bluuebunny/crossref_metadata_2025_split huggingface dataset:
Competing rhythmic neural representations of orientations during concurrent attention to multiple orientation features
Authors: Mo Ce , Lu Junshi , Wu Bichan , Jia Jianrong , Luo Huan , Fang Fang 
Published: November 2019

AbstractWhen a feature is attended, all locations containing this feature are enhanced throughout the visual field. However, how the brain concurrently attends to multiple features remains unknown and cannot be easily deduced from classical attention theories. Here, we recorded human magnetoencephalography signals when subjects concurrently attended to two spatially overlapping orientations. A time-resolved multivariate inverted encoding model was employed to track the ongoing temporal courses of the neural representations of the attended orientations. We show that the two orientation representations alternate with each other and undergo a theta-band (~4 Hz) rhythmic fluctuation over time. Similar temporal profiles are also revealed in the orientation discrimination performance. Computational modeling suggests a tuning competition process between the two neuronal populations that are selectively tuned to one of the attended orientations. Taken together, our findings reveal for the first time a rhythm-based, time-multiplexing neural machinery underlying concurrent multi-feature attention.
Influence of confinement on free radical chemistry in layered nanostructures
Authors: Ghandi Khashayar , Landry Cody , Du Tait , Lainé Maxime , Saul Andres , Le Caër Sophie 
Published: November 2019

AbstractThe purpose of the present work was to study how chemical reactions and the electronic structure of atoms are affected by confinement at the sub-nanometer scale. To reach this goal, we studied the H atom in talc, a layered clay mineral. Talc is a highly 2D-confining material with the width of its interlayer space close to angstrom. We investigated talc with a particle accelerator-based spectroscopic method that uses elementary particles. This technique generates an exotic atom, muonium (Mu), which can be considered as an isotope of the H atom. Moreover, the technique allows us to probe a single atom (H atom) at any time and explore the effects of the layered clay on a single ion (proton) or atom. The cation/electron recombination happens in two time windows: one faster than a nanosecond and the other one at longer than microseconds. This result suggests that two types of electron transfer processes take place in these clay minerals. Calculations demonstrated that the interlayer space acts as a catalytic surface and is the primary location of cation/electron recombination in talc. Moreover, the studies of the temperature dependence of Mu decay rates, due to the formation of the surrogate of H2, is suggestive of an “H2” formation reaction that is thermally activated above 25 K, but governed by quantum diffusion below 25 K. The experimental and computational studies of the hyperfine coupling constant of Mu suggest that it is formed in the interlayer space of talc and that its electronic structure is extremely changed due to confinement. All these results imply that the chemistry could be strongly affected by confinement in the interlayer space of clays.
Twist-to-bend ratio: an important selective factor for many rod-shaped biological structures
Authors: Wolff-Vorbeck Steve , Langer Max , Speck Olga , Speck Thomas , Dondl Patrick 
Published: November 2019

AbstractMechanical optimisation plays a key role in living beings either as an immediate response of individuals or as an evolutionary adaptation of populations to changing environmental conditions. Since biological structures are the result of multifunctional evolutionary constraints, the dimensionless twist-to-bend ratio is particularly meaningful because it provides information about the ratio of flexural rigidity to torsional rigidity determined by both material properties (bending and shear modulus) and morphometric parameters (axial and polar second moment of area). The determination of the mutual contributions of material properties and structural arrangements (geometry) or their ontogenetic alteration to the overall mechanical functionality of biological structures is difficult. Numerical methods in the form of gradient flows of phase field functionals offer a means of addressing this question and of analysing the influence of the cross-sectional shape of the main load-bearing structures on the mechanical functionality. Three phase field simulations were carried out showing good agreement with the cross-sections found in selected plants: (i) U-shaped cross-sections comparable with those of Musa sp. petioles, (ii) star-shaped cross-sections with deep grooves as can be found in the lianoid wood of Condylocarpon guianense stems, and (iii) flat elliptic cross-sections with one deep groove comparable with the cross-sections of the climbing ribbon-shaped stems of Bauhinia guianensis.
DeepIso: A Deep Learning Model for Peptide Feature Detection from LC-MS map
Authors: Zohora Fatema Tuz , Rahman M. Ziaur , Tran Ngoc Hieu , Xin Lei , Shan Baozhen , Li Ming 
Published: November 2019

