bluuebunny/crossref_metadata_2025 huggingface dataset:
Relative and Absolute Effectiveness of High-Dose and Standard-Dose Influenza Vaccine Against Influenza-Related Hospitalization Among Older Adults—United States, 2015–2017
Authors: Doyle Joshua D , Beacham Lauren , Martin Emily T , Talbot H Keipp , Monto Arnold , Gaglani Manjusha , Middleton Donald B , Silveira Fernanda P , Zimmerman Richard K , Alyanak Elif , Smith Emily R , Flannery Brendan L , Rolfes Melissa , Ferdinands Jill M
Published: February 2020

Background

Seasonal influenza causes substantial morbidity and mortality in older adults. High-dose inactivated influenza vaccine (HD-IIV), with increased antigen content compared to standard-dose influenza vaccines (SD-IIV), is licensed for use in people aged ≥65 years. We sought to evaluate the effectiveness of HD-IIV and SD-IIV for prevention of influenza-associated hospitalizations.

Methods

Hospitalized patients with acute respiratory illness were enrolled in an observational vaccine effectiveness study at 8 hospitals in the United States Hospitalized Adult Influenza Vaccine Effectiveness Network during the 2015–2016 and 2016–2017 influenza seasons. Enrolled patients were tested for influenza, and receipt of influenza vaccine by type was recorded. Effectiveness of SD-IIV and HD-IIV was estimated using a test-negative design (comparing odds of influenza among vaccinated and unvaccinated patients). Relative effectiveness of SD-IIV and HD-IIV was estimated using logistic regression.

Results

Among 1487 enrolled patients aged ≥65 years, 1107 (74%) were vaccinated; 622 (56%) received HD-IIV, and 485 (44%) received SD-IIV. Overall, 277 (19%) tested positive for influenza, including 98 (16%) who received HD-IIV, 87 (18%) who received SD-IIV, and 92 (24%) who were unvaccinated. After adjusting for confounding variables, effectiveness of SD-IIV was 6% (95% confidence interval [CI] −42%, 38%) and that of HD-IIV was 32% (95% CI −3%, 54%), for a relative effectiveness of HD-IIV versus SD-IIV of 27% (95% CI −1%, 48%).

Conclusions

During 2 US influenza seasons, vaccine effectiveness was low to moderate for prevention of influenza hospitalization among adults aged ≥65 years. High-dose vaccine offered greater effectiveness. None of these findings were statistically significant.
Waning Vaccine Immunity and Vaccination Responses in Children Treated for Acute Lymphoblastic Leukemia: A Canadian Immunization Research Network Study
Authors: Top Karina A , Vaudry Wendy , Morris Shaun K , Pham-Huy Anne , Pernica Jeffrey M , Tapiéro Bruce , Gantt Soren , Price Victoria E , Rassekh S Rod , Sung Lillian , McConnell Athena , Rubin Earl , Chawla Rupesh , Halperin Scott A
Published: February 2020

Background

There is no uniform guideline for postchemotherapy vaccination of children with acute lymphoblastic leukemia (ALL). We evaluated waning immunity to 14 pneumococcal serotypes, pertussis toxin (PT), tetanus toxoid (TT) and varicella, and immunogenicity of postchemotherapy diphtheria, tetanus, pertussis, hepatitis B, polio, and Haemophilus influenzae type b (DTaP-IPV-Hib) and pneumococcal vaccination among previously vaccinated children treated for ALL.

Methods

This was a multicenter trial of children with ALL enrolled 4–12 months postchemotherapy completion. Exclusion criteria included: infant ALL, relapsed ALL, and stem cell transplant recipients. Immunocompetent children were recruited as controls. Postchemotherapy participants received DTaP-IPV-Hib and 13-valent pneumococcal conjugate vaccine (PCV13) concurrently, followed by 23-valent pneumococcal polysaccharide vaccine (PPV23) 2 months later. Serology was measured at baseline, 2 and 12 months postvaccination. Adverse events were captured via surveys.

