bluuebunny/crossref_metadata_2025 huggingface dataset:
Biological function polarity prediction of missense variants using machine learning
Authors: Ghosh Adhideb , Navarini Alexander A.
Published: April 2020

Functional interpretation is crucial when facing on average 20,000 missense variants per human exome, as the great majority are not associated with any underlying disease.In silicobioinformatics tools can predict the deleteriousness of variants or assess their functional impact by assigning scores, but they cannot predict whether the variant in question results in gain or loss of function at the protein level. Here, we show that machine learning can effectively predict this biological function polarity of missense variants. The new method adapts weighted gradient boosting machine approach on a set of damaging variants (1,288 loss of function and 218 gain of function variants) as annotated by the tools SIFT, PolyPhen2 and CADD. Area under the ROC curve of 0.85 illustrates high discriminative power of the classifier. Predictive performance of the classifier remains consistent against an independent set of damaging variants as highlighted by the area under the ROC curve of 0.83. This new approach may help to guide biological experiments on the clinical relevance of damaging genetic variants.

Author summary

Missense variant occurs when a single genetic alteration in DNA takes place and as a result a new amino acid is translated into the protein. This amino acid change can inactivate the existing protein function causing loss-of-function or produce a new function causing gain-of-function. Therefore, it is very important to interpret these functional consequences of missense variants as they often turn out to be disease causing. Each individual’s genome sequence has thousands of missense variants, out of which very few are actually associated with any underlying disease. Various computational tools have been developed to predict whether missense variants are damaging or not, but none of them can actually predict whether the damaging missense variants cause gain-of-function or loss-of-function. We have developed a new ensemble classifier to predict this biological function polarity at the protein level. The classifier combines the prediction scores of three existing bioinformatics tools and applies machine learning to make effective predictions. We have validated our classifier against an independent data set to show its high predictive power and robustness. The predictions made by our machine learning tool can be used as indicators of biological function polarity, but with further evidence on pathogenicity.
Incorrect Molecular Weights due to inaccurate Prestained Protein Molecular Weight Markers that are used for Gel Electrophoresis and Western Blotting
Authors: Neris Rômulo Leão Silva , Kaur Ajuni , Gomes Aldrin V.
Published: April 2020

The most widely used Western blotting protein standards are prestained proteins of known molecular mass (kDa). They are also utilized for sodium dodecyl sulphate (SDS) Polyacrylamide Gel Electrophoresis (PAGE) to determine the molecular mass of proteins separated by electrophoresis. The objective of this study was to assess the reliability of different commercially available protein standards in predicting accurate protein molecular weights. We performed this experiment by running Criterion TGX gels with five prestained protein standards (Thermo Fisher SeeBlue Plus 2, Bio-Rad Precision Plus Protein Dual-color, Thermo Fisher Spectra Multi-color, Novex-Sharp Pre-stained, and Invitrogen iBright Pre-Stained). To evaluate their accuracy, we utilized highly purified Bovine Serum Albumin (BSA, 66.44 kDa) and Cytochrome C (Cyto C, 11.62 kDa). We also made use of the dimers of BSA (132.88 kDa) and Cyt C (23.24 kDa) that are present on SDS-PAGE gels. Our results suggest that three of the standards were less accurate at higher molecular masses with the iBright marker having the highest error in determining the expected 132.88 kDa molecular weight. The SeeBlue Plus 2 was accurate at identifying the 132.88 kDa molecular weight protein band but was less reliable for the three other lower molecular weight proteins. These findings have significant implications for the determination of protein masses because researchers rely on these standards to evaluate the molecular masses of their protein(s). We suggest that at least two different protein standards should be initially used in electrophoresis gels and for Western blotting in order to get accurate protein molecular weight results.
Whole genome sequences of multi-drug resistantEscherichia coliisolated in a Pastoralist Community of Western Uganda: Phylogenomic changes, virulence and resistant genes
Authors: Iramiot Jacob Stanley , Kajumbula Henry , Bazira Joel , de Villiers Etienne P. , Asiimwe Benon B.
Published: April 2020

Background

The crisis of antimicrobial resistance is already here with us, affecting both humans and animals alike and very soon, small cuts and surgeries will become life threatening. This study aimed at determine the whole genome sequences of multi-drug resistantEscherichia coliisolated in a Pastoralist Community of Western Uganda: phylogenomic changes, virulence and resistant genes.

Methods

This was a laboratory based cross sectional study. Bacterial isolates analyzed in this study were 42 multidrug resistantE. coliisolated from stool samples from both humans and cattle in pastoralist communities collected between January 2018-March 2019. Most of the isolates (41/42) were resistant to three or more antibiotics (multi-drug resistant) and 21/42 isolates were ESBL producers; 13/42 from human and 8/42 from cattle. Whole Genome Sequencing (WGS) was carried out at the facilities of Kenya Medical Research Institute-Wellcome trust, Kilifi, to determine the phylogenomic changes, virulence and resistant genes.

