bluuebunny/crossref_metadata_2025_split huggingface dataset:
Low-Dose Characterization of Kidney Stones Using Spectral Detector Computed Tomography
Authors: Große Hokamp Nils , Salem Johannes , Hesse Albrecht , Holz Jasmin Alexandra , Ritter Manuel , Heidenreich Axel , Maintz David , Haneder Stefan 
Published: March 2018

Objectives
The aim of this study was to investigate the feasibility of kidney stone composition analysis using spectral detector computed tomography scanner (SDCT) with normal- and low-dose imaging protocols.

Methods
A total of 154 stones harvested from nephrolithotripsy or nephrolithotomy with a known monocrystalline composition as determined by infrared spectroscopy were examined in a nonanthropomorphic phantom on an SDCT (IQon, Philips, Best, the Netherlands). Imaging was performed with 120 kVp and (a) 40 mAs and (b) 200 mAs, resulting in a computed tomography dose index (CTDIvol) of 2 and 10 mGy, respectively. Besides conventional CT images (CIs), SDCT enables reconstruction of virtual monoenergetic images (40–200 keV). Spectral coefficient images were calculated by performing a voxel-by-voxel combination of 40 and 200 keV images (Matlab R2017b, Mathworks Inc). All stones were semiautomatically 3D-segmented on CI using a threshold-based algorithm implemented in an offline DICOM viewer. Statistical assessment was performed using Steel-Dwass method to adjust for multiple comparisons.

Results
Ca-phosphate (n = 22), Ca-oxalate (n = 82), cysteine (n = 20), struvite (n = 3), uric acid (n = 18), and xanthine stones (n = 9) were included in the analysis. Stone diameter ranged from 3.0 to 13.5 mm. On CI, attenuation differed significantly between calcific and noncalcific stones only (P ≤ 0.05), the spectral coefficient differed significantly between (//): Ca-oxalate//Ca-phosphate//cystine//struvite//uric acid//xanthine in 10 mGy protocol (all P ≤ 0.05). The same results were found for the 2 mGy-protocol, except that differentiation of Ca-oxalate and Ca-phosphate as well as uric acid and xanthine was not possible (P ≥ 0.05).

Conclusions
Spectral detector CT allows for differentiation of kidney stones using semi-automatic segmentation and advanced image post-processing, even in low-dose imaging protocols.
Jagged1/Notch2 Controls Kidney Fibrosis via Tfam-mediated Metabolic Reprogramming
Authors: Huang Shizheng , Park Jihwan , Qiu Chengxiang , Sirin Yasemin , Han Seung Hyeok , Li Szu-yuan , Taylor Verdon , Zimber-Strobl Ursula , Susztak Katalin 
Published: March 2018

AbstractWhile Notch signaling has been proposed to play a key role in fibrosis, the direct molecular pathways targeted by Notch signaling and the precise ligand and receptor pair that are responsible for kidney disease remain poorly defined.In this study, we found that JAG1 and NOTCH2 showed the strongest correlation with the degree of interstitial fibrosis in a genome wide expression analysis of a large cohort of human kidney samples. RNA sequencing analysis of kidneys of mice with folic acid nephropathy, unilateral ureteral obstruction, or APOL1-associated kidney disease indicated that Jag1 and Notch2 levels were higher in all analyzed kidney fibrosis models. Mice with tubule-specific deletion of Jag1 or Notch2 (Kspcre/Jag1flox/flox, and Kspcre/Notch2flox/flox) had no kidney-specific alterations at baseline, but showed protection from folic acid induced kidney fibrosis. Tubule-specific genetic deletion of Notch1 and global knock-out of Notch3 had no effect on fibrosis. In vitro chromatin immunoprecipitation experiments and genome-wide expression studies identified the mitochondrial transcription factor A (Tfam) as a direct Notch target. Re-expression of Tfam in tubule cells prevented Notch-induced metabolic and profibrotic reprogramming. Kidney tubule specific deletion of Tfam resulted in perinatal lethality.In summary, Jag1/Notch2 plays a key role in kidney fibrosis development by regulating Tfam expression and metabolic reprogramming.
The Kendrick Modelling Platform: Language Abstractions and Tools for Epidemiology
Authors: Bui Mai Anh T. , Papoulias Nick , Stinckwich Serge , Ziane Mikal , Roche Benjamin 
Published: March 2018

