bluuebunny/crossref_metadata_2025_split huggingface dataset:
Access to health care in post-apartheid South Africa: availability, affordability, acceptability
Authors: Burger Ronelle , Christian Carmen 
Published: July 2018

AbstractWe use a reliable, intuitive and simple set of indicators to capture three dimensions of access – availability, affordability and acceptability. Data are from South Africa’s 2009 and 2010 General Household Surveys (n=190,164). Affordability constraints were faced by 23% and are more concentrated amongst the poorest. However, 73% of affordability constraints are due to travel costs which are aligned with findings of the availability constraints dimension. Availability constraints, involving distances and transport costs, particularly in underdeveloped rural areas, and inconvenient opening times, were faced by 27%. Acceptability constraints were noted by only 10%. We approximate acceptability with an indicator measuring the share of community members bypassing the closest health care facility, as we argue that reported health care provider choice is more reliable than stated preferences. However, the indicator assumes a choice of available and affordable providers, which may often not be an accurate assumption in rural areas. We recommend further work on the measurement of acceptability in household surveys, especially considering this dimension’s importance for health reform.
Characterization of Remote Sensing Albedo Over Sloped Surfaces Based on DART Simulations and In Situ Observations
Authors: Wu Shengbiao , Wen Jianguang , You Dongqin , Hao Dalei , Lin Xingwen , Xiao Qing , Liu Qinhuo , Gastellu‐Etchegorry Jean‐Philippe 
Published: July 2018

AbstractIn situ albedo measurement over sloped surfaces is pivotal to a wide range of remote sensing applications, such as the estimation and evaluation of surface energy budget at regional and global scales. However, existing albedo measurements over rugged terrain are limited and controversial and remain a major challenge. In this paper, two commonly measured broadband albedos, which depend on incoming/outgoing geometric conditions, were characterized over sloped surfaces and illustrated. These albedos are the horizontal/horizontal sloped surface albedo (HHSA) and inclined/inclined sloped surface albedo (IISA). The 3‐D Discrete Anisotropic Radiative Transfer (DART) model simulations over varying slopes were utilized to quantify differences in the albedos. In particular, the effects of the slope, aspect, the solar zenith angle, and the proportion of diffuse skylight were investigated. The results show that absolute (relative) biases between HHSA and IISA are significant, reaching up to 0.026 (61.8%), 0.134 (62.4%), and 0.114 (62.3%) in the visible, near‐infrared, and shortwave broadbands, respectively. In addition, the diurnal cycle differences between HHSA and IISA were also compared using DART simulations and in situ observations over four typical slopes. Comparisons reveal that topographic parameters (e.g., slope and aspect) and atmospheric conditions (e.g., diffuse skylight and atmospheric visibility) are the primary factors, while the optical and structural parameters have a smaller effect.
DNA methylation reprogramming of functional elements during mammalian embryonic development
Authors: Li Congru , Fan Yong , Li Guoqiang , Xu Xiaocui , Duan Jialei , Li Rong , Kang Xiangjin , Ma Xin , Chen Xuepeng , Ke Yuwen , Yan Jie , Lian Ying , Liu Ping , Zhao Yue , Zhao Hongcui , Chen Yaoyong , Yu Yang , Liu Jiang 
Published: July 2018

AbstractDNA methylation plays important roles during development. However, the DNA methylation reprogramming of functional elements has not been fully investigated during mammalian embryonic development. Herein, using our modified MethylC-Seq library generation method and published post-bisulphite adapter-tagging (PBAT) method, we generated genome-wide DNA methylomes of human gametes and early embryos at single-base resolution and compared them with mouse methylomes. We showed that the dynamics of DNA methylation in functional elements are conserved between humans and mice during early embryogenesis, except for satellite repeats. We further found that oocyte-specific hypomethylated promoters usually exhibit low CpG densities. Genes with oocyte-specific hypomethylated promoters generally show oocyte-specific hypomethylated genic and intergenic regions, and these hypomethylated regions contribute to the hypomethylation pattern of mammalian oocytes. Furthermore, hypomethylated genic regions with low CG densities correlate with gene silencing in oocytes, whereas hypomethylated genic regions with high CG densities correspond to high gene expression. We further show that methylation reprogramming of enhancers during early embryogenesis is highly associated with the development of almost all human organs. Our data support the hypothesis that DNA methylation plays important roles during mammalian development.
Towards standardized mechanical characterization of microbial biofilms: analysis and critical review
Authors: Boudarel Héloïse , Mathias Jean-Denis , Blaysat Benoît , Grédiac Michel 
Published: July 2018