AbstractLiquid chromatography with tandem mass spectrometry (LC-MS/MS) based quantitative proteomics provides the relative different protein abundance in healthy and disease-afflicted patients, which offers the information for molecular interactions, signaling pathways, and biomarker identification to serve the drug discovery and clinical research. Typical analysis workflow begins with the peptide feature detection and intensity calculation from LC-MS map. We are the first to propose a deep learning based model, DeepIso, that combines recent advances in Convolutional Neural Network (CNN) and Recurrent Neural Network (RNN) to detect peptide features of different charge states, as well as, estimate their intensity. Existing tools are designed with limited engineered features and domain-specific parameters, which are hardly updated despite a huge amount of new coming proteomic data. On the other hand, DeepIso consisting of two separate deep learning based modules, learns multiple levels of representation of high dimensional data itself through many layers of neurons, and adaptable to newly acquired data. The peptide feature list reported by our model matches with 97.43% of high quality MS/MS identifications in a benchmark dataset, which is higher than the matching produced by several widely used tools. Our results demonstrate that novel deep learning tools are desirable to advance the state-of-the-art in protein identification and quantification.
Aerosol gas exchange system (AGES) for nanoparticle sampling at elevated temperatures: Modeling and experimental characterization
Authors: Bainschab Markus , Martikainen Sampsa , Keskinen Jorma , Bergmann Alexander , Karjalainen Panu 
Published: November 2019

AbstractAn aerosol gas exchange system (AGES) for nanoparticle sampling at elevated temperatures was developed, modeled, and further characterized with laboratory tests with respect to gas exchange efficiency and particle losses. The model describing the gas exchange was first verified with oxygen and later studied with several inert gases having molecular masses between 18 and 135 u. The exchange rate of the lightest compounds exceeds 90% efficiency at the flow rates used. In order to reach similarly high removal efficiencies for larger molecules, the residence time in the AGES has to be increased. The removal of sticky gases was studied with gaseous sulfuric acid. Results agreed with the model where the boundary condition is zero concentration on the wall. The AGES exhibits very limited particle losses (<5%) for mono-disperse 6 nm particles. Furthermore, diffusional losses for particles down to 1.2 nm were measured utilizing polydisperse aerosol. The experimental findings are in good agreement with the model derived. As both, gas exchange rate and particle losses, rely on the physical effect of diffusion, an optimization for enhanced gas exchange efficiency will come at the cost of increased diffusional particle losses. The presented model can be used as a tool to redesign and optimize the AGES for a desired application. With an application targeted design, particle dilution can be avoided, which can lead to improved results in many fields of aerosol measurement.
The interplay between Mn and Fe in Deinococcus radiodurans triggers cellular protection during paraquat-induced oxidative stress
Authors: Santos Sandra P. , Yang Yang , Rosa Margarida T. G. , Rodrigues Mafalda A. A. , De La Tour Claire Bouthier , Sommer Suzanne , Teixeira Miguel , Carrondo Maria A. , Cloetens Peter , Abreu Isabel A. , Romão Célia V. 
Published: November 2019

AbstractThe bacterium Deinococcus radiodurans is highly resistant to several stress conditions, such as radiation. According to several reports, manganese plays a crucial role in stress protection, and a high Mn/Fe ratio is essential in this process. However, mobilization of manganese and iron, and the role of DNA-binding-proteins-under-starved-conditions during oxidative-stress remained open questions. We used synchrotron-based X-ray fluorescence imaging at nano-resolution to follow element-relocalization upon stress, and its dependency on the presence of Dps proteins, using dps knockout mutants. We show that manganese, calcium, and phosphorus are mobilized from rich-element regions that resemble electron-dense granules towards the cytosol and the cellular membrane, in a Dps-dependent way. Moreover, iron delocalizes from the septum region to the cytoplasm affecting cell division, specifically in the septum formation. These mechanisms are orchestrated by Dps1 and Dps2, which play a crucial role in metal homeostasis, and are associated with the D. radiodurans tolerance against reactive oxygen species.
De novo cancer incidence after kidney and liver transplantation: Results from a nationwide population based data
Authors: Park Boyoung , Yoon Junghyun , Choi Dongho , Kim Han Joon , Jung Yun Kyung , Kwon Oh Jung , Lee Kyeong Geun 
Published: November 2019

