozzi Piergiorgio , Barras Nicolas , Regamey Julien , Yerly Patrick , Rosner Lorenzo , Marcucci Carlos , Rusca Marco , Liaudet Lucas , Kirsch Matthias 
Published: February 2020

Abstract

OBJECTIVES
The objective of this study was to analyse clinical characteristics, survival and adverse events of patients with advanced heart failure supported using the Abbott HeartMate 3 left ventricular assist device (LVAD).

METHODS
We retrospectively reviewed 42 consecutive HeartMate 3 recipients implanted in our centre between 1 November 2015 and 31 October 2019.

RESULTS
Our series comprised 39 males, aged 56.7 ± 11.8 years. Eleven (26%) patients had preimplant INTERMACS clinical profiles of 1 or 2. The mean duration support was 14.0 ± 10.6 months (range 0.69–44 months). During follow-up, 4 (10%) patients died while on support, 13 (35%) patients received a heart transplant and 25 patients are still ongoing. Actuarial survival after LVAD implantation was 88.4 ± 5.5% and 84.4 ± 6.6% at 1 and 2 years, respectively. There were no cases of pump thrombosis or technical malfunction. Seven (17%) patients required post-implant temporary right ventricular support. Adverse events included bleeding requiring surgery in 13 (31%) patients, gastrointestinal bleeding in 6 (14%) patients, LVAD-specific infections in 19 (45%) patients and non-disabling ischaemic stroke in 5 (12%) patients. The incidence of ischaemic stroke was significantly higher in patients where the outflow graft was anastomosed to the descending aorta as compared to those where it was anastomosed to the ascending aorta (P &lt; 0.003).

CONCLUSIONS
We have observed satisfactory survival rates using the HeartMate 3 LVAD for long-term mechanical circulatory support. The absence of technical failure, pump thrombosis, haemolysis or need for pump exchange during our 4-year experience confirms its technical reliability and improved haemocompatibility, but bleeding complications and infections remain a concern.
Growing season drives the compositional changes and assembly processes of epiphytic bacterial communities of two submerged macrophytes in Taihu Lake
Authors: He Dan , Ren Lijuan , Wu Qinglong L 
Published: February 2020

ABSTRACTLarge amounts of epiphytic bacteria live on the leaf surfaces of submerged macrophytes in freshwater lakes. Despite their important roles in affecting host plant's health and biogeochemical cycling, knowledge about epiphytic bacteria assembly is not sufficient. We studied epiphytic bacteria on two cohabiting plant species in Taihu Lake, China. In comparison with plant identity and geographic distance, the plant-growing season played a prominent role in driving alpha and beta diversity (compositional variations) of epiphytic bacterial communities. Phylogeny-based null model analysis revealed that the growing season also drove the relative importance of deterministic versus stochastic processes underlying bacterial community assembly. In May when both plants start growth, the deterministic processes were most prominent, while in months later than June, the stochastic processes’ effects increased substantially. In addition, we found a significant positive relationship between alpha diversity and compositional stochasticity, implying that stochastic processes may have great effects on the maintenance of diversity and functioning of epiphytic bacteria in aquatic ecosystems. In summary, the growing season overwhelmed plant identity and spatial site in shaping epiphytic bacterial communities in Taihu Lake, which may suggest new clues in understanding the dynamics of epiphytic communities and their roles in large shallow lacustrine ecosystems.
Mapping metabolic activity at single cell resolution in intact volcanic fumarole sediment
Authors: Marlow Jeffrey J , Colocci Isabella , Jungbluth Sean P , Weber Nils Moritz , Gartman Amy , Kallmeyer Jens 
Published: February 2020

ABSTRACT
Interactions among microorganisms and their mineralogical substrates govern the structure, function and emergent properties of microbial communities. These interactions are predicated on spatial relationships, which dictate metabolite exchange and access to key substrates. To quantitatively assess links between spatial relationships and metabolic activity, this study presents a novel approach to map all organisms, the metabolically active subset and associated mineral grains, all while maintaining spatial integrity of an environmental microbiome. We applied this method at an outgassing fumarole of Vanuatu's Marum Crater, one of the largest point sources of several environmentally relevant gaseous compounds, including H2O, CO2 and SO2. With increasing distance from the sediment-air surface and from mineral grain outer boundaries, organism abundance decreased but the proportion of metabolically active organisms often increased. These protected niches may provide more stable conditions that promote consistent metabolic activity of a streamlined community. Conversely, exterior surfaces accumulate more organisms that may cover a wider range of preferred conditions, implying that only a subset of the community will be active under any particular environmental regime. More broadly, the approach presented here allows investigators to see microbial communities ‘as they really are’ and explore determinants of metabolic activity across a range of microbiomes.
Delineation of a Subgroup of the Genus Paraburkholderia, Including P. terrae DSM 17804T, P. hospita DSM 17164T, and Four Soil-Isolated Fungiphiles, Reveals Remarkable Genomic and Ecological Features—Proposal for the Definition of a P. hospita Species Cluster
Authors: Pratama Akbar Adjie , Jiménez Diego Javier , Chen Qian , Bunk Boyke , Spröer Cathrin , Overmann Jörg , van Elsas Jan Dirk 
Published: February 2020