AbstractDeveloping reliable anti-biofilm strategies or efficient biofilm-based bioprocesses strongly depends on having a clear understanding of the mechanisms underlying biofilm development, and knowledge of the relevant mechanical parameters describing microbial biofilm behavior. Many varied mechanical testing methods are available to assess these parameters. The mechanical properties thus identified can then be used to compare protocols such as antibiotic screening. However, the lack of standardization in both mechanical testing and the associated identification methods for a given microbiological goal remains a blind spot in the biofilm community. The pursuit of standardization is problematic, as biofilms are living structures, i.e., both complex and dynamic. Here, we review the main available methods for characterizing the mechanical properties of biofilms through the lens of the relationship linking experimental testing to the identification of mechanical parameters. We propose guidelines for characterizing biofilms according to microbiological objectives that will help the reader choose an appropriate test and a relevant identification method for measuring any given mechanical parameter. The use of a common methodology for the mechanical characterization of biofilms will enable reliable analysis and comparison of microbiological protocols needed for improvement of engineering process and screening.
“Tossing a coin:” defining the excessive use of short-acting beta2-agonists in asthma—the views of general practitioners and asthma experts in primary and secondary care
Authors: McKibben Shauna , Bush Andy , Thomas Mike , Griffiths Chris 
Published: July 2018

AbstractThe National Review of Asthma Deaths (NRAD) identified high prescribing of short–acting beta2-agonists (SABAs) as a key factor in over 40% of deaths. We interviewed asthma experts from both a hospital background (n = 5) and a primary care background (n = 8), and general practitioners delivering asthma care (n = 8), to identify how SABA use is defined and perceived. We identified disparity in how acceptable SABA use is defined, ranging from 0.5 (100 doses/year) to 12 SABA inhalers (2400 doses/year), and complacency in the perception that over-use did not represent a marker for risk of asthma death. Despite current evidence, these findings suggest clinicians of various backgrounds are complacent about excessive SABA use.
Advances in single-scan time-encoding magnetic resonance imaging
Authors: Marhabaie Sina , Bodenhausen Geoffrey , Pelupessy Philippe 
Published: July 2018

AbstractTime-encoding MRI is a single-scan method that uses traditionalk-encoding only in one direction. In the orthogonal “time-encoding” direction, a string of echoes appears in an order that depends on the position of the corresponding spin packets. In one variant of time-encoding, this is achieved by using a series of selective pulses and appropriate gradients in bothk-encoding and time-encoding directions. Although time-encoding offers some advantages over traditional single-scan Fourier methods such as echo planar imaging (EPI), the original time-encoding sequence also has some drawbacks that limit its applications. In this work, we show how one can improve several aspects of the original time-encoding sequence. By using an additional gradient pulse one can change the order in which the echoes appear, leading to identical echo times for all echoes, and hence to a uniform signal attenuation due to transverse relaxation and a reduction in average signal attenuation due to diffusion. By rearranging positive and negative gradients one can reduce the switching rate of the gradients. Furthermore, we show how one can implement time-encoding sequences in an interleaved fashion in order to reduce signal attenuation due to transverse relaxation and diffusion, while increasing the spatial resolution.
Prior object-knowledge sharpens properties of early visual feature-detectors
Authors: Teufel Christoph , Dakin Steven C. , Fletcher Paul C. 
Published: July 2018