Results

The genomes of the humanE. coligenerally clustered together and away from those of cattle origin. TheE. coliisolates were assigned to eight different phylogroups: A, B1, B2, Cladel, D, E, F and G, with a majority being assigned to phylogroup A; while most of the animal isolates were assigned to phylogroup B1. The carriage of multiple AMR genes was higher from theE. colipopulation from humans than those from cattle. Among these were Beta-lactamase; blaOXA-1: Class D beta-lactamases; blaTEM-1, blaTEM-235: Beta-lactamase; catA1: chloramphenicol acetyl transferase; cmlA1: chloramphenicol efflux transporter; dfrA1, dfrA12, dfrA14, dfrA15, dfrA17, dfrA5, dfrA7, dfrA8: macrolide phosphotransferase; oqxB11: RND efflux pump conferring resistance to fluoroquinolone; qacL, qacEdelta1: quinolone efflux pump; qnrS1: quinolone resistance gene; sul1, sul2, sul3: sulfonamide resistant; tet(A), tet(B): tetracycline efflux pump.

A high variation of virulence genes was registered among theE. coligenomes from humans than those of cattle origin.

Conclusion

TheE. coliof human and cattle origin are largely independent with different ancestral origins. Limited sharing of strains and resistance genes presents a challenge to the hypothesis that AMR in humans is as a result of antibiotic misuse on the farm.
Live-cell imaging reveals the spatiotemporal organization of endogenous RNA polymerase II phosphorylation at a single gene
Authors: Forero-Quintero Linda S. , Raymond William , Handa Tetsuya , Saxton Matthew , Morisaki Tatsuya , Kimura Hiroshi , Bertrand Edouard , Munsky Brian , Stasevich Timothy J.
Published: April 2020

The carboxyl-terminal domain of RNA polymerase II is dynamically phosphorylated during transcription in eukaryotic cells. While residue-specific phosphorylation has been mapped with exquisite spatial resolution along the 1D genome in a population of fixed cells using immunoprecipitation-based assays, the timing, kinetics, and spatial organization of phosphorylation along a single-copy gene have not yet been measured in living cells. Here, we achieve this by combining multi-color, single-molecule microscopy with fluorescent antibody-based probes that specifically bind to unphosphorylated and phosphorylated forms of endogenous RNAP2 in living cells. Applying this methodology to a single-copy HIV-1 reporter gene provides live-cell evidence for heterogeneity in the distribution of RNAP2 along the length of the gene as well as clusters of Serine 5 phosphorylated RNAP2 that form around active genes and are separated in both space and time from nascent mRNA synthesis. Computational models fit to our data determine that 5 to 40 RNAP2 cluster around the promoter of a gene during typical transcriptional bursts. Rapid imaging demonstrates nearly all RNAP2 in the cluster acquire Serine 5 phosphorylation within 3-6 seconds of arrival. Transcription from the cluster appears to be highly efficient, with nearly half of the clustered RNAP2 ultimately escaping the promoter in 1.5 minutes on average to elongate a full-length mRNA in approximately five minutes. The highly dynamic and spatially organized concentrations of RNAP2 we observe support the notion of highly efficient transcription clusters that form around promoters and contain high concentrations of RNAP2 phosphorylated at Serine 5.
3D cell culture models demonstrate a role for FGF and WNT signaling in regulation of lung epithelial cell fate and morphogenesis
Authors: Rabata Anas , Fedr Radek , Soucek Karel , Hampl Ales , Koledova Zuzana
Published: April 2020

FGF signaling plays an essential role in lung development, homeostasis, and regeneration. Several FGF ligands were detected in the developing lungs, however, their roles have not been fully elucidated. We employed mouse 3D cell culture models and imaging toex vivostudy ofa)the role of FGF ligands in lung epithelial morphogenesis andb)the interplay of FGF signaling with epithelial growth factor (EGF) and WNT signaling pathways. In non-adherent conditions, FGF signaling promoted formation of lungospheres from lung epithelial stem/progenitor cells (LSPCs). Based on their architecture, we defined three distinct phenotypes of lungospheres. Ultrastructural and immunohistochemical analyses showed that LSPCs produced more differentiated lung cell progeny. In 3D extracellular matrix, FGF2, FGF7, FGF9, and FGF10 promoted lung organoid formation with similar efficiency. However, FGF9 showed reduced capacity to promote lung organoid formation, suggesting that FGF9 has a reduced ability to sustain LSPCs survival and/or initial divisions. Analysis of lung organoid phenotypes revealed that FGF7 and FGF10 produce bigger organoids and induce organoid branching with higher frequency than FGF2 and FGF9. Higher FGF concentration and/or the use of FGF2 with increased stability and affinity to FGF receptors both increased lung organoid and lungosphere formation efficiency, respectively, suggesting that the level of FGF signaling is a crucial driver of LSPC survival and differentiation, and also lung epithelial morphogenesis. EGF signaling played a supportive but nonessential role in FGF-induced lung organoid formation. Moreover, analysis of tissue architecture and cell type composition confirmed that the lung organoids contained alveolar-like regions with cells expressing alveolar type I and type II cell markers, as well as airway-like structures with club cells and ciliated cells. WNT signaling enhanced the efficiency of lung organoid formation, but in the absence of FGF10 signaling, the organoids displayed limited branching and less differentiated phenotype. In summary, we present lung 3D cell culture models as useful tools to study the role and interplay of signaling pathways in lung development and we reveal roles for FGF ligands in regulation of mouse lung morphogenesisex vivo.
A New Dynamic Echodefecography (EDF) Established by Using BK Ultrasound 8838 Transducer and its Testing Results Comparison with X-ray Defecography
Authors: Jin Heiying , Zhang Chunxia
Published: April 2020

Objective

To describe a new dynamic echodefecography(EDF) using BK ultrasound 8838 transducer and compare its testing results with X-ray defecography.

