bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of epigenetics and chromatin structure in transcriptional regulation in malaria parasites
Authors: Abel Steven , Le Roch Karine G 
Published: March 2019

AbstractDue to the unique selective pressures and extreme changes faced by the human malaria parasite Plasmodium falciparum throughout its life cycle, the parasite has evolved distinct features to alter its gene expression patterns. Along with classical gene regulation by transcription factors (TFs), of which only one family, the AP2 TFs, has been described in the parasite genome, a large body of evidence points toward chromatin structure and epigenetic factors mediating the changes in gene expression associated with parasite life cycle stages. These attributes may be critically important for immune evasion, host cell invasion and development of the parasite in its two hosts, the human and the Anopheles vector. Thus, the factors involved in the maintenance and regulation of chromatin and epigenetic features represent potential targets for antimalarial drugs. In this review, we discuss the mechanisms in P. falciparum that regulate chromatin structure, nucleosome landscape, the 3-dimensional structure of the genome and additional distinctive features created by parasite-specific genes and gene families. We review conserved traits of chromatin in eukaryotes in order to highlight what is unique in the parasite.
CliqueMS: a computational tool for annotating in-source metabolite ions from LC-MS untargeted metabolomics data based on a coelution similarity network
Authors: Senan Oriol , Aguilar-Mogas Antoni , Navarro Miriam , Capellades Jordi , Noon Luke , Burks Deborah , Yanes Oscar , Guimerà Roger , Sales-Pardo Marta 
Published: March 2019

Abstract

Motivation
The analysis of biological samples in untargeted metabolomic studies using LC-MS yields tens of thousands of ion signals. Annotating these features is of the utmost importance for answering questions as fundamental as, e.g. how many metabolites are there in a given sample.

Results
Here, we introduce CliqueMS, a new algorithm for annotating in-source LC-MS1 data. CliqueMS is based on the similarity between coelution profiles and therefore, as opposed to most methods, allows for the annotation of a single spectrum. Furthermore, CliqueMS improves upon the state of the art in several dimensions: (i) it uses a more discriminatory feature similarity metric; (ii) it treats the similarities between features in a transparent way by means of a simple generative model; (iii) it uses a well-grounded maximum likelihood inference approach to group features; (iv) it uses empirical adduct frequencies to identify the parental mass and (v) it deals more flexibly with the identification of the parental mass by proposing and ranking alternative annotations. We validate our approach with simple mixtures of standards and with real complex biological samples. CliqueMS reduces the thousands of features typically obtained in complex samples to hundreds of metabolites, and it is able to correctly annotate more metabolites and adducts from a single spectrum than available tools.

Availability and implementation
https://CRAN.R-project.org/package=cliqueMS and https://github.com/osenan/cliqueMS.

Supplementary information
Supplementary data are available at Bioinformatics online.
The Cost-effectiveness of Human Immunodeficiency Virus (HIV) Preexposure Prophylaxis and HIV Testing Strategies in High-risk Groups in India
Authors: Kazemian Pooyan , Costantini Sydney , Kumarasamy Nagalingeswaran , Paltiel A David , Mayer Kenneth H , Chandhiok Nomita , Walensky Rochelle P , Freedberg Kenneth A 
Published: March 2019