AbstractBackgroundMathematical and computational models are widely used for examining transmission, pathogenicity and propagation of infectious diseases. Software implementation of such models and their accompanied modelling tools do not adhere to well established software engineering principles. These principles include bothmodularityandclear separation of concernsthat can promotereproducibilityandreusabilityby other researchers. On the contrary the software written for epidemiology is monolithic, highly coupled and severely heterogeneous. This reality ultimately makes these computational models hard to study and to reuse, both because of the programming competence required and because of the incompatibility of the different approaches involved. Our goal withKendrickis to simplify the creation of epidemiological models through a unified Domain-Specific Language for epidemiology that can support a variety of modelling and simulation approaches classically used in the field. This goal can be achieved by promotingreproducibilityandreusewith modular modelling abstractions.ResultsWe show through several examples how our modular abstractions and tools can reproduce uniformly complex mathematical and computational models of epidemics, despite being simulated by different methods. This is achieved without requiring sophisticated programming skills from the part of the user. We then successfully validate each kind of simulation through statistical analysis between the time series generated and the known theoretical expectations.ConclusionsKendrickis one of the few DSLs for epidemiology that does not burden its users with implementation details or expecting sophisticated programming skills. It is also currently the only language for epidemiology that supports modularity through clear separation of concerns that promote reproducibility and reuse.Kendrick’s wider adoption and further development from the epidemiological community could boost research productivity in epidemiology by allowing researchers to easily reproduce and reuse each other’s software models and simulations. The tool can also be used by people who are not necessarily epidemiology modelers.
Socioeconomic status of indigenous peoples with active tuberculosis in Brazil: a principal components analysis
Authors: Freitas Laís P. , Souza-Santos Reinaldo , Kolte Ida V. , Malacarne Jocieli , Basta Paulo C. 
Published: March 2018

ABSTRACTIndigenous people usually live in precarious conditions and suffer a disproportionally burden of tuberculosis in Brazil. To characterize the socioeconomic status of indigenous peoples with active tuberculosis in Brazil, this cross-sectional study included all Amerindians that started tuberculosis treatment between March 2011 and December 2012 in four municipalities of Mato Grosso do Sul state (Central-Western region). We tested the approach using principal components analysis (PCA) to create three socioeconomic indexes (SEI) using groups of variables: household characteristics, ownership of durable goods, and both. Cases were then classified into tertiles, with the 1st tertile representing the most disadvantaged. A total of 166 indigenous cases of tuberculosis were included. 31.9% did not have durable goods. 25.9% had family bathroom, 9.0% piped water inside the house and 53.0% electricity, with higher proportions in Miranda and Aquidauana. Houses were predominantly made using natural materials in Amambai and Caarapó. Miranda and Aquidauana had more cases in the 3rd tertile (92.3%) and Amambai, in the 1st tertile (37.7%). The indexes showed similar results and consistency for socioeconomic characterization. The percentage of people in the 3rd tertile increased with years of schooling. The majority in the 3rd tertile received Bolsa Família, a social welfare programme. This study confirmed the applicability of the PCA using information on household characteristics and ownership of durable goods for socioeconomic characterization of indigenous groups and provided important evidence of the unfavorable living conditions of Amerindians with tuberculosis in Mato Grosso do Sul.
Opposing roles of endosomal innate immunity proteins IFITM3 and TLR7 in human metapneumovirus infection
Authors: McMichael Temet M. , Zhang Yu , Kenney Adam D. , Zhang Lizhi , Lu Mijia , Chemudupati Mahesh , Li Jianrong , Yount Jacob S. 
Published: March 2018

