bluuebunny/crossref_metadata_2025_split huggingface dataset:
Working Conditions and Work-Related Health Issues of Female Domestic Workers in Four Districts of Karachi
Authors: Tariq Hira , Shaikh Shiraz , Musharaf Mehjabeen 
Published: February 2020

Abstract

Objectives
To determine the working conditions and work-related health issues of female domestic workers (FDWs) in four districts of Karachi.

Methods
Population-based cross-sectional study was conducted in four squatter settlements of Karachi with sample size of 406 FDWs in 2018. Pretested questionnaire was administered to collect data through snowball technique. Multivariate logistic regression examined the association between different factors and experiencing violence, work-related injuries, and chemical exposures.

Results
Only (14.5%) of domestic workers earned Rs 15 000 (75 GBP month−1) and above. &gt;1% had financial support for the health or education of children. Verbal violence included shouting (40.9%), constant critique of work (17.2%), and job threats (13.5%). Common workplace injuries were cuts (30.8%), burns (27.6%), and bruises (23.6%). Doing laundry showed significant positive association with experiencing cuts [odds ratio (OR) = 2.09; 1.15–3.71], looking after children to bruises (OR = 2.29; 1.07–4.88), and cooking to burns (OR = 4.66; 2.68–8.08).

Conclusions
Creating economic environment which is equal for all low wage workers, setting up domestic labor standards and holding employers accountable to them is essential.
CMF-Impute: an accurate imputation tool for single-cell RNA-seq data
Authors: Xu Junlin , Cai Lijun , Liao Bo , Zhu Wen , Yang JiaLiang 
Published: February 2020

Abstract

Motivation
Single-cell RNA-sequencing (scRNA-seq) technology provides a powerful tool for investigating cell heterogeneity and cell subpopulations by allowing the quantification of gene expression at single-cell level. However, scRNA-seq data analysis remains challenging because of various technical noises such as dropout events (i.e. excessive zero counts in the expression matrix).

Results
By taking consideration of the association among cells and genes, we propose a novel collaborative matrix factorization-based method called CMF-Impute to impute the dropout entries of a given scRNA-seq expression matrix. We test CMF-Impute and compare it with the other five state-of-the-art methods on six popular real scRNA-seq datasets of various sizes and three simulated datasets. For simulated datasets, CMF-Impute outperforms other methods in imputing the closest dropouts to the original expression values as evaluated by both the sum of squared error and Pearson correlation coefficient. For real datasets, CMF-Impute achieves the most accurate cell classification results in spite of the choice of different clustering methods like SC3 or T-SNE followed by K-means as evaluated by both adjusted rand index and normalized mutual information. Finally, we demonstrate that CMF-Impute is powerful in reconstructing cell-to-cell and gene-to-gene correlation, and in inferring cell lineage trajectories.

Availability and implementation
CMF-Impute is written as a Matlab package which is available at https://github.com/xujunlin123/CMFImpute.git.

Supplementary information
Supplementary data are available at Bioinformatics online.
Yield, Efficiency, and Costs of Mass Screening Algorithms for Tuberculosis in Brazilian Prisons
Authors: Santos Andrea da Silva , de Oliveira Roberto Dias , Lemos Everton Ferreira , Lima Fabiano , Cohen Ted , Cords Olivia , Martinez Leonardo , Gonçalves Crhistinne , Ko Albert , Andrews Jason R , Croda Julio 
Published: February 2020

Abstract

Background
Tuberculosis (TB) is a major cause of morbidity and mortality among incarcerated populations globally. We performed mass TB screening in 3 prisons and assessed yield, efficiency, and costs associated with various screening algorithms.

Methods
Between 2017 and 2018, inmates from 3 prisons in Brazil were screened for TB by symptom assessment, chest radiography, sputum testing by Xpert MTB/RIF fourth-generation assay, and culture. Chest radiographs were scored by an automated interpretation algorithm (Computer-Aided Detection for Tuberculosis [CAD4TB]) that was locally calibrated to establish a positivity threshold. Four diagnostic algorithms were evaluated. We assessed the yield (percentage of total cases found) and efficiency (prevalence among those screened) for each algorithm. We performed unit costing to estimate the costs of each screening or diagnostic test and calculated the cost per case detected for each algorithm.