AbstractThe fungal-interactive (fungiphilic) strains BS001, BS007, BS110, and BS437 have previously been preliminarily assigned to the species Paraburkholderia terrae. However, in the (novel) genus Paraburkholderia, an as-yet unresolved subgroup exists, that clusters around Paraburkholderia hospita (containing the species P. terrae, P. hospita, and Paraburkholderia caribensis). To shed light on the precise relationships across the respective type strains and the novel fungiphiles, we here compare their genomic and ecophysiological features. To reach this goal, the genomes of the three type strains, with sizes ranging from 9.0 to 11.5 Mb, were de novo sequenced and the high-quality genomes analyzed. Using whole-genome, ribosomal RNA and marker-gene-concatenate analyses, close relationships between P. hospita DSM 17164T and P. terrae DSM 17804T, versus more remote relationships to P. caribensis DSM 13236T, were found. All four fungiphilic strains clustered closely to the two-species cluster. Analyses of average nucleotide identities (ANIm) and tetranucleotide frequencies (TETRA) confirmed the close relationships between P. hospita DSM 17164T and P. terrae DSM 17804T (ANIm = 95.42; TETRA = 0.99784), as compared with the similarities of each one of these strains to P. caribensis DSM 13236T. A species cluster was thus proposed. Furthermore, high similarities of the fungiphilic strains BS001, BS007, BS110, and BS437 with this cluster were found, indicating that these strains also make part of it, being closely linked to P. hospita DSM 17164T (ANIm = 99%; TETRA = 0.99). We propose to coin this cluster the P. hospita species cluster (containing P. hospita DSM 17164T, P. terrae DSM 17804T, and strains BS001, BS007, BS110, and BS437), being clearly divergent from the closely related species P. caribensis (type strain DSM 13236T). Moreover, given their close relatedness to P. hospita DSM 17164T within the cluster, we propose to rename the four fungiphilic strains as members of P. hospita. Analysis of migratory behavior along with fungal growth through soil revealed both P. terrae DSM 17804T and P. hospita DSM 17164T (next to the four fungiphilic strains) to be migration-proficient, whereas P. caribensis DSM 13236T was a relatively poor migrator. Examination of predicted functions across the genomes of the seven investigated strains, next to several selected additional ones, revealed the common presence of features in the P. hospita cluster strains that are potentially important in interactions with soil fungi. Thus, genes encoding specific metabolic functions, biofilm formation (pelABCDEFG, pgaABCD, alginate-related genes), motility/chemotaxis, type-4 pili, and diverse secretion systems were found.
Race, Gender, and Socioeconomic Variations in C-Reactive Protein Using the Health and Retirement Study
Authors: Farmer Heather R , Wray Linda A , Haas Steven A 
Published: February 2020

AbstractObjectivesTo clarify the relationships among race, gender, and socioeconomic status (SES) with C-reactive protein (CRP).MethodThe present study analyzed data from 6,521 Black and White respondents aged 51 and older in the Health and Retirement Study, a nationally representative sample of midlife and older adults, to address two aims. We sought to (i) assess the independent associations between race, gender, and SES with CRP concentrations and (ii) test whether race, gender, and SES interacted to produce unequal CRP concentrations cross-sectionally and over a 4-year follow-up.ResultsThe results demonstrated that race, gender, and SES were each independently associated with baseline CRP, but only SES was associated with CRP at follow-up. Furthermore, race, gender, and education interacted to produce differential CRP levels at baseline. There were incremental benefits for each additional level of education for White men and women, but the relationship between education and CRP was more complicated for Black men and women. Compared with other race/gender groups with less than high school, Black women had the highest and Black men had the lowest levels of CRP. There were no apparent benefits to CRP for Black women with college compared with Black women with high school, while Black men with less than high school and college had similar concentrations of CRP.DiscussionIn clarifying the complexity inherent in CRP disparities, this work contributes to a greater understanding of the biological mechanisms underlying racial disparities in leading causes of morbidity and mortality in the United States.
Development and Validation of the Family Quality of Life in Dementia Scale
Authors: Rose Karen M , Williams Ishan C , Anderson Joel G , Geldmacher David S 
Published: February 2020