AbstractThe cancer risk among solid organ transplantation recipients in East-Asia has been insufficiently studied. This study estimated de novo cancer incidence in kidney and liver recipients 2008–2015, compared with the general population in Korea using nationwide data. This is a retrospective cohort study using nationwide health insurance claims data. The study population was comprised of cancer-free 10,085 kidney recipients and 3,822 liver recipients. Standardized incidence ratio (SIR) of cancer using indirect standardization was calculated. Compared with the general population, the cancer risk increased by 3.19-fold in male and 2.56-fold in female kidney recipients. By cancer type, a notably increased SIR was observed for Kaposi sarcoma, renal cancer, skin cancer, and non-Hodgkin’s lymphoma in male and for bladder cancer, renal cancer, and non-Hodgkin’s lymphoma in female kidney recipients. In liver recipients, the SIR of all cancers was 3.43 in males and 2.30 in females. In male liver recipients, the SIRs for Kaposi sarcoma, non-Hodgkin’s lymphoma, myeloid leukemia, and skin cancer and in female recipients those for non-Hodgkin’s lymphoma and liver cancer were prominent. A greatly higher SIRs for overall cancer and non-Hodgkin’s lymphoma in kidney and liver recipients aged 0–19 were observed, compared with recipients in other age group. The incidence of de novo cancer in kidney and liver recipients was higher than the general population and common types were different. Strategies of cancer prevention and screening after kidney and liver transplantation should be developed in response to the incidence of common types of de novo cancers.
Discovery of novel potential selective HDAC8 inhibitors by combine ligand-based, structure-based virtual screening and in-vitro biological evaluation
Authors: Debnath Sudhan , Debnath Tanusree , Bhaumik Samhita , Majumdar Swapan , Kalle Arunasree M. , Aparna Vema 
Published: November 2019

AbstractNeuroblastoma is the most common extracranial solid tumor found in children and survival rate is extremely meager. HDAC8, a class I zinc-dependent enzyme, is a potential drug target for treatment of neuroblastoma and T cell lymphoma. Most of the HDAC8 inhibitors discovered till date contains a hydroxamic acid group which acts as a zinc binding group. The high binding affinity to the zinc and other ions results in adverse effects. Also, the non-selective inhibition of HDACs cause a variety of side effects. The objective of this is to identify structurally diverse, non-hydroxamate, novel, potential and selective HDAC8 inhibitors. A number of five featured pharmacophore hypotheses were generated using 32 known selective HDAC8 inhibitors. The hypotheses ADDRR.4 were selected for building 3D QSAR model. This model has an excellent correlation coefficient and good predictive ability, which was employed for virtual screening of Phase database containing 4.3 × 106 molecules. The resultant hits with fitness score >1.0 were optimized using in-silico ADMET (absorption, distribution, metabolism, excretion, and toxicity) and XP glide docking studies. On the basis of pharmacophore matching, interacting amino acid residues, XP glide score, more affinity towards HDAC8 and less affinity towards other HDACs, and ADME results five hits- SD-01, SD-02, SD-03, SD-04 and SD-05 with new structural scaffolds, non-hydroxamate were selected for in vitro activity study. SD-01 and SD-02 were found to be active in the nanomolar (nM) range. SD-01 had considerably good selectivity for HDAC8 over HDAC6 and SD-02 had marginal selectivity for HDAC6 over HDAC8. The compounds SD-01 and SD-02 were found to inhibit HDAC8 at concentrations (IC50) 9.0 nM and 2.7 nM, respectively.
Contribution of rare coding mutations in CD36 to type 2 diabetes and cardio-metabolic complications
Authors: Meyre David , Andress Edward J. , Sharma Tanmay , Snippe Marjolein , Asif Hamza , Maharaj Arjuna , Vatin Vincent , Gaget Stefan , Besnard Philippe , Choquet Hélène , Froguel Philippe , Linton Kenneth J. 
Published: November 2019