Results

At enrollment, postchemotherapy participants (n = 74) were less likely than controls (n = 78) to be age-appropriately immunized with DTaP (41% vs 89%, P < .001) and PCV (59% vs 79%, P = .008). Geometric mean concentrations (GMCs) to TT, PT, PCV serotypes, and varicella were lower in postchemotherapy participants than controls after adjusting for previous vaccine doses (P < .001). Two months postvaccination, GMCs to TT, PT, and PCV serotypes increased from baseline (P < .001 for all antigens) and remained elevated at 12 months postvaccination. Antibody levels to PPV23 serotypes also increased postvaccination (P < .001). No serious adverse events were reported.

Conclusions

Children treated for ALL had lower antibody levels than controls against pneumococcal serotypes, tetanus, pertussis, and varicella despite previous vaccination. Postchemotherapy vaccination with DTaP-IPV-Hib, PCV13, and PPV23 was immunogenic and well tolerated. Children with ALL would benefit from systematic revaccination postchemotherapy.

Clinical Trials Registration

NCT02447718.
The Protein Binding of Acetylsalicylic Acid and Salicylic Acid
Authors: Ali M Amir , Routh Joseph I
Published: February 2020

Quantitative experiments to study the binding of acetylsalicylic acid (ASA) and salicylic acid (SA) by human serum albumin (HSA) were carried out using 14C-labeled ASA or SA and gel filtration to separate the free from the bound forms. Two binding procedures were employed: the ASA or SA was incubated with the HSA, or the mixture was placed in an equilibrium dialysis cell. By withdrawing samples at intervals, the extent of binding or the attainment of equilibrium could be assessed. Evidence that filtration by the gel caused unbinding of the bound SA was obtained, with resultant lower percentage binding of SA by HSA than that obtained by equilibrium dialysis without gel filtration. In either case, binding equilibrium was reached in 4-8 hr. The binding of ASA by HSA was markedly different from that of SA. The experiments both with or without gel filtration demonstrated a progressive increase in binding of ASA in the 20- to 53-hr periods studied. In addition, ASA apparently displaces SA from its binding sites on albumin, an observation that may have therapeutic implications.
A Procedure for the Measurement of Urinary 17-Hydroxycorticosteroids, Aldosterone Acid-labile Conjugate, and Free Plasma Cortisol in Patients with Chronic Illness
Authors: Walker Jacqueline Claus
Published: February 2020

The usual steps for steroid isolation are: (1) hydrolysis, acid for the urinary acid-labile aldosterone conjugate, and enzymatic for the urinary 17-hydroxycorticosteroids (17-OHCS); (2) organic solvent extraction of the corticosteroids; and (3) alkaline, acid, and aqueous washing of the organic extracts of steroids.

In the method described the crude extracts are purified by 3 or 4 sequential partitions using solvent systems of increasing polarity. After three chromatographic separations the 17-OHCS are still near the origin, and the fourth solvent system will separate these from each other. For the measurement of 17-OHCS, the mixed steroids are eluted after the third separation. Half of each eluate is analyzed by the Porter-Silber reaction; the other half is used as a blank to obtain the absorbance of the phenylhydrazones by spectrophotometry. For the measurement of aldosterone or cortisol, aldosterone (mixed with cortisone) or cortisol (mixed with tetrahydrocortisone) is eluted after the fourth paper chromatographic separation and acetylated with 100 µg (2 µc) of 14C-acetic anhydride (specific activity, 2 mc/mmol). The labeled acetates are extracted by liquid partition and isolated by paper chromatography after addition of stable carriers. The beta emissions of the isotopic derivatives are counted by liquid scintillation. Concentrations are calculated from data obtained by acetylation and chromatographic separation of pure steroid standards and suitable blanks.
Solid-phase radioimmunoassay with protein-A-bearing Staphylococcus aureus cells used to assay a protein (ferritin) and a hapten (digoxin).
Authors: Gauldie J , Tang H K , Corsini A , Walker W H
Published: February 2020

We compared use of protein-A-containing Staphylococcus aureus bacteria with conventional ammonium sulfate precipitation and second-antibody methods of separating bound and free antigen in the radioimmunoassay of a hapten (digoxin) and protein (ferritin) in human sera. In each case, values obtained with the heat-killed, formalin-fixed bacteria correlated well with those found by established methods. No matrix effects were detected in either hapten or protein measurements. Because of the affinity of S. aureus for rabbit IgG, rabbit antisera could be used with a small number of bacteria to detect antigen in the presence of 50-fold excess human IgG. The availability of S. aureus and ease of handling make this reagent a rapid, economical alternative of general applicability in radioimmunoassay.
Amniotic fluid phosphatidylglycerol and phosphatidylinositol separated by stepwise-development thin-layer chromatography.
Authors: Mitnick M , DeMarco B , Gibbons J M
Published: February 2020