ABSTRACTHuman metapneumovirus (hMPV) utilizes a bifurcated cellular entry strategy, fusing either with the plasma membrane or, after endocytosis, with the endosome membrane. Whether cellular factors restrict or enhance either entry pathway is largely unknown. We found that the interferon-induced transmembrane protein 3 (IFITM3) inhibits hMPV infection to an extent similar to endocytosis-inhibiting drugs, and an IFITM3 variant that accumulates at the plasma membrane in addition to its endosome localization provided increased virus restriction. Mechanistically, IFITM3 blocks hMPV F protein-mediated membrane fusion, and inhibition of infection was reversed by the membrane destabilizing drug amphotericin B. Conversely, we unexpectedly found that infection by some hMPV strains is enhanced by Toll-like receptor 7 (TLR7), an endosomal protein, suggesting that cellular entry via endocytosis may be particularly advantageous for hMPV despite eventual restriction of this pathway upon induction of IFITM3. Overall, our results identify IFITM3 and TLR7 as endosomal factors differentially regulating hMPV infection.
A new approach to design artificial 3D micro-niches with combined chemical, topographical and rheological cues
Authors: Stoecklin Celine , Yue Zhang , Chen Wilhelm W. , de Mets Richard , Fong Eileen , Studer Vincent , Viasnoff Virgile 
Published: March 2018

AbstractThe in vitro methods to recapitulate environmental cues around cells are usually optimized to test a specific property of the environment (biochemical nature or the stiffness of the extra cellular matrix (ECM), or nanotopography) for its capability to induce defined cell behaviors (lineage commitment, migration). Approaches that combine different environmental cues in 3D to assess the biological response of cells to the spatial organization of different biophysical and biochemical cues are growingly being developed. We demonstrate how the lamination of through-hole polymeric bio-functionalized membranes can be implemented to create complex bona fide micro-niches with differential 3D environmental properties using photoactive materials. Our approach enables to create micro-niches ranging in size from single cells to cell aggregates. They are bio-functionalized in 3D simultaneously with topographical featured, protein patterns and structured ECM surrogate with 1 micrometer resolution. We demonstrate how these niches extend in 3D the ability to pattern cells. We exemplify how they can be used to standardize cells shapes in 3D and to trigger the apico-basal polarization of single epithelial cells.
Role of noise and parametric variation in the dynamics of gene regulatory circuits
Authors: Kohar Vivek , Lu Mingyang 
Published: March 2018

AbstractStochasticity in gene expression impacts the dynamics and functions of gene regulatory circuits. Intrinsic noises, including those that are caused by low copy number of molecules and transcriptional bursting, are usually studied by stochastic analysis methods, such as Gillespie algorithm and Langevin simulation. However, the role of extrinsic factors, such as cell-to-cell variability and heterogeneity in microenvironment, is still elusive. To evaluate the effects of both intrinsic and extrinsic noises, we develop a new method, named sRACIPE, by integrating stochastic analysis with random circuit perturbation (RACIPE) method. Unlike traditional methods, RACIPE generates and analyzes an ensemble of mathematical models with random kinetic parameters. Previously, we have shown that the gene expression from random models form robust and functionally related clusters. Under the framework of this randomization-based approach, here we develop two stochastic simulation schemes, aiming to reduce the computational cost without sacrificing the convergence of statistics. One scheme uses constant noise to capture the basins of attraction, and the other one uses simulated annealing to detect the stability of states. By testing the methods on several gene regulatory circuits, we found that high noise, but not large parameter variation, merges clusters together. Our approach quantifies the robustness of a gene circuit in the presence of noise and sheds light on a new mechanism of noise induced hybrid states. We have implemented sRACIPE into a freely available R package.
Natural killer cells inhibit Plasmodium falciparum growth in red blood cells via antibody-dependent cellular cytotoxicity
Authors: Arora Gunjan , Hart Geoffrey T. , Manzella-Lapeira Javier , Doritchamou Justin Y.A. , Narum David L. , Thomas L. Michael , Brzostowski Joseph , Rajagopalan Sumati , Doumbo Ogobara K. , Traore Boubacar , Miller Louis H. , Pierce Susan K. , Duffy Patrick E. , Crompton Peter D. , Desai Sanjay A. , Long Eric O. 
Published: March 2018