AbstractWe sequenced coding regions of the cluster of differentiation 36 (CD36) gene in 184 French individuals of European ancestry presenting simultaneously with type 2 diabetes (T2D), arterial hypertension, dyslipidemia, and coronary heart disease. We identified rare missense mutations (p.Pro191Leu/rs143150225 and p.Ala252Val/rs147624636) in two heterozygous cases. The two CD36 mutation carriers had no family history of T2D and no clustering of cardio-metabolic complications. While the p.Pro191Leu mutation was found in 84 heterozygous carriers from five ethnic groups from the genome aggregation database (global frequency: 0.0297%, N = 141,321), only one European carrier of the p.Ala252Val mutation was identified (global frequency: 0.00040%, N = 125,523). The Pro191 and Ala252 amino acids were not conserved (74.8% and 68.9% across 131 animal species, respectively). In vitro experiments showed that the two CD36 mutant proteins are expressed and trafficked to the plasma membrane where they bind modified low-density-lipoprotein (LDL) cholesterol as normal. However, molecular modelling of the recent CD36 crystal structure showed that Pro191 was located at the exit/entrance gate of the lipid binding chamber and Ala252 was in line with the chamber. Overall, our data do not support a major contribution of CD36 rare coding mutations to T2D and its cardio-metabolic complications in the French population.
Characterization of the expression of LAT1 as a prognostic indicator and a therapeutic target in renal cell carcinoma
Authors: Higuchi Kosuke , Sakamoto Shinichi , Ando Keisuke , Maimaiti Maihulan , Takeshita Nobushige , Okunushi Kentaro , Reien Yoshie , Imamura Yusuke , Sazuka Tomokazu , Nakamura Kazuyoshi , Matsushima Jun , Furihata Tomomi , Ikehara Yuzuru , Ichikawa Tomohiko , Anzai Naohiko 
Published: November 2019

AbstractLarge neutral amino acid transporter 1 (LAT1, SLC7A5) is abundantly expressed in various types of cancer, and it has been thought to assist cancer progression through its activity for uptake of neutral amino acids. However, the roles of LAT1 in renal cell carcinoma (RCC) prognosis and treatment remain uncharacterized. Therefore, we first retrospectively examined the LAT1 expression profile and its associations with clinical factors in RCC tissues (n = 92). The results of immunohistochemistry showed that most of the tissues examined (92%) had cancer-associated LAT1 expression. Furthermore, the overall survival (OS) and progression-free survival (PFS) were shorter in patients with high LAT1 expression levels than in those with low LAT1 expression levels (P = 0.018 and 0.014, respectively), and these associations were further strengthened by the results of univariate and multivariate analyses. Next, we tested the effects of JPH203, which is a selective LAT1 inhibitor, on RCC-derived Caki-1 and ACHN cells. It was found that JPH203 inhibited the growth of these cell types in a dose-dependent manner. Moreover, JPH203 clearly suppressed their migration and invasion activities. Thus, our results show that LAT1 has a great potential to become not only a prognosis biomarker but also a therapeutic target in RCC clinical settings.
An exome-wide rare variant analysis of Korean men identifies three novel genes predisposing to prostate cancer
Authors: Oh Jong Jin , Shivakumar Manu , Miller Jason , Verma Shefali , Lee Hakmin , Hong Sung Kyu , Lee Sang Eun , Lee Younghee , Lee Soo Ji , Sung Joohon , Kim Dokyoon , Byun Seok-Soo 
Published: November 2019

