bluuebunny/crossref_metadata_2025_split huggingface dataset:
Narrow‐band UVB phototherapy and psoralen–ultraviolet A photochemotherapy in the treatment of cutaneous mastocytosis: a study in 20 patients
Authors: Brazzelli Valeria , Grassi Sara , Merante Serena , Grasso Vincenzo , Ciccocioppo Rachele , Bossi Grazia , Borroni Giovanni 
Published: June 2016

SummaryBackgroundIn mastocytosis, the skin is almost invariably involved, and cutaneous symptoms deeply affect patients' quality of life.MethodsA retrospective observational analysis of patients affected by cutaneous mastocytosis (CM) and indolent systemic mastocytosis (ISM) treated with phototherapy/photochemotherapy (PUVA or NB‐UVB) has been conducted. For each patient, total numbers of PUVA or NB‐UVB exposures, the cumulative UV dose (J/cm2), serum tryptase profile, and pruritus, before and after treatment, according to the visual analogue scale (VAS) were considered. Skin lesions of each patient were assessed, before and after treatment, according to a cutaneous scale score.ResultsTwenty patients affected by CM and ISM were studied; in particular, 10 patients received NB‐UVB therapy, and other 10 patients received PUVA. A statistically significant mean reduction of pruritus in both groups (P < 0.01) was observed. The number of treatments necessary to obtain symptom relief was significantly lower in the PUVA group, but the mean exposure dose was significantly higher, if compared to the NB‐UVB group. Serum tryptase levels showed a downward trend. The cutaneous score improved in both groups.LimitationsThis study was a retrospective study with a small sample size and without a control group.ConclusionThis work provides evidence that both NB‐UVB and PUVA represent a safe and useful second‐line therapy of the cutaneous symptoms in mastocytosis.
Pyrodiversity—why managing fire in food webs is relevant to restoration ecology
Authors: Bowman David M. J. S. , Legge Sarah 
Published: June 2016

AbstractThe manipulation of landscape fire to maintain biodiverse, self‐sustaining ecosystems in flammable landscapes is rarely considered by restoration ecologists. Fire regimes can interact with ecological processes, food webs, and biodiversity in complex ways (here called pyrodiversity) and understanding these complexities could be used to promote restoration and resilience. We illustrate this using an example from northern Australia. Understanding and using pyrodiversity in ecological restoration programs will be intellectually and financially challenging. In Australia, the considerable technical and financial resources of the mining industry could support such restoration programs, yet redirecting these resources from the current narrow focus on restoring native vegetation cover at the mine‐affected site requires overcoming entrenched attitudes among policymakers and restoration ecologists.
Ore Genesis of the Lunwei Granite‐Related Scheelite Deposit in the Wuyi Metallogenic Belt, Southeast China: Constraints from Geochronology, Fluid Inclusions, and H–O–S Isotopes
Authors: Wang Hui , Feng Chengyou , Zhao Yiming , Zhang Mingyu , Chen Runsheng , Chen Jinliang 
Published: June 2016

