bluuebunny/crossref_metadata_2025_split huggingface dataset:
Age‐stratified anti‐HAV positivity in Pune, India after two decades: Has voluntary vaccination impacted overall exposure to HAV?
Authors: Arankalle Vidya , Tiraki Divya , Kulkarni Ruta , Palkar Sonali , Malshe Nandini , Lalwani Sanjay , Mishra Akhilesh 
Published: February 2019

SummaryThe degree of transmission of hepatitis A virus (HAV) is inversely proportional to the socioeconomic status of a community. Serosurveys conducted at Pune, India during 1982‐98 documented significant reduction in HAV exposure of paediatric, higher socioeconomic status (HSS) population. Anti‐HAV positivity (ELISA) in age‐stratified Pune population representing HSS and lower middle socioeconomic status (LMSS) (n = 1065) and infants till the age of 15 months (n = 690) was determined in 2017. Anti‐HAV positivity in the LMSS population decreased significantly in 2017 while an increase was seen in the HSS category. The surprising rise in anti‐HAV positivity in the HSS population reflected vaccine‐ and infection‐induced antibodies while only infection‐induced antibodies were present in the LMSS category. Lowest antibody prevalence in infants was at 12 months, the recommended age for hepatitis A vaccination. Improved hygiene and selective immunization practices impacted HAV exposure of the LMSS population. The data emphasize the need for hepatitis A vaccination irrespective of socioeconomic status.
Low recurrence rate of hepatocellular carcinoma following ledipasvir and sofosbuvir treatment in a real‐world chronic hepatitis C patients cohort
Authors: Idilman Ramazan , Demir Mehmet , Aladag Murat , Erol Cihan , Cavus Bilger , Iliaz Raim , Koklu Hayrettin , Cakaloglu Yilmaz , Sahin Memduh , Ersoz Galip , Koksal İftihar , Karasu Zeki , Ozgenel Meric , Turan İlker , Gunduz Feyza , Ataseven Huseyin , Akdogan Meral , Kiyici Murat , Koksal Aydın Seref , Akhan Sila , Gunsar Fulya , Tabak Fehmi , Kaymakoglu Sabahattin , Akarca Ulus S ,   Early Access Program (EAP) Study Group
Published: February 2019

SummaryThe aims of the present study were to evaluate the efficacy and tolerability of ledipasvir/sofosbuvir (LDV/SOF) with or without ribavirin in the treatment of chronic hepatitis C (CHC) in patients with advanced liver disease and to analyse whether the use of LDV/SOF treatment is associated with a new occurrence of hepatocellular carcinoma (HCC) during and after LDV/SOF treatment. The Turkish Early Access Program provided LDV/SOF treatment to a total of 200 eligible CHC patients with advanced liver disease. The median follow‐up period was 22 months. All patients were Caucasian, 84% were infected with genotype 1b, and 24% had a liver transplantation before treatment. The sustained virological response (SVR12) was 86.0% with ITT analysis. SVR12 was similar among patients with Child‐Pugh classes A, B and C disease and transplant recipients. From baseline to SVR12, serum ALT level and MELD score were significantly improved (P < 0.001). LDV/SOF treatment was generally well tolerated. Only one patient developed a new diagnosed HCC. Seventeen of the 35 patients, who had a history of previous HCC, developed HCC recurrence during the LDV/SOF treatment or by a median follow‐up of 6 months after treatment. HCC recurrence was less commonly observed in patients who received curative treatment for HCC compared with those patients who received noncurative treatment (P = 0.007). In conclusion, LDV/SOF with or without ribavirin is an effective and tolerable treatment in CHC patients with advanced liver disease. Eradication is associated with improvements in liver function and a reduced risk of developing a new occurrence of HCC.
Is genomic diversity a useful proxy for census population size? Evidence from a species‐rich community of desert lizards
Authors: Grundler Maggie R. , Singhal Sonal , Cowan Mark A. , Rabosky Daniel L. 
Published: February 2019