Results
We screened 5387 prisoners, of whom 214 (3.9%) were diagnosed with TB. Compared to other screening strategies initiated with chest radiography or symptoms, the trial of all participants with a single Xpert MTB/RIF sputum test detected 74% of all TB cases at a cost of US$249 per case diagnosed. Performing Xpert MTB/RIF screening tests only on those with symptoms had a similar cost per case diagnosed (US$255) but missed 35% more cases (73 vs 54) as screening all inmates.

Conclusions
In this prospective study in 3 prisons in a high TB burden country, we found that testing all inmates with sputum Xpert MTB/RIF was a sensitive approach, while remaining cost-efficient. These results support use of Xpert MTB/RIF for mass screening in TB-endemic prisons.
Two-hour Sephadex column method for assay of unconjugated estriol in serum.
Authors: Haigh W G , Hofman L F , Barron E J 
Published: February 2020

Abstract
The column method of Christner and Fetter (Steroids 24: 327, 1974) has been modified to give a simple, rapid assay for unconjugated estriol in serum. Estriol is isolated from serum by being retained on a Sephadex column, while estriol conjugates and serum proteins are eluted. The sample and labeled estriol compete for antibody on the column. Antibody is eluted, removing proportional amounts of sample and labeled estriol. Our modifications include using stable serum-based standards, shortening the incubation to 10 min, complete removal of conjugates, and regeneration of the columns so that they can be used repeatedly. The assay, which can be completed in 2 h, has a mid-range interassay CV of 8.2%.
Hypophosphatasia (adult form): quantitation of serum alkaline phosphatase isoenzyme activity in a large kindred.
Authors: Millán J L , Whyte M P , Avioli L V , Fishman W H 
Published: February 2020

Abstract
We used heat inactivation, L-phenylalanine inhibition, and electrophoresis on polyacrylamide gel and cellulose acetate membranes--with and without use of specific antisera against the liver-bone, intestinal, and placental isoenzymes--to distinguish and quantitate the different alkaline phosphatase isoenzymes in sera from 23 adult members of a kindred affected by the adult form of hypophosphatasia. Nine subjects had values for total activity more than two standard deviations below the mean values for age- and sex-matched normal persons. Bone isoenzyme was diminished in all nine, whereas liver isoenzyme was subnormal in only four. Phosphoethanolamine and phosphoserine in the urine of eight hypophosphatasemic individuals correlated inversely with both total and liver alkaline phosphatase activity in their serum, but not with the activity of the bone isoenzyme. Total activity in the serum of adult kindred members correlated best with the circulating liver isoenzyme activity. The findings suggest that altered hepatic metabolism is responsible for the increased urinary excretion of phosphoethanolamine, and perhaps phosphoserine, in hypophosphatasia.
Applicability of various quality-control sera to assay of high-density lipoprotein cholesterol.
Authors: Bullock D G , Carter T J , Hughes S V 
Published: February 2020

Abstract
Effective internal quality control and external quality assessment of high-density lipoprotein cholesterol assay is made difficult by analyte instability, and the suitability of quality-control sera for this purpose has not been studied. We have therefore investigated the properties of 25 different control sera from 15 suppliers by estimating within-batch precision for the two precipitation procedures used most widely (phosphotungstate/Mg2+ and heparin/Mn2+ with enzymic measurement of cholesterol. Some sera had properties similar to those of fresh human serum, but others demonstrated poor precision for one or both procedures or contained apparent high-density lipoprotein cholesterol in unphysiological concentrations. A study of six sera indicated that between-batch precision was consistent with the within-batch findings. We found that eight of the 25 batches of quality-control serum we investigated may be used for internal quality control and external quality assessment of high-density lipoprotein cholesterol assay.
Association between the findings of metachronous secondary primary malignancies and the number of Lugol-voiding lesions
Authors: Katada Chikatoshi , Yokoyama Tetsuji , Yano Tomonori , Oda Ichiro , Shimizu Yuichi , Takemura Kenichi , Koike Tomoyuki , Takizawa Kohei , Hirao Motohiro , Okada Hiroyuki , Nakayama Norisuke , Kubota Yutaro , Matsuo Yasumasa , Kawakubo Hirofumi , Ishikawa Hideki , Yokoyama Akira , Muto Manabu 
Published: February 2020

