bluuebunny/crossref_metadata_2025_split huggingface dataset:
From expression footprints to causal pathways: contextualizing large signaling networks with CARNIVAL
Authors: Liu Anika , Trairatphisan Panuwat , Gjerga Enio , Didangelos Athanasios , Barratt Jonathan , Saez-Rodriguez Julio 
Published: November 2019

AbstractWhile gene expression profiling is commonly used to gain an overview of cellular processes, the identification of upstream processes that drive expression changes remains a challenge. To address this issue, we introduce CARNIVAL, a causal network contextualization tool which derives network architectures from gene expression footprints. CARNIVAL (CAusal Reasoning pipeline for Network identification using Integer VALue programming) integrates different sources of prior knowledge including signed and directed protein–protein interactions, transcription factor targets, and pathway signatures. The use of prior knowledge in CARNIVAL enables capturing a broad set of upstream cellular processes and regulators, leading to a higher accuracy when benchmarked against related tools. Implementation as an integer linear programming (ILP) problem guarantees efficient computation. As a case study, we applied CARNIVAL to contextualize signaling networks from gene expression data in IgA nephropathy (IgAN), a condition that can lead to chronic kidney disease. CARNIVAL identified specific signaling pathways and associated mediators dysregulated in IgAN including Wnt and TGF-β, which we subsequently validated experimentally. These results demonstrated how CARNIVAL generates hypotheses on potential upstream alterations that propagate through signaling networks, providing insights into diseases.
Investigation of parameters governing damage resistance of nematic liquid crystals for high-power or peak-intensity laser applications
Authors: Kosc T. Z. , Kozlov A. A. , Papernov S. , Kafka K. R. P. , Marshall K. L. , Demos S. G. 
Published: November 2019

AbstractWe investigate the damage resistance of saturated and unsaturated liquid crystals (LC’s) under a wide range of laser excitation conditions, including 1053-nm pulse durations between 600 fs and 1.5 ns and nanosecond pulse excitation at 351 nm and 532 nm. This study explores the relationship between the LC’s resistance to laser-induced breakdown (damage) and the electronic structure (π-electron delocalization) of the constituent molecules. The laser-induced damage threshold at all wavelengths and pulse durations was consistently higher in saturated materials than in their unsaturated counterparts. The wavelength’s dependence in the results suggests that the energy coupling process that leads to laser-induced breakdown is governed by the energy separation between the ground state and the first and second excited states, while the pulse duration’s dependence in the results reveals the important role of electron relaxation between the excited states. A qualitative description was developed to interpret the experimental observations.
Proposal for a Quantitative 18F-FDG PET/CT Metabolic Parameter to Assess the Intensity of Bone Involvement in Multiple Myeloma
Authors: Takahashi Maria E. S. , Mosci Camila , Souza Edna M. , Brunetto Sérgio Q. , Etchebehere Elba , Santos Allan O. , Camacho Mariana R. , Miranda Eliana , Lima Mariana C. L. , Amorim Barbara J. , de Souza Carmino , Pericole Fernando V. , Lorand-Metze Irene , Ramos Celso D. 
Published: November 2019

AbstractMany efforts have been made to standardize the interpretation of 18F-FDG PET/CT in multiple myeloma (MM) with qualitative visual analysis or with quantitative metabolic parameters using various methods for lesion segmentation of PET images. The aim of this study was to propose a quantitative method for bone and bone marrow evaluation of 18F-FDG PET/CT considering the extent and intensity of bone 18F-FDG uptake: Intensity of Bone Involvement (IBI). Whole body 18F-FDG PET/CT of 59 consecutive MM patients were evaluated. Compact bone tissue was segmented in PET images using a global threshold for HU of the registered CT image. A whole skeleton mask was created and the percentage of its volume with 18F-FDG uptake above hepatic uptake was calculated (Percentage of Bone Involvement - PBI). IBI was defined by multiplying PBI by mean SUV above hepatic uptake. IBI was compared with visual analysis performed by two experienced nuclear medicine physicians. IBI calculation was feasible in all images (range:0.00–1.35). Visual analysis categorized PET exams into three groups (negative/mild, moderate and marked bone involvement), that had different ranges of IBI (multi comparison analysis, p < 0.0001). There was an inverse correlation between the patients’ hemoglobin values and IBI (r = −0.248;p = 0.02). IBI score is an objective measure of bone and bone marrow involvement in MM, allowing the categorization of patients in different degrees of aggressiveness of the bone disease. The next step is to validate IBI in a larger group of patients, before and after treatment and in a multicentre setting.
Unfolding the innovation system for the development of countries: coevolution of Science, Technology and Production
Authors: Pugliese Emanuele , Cimini Giulio , Patelli Aurelio , Zaccaria Andrea , Pietronero Luciano , Gabrielli Andrea 
Published: November 2019