AbstractAntibodies acquired naturally through repeated exposure to Plasmodium falciparum are essential in the control of blood-stage malaria. Antibody-dependent functions may include neutralization of parasite–host interactions, complement activation, and activation of Fc receptor functions. A role of antibody-dependent cellular cytotoxicity (ADCC) by natural killer (NK) cells in protection from malaria has not been established. Here we show that IgG isolated from adults living in a malaria-endemic region activated ADCC by primary human NK cells, which lysed infected red blood cells (RBCs) and inhibited parasite growth in an in vitro assay for ADCC-dependent growth inhibition. RBC lysis by NK cells was highly selective for infected RBCs in a mixed culture with uninfected RBCs. Human antibodies to P. falciparum antigens PfEMP1 and RIFIN were sufficient to promote NK-dependent growth inhibition. As these results implicate acquired immunity through NK-mediated ADCC, antibody-based vaccines that target bloodstream parasites should consider this new mechanism of action.
X Chromosome Dosage Modulates Multiple Molecular and Cellular Properties of Mouse Pluripotent Stem Cells Independently of Global DNA Methylation Levels
Authors: Song Juan , Janiszewski Adrian , Geest Natalie De , Vanheer Lotte , Talon Irene , Bakkali Mouna El , Oh Taeho , Pasque Vincent 
Published: March 2018

ABSTRACTDuring early mammalian development, the two X-chromosomes in female cells are active. Dosage compensation between XX female and XY male cells is then achieved by X-chromosome inactivation in female cells. Reprogramming female mouse somatic cells into induced pluripotent stem cells (iPSCs) leads to X-chromosome reactivation. The extent to which increased X-chromosome dosage (X-dosage) in female iPSCs leads to differences in the molecular and cellular properties of XX and XY iPSCs is still unclear. We show that chromatin accessibility in mouse iPSCs is modulated by X-dosage. Specific sets of transcriptional regulator motifs are enriched in chromatin with increased accessibility in XX or XY iPSCs. We show that the transcriptome, growth and pluripotency exit are also modulated by X-dosage in iPSCs. To understand the mechanisms by which increased X-dosage modulates the molecular and cellular properties of mouse pluripotent stem cells, we used heterozygous deletions of the X-linked gene Dusp9 in XX embryonic stem cells. We show that X-dosage regulates the transcriptome, open chromatin landscape, growth and pluripotency exit largely independently of global DNA methylation. Our results uncover new insights into X-dosage in pluripotent stem cells, providing principles of how gene dosage modulates the epigenetic and genetic mechanisms regulating cell identity.
A Quantitative Tractography Study into the Connectivity, Segmentation and Laterality of the Human Inferior Longitudinal Fasciculus
Authors: Panesar Sandip S , Fang-Cheng Yeh , Jacquesson Timothée , Hula William , Juan C Fernandez-Miranda 
Published: March 2018

AbstractThe human inferior longitudinal fasciculus (ILF) is a ventral, temporo-occipital association tract. Though described in early neuroanatomical works, its existence was later questioned. Application of in vivo tractography to the neuroanatomical study of the ILF has generally confirmed its existence, however consensus is lacking regarding its subdivision, laterality and connectivity. Further, there is a paucity of detailed neuroanatomic data pertaining to the exact anatomy of the ILF. Generalized Q-Sampling imaging (GQI) is a non-tensor tractographic modality permitting high resolution imaging of white-matter structures. As it is a non-tensor modality, it permits visualization of crossing fibers and accurate delineation of close-proximity fiber-systems. We applied deterministic GQI tractography to data from 30 healthy subjects and a large-volume diffusion atlas, to delineate ILF anatomy. Post-mortem white matter dissection was also carried out in a cadaveric specimen for further validation. The ILF was found in all 60 hemispheres. At its occipital extremity, it demonstrated a trifurcated termination pattern which was used to separate the ILF into 3 distinct sub-fascicles: Dorsolateral, ventrolateral and ventromedial. These divisions were consistent across the subject set and within the atlas. We applied quantitative techniques to study connectivity strength of the ILF at its anterior and posterior extremities. Overall, the 3 sub-fascicles, and the whole ILF, demonstrated strong leftward-lateralized connectivity patterns. Leftward-lateralization was also found for ILF volumes across the subject set. Due to connective and volumetric leftward-dominance and ventral location, we postulate the ILFs role in the semantic system. Further, our results are in agreement with functional and lesion-based postulations pertaining to the ILFs role in facial recognition.
Monkeys are Curious about Counterfactual Outcomes
Authors: Wang Maya Zhe , Hayden Benjamin Y. 
Published: March 2018