AbstractEarly stages of visual processing are carried out by neural circuits activated by simple and specific features, such as the orientation of an edge. A fundamental question in human vision is how the brain organises such intrinsically local information into meaningful properties of objects. Classic models of visual processing emphasise a one-directional flow of information from early feature-detectors to higher-level information-processing. By contrast to this view, and in line with predictive-coding models of perception, here, we provide evidence from human vision that high-level object representations dynamically interact with the earliest stages of cortical visual processing. In two experiments, we used ambiguous stimuli that, depending on the observer’s prior object-knowledge, can be perceived as either coherent objects or as a collection of meaningless patches. By manipulating object knowledge we were able to determine its impact on processing of low-level features while keeping sensory stimulation identical. Both studies demonstrate that perception of local features is facilitated in a manner consistent with an observer’s high-level object representation (i.e., with no effect on object-inconsistent features). Our results cannot be ascribed to attentional influences. Rather, they suggest that high-level object representations interact with and sharpen early feature-detectors, optimising their performance for the current perceptual context.
Potential of a polyherbal drug to prevent antimicrobial resistance in bacteria to antibiotics
Authors: Sar Tapas Kumar , Samanta Indranil , Mahanti Achintya , Akhtar Shabnam , Dash Jeevan Ranjan 
Published: July 2018

AbstractPersistence of antibacterial drugs for prolonged period in milk increases the probability of antimicrobial resistance progress. Ceftizoxime was found to be excreted in milk for a prolonged period in goats, cows and buffaloes following intravenous injection of ceftriaxone and ceftizoxime. A single dose of ceftriaxone was administered intravenously in healthy control goats (group I) and a single oral dose of the commercial mammary protective polyherbal drug (1.9 gm) was given one hour prior to intravenous ceftriaxone injection in healthy (group II) and induced mastitic (group III) goats to evaluate milk disposition of ceftizoxime following single intravenous dosing of ceftriaxone at 42.25 mg kg−1.Ceftriaxone/ceftizoxime was analyzed by HPLC. The t1/2α and t1/2β values were 14.755 ± 2.733 and 149.079 ± 18.565 hour, respectively indicating prolonged persistence of ceftizoxime in milk. The polyherbal drug increased the milk concentration at later hours and hastened the excretion of ceftizoxime from milk compared to control group. Ceftriaxone could not be detected in milk. The study suggested that adjunct single or repeated therapy of the polyherbal drug may cause non persistence of ceftriaxone and shorter persistence of ceftizoxime in milk.
Steric interference from intrinsically disordered regions controls dynamin-related protein 1 self-assembly during mitochondrial fission
Authors: Lu Bin , Kennedy Bridget , Clinton Ryan W. , Wang Emily Jue , McHugh Daniel , Stepanyants Natalia , Macdonald Patrick J. , Mears Jason A. , Qi Xin , Ramachandran Rajesh 
Published: July 2018

AbstractThe self-assembling, mechanoenzymatic dynamin superfamily GTPase, dynamin-related protein 1 (Drp1), catalyzes mitochondrial and peroxisomal fission. Distinct intrinsically disordered regions (IDRs) in Drp1 substitute for the canonical pleckstrin homology (PH) domain and proline-rich domain (PRD) of prototypical dynamin, which cooperatively regulate endocytic vesicle scission. Whether the Drp1 IDRs function analogously to the corresponding dynamin domains however remains unknown. We show that an IDR unique to the Drp1 GTPase (G) domain, the ‘extended 80-loop’, albeit dissimilar in location, structure, and mechanism, functions akin to the dynamin PRD by enabling stable Drp1 mitochondrial recruitment and by suppressing Drp1 cooperative GTPase activity in the absence of specific partner-protein interactions. Correspondingly, we find that another IDR, the Drp1 variable domain (VD), in conjunction with the conserved stalk L1N loop, functions akin to the dynamin PH domain; first, in an ‘auto-inhibitory’ capacity that restricts Drp1 activity through a long-range steric inhibition of helical inter-rung G-domain dimerization, and second, as a ‘fulcrum’ for Drp1 self-assembly in the proper helical register. We show that the Drp1 VD is necessary and sufficient for specific Drp1-phospholipid interactions. We further demonstrate that the membrane-dependent VD conformational rearrangement essential for the alleviation of Drp1 auto-inhibition is contingent upon the basal GTP hydrolysis-dependent generation of Drp1 dimers from oligomers in solution. IDRs thus conformationally couple the enzymatic and membrane activities of Drp1 toward membrane fission.
Dynamic Loading and Tendon Healing Affect Multiscale Tendon Properties and ECM Stress Transmission
Authors: Freedman Benjamin R. , Rodriguez Ashley B. , Leiphart Ryan J. , Newton Joseph B. , Ban Ehsan , Sarver Joseph J. , Mauck Robert L. , Shenoy Vivek B. , Soslowsky Louis J. 
Published: July 2018

