bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of Nevirapine Prophylactic and Therapeutic Dosing Regimens for Neonates
Authors: Cressey Tim R. , Punyawudho Baralee , Le Coeur Sophie , Jourdain Gonzague , Saenjum Chalermpong , Capparelli Edmund V. , Jittayanun Kanokwan , Phanomcheong Siriluk , Luvira Anita , Borkird Thitiporn , Puangsombat Achara , Aarons Leon , Sukrakanchana Pra-ornsuda , Urien Saik , Lallemant Marc ,   for the PHPT-5 study team
Published: May 2017

Background:
Nevirapine (NVP) is a key component of antiretroviral prophylaxis and treatment for neonates. We evaluated current World Health Organization (WHO) weight-band NVP prophylactic dosing recommendations and investigated optimal therapeutic NVP dosing for neonates.

Methods:
The PHPT-5 study in Thailand assessed the efficacy of “Perinatal Antiretroviral Intensification” to prevent mother-to-child transmission of HIV in women with <8 weeks of antiretroviral treatment before delivery (NCT01511237). Infants received a 2-week course of zidovudine/lamivudine/NVP (NVP syrup/once daily: 2 mg/kg for 7 days; then 4 mg/kg for 7 days). Infant samples were assessed during the first 2 weeks of life. NVP population pharmacokinetics (PK) parameters were estimated using nonlinear mixed-effects models. Simulations were performed to estimate the probability of achieving target NVP trough concentrations for prophylaxis (>0.10 mg/L) and for therapeutic efficacy (>3.0 mg/L) using different infant dosing strategies.

Results:
Sixty infants (55% male) were included. At birth, median (range) weight was 2.9 (2.3–3.6) kg. NVP concentrations were best described by a 1-compartment PK model. Infant weight and postnatal age influenced NVP PK parameters. Based on simulations for a 3-kg infant, ≥92% would have an NVP trough >0.1 mg/L after 48 hours through 2 weeks using the PHPT-5 and WHO-dosing regimens. For NVP-based therapy, a 6-mg/kg twice daily dose produced a trough >3.0 mg/L in 87% of infants at 48 hours and 80% at 2 weeks.

Conclusion:
WHO weight-band prophylactic guidelines achieved target concentrations. Starting NVP 6 mg/kg twice daily from birth is expected to achieve therapeutic concentrations during the first 2 weeks of life.
EyeBallGUI: A Tool for Visual Inspection and Binary Marking of Multi-channel Bio-signals
Authors: Mohr Kieran S. , Nasseroleslami Bahman , Iyer Parameswaran M. , Hardiman Orla , Lalor Edmund C. 
Published: May 2017

AbstractA wide range of studies in human neuroscience rely on the analysis of electrophysiological bio-signals such as electroencephalogram (EEG) where customized data analysis may require supervised artefact rejection, binary marking through visual inspection, selection of noise and artefact samples for pre-processing algorithms, and selection of clinically-relevant signal segments in neurological conditions. Nevertheless, the existing preprocessing tools do not provide the needed flexibility to handle such tasks efficiently. We therefore developed a free open-source Graphical User Interface (GUI), EyeBallGUI, that allows visualization and flexible, manual marking (binary classification) of multi-channel bio-signal data. EyeBallGUI, developed for MATLAB®, allows the user to interactively and accurately inspect and mark multi-channel digitized data with no restriction on marking periods of data in subsets of channels (a restriction in place in existing tools). The new tool facilitates precise, manual marking of bio-signals by allowing any desired segment of data to be marked in any subset of channels. It is therefore of utility in circumstances where such flexibility is essential. The developed GUI is an auxiliary analysis tool that shall facilitate neural signal (pre-)processing applications where it is desirable to perform accurate supervised artefact rejection, flexible data marking for increased data retention yield, extraction of specific signal segments by expert users from sample data, or labeling of data for clinical and scientific research purposes.
Heterogeneity among estimates of the core genome and pan-genome in different pneumococcal populations
Authors: van Tonder Andries J , Bray James E , Jolley Keith A , Quirk Sigríður J , Haraldsson Gunnsteinn , Maiden Martin CJ , Bentley Stephen D , Haraldsson Ásgeir , Erlendsdóttir Helga , Kristinsson Karl G , Brueggemann Angela B 
Published: May 2017