AbstractWe show that the space in which scientific, technological and economic activities interplay with each other can be mathematically shaped using techniques from statistical physics of networks. We build a holistic view of the innovation system as the tri-layered network of interactions among these many activities (scientific publication, patenting, and industrial production in different sectors), also taking into account the possible time delays. Within this construction we can identify which capabilities and prerequisites are needed to be competitive in a given activity, and even measure how much time is needed to transform, for instance, the technological know-how into economic wealth and scientific innovation, being able to make predictions with a very long time horizon. We find empirical evidence that, at the aggregate scale, technology is the best predictor for industrial and scientific production over the upcoming decades.
Acute Toxic Injuries of Rat’s Visceral Tissues Induced by Different Oximes
Authors: Jaćević Vesna , Nepovimova Eugenie , Kuča Kamil 
Published: November 2019

AbstractCertain AChE reactivators, asoxime, obidoxime, K027, K048, and K075, when taken in overdoses and sometimes even when introduced within therapeutic ranges, may injure the different organs. As a continuation of previously published data, in this study, Wistar rats have sacrificed 24 hrs and 7 days after single im application of 0.1LD50, 0.5LD50 and 1.0LD50 of each reactivator, and examinated tissue samples were obtained for pathohistological and semiquantitative analysis. A severity of tissue alteration, expressed as different tissue damage scores were evaluated. Morphological structure of examinated tissues treated with of 0.1LD50 of all reactivators was comparable with the control group of rats. Moderate injuries were seen in visceral tissues treated with 0.5LD50 of asoxime, obidoxime and K027. Acute damages were enlarged after treatment with 0.5LD50 and 1.0LD50 of all reactivators during the next 7 days. The most prominent changes were seen in rats treated with 1.0LD50 of K048 and K075 (P < 0.001 vs. control and asoxime-treated group). All reactivators given by a single, high, unitary dose regimen, have an adverse effect not only on the main visceral tissue, but on the whole rat as well, but the exact mechanism of cellular injury remains to be confirmed in further investigation.
Magneto-Optical Characteristics of Streptavidin-Coated Fe3O4@Au Core-Shell Nanoparticles for Potential Applications on Biomedical Assays
Authors: Lin Chin-Wei , Chen Jian-Ming , Lin You-Jun , Chao Ling-Wei , Wei Sin-Yi , Wu Chiu-Hsien , Jeng Chien-Chung , Wang Li-Min , Chen Kuen-Lin 
Published: November 2019

AbstractRecently, gold-coated magnetic nanoparticles have drawn the interest of researchers due to their unique magneto-plasmonic characteristics. Previous research has found that the magneto-optical Faraday effect of gold-coated magnetic nanoparticles can be effectively enhanced because of the surface plasmon resonance of the gold shell. Furthermore, gold-coated magnetic nanoparticles are ideal for biomedical applications because of their high stability and biocompatibility. In this work, we synthesized Fe3O4@Au core-shell nanoparticles and coated streptavidin (STA) on the surface. Streptavidin is a protein which can selectively bind to biotin with a strong affinity. STA is widely used in biotechnology research including enzyme-linked immunosorbent assay (ELISA), time-resolved immunofluorescence (TRFIA), biosensors, and targeted pharmaceuticals. The Faraday magneto-optical characteristics of the biofunctionalized Fe3O4@Au nanoparticles were measured and studied. We showed that the streptavidin-coated Fe3O4@Au nanoparticles still possessed the enhanced magneto-optical Faraday effect. As a result, the possibility of using biofunctionalized Fe3O4@Au nanoparticles for magneto-optical biomedical assays should be explored.
Evidence for a transcellular route for vitellogenin transport in the telotrophic ovary of Podisus nigrispinus (Hemiptera: Pentatomidae)
Authors: Assis Mírian Quintão , Dohanik Virgínia Teles , Oliveira Leandro Licursi de , Zanuncio José Cola , Serrão José Eduardo 
Published: November 2019