Method

The BK 8838 ultrasound probe is used to evaluate the static 3D scan, dynamic 3D scan and dynamic 2D scan of pelvic floor and compare its testing results with X-ray defecography and defined its value to evaluate the pelvic floor disease.

Results

Fifty-seven patients were studied (24 male and 33 female). Forty seven patients were diagnosed as anismus by EDF and 46 patients were diagnosed as anismus by X-ray defecography. Sixteen patients were diagnosed as rectocele by X-ray defecography, among which eight were classified as mild(6-15mm), 4 as moderate(16-30mm) and 4 as severe(over 30mm).Fourteen patients with constipation and 2 patients with anal pain were diagnosed as intussusception by EDF, but only 3 patients were diagnosed as intussusception by X-ray defecography. Two patients with constipation were diagnosed as perineal descent by EDF and none by X-ray defecography. Two patients were diagnosed as enterocele by EDF as well as X-ray defecography.

Conclusion

The EDF established by BK 8838 ultrasound probe can show clear anatomy and real time movement of pelvic floor muscle. The EDF is more sensitive to the diagnosis of intussusception, perineal descent(PD) and anal spincter defect than X-ray defecograpgy. For anismus,rectocele and enterocele,the diagnosis results are comparable between EDF and X ray defecography. Further study is needed to determine its clinical values to evaluate the pelvic disease.
Impact of wild boar rooting on small forest‐dwelling rodents
Authors: Mori Emiliano , Ferretti Francesco , Lagrotteria Alessandro , La Greca Leonardo , Solano Emanuela , Fattorini Niccolò
Published: April 2020

Assessing impacts of wild boar on ecosystems is a research priority worldwide, with applied implications for environmental management. We evaluated whether rooting intensity by wild boar affected a rodent community in Central Italy. Rooting intensity was measured within trap transects and all around them, following standard procedures. We live‐trapped rodents in coppiced forests with a gradient of rooting intensity (including a fenced, boar‐proof, area) and evaluated relationships between abundance and rooting for two arboreal and five ground‐dwelling species. Among those, the most abundant ones were the bank vole Myodes glareolus and the yellow‐necked wood mouse Apodemus flavicollis. Rooting within and outside transects correlated to each other, as well as with the local passage rate of the wild boar, assessed through camera‐trapping. We found a negative relationship between rooting intensity and abundance of bank voles, that is, the main food resources of some predators of conservation concern. Rooting activity may trigger effects on ground‐dwelling rodents at the population level.
Significant loss of genetic diversity and accumulation of deleterious genetic variation in a critically endangered azalea species, Rhododendron boninense, growing on the Bonin Islands
Authors: Isagi Yuji , Makino Takashi , Hamabata Tomoko , Cao Ping‐Lin , Narita Satoshi , Komaki Yoshiteru , Kurita Kazuki , Naiki Akiyo , Kameyama Yoshiaki , Kondo Toshiaki , Shibabayashi Mayu
Published: April 2020

Loss of genetic diversity increases the risk of extinction of a population through inbreeding depression. In addition, the number of deleterious genetic variations, which might accumulate in a small population through genetic drift, can also make the population vulnerable. Rhododendron boninense is a critically endangered azalea species, which grows on the Bonin Islands, a UNESCO World Heritage Site; its population size in the wild dropped to only a single individual. Although a governmental program for species conservation has been conducted, no successful natural regeneration or population growth was achieved. We hypothesized that the reduced genetic diversity and accumulated deleterious genetic variation might cause the vulnerability of the species, and conducted comparative genetic and genomic analyses between R. boninense and its congeners. Genetic analysis using microsatellite markers indicated that the genetic diversity of R. boninense was ultimately low; microsatellite loci of this species were all fixed, whereas the congeners maintain high allelic diversity. Based on comprehensive transcriptome analysis, the amount of deleterious variation of R. boninense was significantly greater than that of R. amanoi. Repeated generation transitions of the small population of R. boninense on the oceanic islands is likely to have resulted in low genetic diversity as well as more deleterious variations in the genome, and we speculated that the accumulated deleterious variation might result in vulnerability of R. boninense. This study indicates the possibility of evaluating the feasibility of effective conservation programs based on the genetic diversity and the amount of accumulated deleterious variation in the genome of critically endangered species.
Rural non‐farm diversification, agricultural feminisation and women's autonomy in the farm: evidence from India
Authors: Neog Bhaskar Jyoti , Sahoo Bimal Kishore
Published: April 2020