AbstractSpecies abundance data are critical for testing ecological theory, but obtaining accurate empirical estimates for many taxa is challenging. Proxies for species abundance can help researchers circumvent time and cost constraints that are prohibitive for long‐term sampling. Under simple demographic models, genetic diversity is expected to correlate with census size, such that genome‐wide heterozygosity may provide a surrogate measure of species abundance. We tested whether nucleotide diversity is correlated with long‐term estimates of abundance, occupancy and degree of ecological specialization in a diverse lizard community from arid Australia. Using targeted sequence capture, we obtained estimates of genomic diversity from 30 species of lizards, recovering an average of 5,066 loci covering 3.6 Mb of DNA sequence per individual. We compared measures of individual heterozygosity to a metric of habitat specialization to investigate whether ecological preference exerts a measurable effect on genetic diversity. We find that heterozygosity is significantly correlated with species abundance and occupancy, but not habitat specialization. Demonstrating the power of genomic sampling, the correlation between heterozygosity and abundance/occupancy emerged from considering just one or two individuals per species. However, genetic diversity does no better at predicting abundance than a single day of traditional sampling in this community. We conclude that genetic diversity is a useful proxy for regional‐scale species abundance and occupancy, but a large amount of unexplained variation in heterozygosity suggests additional constraints or a failure of ecological sampling to adequately capture variation in true population size.
The bare necessities: Uncovering essential and condition‐critical genes with transposon sequencing
Authors: Shields Robert C. , Jensen Paul A. 
Published: February 2019

AbstractQuerying gene function in bacteria has been greatly accelerated by the advent of transposon sequencing (Tn‐seq) technologies (related Tn‐seq strategies are known as TraDIS, INSeq, RB‐TnSeq, and HITS). Pooled populations of transposon mutants are cultured in an environment and next‐generation sequencing tools are used to determine areas of the genome that are important for bacterial fitness. In this review we provide an overview of Tn‐seq methodologies and discuss how Tn‐seq has been applied, or could be applied, to the study of oral microbiology. These applications include studying the essential genome as a means to rationally design therapeutic agents. Tn‐seq has also contributed to our understanding of well‐studied biological processes in oral bacteria. Other important applications include in vivo pathogenesis studies and use of Tn‐seq to probe the molecular basis of microbial interactions. We also highlight recent advancements in techniques that act in synergy with Tn‐seq such as clustered regularly interspaced short palindromic repeats (CRISPR) interference and microfluidic chip platforms.
Activity‐based proteomics reveals nine target proteases for the recombinant protein‐stabilizing inhibitor SlCYS8 in Nicotiana benthamiana
Authors: Jutras Philippe V. , Grosse‐Holz Friederike , Kaschani Farnusch , Kaiser Markus , Michaud Dominique , van der Hoorn Renier A.L. 
Published: February 2019

SummaryCo‐expression of protease inhibitors like the tomato cystatin SlCYS8 is useful to increase recombinant protein production in plants, but key proteases involved in protein proteolysis are still unknown. Here, we performed activity‐based protein profiling to identify proteases that are inhibited by SlCYS8 in agroinfiltrated Nicotiana benthamiana. We discovered that SlCYS8 selectively suppresses papain‐like cysteine protease (PLCP) activity in both apoplastic fluids and total leaf extracts, while not affecting vacuolar‐processing enzyme and serine hydrolase activity. A robust concentration‐dependent inhibition of PLCPs occurred in vitro when purified SlCYS8 was added to leaf extracts, indicating direct cystatin–PLCP interactions. Activity‐based proteomics revealed that nine different Cathepsin‐L/‐F‐like PLCPs are strongly inhibited by SlCYS8 in leaves. By contrast, the activity of five other Cathepsin‐B/‐H‐like PLCPs, as well as 87 Ser hydrolases, was unaffected by SlCYS8. SlCYS8 expression prevented protein degradation by inhibiting intermediate and mature isoforms of granulin‐containing proteases from the Resistant‐to‐Desiccation‐21 (RD21) PLCP subfamily. Our data underline the key role of endogenous PLCPs on recombinant protein degradation and reveal candidate proteases for depletion strategies.
Botulinum toxin A for pain reduction in pediatric patients with Parry‐Romberg syndrome
Authors: Mishra Kriti , Sood Arun , Smidt Aimee , Price Harper N. 
Published: February 2019