We describe a stepwise-development thin-layer-chromatographic technique for separating phosphatidylglycerol and phosphatidylinositol in samples of amniotic fluid. Plates are prepared from silica gel G slurried in a 50 g/L ammonium sulfate solution. Phospholipid phosphorus determination is not needed. Phospholipid phosphorus determination is not needed. Phosphatidylglycerol and phosphatidylinositol, measured densitometrically, are expressed as ratios to the sphingomyelin present. These ratios are correlated with the lecithin/sphingomyelin ratio and age of gestation in normal and abnormal pregnancies.
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

There are emerging data that patients <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 <50 years old [median 43 years, range 16–49]. There was no increase in the number of patients <50 years diagnosed with EAC (R = 0.133, P = 0.05). Characteristics of those <50 years versus >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 <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 <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

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 < 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

Large 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

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

The 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

Objectives

To clarify the relationships among race, gender, and socioeconomic status (SES) with C-reactive protein (CRP).

Method

The 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.

Results

The 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.

Discussion

In 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

Background and Objectives

People 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 Methods

Face 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).

Results

Internal 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 Implications

The 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

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

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

Determining 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

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.
Gradient based first- and second-order filters for the demarcation of continental–oceanic boundaries using satellite gravity data
Authors: Maurya Ved P , Fontes Sergio L , Oliveira Jr Vanderlei C , La Terra Emanuele F
Published: February 2020

Demarcating the continental–oceanic boundary (COB) is extremely important as it contributes to an understanding of the tectonic environments of marginal basins through plate reconstructions. In general, the COB is estimated by jointly interpreting the features of the basement geomorphology, bathymetry and geophysical datasets, including gravity, magnetic, seismic and geochemical data. We propose a novel methodology named the tilt-theta angles correlation (TTAC), a second-order filtering approach to estimate the COB using high-resolution satellite gravity data. This method computes the angular difference or correlation angle between the vectors computed from the gradients of the tilt and theta derivative-based first-order filters. Oceanic regions generally exhibit small correlation angles (∼0°), thereby indicating a direct correlation; in contrast, continental regions depict large correlation angles (∼180°) and thus display an inverse correlation. The TTAC method marks the COB at the spatial position where the correlation angles abruptly shift from inverse to direct. Tests using synthetic data and the larger spectral energy content of TTAC for long wavelengths over tilt, theta and minus of the sign of vertical derivative (-SiVD) filters attest the effectiveness of the new methodology over first-order derivative based filters. Additionally, tests utilizing real data over both the West African Transform Margin (WATM) and across the South Atlantic Conjugate Margin (SACM) provide favourable results compared with the previous methodologies used to demarcate the COB. The COB estimates derived using the new methodology are consistent with the COB estimates obtained during recent plate-reconstruction studies. We also compare our results with an earlier interpretation along a conjugate margin encompassing magma-poor and magma-rich regions. In the complex rifted environments of the SACM, in which volcanic rocks are dominant, the TTAC methodology substantially improves the previous COB estimates, thereby establishing it as an efficient edge marker by simultaneously reducing small-scale geological noise and enhancing regional-scale geological contributions.
Adhesion of freshwater sponge cells mediated by carbohydrate–carbohydrate interactions requires low environmental calcium
Authors: Vilanova Eduardo , Ciodaro Priscilla J , Bezerra Francisco F , Santos Gustavo R C , Valle-Delgado Juan J , Anselmetti Dario , Fernàndez-Busquets Xavier , Mourão Paulo A S
Published: February 2020