This study contributes to the literature on the interlinkage between household non‐farm diversification (HND), agricultural feminisation and female autonomy in farming. The study uses unit‐level data from the Indian Human Development Survey for the years 2004 ‐ 2005 and 2011 ‐ 2012. The paper employs instrumental variable regression methods to study such interlinkages. The results show HND to be a significant factor contributing to the feminisation of agriculture. The study finds some evidence that the phenomenon is distress driven. Further, greater participation of women in agriculture, as well as women's access to land rights, significantly contributes to female autonomy in farm decision‐making. The results are robust to the use of alternative indicators of agricultural feminisation.
Film or Film Brand? UK Consumers’ Engagement with Films as Brands
Authors: Kohli Gurdeep Singh , Yen Dorothy , Alwi Sharifah , Gupta Suraksha
Published: April 2020

Many films are produced annually, but only a small number of films reach the state of being considered and identified by consumers as film brands. Film‐brand identification is difficult to achieve, but it leads to engagement behaviours (e.g. repetitive viewing, positive word‐of‐mouth and purchase intention of relevant merchandise/franchise). To help film‐makers better develop films as brands and benefit from their brand status, this paper takes a consumer‐centric approach to investigate how and why films are identified and engaged by consumers as brands. Using an abductive mode of reasoning, a consumer film‐brand engagement framework was developed through qualitative data collected from 35 semi‐structured interviews and then validated using survey data with 1030 participants. This consumer film‐brand engagement framework shows that film identity coherency drives film‐brand identification through the mediation effects of popularity, sequels and emotional bonding, whilst marketing effort, iconic status, franchising/merchandising activities and timelessness are highlighted as key moderators, resulting in positive brand engagement behaviour. The paper sheds new light on film‐branding literature by theoretically explaining and empirically showing a sequential and consolidated process, which consumers go through to identify and engage with films as brands, leading to several managerial and marketing implications for film‐makers.
Evaluating copper isotope fractionation in the metallurgical operational chain: An experimental approach
Authors: Klein S. , Rose T.
Published: April 2020

Until today, raw material information of copper (Cu) objects is mostly gained from impurities and trace elements and not from the Cu itself. This might be obtained using its stable isotopes. However, isotopic fingerprinting requires the absence of fractionation during the smelting process. The Cu isotope evolution during outdoor smelting experiments with Cu sulphide ore was investigated. It is shown that external materials, in particular furnace lining, clay, manure and sand, alter the isotopic composition of the smelting products. Cu isotopes are fractionated within low viscosity slag derived from matte smelting. The produced metallic Cu has a Cu isotope signature close to the ore.
Characterization of ancient building lime mortars of Anhui province, China: A multi‐analytical approach
Authors: Wei G. , Germinario C. , Grifa C. , Ma X.
Published: April 2020

The characterization of lime mortars has become of primary importance in order to obtain information about the raw ingredients and building technology of ancient masonry structures. Five different samples from Anhui province, China, representing two types of lime mortar‐based materials: joint mortars between the bricks of the city wall and lime mortar sealing a tomb coffin, were collected for analysis. Archaeological information about the samples was reported and studies into the microtextural features and mineralogical compositions of those mortars were performed via a multi‐analytical approach. The joint lime mortars between the bricks of city walls, including Mingzhongdu city wall, Mingzhongdu Xihua gate foundation, Zhengyangguan city wall and She county city wall, were found to be aerial lime mortars. The lime mortar from Nanling Tieguai Song dynasty tomb was analysed and found to be a pozzolanic mortar consisting of lime, clay, sand and cocciopesto‐like materials. The analytical results serve as a critical reference for the maintenance and restoration of ancient city walls in Anhui province, and as a starting point for searching for ancient Chinese pozzolanic mortars and technology for making those mortars.
Are Australian parents following feeding guidelines that will reduce their child's risk of dental caries?
Authors: Martin‐Kerry Jacqueline , Gussy Mark , Gold Lisa , Calache Hanny , Boak Rachel , Smith Michael , de Silva Andrea
Published: April 2020

Background

Early childhood is an important time to establish eating behaviours and taste preferences, and there is strong evidence of the association between the early introduction of sugar‐sweetened beverages and obesity and dental caries (tooth decay). Dental caries early in life predicts lifetime caries experience, and worldwide expenditure for dental caries is high.

Methods

Questionnaire data from the Splash! longitudinal birth cohort study of young children in Victoria, Australia was used to examine beverage consumption and parental feeding behaviours of young children, aiming to provide contemporary dietary data and assess consistency with the Australian dietary guidelines.

Results

From 12 months of age, the proportion of children drinking sugar‐sweetened beverages consistently increased with age (e.g. fruit juice consumed by 21.8% at 12 months and 76.7% at 4 years of age). However, the most common beverages for young children are milk and water, consistent with Australian dietary guidelines. In relation to other risk factors for dental caries, at 6 months of age children were sharing utensils, and at 12 months three quarters of carers tasted the child's food before feeding.