AbstractParry‐Romberg syndrome (PRS) is characterized by hemiatrophy of facial structures, including skin, subcutaneous fat, muscle, bone, and cartilage. Complications associated with PRS include headaches, seizures, and chronic facial pain. Protocol for the treatment of chronic facial pain is not clear; reports on the use of botulinum toxin A injections for pain reduction in adults but not in the pediatric/adolescent population are available. Here, we discuss two pediatric PRS cases in which treatment with botulinum toxin A injections reduced or eliminated facial pain.
Melatonin attenuates the detrimental effects of UVA irradiation in human dermal fibroblasts by suppressing oxidative damage and MAPK/AP‐1 signal pathway in vitro
Authors: Koçtürk Semra , Yüksel Egrilmez Mehtap , Aktan Şebnem , Oktay Gülgün , Resmi Halil , Şimşek Keskin Hatice , Sert Serdar Belgin , Erkmen Tugba , Güner Akdogan Gül , Özkan Şebnem 
Published: February 2019

SummaryBackgroundPeople living in Mediterranean countries are mostly exposed to solar ultraviolet (UV) radiation that damages skin and results in photoaging which involves activation of epidermal growth factor receptor (EGFR) and downstream signal transduction through mitogen‐activated protein kinases (MAPKs) in fibroblasts. Generation of reactive oxygen/nitrogen species by UV radiation is also critical for EGFR and MAPKs activation. MAPKs are responsible for activation of AP‐1 subunits in the nucleus which induce matrix metalloproteinases. Melatonin, along with its metabolites, are known to be the most effective free radical scavenger and protective agent due to its ability to react with various radicals, lipophilic/hydrophilic structures.ObjectivesIn this study, we investigated the effects of melatonin on UVA‐irradiated primary human dermal fibroblasts (HDFs) by following the alteration of molecules from cell membrane to the nucleus and oxidative/nitrosative damage status of the cells in a time‐dependent manner which have not been clearly elucidated yet.MethodsTo mimic UVA dosage in Mediterranean countries, HDFs were exposed to UVA with sub‐cytotoxic dosage (20 J/cm2) after pretreatment with melatonin (1 μmol/L) for 1 hour. Changes in the activation of the molecules and oxidative/nitrosative stress damage were analyzed at different time points.ResultsOur results clearly show that melatonin decreases UVA‐induced oxidative/nitrosative stress damage in HDFs. It also suppresses phosphorylation of EGFR, activation of MAPK/AP‐1 signal transduction pathway and production of matrix metalloproteinases in a time‐dependent manner.ConclusionMelatonin can be used as a protective agent for skin damage against intracellular detrimental effects of relatively high dosage of UVA irradiation.
Technological advances in home non‐invasive ventilation monitoring: Reliability of data and effect on patient outcomes
Authors: Borel Jean‐Christian , Palot Alain , Patout Maxime 
Published: February 2019

ABSTRACTHome non‐invasive mechanical ventilation (NIV) has become a well‐established treatment for patients with chronic hypercapnic respiratory failure. NIV monitoring has been developed to evaluate the effectiveness of mechanical ventilation on patient outcomes, with built‐in systems providing data on compliance, leaks and respiratory parameters. Although these data seem intuitively useful, two main concerns have been raised in the literature: (i) are they reliable and (ii) to what extent does their use improve patient outcomes. These two concerns are currently relevant since the very recent development of telemonitoring provides the possibility of adjusting ventilator settings remotely, based on the longitudinal assessment of NIV parameters and respiratory variables provided by the system. This may influence the future management strategies of health organizations for patients under home NIV. This narrative review describes technological advances in patient monitoring using home mechanical ventilation with a main focus on data provided by built‐in NIV monitoring systems. The use of these systems is discussed, including their advantages and limitations in different clinical situations, and perspectives for long‐term patient monitoring are discussed.
TF‐Test Quantified: a new technique for diagnosis of Schistosoma mansoni eggs
Authors: Santos Bianca Martins , Soares Felipe Augusto , Rosa Stefany Laryssa , Gomes Denise da Conceição Ferreira , Oliveira Bruno César Miranda , Peixinho Alan Zanoni , Suzuki Celso Tetsuo Nagase , Bresciani Katia Denise Saraiva , Falcão Alexandre Xavier , Gomes Jancarlo Ferreira 
Published: February 2019

