bluuebunny/crossref_metadata_2025_split huggingface dataset:
New Common and Rare Variants Influencing Metabolic Syndrome and Its Individual Components in a Korean Population
Authors: Lee Ho-Sun , Kim Yongkang , Park Taesung 
Published: April 2018

AbstractTo identify novel loci for susceptibility to MetS, we conducted genome-wide association and exome wide association studies consisting of a discovery stage cohort (KARE, 1946 cases and 6427 controls), and a replication stage cohort (HEXA, 430 cases and 3,264 controls). For finding genetic variants for MetS, with its components, we performed multivariate analysis for common and rare associations, using a standard logistic regression analysis for MetS. From the discovery and replication GWA studies, we confirmed 21 genome-wide signals significantly associated with MetS. Of these 21, four were previously unreported to associate with any MetS components: rs765547 near LPL; rs3782889 in MYL2; and rs11065756 and rs10849915 in CCDC63. Using exome chip variants, gene-based analysis of rare variants revealed three genes, CETP, SH2B1, and ZFP2, in the discovery stage, among which only CETP was confirmed in the replication stage. Finally, CETP D442G (rs2303790) associated, as a less common variant, with decreased risk of MetS. In conclusion, we discovered a total of five new MetS-associated loci, and their overlap with other disease-related components, suggest roles in the various etiologies of MetS, and its possible preventive strategies.
Positive Surgical Margins in the 10 Most Common Solid Cancers
Authors: Orosco Ryan K. , Tapia Viridiana J. , Califano Joseph A. , Clary Bryan , Cohen Ezra E. W. , Kane Christopher , Lippman Scott M. , Messer Karen , Molinolo Alfredo , Murphy James D. , Pang John , Sacco Assuntina , Tringale Kathryn R. , Wallace Anne , Nguyen Quyen T. 
Published: April 2018

AbstractA positive surgical margin (PSM) following cancer resection oftentimes necessitates adjuvant treatments and carries significant financial and prognostic implications. We sought to compare PSM rates for the ten most common solid cancers in the United States, and to assess trends over time. Over 10 million patients were identified in the National Cancer Data Base from 1998–2012, and 6.5 million had surgical margin data. PSM rates were compared between two time periods, 1998–2002 and 2008–2012. PSM was positively correlated with tumor category and grade. Ovarian and prostate cancers had the highest PSM prevalence in women and men, respectively. The highest PSM rates for cancers affecting both genders were seen for oral cavity tumors. PSM rates for breast cancer and lung and bronchus cancer in both men and women declined over the study period. PSM increases were seen for bladder, colon and rectum, and kidney and renal pelvis cancers. This large-scale analysis appraises the magnitude of PSM in the United States in order to focus future efforts on improving oncologic surgical care with the goal of optimizing value and improving patient outcomes.
Imaging beyond ultrasonically-impenetrable objects
Authors: Ilovitsh Tali , Ilovitsh Asaf , Foiret Josquin , Ferrara Katherine W. 
Published: April 2018

AbstractUltrasound images are severely degraded by the presence of obstacles such as bones and air gaps along the beam path. This paper describes a method for imaging structures that are distal to obstacles that are otherwise impenetrable to ultrasound. The method uses an optically-inspired holographic algorithm to beam-shape the emitted ultrasound field in order to bypass the obstacle and place the beam focus beyond the obstruction. The resulting performance depends on the transducer aperture, the size and position of the obstacle, and the position of the target. Improvement compared to standard ultrasound imaging is significant for obstacles for which the width is larger than one fourth of the transducer aperture and the depth is within a few centimeters of the transducer. For such cases, the improvement in focal intensity at the location of the target reaches 30-fold, and the improvement in peak-to-side-lobe ratio reaches 3-fold. The method can be implemented in conventional ultrasound systems, and the entire process can be performed in real time. This method has applications in the fields of cancer detection, abdominal imaging, imaging of vertebral structure and ultrasound tomography. Here, its effectiveness is demonstrated using wire targets, tissue mimicking phantoms and an ex vivo biological sample.
Contrasting epigenetic states of heterochromatin in the different types of mouse pluripotent stem cells
Authors: Tosolini Matteo , Brochard Vincent , Adenot Pierre , Chebrout Martine , Grillo Giacomo , Navia Violette , Beaujean Nathalie , Francastel Claire , Bonnet-Garnier Amélie , Jouneau Alice 
Published: April 2018