AbstractBackgroundThe human immunodeficiency virus (HIV) epidemic in India is concentrated among 3.1 million men who have sex with men (MSM) and 1.1 million people who inject drugs (PWID), with a mean incidence of 0.9–1.4 per 100 person-years. We examined the cost-effectiveness of both preexposure prophylaxis (PrEP) and HIV testing strategies for MSM and PWID in India.MethodsWe populated an HIV microsimulation model with India-specific data and projected clinical and economic outcomes of 7 strategies for MSM/PWID, including status quo; a 1-time HIV test; routine HIV testing every 3, 6, or 12 months; and PrEP with HIV testing every 3 or 6 months. We used a willingness-to-pay threshold of US$1950, the 2017 Indian per capita gross domestic product, to define cost-effectiveness.ResultsHIV testing alone increased life expectancy by 0.07–0.30 years in MSM; PrEP added approximately 0.90 life-years to status quo. Results were similar in PWID. PrEP with 6-month testing was cost-effective for both MSM (incremental cost-effectiveness ratio [ICER], $1000/year of life saved [YLS]) and PWID (ICER, $500/YLS). Results were most sensitive to HIV incidence. PrEP with 6-month testing would increase HIV-related expenditures by US$708 million (MSM) and US$218 million (PWID) over 5 years compared to status quo.ConclusionsWhile the World Health Organization recommends PrEP with quarterly HIV testing, our analysis identifies PrEP with semiannual testing as the cost-effective HIV prevention strategy for Indian MSM and PWID. Since nationwide scale-up would require a substantial fiscal investment, areas of highest HIV incidence may be the appropriate initial targets for PrEP scale-up.
Willingness to Take Multidrug-resistant Tuberculosis (MDR-TB) Preventive Therapy Among Adult and Adolescent Household Contacts of MDR-TB Index Cases: An International Multisite Cross-sectional Study
Authors: Suryavanshi Nishi , Murrill Matthew , Gupta Amita , Hughes Michael , Hesseling Anneke , Kim Soyeon , Naini Linda , Jones Lynne , Smith Betsy , Gupte Nikhil , Dawson Rodney , Mave Vidya , Meshram Sushant , Mendoza-Ticona Alberto , Sanchez Jorge , Kumarasamy Nagalingeswaran , Comins Kyla , Conradie Francesca , Shenje Justin , Nerette Fontain Sandy , Garcia-Prats Anthony , Asmelash Aida , Nedsuwan Supalert , Mohapi Lerato , Lalloo Umesh , Cristina Garcia Ferreira Ana , Okeyo Elisha , Swindells Susan , Churchyard Gavin , Shah N Sarita 
Published: March 2019

Abstract

Background
Household contacts (HHCs) of individuals with multidrug-resistant tuberculosis (MDR-TB) are at high risk of infection and subsequent disease. There is limited evidence on the willingness of MDR-TB HHCs to take MDR-TB preventive therapy (MDR TPT) to decrease their risk of TB disease.

Methods
In this cross-sectional study of HHCs of MDR-TB and rifampicin-resistant tuberculosis (RR-TB) index cases from 16 clinical research sites in 8 countries, enrollees were interviewed to assess willingness to take a hypothetical, newly developed MDR TPT if offered. To identify factors associated with willingness to take MDR TPT, a marginal logistic model was fitted using generalized estimating equations to account for household-level clustering.

Results
From 278 MDR-TB/RR-TB index case households, 743 HHCs were enrolled; the median age of HHCs was 33 (interquartile range, 22–49) years, and 62% were women. HHC willingness to take hypothetical MDR TPT was high (79%) and remained high even with the potential for mild side effects (70%). Increased willingness was significantly associated with current employment or schooling (adjusted odds ratio [aOR], 1.83 [95% confidence interval {CI}, 1.07–3.13]), appropriate TB-related knowledge (aOR, 2.22 [95% CI, 1.23–3.99]), confidence in taking MDR TPT (aOR, 7.16 [95% CI, 3.33–15.42]), and being comfortable telling others about taking MDR TPT (aOR, 2.29 [95% CI, 1.29–4.06]).

Conclusions
The high percentage of HHCs of MDR-TB/RR-TB index cases willing to take hypothetical MDR TPT provides important evidence for the potential uptake of effective MDR TPT when implemented. Identified HHC-level variables associated with willingness may inform education and counseling efforts to increase HHC confidence in and uptake of MDR TPT.
Ciphertext-Policy Attribute-Based Encrypted Data Equality Test and Classification
Authors: Cui Yuzhao , Huang Qiong , Huang Jianye , Li Hongbo , Yang Guomin 
Published: March 2019