AbstractObjectivesLaboratory diagnosis of Schistosoma mansoni eggs is routinely performed by conventional quantitative techniques through the parasitological examination of human faeces. However, the diagnostic sensitivity of this type of exam varies from low to moderate. We aimed to develop a new parasitological technique called TF‐Test Quantified (TFT‐Quant), for the quantitative detection of S. mansoni eggs in human faeces.MethodsFour study stages were performed using 43 mice infected by S. mansoni cercariae. These experiments allowed the definition of an operational protocol for TFT‐Quant and a comparison of this new technique to the conventional Helm‐Teste technique.ResultsThe results show a good diagnostic efficacy of TFT‐Quant, which reached 100% in sensitivity and specificity, indicating an ‘Almost Perfect’ Kappa (k) agreement.ConclusionsThis new technique provided a quantitative gain in the detection of S. mansoni eggs, largely free of faecal debris. The next stage of this study is the field validation of the TFT‐Quant technique with the use of human faecal samples from an endemic region for mansonic schistosomiasis in Brazil (Microregion Jequitinhonha, State of Minas Gerais). In parallel to this validation, computational algorithms will be developed to allow the automated quantitative diagnosis of S. mansoni eggs.
The histone variant H2A.Z and chromatin remodeler BRAHMA act coordinately and antagonistically to regulate transcription and nucleosome dynamics in Arabidopsis
Authors: Torres E. Shannon , Deal Roger B. 
Published: February 2019

SummaryPlants adapt to environmental changes by regulating transcription and chromatin organization. The histone H2A variant H2A.Z and the SWI2/SNF2 ATPase BRAHMA (BRM) have overlapping roles in positively and negatively regulating environmentally responsive genes in Arabidopsis, but the extent of this overlap was uncharacterized. Both factors have been associated with various changes in nucleosome positioning and stability in different contexts, but their specific roles in transcriptional regulation and chromatin organization need further characterization. We show that H2A.Z and BRM co‐localize at thousands of sites, where they interact both cooperatively and antagonistically in transcriptional repression and activation of genes involved in development and responses to environmental stimuli. We identified eight classes of genes that show distinct relationships between H2A.Z and BRM with respect to their roles in transcription. These include activating and silencing transcription both redundantly and antagonistically. We found that H2A.Z contributes to a range of different nucleosome properties, while BRM stabilizes nucleosomes where it binds and destabilizes or repositions flanking nucleosomes. We also found that, at many genes regulated by both BRM and H2A.Z, both factors overlap with binding sites of the light‐regulated transcription factor FAR1‐Related Sequence 9 (FRS9) and that a subset of these FRS9 binding sites are dependent on H2A.Z and BRM for accessibility. Collectively, we comprehensively characterized the antagonistic and cooperative contributions of H2A.Z and BRM to transcriptional regulation, and illuminated several interrelated roles in chromatin organization. The variability observed in their individual functions implies that both BRM and H2A.Z have more context‐dependent roles than previously assumed.
Analysis of Movement Quality in Full-Body Physical Activities
Authors: Niewiadomski Radoslaw , Kolykhalova Ksenia , Piana Stefano , Alborno Paolo , Volpe Gualtiero , Camurri Antonio 
Published: February 2019

Full-body human movement is characterized by fine-grain expressive qualities that humans are easily capable of exhibiting and recognizing in others’ movement. In sports (e.g., martial arts) and performing arts (e.g., dance), the same sequence of movements can be performed in a wide range of ways characterized by different qualities, often in terms of subtle (spatial and temporal) perturbations of the movement. Even a non-expert observer can distinguish between a top-level and average performance by a dancer or martial artist. The difference is not in the performed movements--the same in both cases--but in the “quality” of their performance.
In this article, we present a computational framework aimed at an automated approximate measure of movement quality in full-body physical activities. Starting from motion capture data, the framework computes low-level (e.g., a limb velocity) and high-level (e.g., synchronization between different limbs) movement features. Then, this vector of features is integrated to compute a value aimed at providing a quantitative assessment of movement quality approximating the evaluation that an external expert observer would give of the same sequence of movements.