AbstractThe extracellular matrix (ECM) is the primary biomechanical environment that interacts with tendon cells (tenocytes). Stresses applied via muscle contraction during skeletal movement transfer across structural hierarchies to the tenocyte nucleus in native uninjured tendons. Alterations to ECM structural and mechanical properties due to mechanical loading and tissue healing may affect this multiscale strain transfer and stress transmission through the ECM. This study explores the interface between dynamic loading and tendon healing across multiple length scales using living tendon explants. Results show that macroscale mechanical and structural properties are inferior following high magnitude dynamic loading (fatigue) in uninjured living tendon and that these effects propagate to the microscale. Although similar macroscale mechanical effects of dynamic loading are present in healing tendon compared to uninjured tendon, the microscale properties differed greatly during early healing. Regression analysis identified several variables (collagen and nuclear disorganization, cellularity, and F-actin) that directly predict nuclear deformation under loading. Finite element modeling predicted deficits in ECM stress transmission following fatigue loading and during healing. Together, this work identifies the multiscale response of tendon to dynamic loading and healing, and provides new insight into microenvironmental features that tenocytes may experience following injury and after cell delivery therapies.
Ranking genome-wide correlation measurements improves microarray and RNA-seq based global and targeted co-expression networks
Authors: Liesecke Franziska , Daudu Dimitri , Dugé de Bernonville Rodolphe , Besseau Sébastien , Clastre Marc , Courdavault Vincent , de Craene Johan-Owen , Crèche Joel , Giglioli-Guivarc’h Nathalie , Glévarec Gaëlle , Pichon Olivier , Dugé de Bernonville Thomas 
Published: July 2018

AbstractCo-expression networks are essential tools to infer biological associations between gene products and predict gene annotation. Global networks can be analyzed at the transcriptome-wide scale or after querying them with a set of guide genes to capture the transcriptional landscape of a given pathway in a process named Pathway Level Coexpression (PLC). A critical step in network construction remains the definition of gene co-expression. In the present work, we compared how Pearson Correlation Coefficient (PCC), Spearman Correlation Coefficient (SCC), their respective ranked values (Highest Reciprocal Rank (HRR)), Mutual Information (MI) and Partial Correlations (PC) performed on global networks and PLCs. This evaluation was conducted on the model plantArabidopsis thalianausing microarray and differently pre-processed RNA-seq datasets. We particularly evaluated how dataset × distance measurement combinations performed in 5 PLCs corresponding to 4 well described plant metabolic pathways (phenylpropanoid, carbohydrate, fatty acid and terpene metabolisms) and the cytokinin signaling pathway. Our present work highlights how PCC ranked with HRR is better suited for global network construction and PLC with microarray and RNA-seq data than other distance methods, especially to cluster genes in partitions similar to biological subpathways.
Motion cues modulate responses to emotion in movies
Authors: Dayan Eran , Barliya Avi , de Gelder Beatrice , Hendler Talma , Malach Rafael , Flash Tamar 
Published: July 2018

AbstractFilm theorists and practitioners suggest that motion can be manipulated in movie scenes to elicit emotional responses in viewers. However, our understanding of the role of motion in emotion perception remains limited. On the one hand, movies continuously depictlocal motion- movements of objects and humans, which are crucial for generating emotional responses. Movie scenes also frequently portrayglobal motion, mainly induced by large camera movements, global motion being yet another source of information used by the brain during natural vision. Here we used functional MRI to elucidate the contributions of local and global motion to emotion perception during movie viewing. Subjects observed long (1 min) movie segments depicting emotional or neutral content. Brain activity in areas that showed preferential responses to emotional content was strongly linked over time with frame-wide variations in global motion, and to a lesser extent with local motion information. Similarly, stronger responses to emotional content were recorded within regions of interest whose activity was attuned to global and local motion over time. Since global motion fields are experienced during self-motion, we suggest that camera movements may induce illusory self-motion cues in viewers that interact with the movie’s narrative and with other emotional cues in generating affective responses.
Potent Attractant for Root-Knot Nematodes in Exudates from Seedling Root Tips of Two Host Species
Authors: Čepulytė Rasa , Danquah Wiseborn B. , Bruening George , Williamson Valerie M. 
Published: July 2018