AbstractBackground and ObjectivesPeople with Alzheimer’s disease and related dementias (ADRD) exhibit losses in daily function, as well as behavioral and psychological symptoms, that place a great deal of burden on family caregivers and exert a major influence on the quality of life of these individuals and their families. Despite years of intervention research in the field, there are few studies related to the impact of providing care for a person with ADRD on the family as the unit of analysis. While numerous findings have reported the effects of the chronic stress of caregiving for an individual, analysis of family quality of life is a concept that has been generally overlooked in the ADRD field. The purpose of the present study was to develop and test the Family Quality of Life in Dementia (FQOL-D) scale.Research Design and MethodsFace validity was obtained via a Delphi survey of a multidisciplinary team of dementia providers and researchers; initial psychometric evaluation of the instrument was obtained via family respondents (N = 244).ResultsInternal consistency and reliability were established for the instrument. The FQOL-D scale exhibited excellent factorability and concurrent validity with existing scales assessing family psychosocial measures.Discussion and ImplicationsThe initial psychometric testing of the FQOL-D instrument is favorable. Additional use of the FQOL-D instrument in health care settings is warranted to evaluate further the clinical utility of the instrument.
Evaluating the genome and resistome of extensively drug-resistant Klebsiella pneumoniae using native DNA and RNA Nanopore sequencing
Authors: Pitt Miranda E , Nguyen Son H , Duarte Tânia P S , Teng Haotian , Blaskovich Mark A T , Cooper Matthew A , Coin Lachlan J M 
Published: February 2020

Abstract

Background
Klebsiella pneumoniae frequently harbours multidrug resistance, and current diagnostics struggle to rapidly identify appropriate antibiotics to treat these bacterial infections. The MinION device can sequence native DNA and RNA in real time, providing an opportunity to compare the utility of DNA and RNA for prediction of antibiotic susceptibility. However, the effectiveness of bacterial direct RNA sequencing and base-calling has not previously been investigated. This study interrogated the genome and transcriptome of 4 extensively drug-resistant (XDR) K. pneumoniae clinical isolates; however, further antimicrobial susceptibility testing identified 3 isolates as pandrug-resistant (PDR).

Results
The majority of acquired resistance (≥75%) resided on plasmids including several megaplasmids (≥100 kb). DNA sequencing detected most resistance genes (≥70%) within 2 hours of sequencing. Neural network–based base-calling of direct RNA achieved up to 86% identity rate, although ≤23% of reads could be aligned. Direct RNA sequencing (with ~6 times slower pore translocation) was able to identify (within 10 hours) ≥35% of resistance genes, including those associated with resistance to aminoglycosides, β-lactams, trimethoprim, and sulphonamide and also quinolones, rifampicin, fosfomycin, and phenicol in some isolates. Direct RNA sequencing also identified the presence of operons containing up to 3 resistance genes. Polymyxin-resistant isolates showed a heightened transcription of phoPQ (≥2-fold) and the pmrHFIJKLM operon (≥8-fold). Expression levels estimated from direct RNA sequencing displayed strong correlation (Pearson: 0.86) compared to quantitative real-time PCR across 11 resistance genes.

Conclusion
Overall, MinION sequencing rapidly detected the XDR/PDR K. pneumoniae resistome, and direct RNA sequencing provided accurate estimation of expression levels of these genes.
Genomic diversity affects the accuracy of bacterial single-nucleotide polymorphism–calling pipelines
Authors: Bush Stephen J , Foster Dona , Eyre David W , Clark Emily L , De Maio Nicola , Shaw Liam P , Stoesser Nicole , Peto Tim E A , Crook Derrick W , Walker A Sarah 
Published: February 2020

Abstract

Background
Accurately identifying single-nucleotide polymorphisms (SNPs) from bacterial sequencing data is an essential requirement for using genomics to track transmission and predict important phenotypes such as antimicrobial resistance. However, most previous performance evaluations of SNP calling have been restricted to eukaryotic (human) data. Additionally, bacterial SNP calling requires choosing an appropriate reference genome to align reads to, which, together with the bioinformatic pipeline, affects the accuracy and completeness of a set of SNP calls obtained. This study evaluates the performance of 209 SNP-calling pipelines using a combination of simulated data from 254 strains of 10 clinically common bacteria and real data from environmentally sourced and genomically diverse isolates within the genera Citrobacter, Enterobacter, Escherichia, and Klebsiella.