AbstractA granite‐related scheelite deposit has been recently discovered in the Wuyi metallogenic belt of southeast China. The veinlet–disseminated scheelite occurs mainly in the inner and outer contact zones of the porphyritic biotite granite, spatially associated with potassic feldspathization and silicification. Re–Os dating of molybdenite intergrowths with scheelite yield a well‐constrained isochron age of 170.4 ± 1.2 Ma, coeval with the LA–MC–ICP–MS concordant zircon age of porphyritic biotite granite (167.6 ± 2.2 Ma), indicating that the Lunwei W deposit was formed in the Middle Jurassic (~170 Ma). We identify three stages of ore formation (from early to late): (I) the quartz–K‐feldspar–scheelite stage; (II) the quartz–polymetallic sulfide stage; and (III) the quartz–carbonate stage. Based on petrographic observations and microthermometric criteria, the fluid inclusions in the scheelite and quartz are determined to be mainly aqueous two‐phase (liquid‐rich and gas‐rich) fluid inclusions, with minor gas‐pure and CO2‐bearing fluid inclusions. Ore‐forming fluids in the Lunwei W deposit show a successive decrease in temperature and salinity from Stage I to Stage III. The homogenization temperature decreases from an average of 299 °C in Stage I, through 251 °C in Stage II, to 212 °C in Stage III, with a corresponding change in salinity from an average of 5.8 wt.%, through 5.2 wt.%, to 3.4 wt.%. The ore‐forming fluids have intermediate to low temperatures and low salinities, belonging to the H2O–NaCl ± CO2 system. The δ18OH2O values vary from 1.8‰ to 3.3‰, and the δDV‐SMOW values vary from –66‰ to –76‰, suggesting that the ore‐forming fluid was primarily of magmatic water mixed with various amounts of meteoric water. Sulfur isotope compositions of sulfides (δ34S ranging from –1.1‰ to +2.4‰) and Re contents in molybdenite (1.45–19.25 µg/g, mean of 8.97 µg/g) indicate that the ore‐forming materials originated mainly in the crust. The primary mechanism for mineral deposition in the Lunwei W deposit was a decrease in temperature and the mixing of magmatic and meteoric water. The Lunwei deposit can be classified as a porphyry‐type scheelite deposit and is a product of widespread tungsten mineralization in South China. We summarize the geological characteristics of typical W deposits (the Xingluokeng, Shangfang, and Lunwei deposits) in the Wuyi metallogenic belt and suggest that porphyry and skarn scheelite deposits should be considered the principal exploration targets in this area.
Randomization-based Instrumental Variables methods for Binary outcomes with an Application to the ‘IMPROVE’ trial
Authors: Keele Luke , Small Dylan , Grieve Richard 
Published: June 2016

SummaryIn randomized controlled trials with non-adherence, instrumental variable (IV) methods are frequently used to report the complier average causal effect. With binary outcomes, many of the available IV estimation methods impose distributional assumptions. We develop a randomization-inference-based method of IV estimation for binary outcomes. The method is non-parametric and is based on Fisher's exact test, and estimates can be easily calculated from a set of 2×2 or 2×2×2 tables. Although we retain the standard IV identification assumptions for confidence regions and point estimates, the IV estimand under randomization inference is sample specific and does not assume that the randomized controlled trials participants are a random sample from the target population. We illustrate the method with the ‘IMPROVE’ trial that compares emergency endovascular versus open surgical repair for patients with ruptured aortic aneurysms.
A hybrid approach to modeling territorial control in violent armed conflicts
Authors: Tao Ran , Strandow Daniel , Findley Michael , Thill Jean‐Claude , Walsh James 
Published: June 2016

AbstractTerritorial control is central to the understanding of violent armed conflicts, yet reliable and valid measures of this concept do not exist. We argue that geospatial analysis provides an important perspective to measure the concept. In particular, measuring territorial control can be seen as an application of calculating service areas around points of control. The modeling challenge is acute for areas with limited road infrastructure, where no complete network is available to perform the analysis, and movements largely occur off road. We present a new geospatial approach that applies network analysis on a hybrid transportation network with both actual road data and hexagon‐fishnet‐based artificial road data representing on‐road and off‐road movements, respectively. Movement speed or restriction can be readily adjusted using various input data. Simulating off‐road movement with hexagon‐fishnet‐based artificial road data has a number of advantages including scalability to small or large study areas and flexibility to allow all‐directional travel. We apply this method to measuring territorial control of armed groups in Sub‐Saharan Africa where inferior transport infrastructure is the norm. Based on the Uppsala Conflict Data Program's (UCDP) Georeferenced Event Data (GED) as well as spatial data on terrain, population locations, and limited transportation networks, we enhance the delineation of the specific areas directly controlled by each warring party during civil wars within a given travel time.
Crowdsensing smart ambient environments and services
Authors: Regalia Blake , McKenzie Grant , Gao Song , Janowicz Krzysztof 
Published: June 2016