AbstractSince prostate cancer is highly heritable, common variants associated with prostate cancer have been studied in various populations, including those in Korea. However, rare and low-frequency variants have a significant influence on the heritability of the disease. The contributions of rare variants to prostate cancer susceptibility have not yet been systematically evaluated in a Korean population. In this work, we present a large-scale exome-wide rare variant analysis of 7,258 individuals (985 cases with prostate cancer and 6,273 controls). In total, 19 rare variant loci spanning 7 genes contributed to an association with prostate cancer susceptibility. In addition to replicating previously known susceptibility genes (e.g., CDYL2, MST1R, GPER1, and PARD3B), 3 novel genes were identified (FDR q < 0.05), including the non-coding RNAs ENTPD3-AS1, LOC102724438, and protein-coding gene SPATA3. Additionally, 6 pathways were identified based on identified variants and genes, including estrogen signaling pathway, signaling by MST1, IL-15 production, MSP-RON signaling pathway, and IL-12 signaling and production in macrophages, which are known to be associated with prostate cancer. In summary, we report novel genes and rare variants that potentially play a role in prostate cancer susceptibility in the Korean population. These observations demonstrated a path towards one of the fundamental goals of precision medicine, which is to identify biomarkers for a subset of the population with a greater risk of disease than others.
Machine Learning Approach for Prescriptive Plant Breeding
Authors: Parmley Kyle A. , Higgins Race H. , Ganapathysubramanian Baskar , Sarkar Soumik , Singh Asheesh K. 
Published: November 2019

AbstractWe explored the capability of fusing high dimensional phenotypic trait (phenomic) data with a machine learning (ML) approach to provide plant breeders the tools to do both in-season seed yield (SY) prediction and prescriptive cultivar development for targeted agro-management practices (e.g., row spacing and seeding density). We phenotyped 32 SoyNAM parent genotypes in two independent studies each with contrasting agro-management treatments (two row spacing, three seeding densities). Phenotypic trait data (canopy temperature, chlorophyll content, hyperspectral reflectance, leaf area index, and light interception) were generated using an array of sensors at three growth stages during the growing season and seed yield (SY) determined by machine harvest. Random forest (RF) was used to train models for SY prediction using phenotypic traits (predictor variables) to identify the optimal temporal combination of variables to maximize accuracy and resource allocation. RF models were trained using data from both experiments and individually for each agro-management treatment. We report the most important traits agnostic of agro-management practices. Several predictor variables showed conditional importance dependent on the agro-management system. We assembled predictive models to enable in-season SY prediction, enabling the development of a framework to integrate phenomics information with powerful ML for prediction enabled prescriptive plant breeding.
The association between high-arched feet, plantar pressure distribution and body posture in young women
Authors: Woźniacka Renata , Oleksy Łukasz , Jankowicz-Szymańska Agnieszka , Mika Anna , Kielnar Renata , Stolarczyk Artur 
Published: November 2019

AbstractThe aim of this study was to examine the effect of excessive feet arching (symmetrical and asymmetrical) on plantar pressure distribution and on the alignment of pelvis, spine and shoulder girdle. Eighty-one women (20–40 years old, 61 +/− 12 kg, 165 +/− 5 cm) were divided into 3 groups based on the foot arch index (Group 1 - with normally arched feet, Group 2 with one foot properly arched and the other high-arched, Group 3 with both feet high-arched). Plantar pressure distribution between the right and left foot for the forefoot, midfoot and rearfoot, respectively and body posture were assessed. A slight increase in longitudinal arch of the foot caused changes in the distribution of feet loads both between limbs and between the forefoot and rearfoot and also influenced the whole body. Asymmetrical high-arching of the feet resulted in asymmetry of lower limb load and in the height of the shoulder girdle. We have suggested that any alteration of the foot arch may be harmful to body tissues and should not be considered as correct. Due to the fact that slight increases in longitudinal arch of the foot are very common, they should be considered as a foot defect, and appropriate corrective exercises should be used to prevent forefoot overload and alterations in body posture.