AbstractBackgroundUnderstanding the structure of a bacterial population is essential in order to understand bacterial evolution, or which genetic lineages cause disease, or the consequences of perturbations to the bacterial population. Estimating the core genome, the genes common to all or nearly all strains of a species, is an essential component of such analyses. The size and composition of the core genome varies by dataset, but our hypothesis was that variation between different collections of the same bacterial species should be minimal. To test this, the genome sequences of 3,121 pneumococci recovered from healthy individuals in Reykjavik (Iceland), Southampton (United Kingdom), Boston (USA) and Maela (Thailand) were analysed.ResultsThe analyses revealed a ‘supercore’ genome (genes shared by all 3,121 pneumococci) of only 303 genes, although 461 additional core genes were shared by pneumococci from Reykjavik, Southampton and Boston. Overall, the size and composition of the core genomes and pan-genomes among pneumococci recovered in Reykjavik, Southampton and Boston were very similar, but pneumococci from Maela were distinctly different. Inspection of the pan-genome of Maela pneumococci revealed several >25 Kb sequence regions that were homologous to genomic regions found in other bacterial species.ConclusionsSome subsets of the global pneumococcal population are highly heterogeneous and thus our hypothesis was rejected. This is an essential point of consideration before generalising the findings from a single dataset to the wider pneumococcal population.
DeepDeath: Learning to Predict the Underlying Cause of Death with Big Data
Authors: Hassanzadeh Hamid Reza , Sha Ying , Wang May D. 
Published: May 2017

AbstractMultiple cause-of-death data provides a valuable source of information that can be used to enhance health standards by predicting health related trajectories in societies with large populations. These data are often available in large quantities across U.S. states and require Big Data techniques to uncover complex hidden patterns. We design two different classes of models suitable for large-scale analysis of mortality data, a Hadoop-based ensemble of random forests trained over N-grams, and the DeepDeath, a deep classifier based on the recurrent neural network (RNN). We apply both classes to the mortality data provided by the National Center for Health Statistics and show that while both perform significantly better than the random classifier, the deep model that utilizes long short-term memory networks (LSTMs), surpasses the N-gram based models and is capable of learning the temporal aspect of the data without a need for building ad-hoc, expert-driven features.
A carbon nanotube optical reporter maps endolysosomal lipid flux
Authors: Jena Prakrit V. , Roxbury Daniel , Galassi Thomas V. , Akkari Leila , Horoszko Christopher P. , Iaea David B. , Budhathoki-Uprety Januka , Pipalia Nina H. , Haka Abigail S. , Harvey Jackson D. , Mittal Jeetain , Maxfield Frederick R. , Joyce Johanna A. , Heller Daniel A. 
Published: May 2017

ABSTRACTLipid accumulation within the lumen of endolysosomal vesicles is observed in various pathologies including atherosclerosis, liver disease, neurological disorders, lysosomal storage disorders, and cancer. Current methods cannot measure lipid flux specifically within the lysosomal lumen of live cells. We developed an optical reporter, composed of a photoluminescent carbon nanotube of a single chirality, which responds to lipid accumulation via modulation of the nanotube’s optical bandgap. The engineered nanomaterial, composed of short-single stranded DNA and a single nanotube chirality, localizes exclusively to the lumen of endolysosomal organelles without adversely affecting cell viability or proliferation, or organelle morphology, integrity, or function. The emission wavelength of the reporter can be spatially resolved from within the endolysosomal lumen to generate quantitative maps of lipid content in live cells. Endolysosomal lipid accumulation in cell lines, an example of drug-induced phospholipidosis (DIPL), was observed for multiple drugs in macrophages, and measurements of patient-derived Niemann-Pick type C fibroblasts identified lipid accumulation and phenotypic reversal of this lysosomal storage disease. Single-cell measurements using the reporter discerned sub-cellular differences in equilibrium lipid content, illuminating significant intracellular heterogeneity among endolysosomal organelles of differentiating bone marrow-derived monocytes. Single-cell kinetics of lipoprotein-derived cholesterol accumulation within macrophages revealed rates that differed among cells by an order of magnitude. This carbon nanotube optical reporter of endolysosomal lipid content in live cells confers new capabilities for drug development processes and the investigation of lipid-linked diseases.
Homology modeling in a dynamical world
Authors: Monzon Alexander Miguel , Zea Diego Javier , Marino-Buslje Cristina , Parisi Gustavo 
Published: May 2017