Marine ancestors of freshwater sponges had to undergo a series of physiological adaptations to colonize harsh and heterogeneous limnic environments. Besides reduced salinity, river-lake systems also have calcium concentrations far lower than seawater. Cell adhesion in sponges is mediated by calcium-dependent multivalent self-interactions of sulfated polysaccharide components of membrane-bound proteoglycans named aggregation factors. Cells of marine sponges require seawater average calcium concentration (10 mM) to sustain adhesion promoted by aggregation factors. We demonstrate here that the freshwater sponge Spongilla alba can thrive in a calcium-poor aquatic environment and that their cells are able to aggregate and form primmorphs with calcium concentrations 40-fold lower than that required by marine sponges cells. We also find that their gemmules need calcium and other micronutrients to hatch and generate new sponges. The sulfated polysaccharide purified from S. alba has sulfate content and molecular size notably lower than those from marine sponges. Nuclear magnetic resonance analyses indicated that it is composed of a central backbone of non- and 2-sulfated α- and β-glucose units decorated with branches of α-glucose. Assessments with atomic force microscopy/single-molecule force spectroscopy show that S. alba glucan requires 10-fold less calcium than sulfated polysaccharides from marine sponges to self-interact efficiently. Such an ability to retain multicellular morphology with low environmental calcium must have been a crucial evolutionary step for freshwater sponges to successfully colonize inland waters.
Impact of the ‘Seguro Médico Siglo XXI’ medical insurance programme on neonatal and infant mortality in Mexico, 2006–14: an ecological approach to estimation
Authors: Urquieta-Salomón José , Lamadrid-Figueroa Héctor , Angeles Gustavo , Montoya Alejandra , Rojas-Martínez Rosalba , Martínez-Nolasco Alejandro , Torres-Pereda Pilar , O’Shea Gabriel , Villagrán Victor M , Halley Elizabeth , Delgado-Sánchez Verónica , Lazcano-Ponce Eduardo
Published: February 2020

The ‘Seguro Médico Siglo XXI’ (SMSXXI), a universal coverage medical insurance programme for children under 5 years of age, started in 2006 to help avoid catastrophic health expenditures in poor families without social security in Mexico. The study used information from the National Health Information System for the 2006–14 period. An ecological approach was followed with a panel of the 2457 municipalities of Mexico as the units of analysis. The outcome variables were the municipality-level neonatal mortality and infant mortality rates in population without access to social security. The programme variable was the coverage of the SMSXXI programme at the municipality level, expressed as a proportion. Demographic and economic variables defined at the municipality level were included as covariates. Impact was estimated by fitting a fixed-effects negative binomial regression model. Results reveal that the SMSXXI significantly reduced both infant and neonatSal mortality in the target population, although in a non-linear fashion, with minimum mortality levels found around the 70% coverage range. The effect is mostly given by the transition from the first quintile to the fourth quintile of coverage (<13% vs 70.5–93.7% coverage), and it is attenuated significantly at coverage levels very close to or at 100%. The observed risk reduction amounted to an estimated total of 11 358 infant deaths being avoided due to the SMSXXI during the 2006–14 period, of which 48% were neonatal. In conclusion, we found a significant impact of the SMSXXI programme on both infant mortality and neonatal mortality. An attenuation of the effect of the insurance on mortality rates at levels close to 100% coverage may reflect the saturation of health units in detriment of the quality of care.
CHCHD2 harboring Parkinson’s disease-linked T61I mutation precipitates inside mitochondria and induces precipitation of wild-type CHCHD2
Authors: Cornelissen Tom , Spinazzi Marco , Martin Shaun , Imberechts Dorien , Vangheluwe Peter , Bird Matthew , De Strooper Bart , Vandenberghe Wim
Published: February 2020

The T61I mutation in coiled-coil-helix-coiled-coil-helix domain containing 2 (CHCHD2), a protein residing in the mitochondrial intermembrane space (IMS), causes an autosomal dominant form of Parkinson’s disease (PD), but the underlying pathogenic mechanisms are not well understood. Here, we compared the subcellular localization and solubility of wild-type (WT) and T61I mutant CHCHD2 in human cells. We found that mitochondrial targeting of both WT and T61I CHCHD2 depended on the four cysteine residues in the C-terminal coiled-coil-helix-coiled-coil-helix (CHCH) domain but not on the N-terminal predicted mitochondrial targeting sequence. The T61I mutation did not interfere with mitochondrial targeting of the mutant protein but induced its precipitation in the IMS. Moreover, T61I CHCHD2 induced increased mitochondrial production of reactive oxygen species and apoptosis, which was prevented by treatment with anti-oxidants. Retention of T61I CHCHD2 in the cytosol through mutation of the cysteine residues in the CHCH domain prevented its precipitation as well as its apoptosis-inducing effect. Importantly, T61I CHCHD2 potently impaired the solubility of WT CHCHD2. In conclusion, our data show that the T61I mutation renders mutant CHCHD2 insoluble inside mitochondria, suggesting loss of function of the mutant protein. In addition, T61I CHCHD2 exerts a dominant-negative effect on the solubility of WT CHCHD2, explaining the dominant inheritance of this form of PD.
The Contribution of Cognitive Linguistics to the Acquisition of Polysemy: A Dictionary Entry-Based Study with Chinese Learners of English
Authors: Lu Huaguo , Zhang Ya , Hao Xia
Published: February 2020