AbstractWhether it be Smart Cities, Ambient Intelligence, or the Internet of Things, current visions for future urban spaces share a common core, namely the increasing role of distributed sensor networks and the on‐demand integration of their data to power real‐time services and analytics. Some of the greatest hurdles to implementing these visions include security risks, user privacy, scalability, the integration of heterogeneous data, and financial cost. In this work, we propose a crowdsensing mobile‐device platform that empowers citizens to collect and share information about their surrounding environment via embedded sensor technologies. This approach allows a variety of urban areas (e.g., university campuses, shopping malls, city centers, suburbs) to become equipped with a free ad‐hoc sensor network without depending on proprietary instrumentation. We present a framework, namely the GeoTracer application, as a proof‐of‐concept to conduct multiple experiments simulating use‐case scenarios on a university campus. First, we demonstrate that ambient sensors (e.g. temperature, pressure, humidity, magnetism, illuminance, and audio) can help determine a change in environment (e.g. moving from indoors to outdoors, or floor changes inside buildings) more accurately than typical positioning technologies (e.g. global navigation satellite system, Wi‐Fi, etc.). Furthermore, each of these sensors contributes a different amount of data to detecting events. for example, illuminance has the highest information gain when trying to detect changes between indoors and outdoors. Second, we show that through this platform it is possible to detect and differentiate place types on a university campus based on inferences made through ambient sensors. Lastly, we train classifiers to determine the activities that a place can afford at different times (e.g. good for studying or not, basketball courts in use or empty) based on sensor‐driven semantic signatures.
Map algebra based analysis for directed flow networks
Authors: She Jiangfeng , Li Xingong 
Published: June 2016

AbstractBased on the concept of map algebra, this research developed a network neighborhood analysis framework for directed flow networks. The analysis framework has two components: the first component defines how neighborhoods are delineated on networks and the second component calculates various statistics within the neighborhoods. The power and value of the analysis framework lie in its capability to delineate versatile network neighborhoods and its flexibility in calculating various statistics within the neighborhoods. It extends the raster map algebra to networks and provides a consistent analysis framework for the raster, vector, and network data models. Using a small section of the National Hydrography Dataset (NHD) networks, a prototype Web application is implemented to experiment and demonstrate the concept and uses of the analysis framework.
Analysis of transposable elements and organellar DNA in male and female genomes of a species with a huge Y chromosome reveals distinct Y centromeres
Authors: Sousa Aretuza , Bellot Sidonie , Fuchs Jörg , Houben Andreas , Renner Susanne S. 
Published: June 2016

SummaryFew angiosperms have distinct Y chromosomes. Among those that do are Silene latifolia (Caryophyllaceae), Rumex acetosa (Polygonaceae) and Coccinia grandis (Cucurbitaceae), the latter having a male/female difference of 10% of the total genome (female individuals have a 0.85 pg genome, male individuals 0.94 pg), due to a Y chromosome that arose about 3 million years ago. We compared the sequence composition of male and female C. grandis plants and determined the chromosomal distribution of repetitive and organellar DNA with probes developed from 21 types of repetitive DNA, including 16 mobile elements. The size of the Y chromosome is largely due to the accumulation of certain repeats, such as members of the Ty1/copia and Ty3/gypsy superfamilies, an unclassified element and a satellite, but also plastome‐ and chondriome‐derived sequences. An abundant tandem repeat with a unit size of 144 bp stains the centromeres of the X chromosome and the autosomes, but is absent from the Y centromere. Immunostaining with pericentromere‐specific markers for anti‐histone H3Ser10ph and H2AThr120ph revealed a Y‐specific extension of these histone marks. That the Y centromere has a different make‐up from all the remaining centromeres raises questions about its spindle attachment, and suggests that centromeric or pericentromeric chromatin might be involved in the suppression of recombination.
KymoRod: a method for automated kinematic analysis of rod‐shaped plant organs
Authors: Bastien Renaud , Legland David , Martin Marjolaine , Fregosi Lucien , Peaucelle Alexis , Douady Stéphane , Moulia Bruno , Höfte Herman 
Published: June 2016