AbstractA key concept in template-based modeling is the high correlation between sequence and structural divergence, with the practical consequence that homologous proteins that are similar at the sequence level will also be similar at the structural level. However, conformational diversity of the native state will reduce the correlation between structural and sequence divergence, because structural variation can appear without sequence diversity.In this work, we explore the impact that conformational diversity has on the relationship between structural and sequence divergence. We find that the extent of conformational diversity can be as high as the maximum structural divergence among families. Also, as expected, conformational diversity impairs the well-established correlation between sequence and structural divergence, which is nosier than previously suggested. However, we found that this noise can be resolved usinga prioriinformation coming from the structure-function relationship. We show that protein families with low conformational diversity show a well-correlated relationship between sequence and structural divergence, which is severely reduced in proteins with larger conformational diversity. This lack of correlation could impair Template-based modelling (TMB) results in highly dynamical proteins. Finally, we also find that the presence of order/disorder can provide useful beforehand information for better TBM performance.Author summaryTemplate-based modelling (TBM) is the most reliable and fastest approach to obtain protein structural models. TBM relies in the high correlation between sequence and structural divergence, with the practical consequence that proteins that are similar at the sequence level will also be similar at the structural level, allowing in this way the selection of the better template to obtain the 3D model of the target sequence. However, protein native state could be described by a collection of conformers in equilibrium where their structural differences are called conformational diversity.In this work, we explore the impact that conformational diversity has on the relationship between structural and sequence divergence. We firstly found that the extent of conformational diversity can be as high as the maximum structural differences reached by families differing in their sequences. In these proteins with higher conformational diversity levels, the well-established correlation between sequence and structural divergence is nosier than previously suggested due to the presence of structural change without sequence variation. This lack of correlation could impair TBM results due to the uncertainty in the correct template selection. Finally, we also found that the presence of order/disorder can provide useful beforehand information for better TBM performance.
Two loci single particle trajectories analysis: constructing a first passage time statistics of local chromatin exploration
Authors: Shukron O. , Hauer MH. , Holcman D. 
Published: May 2017

AbstractStochastic single particle trajectories are used to explore the local chromatin organization. We present here a statistical analysis of the first contact time distributions between two tagged loci recorded experimentally. First, we extract the association and dissociation times from data for various genomic distances between loci and we show that the looping time occurs in confined nanometer regions. Second, we characterize the looping time distribution for two loci in the presence of multiple DNA damages. Finally, we construct a polymer model that accounts for the local chromatin organization before and after a double-stranded DNA break (DSB) to estimate the level of chromatin decompaction. This novel passage time statistics method allows extracting transient dynamic at scales from one to few hundreds of nanometers, predicts the local changes in the number of binding molecules following DSB and can be used to better characterize the local dynamic of the chromatin.
Developing a comprehensive performance measurement system forwaqfinstitutions
Authors: Noordin Nazrul Hazizi , Haron Siti Nurah , Kassim Salina 
Published: May 2017