AbstractMouse embryonic stem cells (ESCs) and epiblast stem cells (EpiSCs) represent naive and primed pluripotency states, respectively, and are maintained in vitro by specific signalling pathways. Furthermore, ESCs cultured in serum-free medium with two kinase inhibitors (2i-ESCs) are thought to be the ground naïve pluripotent state. Here, we present a comparative study of the epigenetic and transcriptional states of pericentromeric heterochromatin satellite sequences found in these pluripotent states. We show that 2i-ESCs are distinguished from other pluripotent cells by a prominent enrichment in H3K27me3 and low levels of DNA methylation at pericentromeric heterochromatin. In contrast, serum-containing ESCs exhibit higher levels of major satellite repeat transcription, which is lower in 2i-ESCs and even more repressed in primed EpiSCs. Removal of either DNA methylation or H3K9me3 at PCH in 2i-ESCs leads to enhanced deposition of H3K27me3 with few changes in satellite transcript levels. In contrast, their removal in EpiSCs does not lead to deposition of H3K27me3 but rather removes transcriptional repression. Altogether, our data show that the epigenetic state of PCH is modified during transition from naive to primed pluripotency states towards a more repressive state, which tightly represses the transcription of satellite repeats.
Retraction of the dissolution front in natural porous media
Authors: Yang Y. , Bruns S. , Rogowska M. , Hakim S. S. , Hammel J. U. , Stipp S. L. S. , Sørensen H. O. 
Published: April 2018

AbstractThe dissolution of porous materials in a flow field controls the fluid pathways through rocks and soils and shapes the morphology of landscapes. Identifying the dissolution front, the interface between the reactive and the unreactive volumes in a dissolving medium, is a prerequisite for describing dissolution-induced structure emergence and transformation. Despite its fundamental importance, the report on the dynamics of a dissolution front in an evolving natural microstructure is scarce. Here we show an unexpected, spontaneous migration of the dissolution front against the flow direction. This retraction stems from infiltration instability induced surface generation, which leads to an increase in reactive surface area when a porous medium dissolves in an imposing flow field. There is very good agreement between observations made with in situ, X-ray tomography and model predictions. Both show that the value of reactive surface area reflects a balance between flow-dependent surface generation and destruction, i.e. the “dry” geometric surface area of a porous material, measured without a flow field, is not necessarily the upper limit of its reactive surface area when in contact with reactive flow. This understanding also contributes to reconciling the discrepancies between field and laboratory derived solid-fluid reaction kinetics.
Correcting B0 Field Distortions in MRI Caused by Stainless Steel Orthodontic Appliances at 1.5 T Using Permanent Magnets – A Head Phantom Study
Authors: Wang Zhiyue J. , Park Yong Jong , Morriss Michael C. , Seo Youngseob , Nguyen Trung , Hallac Rami R. , Nava Ana , Chopra Rajiv , Chatzinoff Yonatan , Price Khyana , Rollins Nancy K. 
Published: April 2018

AbstractSusceptibility artifacts caused by stainless steel orthodontic appliances (braces) pose significant challenges in clinical brain MRI examinations. We introduced field correction device (FCD) utilizing permanent magnets to cancel the induced B0inhomogeneity and mitigate geometric distortions in MRI. We evaluated a prototype FCD using a 3D-printed head phantom in this proof of concept study. The phantom was compartmented into anterior frontal lobe, temporal lobe, fronto-parieto-occipital lobe, basal ganglia and thalami, brain stem, and cerebellum and had built-in orthogonal gridlines to facilitate the quantification of geometric distortions and volume obliterations. Stainless steel braces were mounted on dental models of three different sizes with total induced magnetic moment 0.15 to 0.17 A·m2. With braces B0standard deviation (SD) ranged from 2.8 to 3.7 ppm in the temporal and anterior frontal lobes vs. 0.2 to 0.3 ppm without braces. The volume of brain regions in diffusion weighted imaging was obliterated by 32–38% with braces vs. 0% without braces in the cerebellum. With the FCD the SD of B0ranged from 0.3 to 1.2 ppm, and obliterated volume ranged from 0 to 6% in the corresponding brain areas. These results showed that FCD can effectively decrease susceptibility artifacts from orthodontic appliances.
Ion Permeation Mechanism in Epithelial Calcium Channel TRVP6
Authors: Sakipov Serzhan , Sobolevsky Alexander I. , Kurnikova Maria G. 
Published: April 2018