Conclusions

The increasing consumption of sugar‐sweetened beverages and prevalence of other risk factors for dental caries and obesity through early childhood continues to be a problem despite efforts to raise awareness of these issues with parents.
Epigenetic variations due to nutritional status in early‐life and its later impact on aging and disease
Authors: Gomez‐Verjan Juan C. , Barrera‐Vázquez Oscar S. , García‐Velázquez Lizbeth , Samper‐Ternent Rafael , Arroyo Pedro
Published: April 2020

Epigenetics refers to changes in gene function, not resulting from the primary DNA sequence, influenced by the environment. It provides a link between the molecular regulation of the genome and the environmental signals exposed during the life of individuals (including lifestyle, social behavior, development, and nutrition). Notably, early development (intrauterine or postnatal) is highly influenced by the adverse socioeconomic status that leads to malnutrition or obesity; these conditions induce changes over the fetal epigenetic programming and can be transferred by transgenerational inheritance, inducing alterations of the transcription of genes related to several metabolic and neurological processes. Moreover, obesity during pregnancy, and excessive gestational weight gain are associated with an increased risk of fatal pregnancy complications, and adverse cardio‐metabolic, respiratory and cognitive‐related outcomes of the future child. However, most of our knowledge in this field comes from experimental animal models, that partially resemble the nutritional effects of humans. In this context, nutritional effects implicated in historical famines represent valuable information about the transgenerational effects of undernutrition and stress. In the present review, we attempt to describe the most outstanding results from the most studied famines about the impact of malnutrition on the epigenome.
Endogenous α1‐antitrypsin levels in the perilymphatic fluid correlates with severity of hearing loss
Authors: El‐Saied Sabri , Schmitt Heike , Durisin Martin , Joshua Ben‐Zion , Abu Tailakh Muhammad , Prenzler Nils , Lenarz Thomas , Kaplan Daniel M. , Lewis Eli C. , Warnecke Athanasia
Published: April 2020

Objectives

To determine the levels of endogenous α1‐antitrypsin in the perilymph of patients undergoing cochlear implant (CI), and its reverse association with the severity of hearing loss.

Study Design

Retrospective study.

Setting

Tertiary care university hospital.

Participants

The study includes 38 patients undergoing CI surgery, 11 patients diagnosed with congenital deafness and 27 non‐congenital deafness, eight patients diagnosed with moderate hearing loss (N = 8; PTA = 70 dB), severe hearing loss (N = 11; PTA 70‐90 dB) and profound hearing loss (N = 19; PTA > 90 dB).

Main outcome and measure

1 to 12 μL perilymphatic fluids were collected by micropipette. α1‐antitrypsin levels were determined, and current and historic audiological parameters were obtained.

Results

The congenital and non‐congenital group exhibited AAT concentrations of 2.5 ± 1.9 × 106 LFQ and 3.2 ± 1.2 × 106 LFQ, respectively (mean ± SD; P = .38). Mean levels of α1‐antitrypsin in the perilymph fluid within the moderate group was 3.64 × 106 ± 2.1 × 106 LFQ vs 3.5 × 106 ± 1.2 × 106 in severe hearing loss (P = .81) and 2.4 × 106 ± 1.1 × 106 LFQ in the profound hearings loss group (P = .06). The difference in levels of AAT in samples from the severe hearings loss group vs the profound hearings loss group reached statistical significance (P = .04).

Conclusion

Insufficiency in α1‐antitrypsin levels in the perilymph fluid of the inner ear appears to display a relationship with the severity of hearing loss. The prospect of introducing clinical‐grade plasma‐purified α1‐antitrypsin directly onto the site of cochlear injury deserves thorough investigation.
An experimental test of the genetic consequences of population augmentation in an amphibian
Authors: Byrne Phillip G. , Silla Aimee J.
Published: April 2020

Supplementing declining populations with individuals from different populations (population augmentation) is increasingly being considered an effective way to genetically rescue threatened species. However, the general value of population augmentation remains contentious, largely because few studies have experimentally tested the genetic consequences of mixing individuals from different populations. Among amphibians, which typically display fine‐scale genetic structuring, there is a high risk that population augmentation might exacerbate population decline via outbreeding depression. Here, we use artificial fertilization techniques combined with a cross‐classified breeding design (North Carolina Type II) to investigate the fitness consequences of outbreeding in the near threatened brown toadlet (Pseudophryne bibronii). Our results revealed that outcrossed families suffered from significantly lower fertilization success, hatching success and larval survival to metamorphosis. These findings suggest that inter‐population crosses might be susceptible to genetic incompatibility and outbreeding depression. However, because genetic factors specific to one of our study populations may have caused outcrossed families to have reduced fitness, an additional breeding experiment involving full factorial crosses will be required to draw firm conclusions. Nevertheless, our findings underscore the need for caution when conducting population augmentation in amphibians. Before mixing populations that might be evolutionary distinct, we encourage conservation managers to use artificial fertilization techniques and cross‐classified breeding designs to critically assess the risk of outbreeding depression. We argue that widespread adoption of this approach will enable more rapid assessment of the risks associated with population augmentation and improve the management of threatened amphibians globally.
Role of fractal dimension in distinguishing benign from malignant endometrial clusters in liquid‐based cervical samples
Authors: Gupta Parikshaa , Gupta Nalini , Rajwanshi Arvind , Dey Pranab
Published: April 2020

Introduction

Exfoliated endometrial cells are often seen as hyperchromatic crowded groups (HCGs) in cervical samples. It is challenging for the cytopathologists to discriminate between HCGs of benign and malignant endometrial cells. Fractal dimension (FD) analysis has proved to be a useful tool in discriminating between different types of cell groups in previous studies.