AbstractVitellogenin is the main yolk precursor protein in insect oocytes. It is synthesized in the fat body and released into the hemolymph. To reach the oocyte surface, vitellogenin must cross a single layer of follicular epithelium cells. The transport of vitellogenin across the follicular epithelium has been suggested to occur through the enlarged intercellular spaces (patency) by a paracellular route or by endocytosis by follicular cells and release onto oocyte surface in a transcelluar route. In this study, we investigated whether vitellogenin transport in the meroistic telotrophic ovary of Podisus nigrispinus (Hemiptera) occurs via a paracellular or transcellular route. Light and transmission electron microscopies showed that short cell–cell contacts with well-developed occluding septate junctions were present in follicular cells with patency. Immunofluorescence microscopy revealed the presence of vitellogenin receptors in the plasma membrane and of vitellogenin in the cytoplasm of follicular cells. Data suggest that cell–cell contacts serve as a barrier to large vitellogenin molecules and that this protein is transported via a transcellular route of receptor-mediated endocytosis.
The characteristics of krill swarms in relation to aggregating Antarctic blue whales
Authors: Miller E. J. , Potts J. M. , Cox M. J. , Miller B. S. , Calderan S. , Leaper R. , Olson P. A. , O’Driscoll R. L. , Double M. C. 
Published: November 2019

AbstractWe model the presence of rare Antarctic blue whales (Balaenoptera musculus intermedia) in relation to the swarm characteristics of their main prey species, Antarctic krill (Euphausia superba). A combination of visual observations and recent advances in passive acoustic technology were used to locate Antarctic blue whales, whilst simultaneously using active underwater acoustics to characterise the distribution, size, depth, composition and density of krill swarms. Krill swarm characteristics and blue whale presence were examined at a range of spatiotemporal scales to investigate sub meso-scale (i.e., <100 km) foraging behaviour. Results suggest that at all scales, Antarctic blue whales are more likely to be detected within the vicinity of krill swarms with a higher density of krill, those found shallower in the water column, and those of greater vertical height. These findings support hypotheses that as lunge-feeders of extreme size, Antarctic blue whales target shallow, dense krill swarms to maximise their energy intake. As both Antarctic krill and blue whales play a key role in the Southern Ocean ecosystem, the nature of their predator-prey dynamics is an important consideration, not only for the recovery of this endangered species in a changing environment, but for the future management of Antarctic krill fisheries.
Estimating growth and photosynthetic properties of wheat grown in simulated saline field conditions using hyperspectral reflectance sensing and multivariate analysis
Authors: El-Hendawy Salah , Al-Suhaibani Nasser , Alotaibi Majed , Hassan Wael , Elsayed Salah , Tahir Muhammad Usman , Mohamed Ahmed Ibrahim , Schmidhalter Urs 
Published: November 2019

AbstractThe timely estimation of growth and photosynthetic-related traits in an easy and nondestructive manner using hyperspectral data will become imperative for addressing the challenges of environmental stresses inherent to the agricultural sector in arid conditions. However, the handling and analysis of these data by exploiting the full spectrum remains the determining factor for refining the estimation of crop variables. The main objective of this study was to estimate growth and traits underpinning photosynthetic efficiency of two wheat cultivars grown under simulated saline field conditions and exposed to three salinity levels using hyperspectral reflectance information from 350–2500 nm obtained at two years. Partial least squares regression (PLSR) based on the full spectrum was applied to develop predictive models for estimating the measured parameters in different conditions (salinity levels, cultivars, and years). Variable importance in projection (VIP) of PLSR in combination with multiple linear regression (MLR) was implemented to identify important waveband regions and influential wavelengths related to the measured parameters. The results showed that the PLSR models exhibited moderate to high coefficients of determination (R2) in both the calibration and validation datasets (0.30–0.95), but that this range of R2 values depended on parameters and conditions. The PLSR models based on the full spectrum accurately and robustly predicted three of four parameters across all conditions. Based on the combination of PLSR-VIP and MLR analysis, the wavelengths selected within the visible (VIS), red-edge, and middle near-infrared (NIR) wavebands were the most sensitive to all parameters in all conditions, whereas those selected within the shortwave infrared (SWIR) waveband were effective for some parameters in particular conditions. Overall, these results indicated that the PLSR analysis and band selection techniques can offer a rapid and nondestructive alternative approach to accurately estimate growth- and photosynthetic-related trait responses to salinity stress.
Early embryonic exposure of freshwater gastropods to pharmaceutical 5-alpha-reductase inhibitors results in a surprising open-coiled “banana-shaped” shell
Authors: Baynes Alice , Montagut Pino Gemma , Duong Giang Huong , Lockyer Anne E. , McDougall Carmel , Jobling Susan , Routledge Edwin J. 
Published: November 2019