Abstract
Thanks to the ease of access and low expenses, it is now popular for people to store data in cloud servers. To protect sensitive data from being leaked to the outside, people usually encrypt the data in the cloud. However, management of these encrypted data becomes a challenging problem, e.g. data classification. Besides, how to selectively share data with other users is also an important and interesting problem in cloud storage. In this paper, we focus on ciphertext-policy attribute based encryption with equality test (CP-ABEET). People can use CP-ABEET to implement not only flexible authorization for the access to encrypted data, but also efficient data label classification, i.e. test of whether two encrypted data contain the same message. We construct an efficient CP-ABEET scheme, and prove its security based on a reasonable number-theoretic assumption. Compared with the only existing CP-ABEET scheme, our construction is more efficient in key generation, and has shorter attribute-related secret keys and better security.
Clinicopathological, immunophenotypic and genetic studies of mediastinal paragangliomas†
Authors: Hsu Ying-Han R , Torres-Mora Jorge , Kipp Benjamin R , Sukov William R , Jenkins Sarah M , Voss Jesse S , Barr Fritcher Emily G , Schaff Hartzell V , Cassivi Stephen D , Roden Anja C 
Published: March 2019

Abstract

OBJECTIVES
Paragangliomas have unique features in the mediastinum, in part due to their location. Because of their paucity, they have not been thoroughly investigated. We studied the clinical, pathological, immunohistochemical and molecular features of mediastinal paragangliomas.

METHODS
Immunohistochemistry, next-generation sequencing mutation panel and the Oncoscan assay were performed.

RESULTS
Twenty-four patients with mediastinal paraganglioma (7 men, 29.2%) had a median age of 45.5 years (19.8–72.2). Twenty-one (87.5%) paragangliomas were completely resected. Six (of 24, 25.0%) tumours were considered metastatic. Mitotic activity occurred in 11 (of 24, 45.8%) paragangliomas. Programmed death-ligand 1 (PD-L1) (n = 23) was expressed in 6 (26%) patients in 10% (n = 2) and 1% (n = 4) of tumour cells, respectively. SDHB expression was lost in 19 (of 22, 86.4%) cases. ATRX expression was lost in 11 (of 23, 47.8%) cases. Next-generation sequencing revealed a single pathogenic mutation in 10 (of 19) specimens including SDHB (n = 4), SDHD (n = 6), SDHC (n = 1), ATRX (n = 1), and ≥2 mutations in 2 cases [SDHC and TERT (n = 1); SDHB, ATRX and TP53 (n = 1)]. Germline mutation analysis revealed the same succinate dehydrogenase mutation (or lack thereof) as identified in the paraganglioma in 11 (of 12) cases. During a median follow-up (n = 21) of 4.8 years (0.8–14.9), 3 patients developed metastases; 4 patients died, at least 1 of disease.

CONCLUSIONS
Mediastinal paragangliomas can be associated with morbidity and mortality. Many mediastinal paragangliomas have been reported to be associated with syndromes such as multiple endocrine neoplasia, von Hippel-Lindau or succinate dehydrogenase syndrome with mutation profiles dominated by alterations in genes associated with these syndromes.
Impact of the 2017 measles outbreak on the emergency care system of a large tertiary-care teaching hospital in Italy: a retrospective analysis
Authors: Ceccarelli Giancarlo , Spagnolello Ornella , Borrazzo Cristian , Vullo Francesco , Cuomo Maria Rosaria , Milocco Mimosa , Angeletti Silvia , Ciccozzi Massimo , Mastroianni Claudio M , d’Ettorre Gabriella , Bertazzoni Giuliano 
Published: March 2019

Abstract

Background
A large outbreak of measles has spread across Italy over the year 2017. Its impact on emergency department (ED) of a tertiary-care teaching hospital and the related critical issues in public health were evaluated.

Methods
Medical records of adults discharged from January to December 2017 with diagnosis of ‘measles’ or ‘measles suspicion’ were collected and analyzed.

Results
From a total of 58 579 admissions, 218 medical records matched enrollment criteria. Measles infection was confirmed in 55.3% of patients, excluded in 26.2%, and judged as possible or probable in 18.3% of cases. Considered that the vaccination status was unknown in 89.2% of patients, the mean time spent in temporary isolation rooms (TIRs) waiting serological results was 1.7 ± 0.8 days. Measles-free patients spent a mean of 1.9 ± 0.9 days in TIRs, meaning a cumulative unnecessary time of isolation of 106.4 days. Despite most of patients were pauci-simptomatic and with a low burden of comorbidities, only 28.6% of them reported a previous out-of-hospital medical contact. Moreover an assessment of moderately critical conditions was assigned to 89.6% of cases, representing an over-valuation of the severity of the cases. Antibiotic therapy had been prescribed in 69.0% of cases and 57.7% of patients were hospitalized. We found no differences in terms of median time spent in TIRs, rate of hospitalization and antibiotic prescription between measles cases and measles-free patients.