Aims

This study was conducted to evaluate the utility of FD for differentiating between benign and malignant endometrial HCGs, in liquid‐based cervical samples.

Methods

Two groups of cervical samples, with subsequent histopathology, were selected: Group A: 30 cases with benign endometrial HCGs; and Group B: 39 cases with malignant endometrial HCGs. Image J, NIH and FracLac software were used for selecting and measuring the FD of the HCGs. Student t‐test was used for statistical analysis.

Results

The mean FD for benign endometrial HCGs (1.066943 ± 0.0699) was significantly lower than that of the malignant endometrial HCGs (1.086271 ± 0.05121; P = .001). Using receiver operator characteristic curve analysis, we determined that an FD cut‐off value of 1.01 would yield sensitivity of 90.3%, specificity of 26.1%, positive predictive value of 47.3% and negative predictive value of 78.6%.

Conclusion

The measurement of FD of HCGs in cervical samples can serve as a useful screening adjunct to differentiate malignant from benign HCGs, owing to its high sensitivity. However, in view of its low specificity and positive predictive value, we recommend that cases labelled as malignant by the FD value be confirmed for malignancy by other methods.
Psoriasis 2.0: Facebook as a source of disease‐related information for patients with psoriasis
Authors: Schuster Barbara , Ziehfreund Stefanie , Biedermann Tilo , Zink Alexander
Published: April 2020

Background and objectives

The Internet is a commonly used source of health‐related information. Social media allow psoriasis patients to seek and share information about their disease. However, they also involve risks such as misinformation and envy. The aim of this study was to explore the relevance and suitability of Facebook as a source of disease‐related information for patients with psoriasis.

Patients and methods

Cross‐sectional study consisting of an online survey (11/2017–01/2018). The link was published on a German information website focused on psoriasis. We also collected data about the respondents' general and disease‐related Facebook habits as well as their assessment of opportunities and risks of Facebook in the context of psoriasis.

Results

101 participants with psoriasis completed the questionnaire. Of these, 75 % reported using Facebook at least once a month, and 72 % of Facebook users stated that they had searched for disease‐related information on Facebook. Active members of psoriasis‐related Facebook groups deemed Facebook more helpful for coping with psoriasis. 60 % of Facebook users reported unreliable information and 57 % reported sales promotions regarding psoriasis when using Facebook.

Conclusions

We found that Facebook is a relevant source of information for psoriasis patients. However, the quality of information offered seems insufficient and needs to be improved.
A novel method for sexing live adult Alphitobius diaperinus
Authors: Arena Julieta Soledad , Defagó María Teresa
Published: April 2020

This work aimed to identify discriminant morphological characteristics in Alphitobius diaperinus Panzer (Coleoptera: Tenebrionidae) adults that enable live males and females to be distinguished. The method of sexing proposed here is based on dimorphism of the 8th abdominal sternite and is 100% accurate. The method allows differentiation of the sexes non‐destructively.
Structural analysis of β‐L‐arabinobiose‐binding protein in the metabolic pathway of hydroxyproline‐rich glycoproteins in Bifidobacterium longum
Authors: Miyake Masayuki , Terada Tohru , Shimokawa Michiko , Sugimoto Naohisa , Arakawa Takatoshi , Shimizu Kentaro , Igarashi Kiyohiko , Fujita Kiyotaka , Fushinobu Shinya
Published: April 2020

Bifidobacterium longum is a symbiotic human gut bacterium that has a degradation system for β‐arabinooligosaccharides, which are present in the hydroxyproline‐rich glycoproteins of edible plants. Whereas microbial degradation systems for α‐linked arabinofuranosyl carbohydrates have been extensively studied, little is understood about the degradation systems targeting β‐linked arabinofuranosyl carbohydrates. We functionally and structurally analyzed a substrate‐binding protein (SBP) of a putative ABC transporter (BLLJ_0208) in the β‐arabinooligosaccharide degradation system. Thermal shift assays and isothermal titration calorimetry revealed that the SBP specifically bound Araf‐β1,2‐Araf (β‐Ara2) with a Kd of 0.150 μm, but did not bind L‐arabinose or methyl‐β‐Ara2. Therefore, the SBP was termed β‐arabinobiose‐binding protein (BABP). Crystal structures of BABP complexed with β‐Ara2 were determined at resolutions of up to 1.78 Å. The findings showed that β‐Ara2 was bound to BABP within a short tunnel between two lobes as an α‐anomeric form at its reducing end. BABP forms extensive interactions with β‐Ara2, and its binding mode was unique among SBPs. A molecular dynamics simulation revealed that the closed conformation of substrate‐bound BABP is stable, whereas substrate‐free form can adopt a fully open and two distinct semi‐open states. The importer system specific for β‐Ara2 may contribute to microbial survival in biological niches with limited amounts of digestible carbohydrates.