This paper reported on a quasi-experimental study into the effectiveness of two types of entries – entries enhanced with cognitive linguistic insights (CL entries) and linearly ordered entries (LO entries) – in promoting L2 learners’ acquisition of English polysemes. Sixty-five college students majoring in English were divided into an experimental group (EG) and a reference group (RG). EG received the CL entries for lift and break in and RG were presented with the corresponding LO entries. Both groups were given twenty minutes to read the entries and to learn the twenty-seven senses. To examine the effectiveness of the two types of entries, an English-Chinese translation test was administered before the learning session (as Test 1), immediately after it (as Test 2) and two weeks later (as Test 3). The results showed that: (1) EG outperformed RG in the comprehension of the target senses on both Test 2 and Test 3. (2) The CL entries were more effective in promoting short-term retention than the LO entries, but had no advantage over the latter in long-term retention. (3) The CL entry for lift facilitated the learning of the target senses more than the LO entry did, but the CL entry for break in was no more effective than the LO entry in helping L2 learners acquire the target senses. The study suggests that the cognitive linguistic view can and should be further applied to treating polysemy in learner’s dictionaries, but the model for CL entries is not always recommendable and the knowledge gained from reading the CL entries needs consolidating.
Postvaccination Serum Antirotavirus Immunoglobulin A as a Correlate of Protection Against Rotavirus Gastroenteritis Across Settings
Authors: Baker Julia M , Tate Jacqueline E , Leon Juan , Haber Michael J , Pitzer Virginia E , Lopman Benjamin A
Published: February 2020

Background

A correlate of protection for rotavirus gastroenteritis would facilitate rapid assessment of vaccination strategies and the next generation of rotavirus vaccines. We aimed to quantify a threshold of postvaccine serum antirotavirus immunoglobulin A (IgA) as an individual-level immune correlate of protection against rotavirus gastroenteritis.

Methods

Individual-level data on 5074 infants in 9 GlaxoSmithKline Rotarix Phase 2/3 clinical trials from 16 countries were pooled. Cox proportional hazard models were fit to estimate hazard ratios (HRs) describing the relationship between IgA thresholds and occurrence of rotavirus gastroenteritis.

Results

Seroconversion (IgA ≥ 20 U/mL) conferred substantial protection against any and severe rotavirus gastroenteritis to age 1 year. In low child mortality settings, seroconversion provided near perfect protection against severe rotavirus gastroenteritis (HR, 0.04; 95% confidence interval [CI], .01–.31). In high child mortality settings, seroconversion dramatically reduced the risk of severe rotavirus gastroenteritis (HR, 0.46; 95% CI, .25–.86). As IgA threshold increased, risk of rotavirus gastroenteritis generally decreased. A given IgA threshold provided better protection in low compared to high child mortality settings.

Discussion

Postvaccination antirotavirus IgA is a valuable correlate of protection against rotavirus gastroenteritis to age 1 year. Seroconversion provides an informative threshold for assessing rotavirus vaccine performance.
Thinking outside the Box: Globalization, Labor Rights, and the Making of Preferential Trade Agreements
Authors: Wang Zhiyuan
Published: February 2020