Conclusion
A preventable high-infective disease outbreak can lead to a misapply of ED facilities in terms of unjustified admissions, time spent in TIRs, antibiotic prescription and in hospitalization rate.
Evaluating vaccination policies to accelerate measles elimination in China: a meta-population modelling study
Authors: Hao Lixin , Glasser John W , Su Qiru , Ma Chao , Feng Zhilan , Yin Zundong , Goodson James L , Wen Ning , Fan Chunxiang , Yang Hong , Rodewald Lance E , Feng Zijian , Wang Huaqing 
Published: March 2019

Abstract

Background
Measles is among the most highly infectious human diseases. By virtue of increasingly effective childhood vaccination, together with targeted supplemental immunization activities (SIAs), health authorities in the People’s Republic of China have reduced measles’ reproduction number from about 18 to 2.3. Despite substantial residual susceptibility among young adults, more in some locales than others, sustained routine childhood immunization likely would eliminate measles eventually. To support global eradication efforts, as well as expedite morbidity and mortality reductions in China, we evaluated alternative SIAs via mechanistic mathematical modelling.

Methods
Our model Chinese population is stratified by immune status (susceptible to measles infection; infected, but not yet infectious; infectious; and recovered or immunized), age (0, 1–4, 5–9, …, 65+ years) and location (31 provinces). Contacts between sub-populations are either empirical or a mixture of preferential and proportionate with respect to age and decline exponentially with distance between locations at age-dependent rates. We estimated initial conditions and most parameters from recent cross-sectional serological surveys, disease surveillance and demographic observations. Then we calculated the reproduction numbers and gradient of the effective number with respect to age- and location-specific immunization rates. We corroborated these analytical results by simulating adolescent and young adult SIAs using a version of our model in which the age-specific contact rates vary seasonally.

Results
Whereas the gradient indicates that vaccinating young adults generally is the optimal strategy, simulations indicate that a catch-up campaign among susceptible adolescent schoolchildren would accelerate elimination, with timing dependent on uptake.

Conclusions
These results are largely due to indirect effects (i.e. fewer infections than immunized people might otherwise cause), which meta-population models with realistic mixing are uniquely capable of reproducing accurately.
Loss of GLK1 transcription factor function reveals new insights in chlorophyll biosynthesis and chloroplast development
Authors: Gang Huixin , Li Ranhong , Zhao Yuming , Liu Guifeng , Chen Su , Jiang Jing 
Published: March 2019

AbstractBirch (Betula platyphylla × B. pendula) is an important tree for landscaping due to its attractive white bark and straight trunk. In this study, we characterized a T-DNA yellow-green leaf mutant, yl. We identified six insertion sites (ISs) in the mutant by genome resequencing and found a 40-kb deletion containing BpGLK1 around IS2 on chromosome 2. Complementation experiments with the yl mutant and repression of BpGLK1 in wild-type plants confirmed that BpGLK1 was responsible for the mutated phenotype. Physiological and ultrastructural analyses showed that the leaves of the yl mutant and BpGLK1-repression lines had decreased chlorophyll content and defective chloroplast development compared to the wild-type. Furthermore, the loss function of BpGLK1 also affected photosynthesis in leaves. Transcriptomics, proteomics, and ChIP-PCR analysis revealed that BpGLK1 directly interacted with the promoter of genes related to antenna proteins, chlorophyll biosynthesis, and photosystem subunit synthesis, and regulated their expression. Overall, our research not only provides new insights into the mechanism of chloroplast development and chlorophyll biosynthesis regulated by BpGLK1, but also provides new transgenic birch varieties with various levels of yellowing leaves by repressing BpGLK1 expression.
Nitric oxide and plant mineral nutrition: current knowledge
Authors: Buet Agustina , Galatro Andrea , Ramos-Artuso Facundo , Simontacchi Marcela 
Published: March 2019