Summary
This study was designed to evaluate the relation between dysplastic squamous epithelium in the esophageal mucosa and the development of metachronous secondary primary malignancies (mSPM) other than esophagus after endoscopic resection (ER) in patients with early esophageal squamous cell carcinoma (SCC). We studied 330 patients with early esophageal SCC who underwent ER as a post hoc analysis of a prospective multicenter cohort study (UMIN Clinical Trials Registry ID UMIN000001676). Lugol-voiding lesions (LVL) were graded into 3 categories (A = no lesion; B = 1 to 9 lesions; C ≥ 10 lesions). The following variables were studied: (i) the incidences of mSPM other than esophagus; (ii) the standardized incidence ratios (SIRs) of mSPM; (iii) the cumulative incidence and total number of mSPM other than esophagus; and (iv) predictors of mSPM other than esophagus on analysis with a multivariate Cox proportional-hazards model. After a median follow-up of 46.6 months, mSPM other than esophagus was diagnosed in a total of 73 patients (90 lesions). Among the 106 patients in group C, 37 patients had mSPM (51 lesions), including head and neck cancer in 14 patients (24 lesions) and gastric cancer in 12 patients (16 lesions). The SIR of mSPM was 3.61 in this study subjects. An increase in the LVL grade (A to B to C) was associated with a progressive increase in the cumulative incidence rate of mSPM other than esophagus (P = 0.017 for A vs. C, P = 0.023 for B vs. C). An increase in the LVL grade (A to B to C) was also associated with a progressive increase in the total number of mSPM other than esophagus per 100 person-years (primary events, relative risk [RR] = 1.66 and 3.24 for grades B and C, respectively, vs. A, P = 0.002 for trend; all events, RR = 1.81 and 4.66 for grades B and C, respectively, vs. A, P &lt; 0.0001 for trend). LVL grade C was a strong predictor of mSPM other than esophagus (RR = 3.41 for A vs. C). LVL grade may be a useful predictor of the risk of mSPM other than esophagus after ER in patients with early esophageal SCC.
Links between metabolic syndrome and the microbiome
Authors: Gildner Theresa E 
Published: February 2020

Abstract
Metabolic syndrome (MetS) is a cluster of harmful conditions which occur together, such as insulin resistance, abdominal obesity, and hypertension. The global prevalence of MetS is growing rapidly, with some estimates suggesting over one billion people worldwide experience increased morality and disease rates linked with this syndrome. One possible factor contributing to MetS risk is changes in microbiome composition. Approximately 100 trillion bacteria and other microbes reside in the human intestinal tract, collectively termed the gut microbiome. Humans and microbes share a long evolutionary history, with many of these microbes influencing human health outcomes. However, environmental conditions have changed dramatically with human technological innovations; many of these changes (e.g., diets high in processed foods and sedentary lifestyles) appear to impact human-microbe relationships. In general, recent changes in diet and activity patterns have been linked to decreased microbiome diversity, elevating inflammation and metabolic disease risk and likely promoting the development of MetS. Targeting patient diet or exercise patterns may therefore help doctors better treat patients suffering from MetS. Still, additional work is needed to determine how the microbiome responds to changes in patient activity and diet patterns across culturally and biologically diverse human populations.
Insect—Symbiont Gene Expression in the Midgut Bacteriocytes of a Blood-Sucking Parasite
Authors: Husnik Filip , Hypsa Vaclav , Darby Alistair 
Published: February 2020