PurposeThe purpose of this paper is to contribute to the literature on management ofwaqfinstitutions by developing a contingency framework and outlining approaches that can be followed to instigate a comprehensive performance measurement system (PMS).Design/methodology/approachIt conducts a thorough and critical review of the literature on relevant performance measurement literature of third sector organizations andwaqfinstitutions.FindingsThe findings suggest that an effective PMS is undoubtedly significant in promoting good governance and ethical management ofwaqfinstitutions. However, the current practice of performance measurement inwaqfinstitutions is less standardized and does not cover its entire aspects of performance as a religious as well as a voluntary organization. It is also found that mostwaqfinstitutions’ management and researchers primarily rely on financial reporting and economic indicators to report to the stakeholders about the performance ofwaqfinstitutions.Practical implicationsThe contributions of this paper are twofold. First, the authors develop a contingency framework for assessing performance ofwaqfinstitutions. Second, the authors outline eight necessary steps that can serve as guidelines forwaqfinstitutions in designing their own comprehensive PMS.Originality/valueThe novelty of this paper lies in highlighting the feasibility of adopting qualitative approaches bywaqfinstitutions. This study hopes to shed light on a standard measurement system that can be adopted by thewaqfinstitutions to ensure efficiency and sustainability of thewaqfinstitutions, not just in Malaysia but in the Muslim world.
Methods of evaluation of intangible assets and intellectual capital
Authors: Osinski Marilei , Selig Paulo Mauricio , Matos Florinda , Roman Darlan José 
Published: May 2017

Purpose
The competitive model has changed. In this context, society entered into an era in which intangible assets are the greatest assets of a company. However, some gaps and uncertainties are presented in the literature as to understand the value of a company based on knowledge intensive activities. The purpose of this paper is to analyze the methods of evaluation of intangible assets in the context of business, economic and strategic management.

Design/methodology/approach
This is a qualitative research. This research is characterized as descriptive, bibliographic, inductive.

Findings
The main results of this research can highlight the existence of valuation methods of intangible assets intended for specific industries, as public and/or private, that can be better aligned to the context of business; economic and/or strategic management.

Originality/value
It was found that intangible assets are a current topic and increasingly addressed in the literature.
Switching of biologics in psoriasis: Reasons and results
Authors: Honda Hiromi , Umezawa Yoshinori , Kikuchi Sota , Yanaba Koichi , Fukuchi Osamu , Ito Toshihiro , Nobeyama Yoshimasa , Asahina Akihiko , Nakagawa Hidemi 
Published: May 2017

AbstractEfficacy and safety profiles of biologics have been established for moderate to severe psoriasis. However, inefficacy or adverse events sometimes require changing the treatment to other biologics. Here, we examine the effectiveness of this strategy. We retrospectively investigated cases requiring switching biologics. We enrolled 275 psoriatic patients treated with biologics between January 2010 and December 2014 in our hospital. Of these, 51 required a switch to another biologic. First‐line therapies were infliximab (IFX, n = 26), adalimumab (ADA, n = 18) and ustekinumab (UST, n = 7), and second‐line therapies were IFX (n = 5), ADA (n = 21) and UST (n = 25). Reasons for switching were inefficacy (n = 38), adverse events (n = 11) and others (n = 2). The details were primary failure (n = 15), secondary failure (n = 23) and infusion reactions (n = 8). In 49 patients who switched biologics due to inefficacy and adverse events, the mean Psoriasis Area and Severity Index (PASI) score at week 16 was 4.3 for first‐line therapies and 2.9 for second‐line therapies (P < 0.05). Switching to a second biologic therapy to address the first's inefficacy or adverse events often results in significant improvement in moderate to severe psoriasis.
Experimental verification of effective anisotropic crack theories in variable crack aspect ratio medium
Authors: Henriques Jessica P. , de Figueiredo Jose J. S. , Santos Leo K. , Macedo Daniel L. , Coutinho Icaro , da Silva Carolina B. , Melo Alberto L. , Sousa Mykel , Azevedo Felipe L. 
Published: May 2017