Results
We evaluated the performance of 209 SNP-calling pipelines, aligning reads to genomes of the same or a divergent strain. Irrespective of pipeline, a principal determinant of reliable SNP calling was reference genome selection. Across multiple taxa, there was a strong inverse relationship between pipeline sensitivity and precision, and the Mash distance (a proxy for average nucleotide divergence) between reads and reference genome. The effect was especially pronounced for diverse, recombinogenic bacteria such as Escherichia coli but less dominant for clonal species such as Mycobacterium tuberculosis.

Conclusions
The accuracy of SNP calling for a given species is compromised by increasing intra-species diversity. When reads were aligned to the same genome from which they were sequenced, among the highest-performing pipelines was Novoalign/GATK. By contrast, when reads were aligned to particularly divergent genomes, the highest-performing pipelines often used the aligners NextGenMap or SMALT, and/or the variant callers LoFreq, mpileup, or Strelka.
Crustal structure of the Azores Archipelago from Rayleigh wave ellipticity data
Authors: Ferreira Ana M G , Marignier Augustin , Attanayake Januka , Frietsch Michael , Berbellini Andrea 
Published: February 2020

SUMMARYDetermining the crustal structure of ocean island volcanoes is important to understand the formation and tectonic evolution of the oceanic lithosphere and tectonic swells in marine settings, and to assess seismic hazard in the islands. The Azores Archipelago is located near a triple junction system and is possibly under the influence of a mantle plume, being at the locus of a wide range of geodynamic processes. However, its crustal structure is still poorly constrained and debated due to the limited seismic coverage of the region and the peculiar linear geometry of the islands. To address these limitations, in this study we invert teleseismic Rayleigh wave ellipticity measurements for 1-D shear wave speed (VS) crustal models of the Azores Archipelago. Moreover, we test the reliability of these new models by using them in independent moment tensor inversions of local seismic data and demonstrate that our models improve the waveform fit compared to previous models. We find that data from the westernmost seismic stations used in this study require a shallower Moho depth (∼10 km) than data from stations in the eastern part of the archipelago (∼13–16 km). This apparent increase in the Moho depth with increasing distance from the mid-Atlantic ridge (MAR) is expected. However, the rate at which Moho deepens away from the MAR is greater than that predicted from a half-space cooling model, suggesting that local tectonic perturbations have modified crustal structure. The 1-D VS models obtained beneath the westernmost seismic stations also show higher wave speeds than for the easternmost stations, which correlates well with the ages of the islands except Santa Maria Island. We interpret the relatively low VS profile found beneath Santa Maria Island as resulting from underplating, which agrees with previous geological studies of the island. Compared to a recent receiver function study of the region, the shallow structure (top ∼2 km) in our models shows lower shear wave speed, which may have important implications for future hazard studies of the region. More generally, the new seismic crustal models we present in this study will be useful to better understand the tectonics, seismicity, moment tensors and strong ground motions in the region.
Frequency-dependent anisotropy due to two orthogonal sets of mesoscale fractures in porous media
Authors: Shuai Da , Stovas Alexey , Wei Jianxin , Di Bangrang 
Published: February 2020

SUMMARY
Seismic anisotropy can occur in rocks that have complicated internal structures and thin layering. Wave-induced fluid flow (WIFF) is one of the major causes of elastic wave dispersion and anisotropy. The principle goal of this paper is to combine the effects of WIFF and layer-induced anisotropy in orthorhombic (OTR) models that are often used in the seismic industry nowadays to describe azimuthal and polar anisotropy. We derive the effective frequency-dependent anisotropy parameters based on the Chapman model that accounts for the WIFF mechanism. First, we summarize two major problems to establish the link between the frequency-dependent seismic anisotropy and the multiple sets of fractures with different scales and orientations. Then we specify the multiple mesoscale fractures to be vertical and orthogonal so as to simplify the rock physics model to be an ORT medium. We also give the explicit expressions for the effective stiffness and the Thomsen-style parameters (vP0, vS0, ϵ1, ϵ2, γ1, γ2, δ1, δ2, δ3). Finally, we derive the effective frequency-dependent anisotropy parameters for ORT multiple layers using the Backus averaging under the approximation of weak contrast between layers. We also investigate the influence of frequency, fracture parameters (density and scale), effective porosity and volume fraction on the Thomsen-style parameters.