AbstractPlants under conditions of essential mineral deficiency trigger signaling mechanisms that involve common components. Among these components, nitric oxide (NO) has been identified as a key participant in responses to changes in nutrient availability. Usually, nutrient imbalances affect the levels of NO in specific plant tissues, via modification of its rate of synthesis or degradation. Changes in the level of NO affect plant morphology and/or trigger responses associated with nutrient homeostasis, mediated by its interaction with reactive oxygen species, phytohormones, and through post-translational modification of proteins. NO-related events constitute an exciting field of research to understand how plants adapt and respond to conditions of nutrient shortage. This review summarizes the current knowledge on NO as a component of the multiple processes related to plant performance under conditions of deficiency in mineral nutrients, focusing on macronutrients such as nitrogen, phosphate, potassium, and magnesium, as well as micronutrients such as iron and zinc.
Similar hydraulic efficiency and safety across vesselless angiosperms and vessel-bearing species with scalariform perforation plates
Authors: Trueba Santiago , Delzon Sylvain , Isnard Sandrine , Lens Frederic 
Published: March 2019

AbstractThe evolution of xylem vessels from tracheids is put forward as a key innovation that boosted hydraulic conductivity and photosynthetic capacities in angiosperms. Yet, the role of xylem anatomy and interconduit pits in hydraulic performance across vesselless and vessel-bearing angiosperms is incompletely known, and there is a lack of functional comparisons of ultrastructural pits between species with different conduit types. We assessed xylem hydraulic conductivity and vulnerability to drought-induced embolism in 12 rain forest species from New Caledonia, including five vesselless species, and seven vessel-bearing species with scalariform perforation plates. We measured xylem conduit traits, along with ultrastructural features of the interconduit pits, to assess the relationships between conduit traits and hydraulic efficiency and safety. In spite of major differences in conduit diameter, conduit density, and the presence/absence of perforation plates, the species studied showed similar hydraulic conductivity and vulnerability to drought-induced embolism, indicating functional similarity between both types of conduits. Interconduit pit membrane thickness (Tm) was the only measured anatomical feature that showed a relationship to significant vulnerability to embolism. Our results suggest that the incidence of drought in rain forest ecosystems can have similar effects on species bearing water-conducting cells with different morphologies.
Properties of ionized outflows in MaNGA DR2 galaxies
Authors: Rodríguez del Pino Bruno , Arribas Santiago , Piqueras López Javier , Villar-Martín Montserrat , Colina Luis 
Published: March 2019

ABSTRACT
We present the results from a systematic search and characterization of ionized outflows in nearby galaxies using the data from the second Data Release of the Mapping Nearby Galaxies at Arecibo Point Observatory (MaNGA) Survey (DR2; &gt;2700 galaxies, z ≤ 0.015). Using the spatially resolved spectral information provided by the MANGA data, we have identified ∼5200 H α-emitting regions across the galaxies and searched for signatures of ionized outflows. We find evidence for ionized outflows in 105 regions from 103 galaxies, roughly 7 per cent of all the H α-emitting galaxies identified in this work. Most of the outflows are nuclear, with only two cases detected in off-nuclear regions. Our analysis allows us to study ionized outflows in individual regions with star formation rates (SFRs) down to ∼0.01 M⊙ yr−1, extending the ranges probed by previous works. The kinematics of the outflowing gas is strongly linked to the type of ionization mechanism: regions characterized by low-ionization emission region emission (LIER) host the outflows with more extreme kinematics (FWHMbroad ∼ 900 km s−1), followed by those originated in active galactic nuclei (550 km s−1), ‘Intermediate’ (450 km s−1), and star-forming (350 km s−1) regions. Moreover, in most of the outflows we find evidence for gas ionized by shocks. We find a trend for higher outflow kinematics towards larger stellar masses of the host galaxies but no significant variation as a function of star formation properties within the SFR regime we probe (∼0.01–10 M⊙ yr−1). Our results also show that the fraction of outflowing gas that can escape from galaxies decreases towards higher dynamical masses, contributing to the preservation of the mass–metallicity relation by regulating the amount of metals in galaxies. Finally, assuming that the extensions of the outflows are significantly larger than the individual star-forming regions, as found in previous works, our results also support the presence of star formation within ionized outflows, as recently reported by Maiolino et al. (2017) and Gallagher et al. (2018).