Abstract
Animals interact with a diverse array of both beneficial and detrimental microorganisms. In insects, these symbioses in many cases allow feeding on nutritionally unbalanced diets. It is, however, still not clear how are obligate symbioses maintained at the cellular level for up to several hundred million years. Exact mechanisms driving host–symbiont interactions are only understood for a handful of model species and data on blood-feeding hosts with intracellular bacteria are particularly scarce. Here, we analyzed interactions between an obligately blood-sucking parasite of sheep, the louse fly Melophagus ovinus, and its obligate endosymbiont, Arsenophonus melophagi. We assembled a reference transcriptome for the insect host and used dual RNA-Seq with five biological replicates to compare expression in the midgut cells specialized for housing symbiotic bacteria (bacteriocytes) to the rest of the gut (foregut–hindgut). We found strong evidence for the importance of zinc in the system likely caused by symbionts using zinc-dependent proteases when acquiring amino acids, and for different immunity mechanisms controlling the symbionts than in closely related tsetse flies. Our results show that cellular and nutritional interactions between this blood-sucking insect and its symbionts are less intimate than what was previously found in most plant-sap sucking insects. This finding is likely interconnected to several features observed in symbionts in blood-sucking arthropods, particularly their midgut intracellular localization, intracytoplasmic presence, less severe genome reduction, and relatively recent associations caused by frequent evolutionary losses and replacements.
Age-Related Differences in the Gut Microbiome of Rhesus Macaques
Authors: Adriansjach Julie , Baum Scott T , Lefkowitz Elliot J , Van Der Pol William J , Buford Thomas W , Colman Ricki J 
Published: February 2020

AbstractAging is a multifactorial process characterized by progressive changes in gut physiology and the intestinal mucosal immune system. These changes, along with alterations in lifestyle, diet, nutrition, inflammation and immune function alter both composition and stability of the gut microbiota. Given the impact of environmental influences on the gut microbiota, animal models are particularly useful in this field. To understand the relationship between the gut microbiota and aging in nonhuman primates, we collected fecal samples from 20 male and 20 female rhesus macaques (Macaca mulatta), across the natural macaque age range, for 16S rRNA gene analyses. Operational taxonomic units were then grouped together to summarize taxon abundance at different hierarchical levels of classification and alpha- and beta-diversity were calculated. There were no age or sex differences in alpha diversity. At the phylum level, relative abundance of Proteobacteria and Firmicutes and Firmicutes to Bacteriodetes ratio were different between age groups though significance disappeared after correction for multiple comparisons. At the class level, relative abundance of Firmicutes_Bacilli decreased and Proteobacteria_Alphaproteobacteria and Proteobacteria_Betaproteobacteria increased with each successively older group. Only differences in Firmicutes_Bacilli remained significant after correction for multiple comparisons. No sex differences were identified in relative abundances after correction for multiple comparisons. Our results are not surprising given the known impact of environmental factors on the gut microbiota.
Seismic inversion of soil damping and stiffness using multichannel analysis of surface wave measurements in the marine environment
Authors: Armstrong M A , Ravasio M , Versteijlen W G , Verschuur D J , Metrikine A V , van Dalen K N 
Published: February 2020

SUMMARY
Determination of soil material damping is known to be difficult and uncertain, especially in the offshore environment. Using an advanced inversion methodology based on multichannel spectral analysis, Scholte and Love wave measurements are used to characterize subsea soil from a North Sea site. After normalization, a determinant-based objective function is used in a genetic algorithm optimization to estimate the soil shear modulus. The inverted shear-modulus profile is comparable to previously published results for the same data, although a higher degree of certainty is achieved in the near-surface layers. The half-power bandwidth method is used for extracting the attenuation curve from the measurements and efficient reference data points are chosen based on wavelet compression. The material-damping ratio inversion is performed using a modified stochastic optimization algorithm. Accounting for measurement errors, the material-damping ratio profile is retrieved from the fundamental-mode Scholte wave with a high degree of certainty. Furthermore, a method is proposed for identifying the frequency dependence of the material-damping ratio from in situ measurements. No evidence for frequency dependence is found and the small-strain soil material-damping ratio at this site can be said to be frequency independent for the measured conditions.
Transfer functions between teleseismic data components
Authors: Frederiksen A W 
Published: February 2020

SUMMARYDifferent data components of teleseismic waveforms are related by transfer functions that depend only on receiver-side structure. This is the common basis of a number of teleseismic techniques, including receiver functions and shear wave splitting analysis. Common trace misfits used in these analysis techniques are shown to be equivalent to band-limited comparisons of real and synthetic transfer functions. The data deconvolution used in receiver function analysis leads to reduced structural resolution compared to direct trace-based misfits such as cross-convolution, with direct transfer function modelling of a data trace having the particular advantage of a physically meaningful misfit. Having established that the intertrace transfer function contains all available structural information, the sensitivity of transfer functions to structure is examined for a series of teleseismic scenarios. Transfer functions for the teleseismic P coda show a strong sensitivity to shallow low-velocity structures such as sedimentary basins; the Sp precursors used in S receiver functions are less affected. Examination of transfer functions for shear wave splitting shows that response complexities occur at frequencies too high to be observable in teleseismic studies, and that the dominant control on the response is the splitting intensity.
Stent and leaflet stresses across generations of balloon-expandable transcatheter aortic valves
Authors: Xuan Yue , Dvir Danny , Wang Zhongjie , Ye Jian , Guccione Julius M , Ge Liang , Tseng Elaine E 
Published: February 2020