Next, a system representing a concrete implementation of the framework is proposed. Karate is adopted as a testbed. We selected two different katas (i.e., detailed choreographies of movements in karate) characterized by different overall attitudes and expressions (aggressiveness, meditation), and we asked seven athletes, having various levels of experience and age, to perform them. Motion capture data were collected from the performances and were analyzed with the system. The results of the automated analysis were compared with the scores given by 14 karate experts who rated the same performances. Results show that the movement-quality scores computed by the system and the ratings given by the human observers are highly correlated (Pearson’s correlations
r
= 0.84,
p
= 0.001 and
r
= 0.75,
p
= 0.005).
The Current Status of Accessibility in Mobile Apps
Authors: Yan Shunguo , Ramachandran P. G. 
Published: February 2019

This study evaluated the status of accessibility in mobile apps by investigating the graphical user interface (GUI) structures and conformance to accessibility guidelines of 479 Android apps in 23 business categories from Google Play. An automated tool, IBM Mobile Accessibility Checker (MAC), was used to identify the accessibility issues, which were categorized as a violation (V), potential violation (PV), or warning (W). The results showed 94.8%, 97.5%, and 66.4% of apps studied contained issues related to V, PV, or W, respectively. Five widget categories (TextView, ImageView, View, Button, and ImageButton) were used to create 92% of the total number of the GUI elements and caused 89%, 78%, and 86% of V, PV, and W, respectively. These accessibility issues were mainly caused by lack of element focus, missing element description, low text color contrast, lack of sufficient spacing between elements, and less than minimum sizes of text fonts and elements. Together, these accessibility issues accounted for 97.0%, 77.8%, and 94.5% of V, PV, and W, respectively.
This study proposed coverage measures to estimate the percentage of accessibility issues identified by an automated tool. The result showed that MAC, on average, identified about 67% of accessibility issues in mobile apps.
Two new accessibility conformance measures were proposed in this study: inaccessible element rate (IAER) and accessibility issue rate (AIR). IAER estimates the percentage of GUI elements that are inaccessible. AIR calculates the percentage of the actual number of accessibility issues relative to the maximum number of accessibility issues. Average IAER and AIR scores were 27.3%, 19.9%, 6.3% and 20.7%, 15.0%, 5.4% for V, PV, and W, respectively, for the studied apps. The IAER score showed approximately 30% of the GUI elements had accessibility issues, and the AIR score indicated that 15% of the accessibility issues remained and need to be fixed to make the apps accessible.
Comparison of polyglycolic acid acupoint catgut embedding therapy monofilaments for a juvenile pseudo-myopia surface modified by two processing methods
Authors: Fu Shaoju , Lu Yao , Zhang Peihua 
Published: February 2019

Polyglycolic acid (PGA) acupoint catgut embedding therapy (ACET) monofilament has been heavily used for juvenile pseudopia in the recent years. However, poor hydrophilicity and cytocompatibility have limited its development and wide practical application. In this context, this work is aimed to develop ACET materials with good comprehensive properties by surface modifications.  Two different methods, namely ultrasound and plasma technologies, were selected to modify the surface property of PGA monofilaments to improve their wetting and compatibility with tissues, while minimizing degradation of the fibers. Moreover, the effects of these two processing methods on the structure, mechanical and in vitro properties of PGA were fully characterized.  Both the ultrasound and plasma modified samples were observed to have a larger surface roughness, and their weights and diameters were decreased. Samples P-PGA1 (76.2° ± 1.4°) and P-PGA2 (73.5° ± 1.9°) exhibited the smallest contact angle values among their groups, respectively. The tensile properties and bending stiffness values of modified PGA decreased slightly, while their swelling ratios were greatly improved. All the prepared samples presented no toxicity (more than 75% cells being viable), and their cell attachment ratios (cultured for 48 h) were also enhanced.  In summary, plasma and ultrasound modified PGA showed better hydrophilicity and in vitro properties compared to that of unmodified samples, while retaining the other excellent characteristics. These findings illustrated that the two processing methods were feasible and warrant further study in the application of ACET materials.