Database

Atomic coordinates and structure factors (codes 6LCE and 6LCF) have been deposited in the Protein Data Bank (http://wwpdb.org/).
On the application of laser shock peening for retardation of surface fatigue cracks in laser beam‐welded AA6056
Authors: Kashaev Nikolai , Ushmaev Dmitrii , Ventzke Volker , Klusemann Benjamin , Fomin Fedor
Published: April 2020

The present study aims to investigate the extent to which the fatigue behaviour of laser beam‐welded AA6056‐T6 butt joints with an already existing crack can be improved through the application of laser shock peening. Ultrasonic testing was utilized for in situ (nondestructive) measurement of fatigue crack growth during the fatigue test. This procedure allowed the preparation of welded specimens with surface fatigue cracks with a depth of approximately 1.2 mm. The precracked specimens showed a 20% reduction in the fatigue limit compared with specimens without cracks in the as‐welded condition. Through the application of laser shock peening on the surfaces of the precracked specimens, it was possible to recover the fatigue life to the level of the specimens tested in the as‐welded condition. The results of this study show that laser shock peening is a very promising technique to recover the fatigue life of welded joints with surface cracks, which can be detected by nondestructive testing.
Gendered labour activism in the Vietnamese manufacturing industry
Authors: Chi Do Quynh , van den Broek Di
Published: April 2020

This article analyses the nature of female activism within the context of the Vietnamese export‐oriented manufacturing industry. It highlights women's potential as change agents within the industrial fabric of Vietnamese society and identifies how gendered perceptions shaped the nature of industrial action in the country. The three examples of industrial action presented here indicate that although the activism undertaken by female rank‐and‐file workers in industrial zones was informal, it played a crucial role in the progressive changes to labour relations in Vietnam. Further, it shows how women's agency was shaped by their own gender perceptions, which in turn guided their industrial strategies and outcomes.
Characterizing female patients with haemophilia A: Administrative claims analysis and medical chart review
Authors: Farej Ryan , Batt Katharine , Afonja Olubunmi , Martin Carolyn , Aubert Ronald , Carlyle Maureen , White John , Sidonio Robert F.
Published: April 2020

Aim

Haemophilia A (HA) is a male‐predominant disorder, yet women and girls can have factor VIII (FVIII) deficiency with bleeding events requiring treatment. This study aimed to identify and characterize female patients with HA.

Methods

Administrative claims dated 01 January 2012‐31 July 2016 were accessed for patients with 18 months’ coverage by commercial or Medicare Advantage with Part D insurance. Patients were included by HA diagnoses or treatments and/or bleeding‐related diagnoses or procedures, and excluded by haemophilia B or qualitative platelet disorder diagnoses. A sample of charts was examined for bleeding history, HA therapies and bleeding treatments. All‐cause healthcare utilization and costs were also described.

Results

Among 353 patients meeting initial inclusion criteria, 86 charts were procured, with 8 patients identified as having HA. Their mean age was 60 ± 17 years and most were Medicare‐insured. The mean Charlson Comorbidity Index score was 2.50 ± 2.56; the most prevalent comorbid conditions involved coagulation/haemorrhage, fluid/electrolyte balance and non‐traumatic joint disorders. Over 18 months, a mean of 54 ambulatory visits and 120 pharmacy fills were observed; mean medical costs were $86 694 and pharmacy costs were $25 396.

Conclusions

Identifying females with HA is challenging using healthcare claims, because diagnostic nomenclature is unclear for female patients treated for bleeding events. Although chart abstraction enhanced claims data, very few female patients were identified with HA. Nevertheless, even in a small sample, sizeable burden in comorbidity and healthcare use was observed. Improved nomenclature and coding for HA diagnoses for women and girls is key to improving research and treatment.
Interstitial cystitis/bladder pain syndrome: The evolving landscape, animal models and future perspectives
Authors: Akiyama Yoshiyuki , Luo Yi , Hanno Philip M , Maeda Daichi , Homma Yukio
Published: April 2020

Interstitial cystitis/bladder pain syndrome is a debilitating condition of unknown etiology characterized by persistent pelvic pain with lower urinary tract symptoms and comprises a wide variety of potentially clinically useful phenotypes with different possible etiologies. Current clinicopathological and genomic evidence suggests that interstitial cystitis/bladder pain syndrome should be categorized by the presence or absence of Hunner lesions, rather than by clinical phenotyping based on symptomatology. The Hunner lesion subtype is a distinct inflammatory disease with proven bladder etiology characterized by epithelial denudation and enhanced immune responses frequently accompanied by clonal expansion of infiltrating B cells, with potential engagement of infection. Meanwhile, the non‐Hunner lesion subtype is a non‐inflammatory disorder with little evidence of bladder etiology. It is potentially associated with urothelial malfunction and neurophysiological dysfunction, and frequently presents with somatic and/or psychological symptoms, that commonly result in central nervous sensitization. Animal models of autoimmune cystitis and neurogenic sensitization might serve as disease models for the Hunner lesion and non‐Hunner lesion subtypes, respectively. Here, we revisit the taxonomy of interstitial cystitis/bladder pain syndrome according to current research, and discuss its potential pathophysiology and representative animal models. Categorization of interstitial cystitis/bladder pain syndrome based on cystoscopy is mandatory to design optimized treatment and research strategies for each subtype. A tailored approach that specifically targets the characteristic inflammation and epithelial denudation for the Hunner lesion subtype, or the urothelial malfunction, sensitized/altered nervous system and psychosocial problems for the non‐Hunner lesion subtype, is essential for better clinical management and research progress in this complex condition.
Medical masks vs N95 respirators for preventing COVID‐19 in healthcare workers: A systematic review and meta‐analysis of randomized trials
Authors: Bartoszko Jessica J. , Farooqi Mohammed Abdul Malik , Alhazzani Waleed , Loeb Mark
Published: April 2020

Background

Respiratory protective devices are critical in protecting against infection in healthcare workers at high risk of novel 2019 coronavirus disease (COVID‐19); however, recommendations are conflicting and epidemiological data on their relative effectiveness against COVID‐19 are limited.