SummaryA major challenge in plant systems biology is the development of robust, predictive multiscale models for organ growth. In this context it is important to bridge the gap between the, rather well‐documented molecular scale and the organ scale by providing quantitative methods to study within‐organ growth patterns. Here, we describe a simple method for the analysis of the evolution of growth patterns within rod‐shaped organs that does not require adding markers at the organ surface. The method allows for the simultaneous analysis of root and hypocotyl growth, provides spatio‐temporal information on curvature, growth anisotropy and relative elemental growth rate and can cope with complex organ movements. We demonstrate the performance of the method by documenting previously unsuspected complex growth patterns within the growing hypocotyl of the model species Arabidopsis thaliana during normal growth, after treatment with a growth‐inhibiting drug or in a mechano‐sensing mutant. The method is freely available as an intuitive and user‐friendly Matlab application called KymoRod.
In the Limelight: Photoreceptors in Cyanobacteria
Authors: Bhaya Devaki 
Published: June 2016

ABSTRACT
Certain cyanobacteria look green if grown in red light and vice versa. This dramatic color change, called complementary chromatic adaptation (CCA), is caused by alterations of the major colored light-harvesting proteins. A major controller of CCA is the cyanobacteriochrome (CBCR) RcaE, a red-green reversible photoreceptor that triggers a complex signal transduction pathway. Now, a new study demonstrates that CCA is also modulated by DpxA, a CBCR that senses yellow and teal (greenish blue) light. DpxA acts to expand the range of wavelengths that can impact CCA, by fine-tuning the process. This dual control of CCA might positively impact the fitness of cells growing in the shade of competing algae or in a water column where light levels and spectral quality change gradually with depth. This discovery adds to the growing number of light-responsive phenomena controlled by multiple CBCRs. Furthermore, the diverse CBCRs which are exclusively found in cyanobacteria have significant biotechnological potential.
Dengue Virus Genome Uncoating Requires Ubiquitination
Authors: Byk Laura A. , Iglesias Néstor G. , De Maio Federico A. , Gebhard Leopoldo G. , Rossi Mario , Gamarnik Andrea V. 
Published: June 2016

ABSTRACT
The process of genome release or uncoating after viral entry is one of the least-studied steps in the flavivirus life cycle. Flaviviruses are mainly arthropod-borne viruses, including emerging and reemerging pathogens such as dengue, Zika, and West Nile viruses. Currently, dengue virus is one of the most significant human viral pathogens transmitted by mosquitoes and is responsible for about 390 million infections every year around the world. Here, we examined for the first time molecular aspects of dengue virus genome uncoating. We followed the fate of the capsid protein and RNA genome early during infection and found that capsid is degraded after viral internalization by the host ubiquitin-proteasome system. However, proteasome activity and capsid degradation were not necessary to free the genome for initial viral translation. Unexpectedly, genome uncoating was blocked by inhibiting ubiquitination. Using different assays to bypass entry and evaluate the first rounds of viral translation, a narrow window of time during infection that requires ubiquitination but not proteasome activity was identified. In this regard, ubiquitin E1-activating enzyme inhibition was sufficient to stabilize the incoming viral genome in the cytoplasm of infected cells, causing its retention in either endosomes or nucleocapsids. Our data support a model in which dengue virus genome uncoating requires a nondegradative ubiquitination step, providing new insights into this crucial but understudied viral process.

IMPORTANCE
Dengue is the most significant arthropod-borne viral infection in humans. Although the number of cases increases every year, there are no approved therapeutics available for the treatment of dengue infection, and many basic aspects of the viral biology remain elusive. After entry, the viral membrane must fuse with the endosomal membrane to deliver the viral genome into the cytoplasm for translation and replication. A great deal of information has been obtained in the last decade regarding molecular aspects of the fusion step, but little is known about the events that follow this process, which leads to viral RNA release from the nucleocapsid. Here, we investigated the fate of nucleocapsid components (capsid protein and viral genome) during the infection process and found that capsid is degraded by the ubiquitin-proteasome system. However, in contrast to that observed for other RNA and DNA viruses, dengue virus capsid degradation was not responsible for genome uncoating. Interestingly, we found that dengue virus genome release requires a nondegradative ubiquitination step. These results provide the first insights into dengue virus uncoating and present new opportunities for antiviral intervention.
Evaluating the accessibility and utility of HIV-related point-of-care diagnostics for maternal health in rural South Africa: a study protocol
Authors: Mashamba-Thompson T P , Drain P K , Sartorius B 
Published: June 2016