AbstractRoot-knot nematodes (RKN; Meloidogyne spp.) can parasitize over 2,000 plant species and are generally considered to be the most agriculturally damaging group of plant-parasitic nematodes worldwide. Infective juveniles (J2) are non-feeding and must locate and invade a host before their reserves are depleted. However, what attracts J2 to appropriate root entry sites is not known. An aim of this research is to identify semiochemicals that attract RKN to roots. J2 of the three RKN species tested are highly attracted to root tips of both tomato and Medicago truncatula. For both hosts, mutants defective in ethylene signaling were found to be more attractive than those of wild type. We determined that cell-free exudates collected from tomato and M. truncatula seedling root tips were highly attractive to M. javanica J2. Using a pluronic gel-based microassay to monitor chemical fractionation, we determined that for both plant species the active component fractionated similarly and had a mass of ~400 based on size-exclusion chromatography. This characterization is a first step toward identification of a potent and specific attractant from host roots that attracts RKN. Such a compound is potentially a valuable tool for developing novel and safe control strategies.
Automatic multiple zebrafish tracking based on improved HOG features
Authors: Bai Yun-Xiang , Zhang Shu-Hui , Fan Zhi , Liu Xing-Yu , Zhao Xin , Feng Xi-Zeng , Sun Ming-Zhu 
Published: July 2018

AbstractAs an excellent model organism, zebrafish have been widely applied in many fields. The accurate identification and tracking of individuals are crucial for zebrafish shoaling behaviour analysis. However, multi-zebrafish tracking still faces many challenges. It is difficult to keep identified for a long time due to fish overlapping caused by the crossings. Here we proposed an improved Histogram of Oriented Gradient (HOG) algorithm to calculate the stable back texture feature map of zebrafish, then tracked multi-zebrafish in a fully automated fashion with low sample size, high tracking accuracy and wide applicability. The performance of the tracking algorithm was evaluated in 11 videos with different numbers and different sizes of zebrafish. In the Right-tailed hypothesis test of Wilcoxon, our method performed better than idTracker, with significant higher tracking accuracy. Throughout the video of 16 zebrafish, the training sample of each fish had only 200–500 image samples, one-fifth of the idTracker’s sample size. Furthermore, we applied the tracking algorithm to analyse the depression and hypoactivity behaviour of zebrafish shoaling. We achieved correct identification of depressed zebrafish among the fish shoal based on the accurate tracking results that could not be identified by a human.
Engineering the oleaginous red yeast Rhodotorula glutinis for simultaneous β-carotene and cellulase production
Authors: Pi Hong-Wei , Anandharaj Marimuthu , Kao Yi-Ying , Lin Yu-Ju , Chang Jui-Jen , Li Wen-Hsiung 
Published: July 2018

AbstractRhodotorula glutinis, an oleaginous red yeast, intrinsically produces several bio-products (i.e., lipids, carotenoids and enzymes) and is regarded as a potential host for biorefinery. In view of the limited available genetic engineering tools for this yeast, we have developed a useful genetic transformation method and transformed the β-carotene biosynthesis genes (crtI, crtE, crtYB and tHMG1) and cellulase genes (CBHI, CBHII, EgI, EgIII, EglA and BGS) into R. glutinis genome. The transformant P4-10-9-63Y-14B produced significantly higher β-carotene (27.13 ± 0.66 mg/g) than the wild type and also exhibited cellulase activity. Furthermore, the lipid production and salt tolerance ability of the transformants were unaffected. This is the first study to engineer the R. glutinis for simultaneous β-carotene and cellulase production. As R. glutinis can grow in sea water and can be engineered to utilize the cheaper substrates (i.e. biomass) for the production of biofuels or valuable compounds, it is a promising host for biorefinery.