Purpose

To compare medical masks to N95 respirators in preventing laboratory‐confirmed viral infection and respiratory illness including coronavirus specifically in healthcare workers.

Data Sources

MEDLINE, Embase, and CENTRAL from January 1, 2014, to March 9, 2020. Update of published search conducted from January 1, 1990, to December 9, 2014.

Study Selection

Randomized controlled trials (RCTs) comparing the protective effect of medical masks to N95 respirators in healthcare workers.

Data Extraction

Reviewer pair independently screened, extracted data, and assessed risk of bias and the certainty of the evidence.

Data Synthesis

Four RCTs were meta‐analyzed adjusting for clustering. Compared with N95 respirators; the use of medical masks did not increase laboratory‐confirmed viral (including coronaviruses) respiratory infection (OR 1.06; 95% CI 0.90‐1.25; I2 = 0%; low certainty in the evidence) or clinical respiratory illness (OR 1.49; 95% CI: 0.98‐2.28; I2 = 78%; very low certainty in the evidence). Only one trial evaluated coronaviruses separately and found no difference between the two groups (P = .49).

Limitations

Indirectness and imprecision of available evidence.

Conclusions

Low certainty evidence suggests that medical masks and N95 respirators offer similar protection against viral respiratory infection including coronavirus in healthcare workers during non–aerosol‐generating care. Preservation of N95 respirators for high‐risk, aerosol‐generating procedures in this pandemic should be considered when in short supply.
Inefficient incentives and nonprice allocations: Experimental evidence from big‐box restaurants
Authors: Kapoor Sacha
Published: April 2020

Queues are puzzling because they are consistent with wasted profit in equilibrium. Standard rationales trace the puzzle to the pricing of goods. This article uses field experimental evidence from large‐scale restaurants to trace the puzzle to the pricing of labor. The customary wage contract in these settings fosters congestion and longer queues because it can encourage workers to emphasize the quality rather than quantity of output. To study this problem, the field experiment pays waiters bonuses for customer volume on days with excess demand, in addition to the tips and hourly wages they customarily receive. The experimental contract shortens queues substantially, generating surplus gains for consumers with no discernible cost in terms of perceived service quality. Workers earn more via the bonuses and because they earn more in tips. Short‐run profits increase by at least 49%. There is no discernible reduction in long‐run profit. The firm reverted to the baseline contract on excess demand days after many months of evidence, even after acknowledging the gains from the experimental contract. The evidence suggests the puzzle may partly be explained by inefficient wage contracting.
In the intimacy of the darkness: Genetic polyandry in deep‐sea luminescent lanternsharks Etmopterus spinax and Etmopterus molleri (Squaliformes, Etmopteridae)
Authors: Duchatelet Laurent , Oury Nicolas , Mallefet Jérôme , Magalon Hélène
Published: April 2020

Multiple paternity seems common within elasmobranchs. Focusing on two deep‐sea shark species, the velvet belly lanternshark (Etmopterus spinax) and the slendertail lanternshark (Etmopterus molleri) we inferred the paternity in 31 E. spinax litters from Norway (three to 18 embryos per litter) and six E. molleri litters from Japan (three to six embryos), using 21 and 10 specific microsatellites, respectively. At least two E. spinax litters were sired from multiple fathers each, with highly variable paternal skew (1:1 to 9:1). Conversely, no clear signal of genetic polyandry was found in E. molleri.
Consequences of Later‐Life Divorce and Widowhood for Adult Well‐Being: A Call for the Convalescence Model
Authors: Lin I‐Fen , Brown Susan L.
Published: April 2020

Later‐life marital dissolution increasingly occurs through divorce, not widowhood, and this is reflected in the rising rate of divorce among older adults and gains in life expectancy. Yet the consequences of later‐life divorce for individual well‐being are poorly understood. Prior work on later‐life marital dissolution focuses on bereavement, positing either a short‐term, acute grief period or chronic, unrelenting grief. The divorce literature offers an analogous bifurcated explanation in the stress‐adjustment perspective on divorce. Adjustment either occurs during a brief crisis period or is elusive as divorce creates chronic strain. After describing these entrenched conceptual models of postdissolution adjustment, we introduce a third trajectory that is emergent in recent, longitudinal studies: the convalescence model. Drawing on Pearlin's stress process perspective, we theorize why spousal loss and divorce alike may result in a protracted period of recovery. We conclude with directions for future research to encourage conceptual and methodological advancements in the field.