AbstractCalcium is the most abundant metal in the human body that plays vital roles as a cellular electrolyte as well as the smallest and most frequently used signaling molecule. Calcium uptake in epithelial tissues is mediated by tetrameric calcium-selective transient receptor potential (TRP) channels TRPV6 that are implicated in a variety of human diseases, including numerous forms of cancer. We used TRPV6 crystal structures as templates for molecular dynamics simulations to identify ion binding sites and to study the permeation mechanism of calcium and other ions through TRPV6 channels. We found that at low Ca2+ concentrations, a single calcium ion binds at the selectivity filter narrow constriction formed by aspartates D541 and allows Na+ permeation. In the presence of ions, no water binds to or crosses the pore constriction. At high Ca2+ concentrations, calcium permeates the pore according to the knock-off mechanism that includes formation of a short-lived transition state with three calcium ions bound near D541. For Ba2+, the transition state lives longer and the knock-off permeation occurs slower. Gd3+ binds at D541 tightly, blocks the channel and prevents Na+ from permeating the pore. Our results provide structural foundations for understanding permeation and block in tetrameric calcium-selective ion channels.
Effects of oil-film layer and surfactant on the siphonal respiration and survivorship in the fourth instar larvae of Aedes togoi mosquito in laboratory conditions
Authors: Lee Sang Joon , Kim Jun Ho , Lee Seung Chul 
Published: April 2018

AbstractMosquitoes transmit various diseases; thus, controlling them is necessary to prevent mosquito-borne infections. Unlike flying adult mosquitoes, those in the immature stages are easy to control because of being restricted to their habitats found in an aquatic environment. In this study, we aimed to evaluate of respiration and survivorship in the larvae of Aedes togoi. The mechanism of actions of the oil-film layer and the surfactant as well as their effects on the siphonal respiration of submerged Aedes togoi larvae were analyzed by checking the survival time of mosquito larvae against oil-film layer and surfactant, and conducting experiments using a siphon-model. Compared with an impermeable membrane used for reference (762.4 min; average time in all cases), the survival time of mosquito larvae was 5% longer for the oil-film layer (808.1 min) and 40% longer for the surfactant (1086.9 min). The surface of the siphon was changed from hydrophobic to hydrophilic by addition of a surfactant. In addition, the surface tension and wettability have a significant influence on the opening and closing of siphon. This study would be helpful for understanding the basic mechanism of physical control measures for disturbing the siphonal respiration of mosquito larvae in a way of dissolved oxygen and surface tension. The present results would guide the establishment of effective control measures for mosquitoes.
Metabolomics and proteomics reveal drought-stress responses of leaf tissues from spring-wheat
Authors: Michaletti Anna , Naghavi Mohammad Reza , Toorchi Mahmoud , Zolla Lello , Rinalducci Sara 
Published: April 2018