ABSTRACTWhile many non-human animals show basic exploratory behaviors, it remains unclear whether any animals possess human-like curiosity. We propose that human-like curiosity satisfies three formal criteria: (1) willingness to pay (or to sacrifice reward) to obtain information, (2) that the information provides no instrumental or strategic benefit (and the subject understands this), and (3) the amount the subject is willing to pay scales with the amount of information available. Although previous work, including our own, demonstrates that some animals will sacrifice juice rewards for information, that information normally predicts upcoming rewards and their ostensible curiosity may therefore be a byproduct of reinforcement processes. Here we get around this potential confound by showing that macaques sacrifice juice to obtain information about counterfactual outcomes (outcomes that could have occurred had the subject chosen differently). Moreover, willingness-to-pay scales with the information (Shannon entropy) offered by the counterfactual option. These results demonstrate human-like curiosity in non-human animals according to our strict criteria, which circumvent several confounds associated with less stringent criteria.
What influences the willingness of Vietnamese accountants to adopt International Financial Reporting Standards (IFRS) by 2025?
Authors: Phan Duc , Joshi Mahesh , Mascitelli Bruno 
Published: March 2018

PurposeThe purpose of this paper is to examine the effects of perceived implications of International Financial Reporting Standards (IFRS) adoption on the willingness to adopt IFRS.Design/methodology/approachThe study analysed the causal relationships between perceptions and the willingness of the accountants to adopt IFRS.FindingsThe findings revealed that perceived benefits drove the willingness to adopt IFRS whereas the perceived disadvantages and challenges diminished the willingness. Knowledge of IFRS enhanced the willingness towards IFRS adoption. Also, legitimacy desire enhanced the association between the perceived implications and the willingness to adopt IFRS.Originality/valueThe study contributes significantly to theory and practice as Vietnamese policy makers recently announced their strategic planning to full IFRS adoption by 2025.
On the news today: challenging homelessness through participatory action research
Authors: De Oliveira Bruno 
Published: March 2018

Purpose
How can people with lived experience of homelessness actively participate in contesting their marginalisation? The purpose of this paper is to suggest that involving people who are homeless in participatory action research (PAR) is one such strategy. This paper shows that such an approach can have a significant impact on empowering people with direct of experience of homelessness to challenge prevailing social discourses, particularly in terms of the way in which the local media presents homelessness as a social issue.

Design/methodology/approach
A PAR approach informed the design, development and dissemination of the study on which this paper is based. Analytically, it is underpinned by Foucauldian discourse analysis (FDA). FDA, with its focus on power relations in society, is noted to be particularly useful for analysing local media representations of homeless people.

Findings
The research reported here found that academic practitioners and homeless people can work together to challenge media discourses, which serve to marginalise people affected by homelessness.

Research limitations/implications
The research reported here served to challenge some of the ways in homeless people are victimized and stigmatized.

Practical implications
The research reported here has the potential to inform future research concerned with understanding media presentations of homeless people. It can be seen as a model for how people affected by a particularly pernicious social issue can contribute to research in ways that go beyond researching for the sake of research.

Originality/value
The research reported here provides evidence of the emancipatory value of research that seeks to bring academic practitioners and homeless people together in a partnership to challenge vital social issues such as the power of the local media to frame understandings of homelessness.