ABSTRACTPhysical modelling of cracked/fractured media using downscaled laboratory experiments has been used with great success as a useful alternative for understanding the effect of anisotropy in the hydrocarbon reservoir characterization and in the crustal and mantle seismology. The main goal of this work was to experimentally verify the predictions of effective elastic parameters in anisotropic cracked media by Hudson and Eshelby–Cheng's effective medium models. For this purpose, we carried out ultrasonic measurements on synthetic anisotropic samples with low crack densities and different aspect ratios. Twelve samples were prepared with two different crack densities, 5% and 8%. Three samples for each crack density presented cracks with only one crack aspect ratio, whereas other three samples for each crack density presented cracks with three different aspect ratios in their composition. It results in samples with aspect ratio values varying from 0.13 to 0.26. All the cracked samples were simulated by penny‐shaped rubber inclusions in a homogeneous isotropic matrix made with epoxy resin. Moreover, an isotropic sample for reference was constructed with epoxy resin only. Regarding velocity predictions performed by the theoretical models, Eshelby–Cheng shows a better fit when compared with the experimental results for samples with single and mix crack aspect ratio (for both crack densities). From velocity values, our comparisons were also performed in terms of the ε, γ, and δ parameters (Thomsen parameters). The results show that Eshelby–Cheng effective medium model fits better with the measurements of ε and γ parameters for crack samples with only one type of crack aspect ratio.
The segregation of generations: ancestral groups in Sydney, 2011
Authors: Johnston Ron , Forrest James , Manley David , Jones Kelvyn 
Published: May 2017

AbstractMost models of immigrant minority enclave formation in cities represent their situation as relatively transient elements in urban residential mosaics. As minority group members become both economically integrated and socially–culturally assimilated into the host society, so they move away from the enclaves where they initially concentrated. Such shifts are especially likely in the second and later generations of group members, who are more likely to overcome the disadvantages experienced by many of the original settlers with regard to human capital. This paper evaluates that model using data on the residential distributions of three generations of those claiming one of 19 different ancestral groups in Sydney in 2011, at four nested spatial scales, deploying a recently developed inferential method for evaluating the intensity of residential segregation. The findings are not consistent with the model: in general, members of the second and third generations in any ancestral group are as segregated as the first generation (that is, those born outside Australia) at both regional and neighbourhood scales.
A randomized clinical trial comparing two two‐phase treatment strategies for in‐patients with severe depression
Authors: Vermeiden M. , Kamperman A. M. , Hoogendijk W. J. G. , van den Broek W. W. , Birkenhäger T. K. 
Published: May 2017

ObjectiveTo compare the efficacy of two antidepressant treatment strategies in severely depressed in‐patients, that is, imipramine vs. venlafaxine, both with subsequent lithium addition in non‐responders.MethodIn‐patients (n = 88) with major depressive disorder were randomized to 7‐week treatment with imipramine or venlafaxine (phase I). All non‐responders (n = 44) received 4‐week plasma level‐targeted dose lithium addition (phase II). Efficacy was evaluated after 11 weeks of treatment.ResultsAnalyzing phases I and II combined, non‐inferiority was established and the difference in the proportion of responders (HAM‐D score reduction ≥50%) by the end of phase II demonstrated the venlafaxine‐lithium treatment strategy to be significantly superior to the imipramine‐lithium treatment strategy (77% vs. 52%) (χ2(1) = 6.03; P = 0.01). Regarding remission (HAM‐D score ≤ 7), 15 of 44 (34%) patients in the imipramine‐lithium treatment group were remitters compared to 22 of 44 (50%) patients in the venlafaxine‐lithium treatment group, a non‐significant difference. Patients in the venlafaxine‐lithium treatment group had a non‐significant larger mean HAM‐D score reduction compared with patients in the imipramine‐lithium treatment group (16.1 vs. 13.5 points, respectively; Cohen's d = 0.30).ConclusionThe venlafaxine‐lithium treatment strategy can be considered a valuable alternative for the imipramine‐lithium treatment strategy in the treatment of severely depressed in‐patients.