States can seemingly defy the dictates of globalization. In practice, although being pressured by their competitors, states rarely engage in the race to the bottom by downgrading labor rights laws that are politically costly to pursue. I argue that states’ resistance is made possible by adopting more viable policy alternatives, i.e., concluding preferential trade agreements (PTAs). PTAs can generate considerable economic gains in a less politically costly way than does reducing legal labor protection. As a result, it is expected that a pair of states is more likely to form a PTA in the face of policy pressure to lower legal labor protection. I also argue that facing such pressure, these states are more likely to include strong labor provisions in PTAs. Finally, in the face of the policy pressure, states may feel that signing a PTA is a bit less urgent when they are able to diminish practical labor protection. Applying structural equivalence technique to a new global labor rights dataset to capture the policy pressure to lower legal labor protection, I find robust evidence in support of these conjectures.
Inactivation of thymidine kinase as a cause of resistance to zidovudine in clinical isolates of Escherichia coli: a phenotypic and genomic study
Authors: Peyclit Lucie , Ben Khedher Maryem , Zerrouki Lotfi , Diene Seydina M , Baron Sophie Alexandra , Rolain Jean-Marc
Published: February 2020

Objectives

The antiviral zidovudine has been recently identified as an active drug against resistant Enterobacteriaceae, but prevalence of resistance to this compound remains unknown. The aim was to estimate the prevalence of clinical Escherichia coli isolates resistant to zidovudine and to decipher the mechanism of zidovudine resistance.

Methods

We screened 537 isolates on zidovudine-containing agar plates and studied their thymidine kinase (tdk) gene sequences, the putative target involved in zidovudine resistance. Moreover, sequence analysis of 633 complete genomes of E. coli was performed to investigate mutation in the tdk gene. A comparative genomic analysis was done on an in vitro zidovudine-resistant mutant.

Results

After screening on our medium containing 2.7 mg/L (10 μM) zidovudine, nine strains had a zidovudine MIC >26.7 mg/L. The gene was absent in three isolates, inactivated by an IS (IS1X2 and ISApl1) in two isolates and mutated in four isolates. A genomic analysis of 633 E. coli genomes showed heterogeneity of the tdk gene sequence, with 27 different sequences. Among them, three genomes showed an inactivation of the gene (IS, stop codon and no tdk gene sequence). The in vitro mutant E. coli had 27 SNPs in eight genes of the core genome compared with the initial strain.

Conclusions

Our study reports zidovudine-resistant clinical isolates of E. coli, presumably related to tdk inactivation. Diversity of Tdk in bacterial genomes can be large. Other mechanisms need to be considered in zidovudine resistance. The use of zidovudine in antibiotic-resistant infections needs to be in combination and should be tested before clinical administration.
BL30SEC Method for Detection of Beta-Lactams in Raw Commingled Cow Milk: AOAC Performance Tested MethodSM 061902
Authors: Markovsky Robert J , Douglas David W , Sullivan Ryan , Tran Alan C , Legg David R , McRobbie Lindsey W , Schwartz Janine A , Salter Robert S , Klass Nicole , Knoop Sarah , Bastin Benjamin , Crowley Erin , Agin James , Goins David , Kalinowsky Emily
Published: February 2020

Testing milk for antibiotics before acceptance into dairies is required by the U.S. Pasteurized Milk Ordinance. Technological advances in tests have reduced screening times and improved detection accuracy. This work describes the validation of the Charm Rapid One Step Assay Beta-Lactam 30 Second Test according to the U.S. Food and Drug Administration Center for Veterinary Medicine protocol for raw commingled milk. Milk is added to the lateral flow test strip in an incubator/reader to deliver a 30 second result. Independent laboratory validation followed sensitivity, interference, and incurred residue protocols. Sensitivity, in parts per billion (ppb = µg/kg), using a probit curve determined 90% percent detection with 95% confidence, which met National Conference of Interstate Milk Shipments (NCIMS) specifications. Six U.S. approved beta-lactam drugs were detected below, but within 50% of, target/tolerance levels for penicillin G 2.9 ppb, ampicillin 5.9 ppb, amoxicillin 5.8 ppb, cephapirin 13 ppb, cloxacillin 8.1 ppb, and ceftiofur metabolites 73 ppb. No interferences were observed from 33 animal drugs at 100 ppb, somatic cells at 1.2 million/mL, or bacterial levels of >300 000 CFU/mL. Incurred residue detection levels were similar to levels determined with the spiked parent compound. The data support NCIMS that the BL30SEC method met U.S. criteria for testing milk for beta-lactams.