IntroductionPoor healthcare access is a major barrier to receiving antenatal care and a cause of high maternal mortality in South Africa (SA). ‘Point-of-care’ (POC) diagnostics is a powerful emerging healthcare approach to improve healthcare access. This study focuses on evaluating the accessibility and utility of POC diagnostics for maternal health in rural SA primary healthcare (PHC) clinics in order to generate a model framework of implementation of POC diagnostics in rural South African clinics.Method and analysesWe will use several research methods, including a systematic review, quasi-experiments, survey, key informant interviews and audits. We will conduct a systematic review and experimental study to determine the impact of POC diagnostics on maternal health. We will perform a cross-sectional case study of 100 randomly selected rural primary healthcare clinics in KwaZulu-Natal to measure the context and patterns of POC diagnostics access and usage by maternal health providers and patients. We will conduct interviews with relevant key stakeholders to determine the reasons for POC deficiencies regarding accessibility and utility of HIV-related POC diagnostics for maternal health. We will also conduct a vertical audit to investigate all the quality aspects of POC diagnostic services including diagnostic accuracy in a select number of clinics. On the basis of information gathered, we will propose a model framework for improved implementation of POC diagnostics in rural South African public healthcare clinics. Statistical (Stata-13) and thematic (NVIVO) data analysis will be used in this study.Ethics and disseminationThe study protocol was approved by the Ethics Committee of the University of KwaZulu-Natal (BE 484/14) and the KwaZulu-Natal Department of Health based on the Helsinki Declaration (HRKM 40/15). Findings of this study will be disseminated electronically and in print. They will be presented to conferences related to HIV/AIDS, diagnostics, maternal health and strengthening of health systems.
Prevalence of clinically significant decisional conflict: an analysis of five studies on decision-making in primary care
Authors: Thompson-Leduc Philippe , Turcotte Stéphane , Labrecque Michel , Légaré France 
Published: June 2016

ObjectivesUnresolved clinically significant decisional conflict (CSDC) in patients following a consultation with health professionals is often the result of inadequate patient involvement in decision-making and may result in poor outcomes. We sought to identify the prevalence of CSDC in studies on decision-making in primary care and to explore its risk factors.SettingWe performed a secondary analysis of existing data sets from studies conducted in Primary Care Practice-Based Research Networks in Québec and Ontario, Canada.ParticipantsEligible studies included a patient-reported measure on the 16-item Decisional Conflict Scale (DCS) following a decision made with a healthcare professional with no study design restriction.Primary and secondary outcome measuresCSDC was defined as a score ≥25/100 on the DCS. The prevalence of CSDC was stratified by sex; and patient-level logistic regression analysis was performed to explore its potential risk factors. Data sets of studies were analysed individually and qualitatively compared.Results5 projects conducted between 2003 and 2010 were included. They covered a range of decisions: prenatal genetic screening, antibiotics for acute respiratory infections and miscellaneous. Altogether, the 5 projects gathered data from encounters with a total of 1338 primary care patients (69% female; range of age 15–83). The prevalence of CSDC in patients varied across studies and ranged from 10.3% (95% CI 7.2% to 13.4%) to 31.1% (95% CI 26.6% to 35.6%). Across the 5 studies, risk factors of CSDC included being male, living alone and being 45 or older.ConclusionsPrevalence of CSDC in patients who had enrolled in studies conducted in primary care contexts was substantial and appeared to vary according to the type of decision as well as to patient characteristics such as sex, living arrangement and age. Patients presenting risk factors of CSDC should be offered tools to increase their involvement in decision-making.