AbstractOBJECTIVESTranscatheter aortic valve replacement (TAVR) is established therapy for severe aortic stenosis patients with intermediate-, high- and prohibitive-risk for surgery. A significant challenge when expanding TAVR to low-risk and younger patients is the unknown long-term durability. High leaflet stresses have been associated with surgical bioprosthetic valve degeneration. In this study, we examined the impact of changes in valve design across 3 generations of same-sized TAVR devices on stent and leaflet stresses.METHODSThe 26-mm Edwards SAPIEN, 23, 26 and 29 mm SAPIEN XT (XT) and 26 mm SAPIEN 3 (S3) (n = 1 each) underwent micro-computed tomography (micro-CT) scanning. Dynamic finite element computational simulations of 23–26 mm SAPIEN, 23–29 mm XT and 23–29 mm S3 were performed with physiological loading and micro-CT or scaled geometries.RESULTSPeak stresses were concentrated in the commissure area and along the bottom of the suture, representing areas most likely to develop structural valve degeneration across TAVR generations. Latest-generation S3 showed greatest 99th percentile principal stress on commissural leaflets for 26 and 29 mm, and increased stresses over XT for 23 mm. Percentage of higher stress areas within the leaflets steadily increased across generations, 3.8%, 3.9% and 5.7%, respectively, for 26 mm SAPIEN, XT and S3 with similar trend for 29-mm valves.CONCLUSIONSUsing computational simulations based on high-fidelity modelling of balloon-expandable TAVRs, our study demonstrated that maximum stress areas existed in similar leaflet locations across SAPIEN generations, while the latest model S3 had the highest magnitude for both 26- and 29-mm valves. S3 also had the largest area of higher stresses than other generations, which would be prone to degeneration. Our study coupled with future long-term clinical outcomes &gt;10 years will provide insight on biomechanics of TAVR degeneration.
Overconstrained gravitational lens models and the Hubble constant
Authors: Kochanek C S 
Published: February 2020

ABSTRACT
It is well known that measurements of H0 from gravitational lens time delays scale as H0 ∝ 1 − κE, where κE is the mean convergence at the Einstein radius RE but that all available lens data other than the delays provide no direct constraints on κE. The properties of the radial mass distribution constrained by lens data are RE and the dimensionless quantity ξ = REα″(RE)/(1 − κE), where α″(RE) is the second derivative of the deflection profile at RE. Lens models with too few degrees of freedom, like power-law models with densities ρ ∝ r−n, have a one-to-one correspondence between ξ and κE (for a power-law model, ξ = 2(n − 2) and κE = (3 − n)/2 = (2 − ξ)/4). This means that highly constrained lens models with few parameters quickly lead to very precise but inaccurate estimates of κE and hence H0. Based on experiments with a broad range of plausible dark matter halo models, it is unlikely that any current estimates of H0 from gravitational lens time delays are more accurate than ${\sim} 10{{\ \rm per\ cent}}$, regardless of the reported precision.
Chromospheric plasma ejection above a pore
Authors: Bharti L , Sobha B , Quintero Noda C , Joshi C , Pandya U 
Published: February 2020

ABSTRACT
We present high spatial resolution observations of short-lived transients, ribbons and jet-like events above a pore in Ca ii H images where fine structure, like umbral dots, light bridges and penumbral microfilaments, is present in the underlying photosphere. We found that current layers are formed at the edges of the convective fine structure, due to the shear between their horizontal field and the ambient vertical field. High vertical electric current density patches are observed in the photosphere around these events, which indicates the formation of a current sheet at the reconnection site. In the framework of past studies, low altitude reconnection could be the mechanism that produces such events. The reconnection is caused by an opposite polarity field produced by the bending of field lines by convective downflows at the edge of pore fine structure.