AbstractTo reveal the integrative biochemical networks of wheat leaves in response to water deficient conditions, proteomics and metabolomics were applied to two spring-wheat cultivars (Bahar, drought-susceptible; Kavir, drought-tolerant). Drought stress induced detrimental effects on Bahar leaf proteome, resulting in a severe decrease of total protein content, with impairments mainly in photosynthetic proteins and in enzymes involved in sugar and nitrogen metabolism, as well as in the capacity of detoxifying harmful molecules. On the contrary, only minor perturbations were observed at the protein level in Kavir stressed leaves. Metabolome analysis indicated amino acids, organic acids, and sugars as the main metabolites changed in abundance upon water deficiency. In particular, Bahar cv showed increased levels in proline, methionine, arginine, lysine, aromatic and branched chain amino acids. Tryptophan accumulation via shikimate pathway seems to sustain auxin production (indoleacrylic acid), whereas glutamate reduction is reasonably linked to polyamine (spermine) synthesis. Kavir metabolome was affected by drought stress to a less extent with only two pathways significantly changed, one of them being purine metabolism. These results comprehensively provide a framework for better understanding the mechanisms that govern plant cell response to drought stress, with insights into molecules that can be used for crop improvement projects.
Growth mechanism of epitaxial YSZ on Si by Pulsed Laser Deposition
Authors: Dubbink David , Koster Gertjan , Rijnders Guus 
Published: April 2018

AbstractThe epitaxial growth of yttria-stabilized zirconia (YSZ) on silicon with native oxide was investigated in order to gain more insight in the growth mechanism. Specifically, attention was paid to the possibilities to control the chemical interactions between YSZ, silicon and oxygen during initial growth. The sources of oxygen during growth proved to play an important role in the growth process, as shown by individual manipulation of all sources present during Pulsed Laser Deposition. Partial oxidation of the YSZ plasma and sufficient delivery of oxygen to the growing film were necessary to prevent silicide formation and obtain optimal YSZ crystalline qualities. In these conditions, thickness increase of the silicon native oxide before growth just started to occur, while a much faster regrowth of silicon oxide at the YSZ-Si interface occurred during growth. Control of all these contributions to the growth process is necessary to obtain reproducible growth of high quality YSZ.
Temporal and spatial changes of macrobenthos community in the regions frequently occurring black water aggregation in Lake Taihu
Authors: Chen Jianqin , Hu Dongfang , Zhang Chenling , Ding Zhengfeng 
Published: April 2018

AbstractSeasonal survey was performed from August 2015 to May 2016 at 50 sampling sites in Lake Taihu to determine the spatial and temporal changes in macrobenthos community and their relationships with environmental variables. A total of 58 macrobenthos species were collected and identified, including 28 species of annelids, 17 species of molluscs, and 12 species of arthropods. Both the community composition and the dominant species changed temporally and spatially. Correspondingly, the macrobenthos biodiversity differed among regions and seasons. The macrobenthos density decreased with increased sediment depth, which is the first report about the vertical distribution of macrobenthos in Lake Taihu. The majority of benthic animals were located within the sediment depth of 0–5 cm and 5–10 cm, accounting for 39.25% and 24.87% of the total abundance respectively. Redundancy discriminate analysis revealed that the main environmental factors affecting the most contributing macrobenthos species were temperature in summer, transparency, dissolved oxygen and pH in autumn, and water depth and dissolved oxygen in winter. Particularly, salinity and conductivity showed high correlation with the macrobenthos community through the whole sampling period. The investigation reveals the inherent spatiotemporal variation of macrobenthos community, and provides references for the biological assessment of water quality in Lake Taihu.
Sunlight-Induced photochemical synthesis of Au nanodots on α-Fe2O3@Reduced graphene oxide nanocomposite and their enhanced heterogeneous catalytic properties
Authors: Bharath G. , Anwer Shoaib , Mangalaraja R. V. , Alhseinat Emad , Banat Fawzi , Ponpandian N. 
Published: April 2018

AbstractIn this present study, we report the synthesis of Au nanodots on α-Fe2O3@reduced graphene oxide (RGO) based hetero-photocatalytic nanohybrids through a chlorophyll mediated photochemical synthesis. In this process, chlorophyll induces a rapid reduction (30 min) of Au3+ions to Au° metallic nanodots on α-Fe2O3@RGO surface under sunlight irradiation. The nucleation growth process, photo-induced electron-transfer mechanism and physico-chemical properties of the Au@α-Fe2O3@RGO ternary nanocomposites were systematically studied with various analytical techniques. This novel photochemical synthesis process is a cost-effective, convenient, surfactant-less, and scalable method. Moreover, the prepared ternary nanocomposites enhanced catalytic activity as compared to pure α-Fe2O3and α-Fe2O3@RGO. The advantages and synergistic effect of Au@α-Fe2O3@RGO exhibit, (i) a broader range of visible-light absorption due to visible light band gap of α-Fe2O3, (ii) lower recombination possibility of photo-generated electrons and holes due to effect of Au and (iii) faster electron transfer due to higher conductivity of RGO. Therefore, the prepared Au@α-Fe2O3@RGO hetero-photocatalytic nanohybrids exhibited a remarkable photocatalytic activity, thus enabling potential active hetero-photocatalyst for industrial and environmental applications.
Distinguishing butchery cut marks from crocodile bite marks through machine learning methods
Authors: Domínguez-Rodrigo Manuel , Baquedano Enrique 
Published: April 2018

AbstractAll models of evolution of human behaviour depend on the correct identification and interpretation of bone surface modifications (BSM) on archaeofaunal assemblages. Crucial evolutionary features, such as the origin of stone tool use, meat-eating, food-sharing, cooperation and sociality can only be addressed through confident identification and interpretation of BSM, and more specifically, cut marks. Recently, it has been argued that linear marks with the same properties as cut marks can be created by crocodiles, thereby questioning whether secure cut mark identifications can be made in the Early Pleistocene fossil record. Powerful classification methods based on multivariate statistics and machine learning (ML) algorithms have previously successfully discriminated cut marks from most other potentially confounding BSM. However, crocodile-made marks were marginal to or played no role in these comparative analyses. Here, for the first time, we apply state-of-the-art ML methods on crocodile linear BSM and experimental butchery cut marks, showing that the combination of multivariate taphonomy and ML methods provides accurate identification of BSM, including cut and crocodile bite marks. This enables empirically-supported hominin behavioural modelling, provided that these methods are applied to fossil assemblages.
From cooperative to uncorrelated clogging in cross-flow microfluidic membranes
Authors: van Zwieten R. , van de Laar T. , Sprakel J. , Schroën K. 
Published: April 2018

AbstractThe operational lifetime of filtration membranes is reduced by the clogging of pores and subsequent build-up of a fouling or cake layer. Designing membrane operations in which clogging is delayed or even mitigated completely, requires in-depth insight into its origins. Due to the complexity of the clogging process, simplified model membranes fabricated in microfluidic chips have emerged as a powerful tool to study how clogs emerge and deteriorate membrane efficiency. However, to date, these have focussed solely on dead-end filtration, while cross-flow filtration is of greater practical relevance at the industrial scale. As such, the microscopic mechanisms of clogging in crossflow geometries have remained relatively ill-explored. Here we use a microfluidic filtration model to probe the kinetics and mechanisms of clogging in crossflow. Our study exposes two findings: (i) the primary clogging rate of individual pores depends only on the trans-membrane flux, whose strong effects are explained quantitatively by extending existing models with a term for flux-controlled flow-enhanced barrier crossing, (ii) cross-membrane flow affects the pore-pore communication, leading to a transition from correlated to uncorrelated clogging of the membrane, which we explain qualitatively by deriving a dimensionless number which captures two essential regimes of clogging at the microscale.
Using nested discretization for a detailed yet computationally efficient simulation of local hydrology in a distributed hydrologic model
Authors: Wang Dongdong , Liu Yanlan , Kumar Mukesh 
Published: April 2018

AbstractFully distributed hydrologic models are often used to simulate hydrologic states at fine spatio-temporal resolutions. However, simulations based on these models may become computationally expensive, constraining their applications to smaller domains. This study demonstrates that a nested-discretization based modeling strategy can be used to improve the efficiency of distributed hydrologic simulations, especially for applications where fine resolution estimates of hydrologic states are of the focus only within a part of a watershed. To this end, we consider two applications where the goal is to capture the groundwater dynamics within a defined target area. Our results show that at the target locations, a nested simulation is able to competently replicate the estimates of groundwater table as obtained from the fine simulation, while yielding significant computational savings. The results highlight the potential of using nested discretization for a detailed yet computationally efficient estimation of hydrologic states in part of the model domain.