AbstractIn vertebrates, the steroidogenesis enzyme 5α-reductase converts testosterone to the more potent androgen 5α-dihydrotestosterone. Homologues of 5α-reductase genes have been identified in molluscs. However, recent findings suggest that vertebrate-type steroid androgens are not utilised in molluscan reproductive development. Genomic searches have revealed that molluscs do not possess many of the steroidogenic enzymes required to make testosterone, nor a nuclear androgen receptor. Consequently, the role of 5α-reductase in molluscs presents a mystery. Here, developmental exposures ofBiomphalaria glabratato selective pharmaceutical 5α-reductase inhibitors elicited a strong, highly reproducible phenotypic response characterised by the development of elongated “banana-shaped” shell morphology. In comparison to untreated snails, the shells are open-coiled and the whorls are unattached. Dutasteride (5α-reductase inhibitor) is approximately 10-times more potent at provoking the banana-shaped shell phenotype than finasteride, paralleling the pharmaceuticals’ efficacy in humans. Other enzyme inhibitors with different modes of action were tested to investigate the specificity of the phenotype. However, only the pharmaceutical 5α-reductase inhibitors provoked the response. Dutasteride elicited the same phenotype in a second gastropod,Physella acuta. In the absence of evidence forde novoandrogen steroidogenesis in molluscs, these findings suggest that novel substrates for 5α-reductase exist in gastropods, lending support to the contention that molluscan endocrinology differs from the well-characterised vertebrate endocrine system.
Split-Belt walking induces changes in active, but not passive, perception of step length
Authors: Sombric Carly , Gonzalez-Rubio Marcela , Torres-Oviedo Gelsy 
Published: November 2019

AbstractSuccessful motor control requires accurate estimation of our body in space for planning, executing, and evaluating the outcome of our actions. It has been shown that the estimation of limb position is susceptible to motor adaptation. However, a similar effect has not been found in locomotion, possibly due to how it was tested. We hypothesized that split-belt walking with the legs moving at different speeds changes the estimation of the legs’ position when taking a step. Thus, we assessed young subjects’ perception of step length (i.e., inter-feet distance at foot landing) when they moved their legs (active perception) or when the legs were moved by the experimenter (passive perception). We found that the active perception of step length was substantially altered following split-belt walking, whereas passive perception exhibited minor changes. This suggests that split-belt walking induced the adaptation of efferent signals, without altering sensory signals. We also found that active perceptual shifts were sensitive to how they were tested: they were most salient in the trailing leg and at short step lengths. Our results suggest that split-belt walking could modulate the deficient perception of step length post-stroke, which may contribute to gait asymmetries impairing patients’ mobility.
A quantitative method to decompose SWE differences between regional climate models and reanalysis datasets
Authors: Xu Yun , Jones Andrew , Rhoades Alan 
Published: November 2019

AbstractThe simulation of snow water equivalent (SWE) remains difficult for regional climate models. Accurate SWE simulation depends on complex interacting climate processes such as the intensity and distribution of precipitation, rain-snow partitioning, and radiative fluxes. To identify the driving forces behind SWE difference between model and reanalysis datasets, and guide model improvement, we design a framework to quantitatively decompose the SWE difference contributed from precipitation distribution and magnitude, ablation, temperature and topography biases in regional climate models. We apply this framework within the California Sierra Nevada to four regional climate models from the North American Coordinated Regional Downscaling Experiment (NA-CORDEX) run at three spatial resolutions. Models generally predict less SWE compared to Landsat-Era Sierra Nevada Snow Reanalysis (SNSR) dataset. Unresolved topography associated with model resolution contribute to dry and warm biases in models. Refining resolution from 0.44° to 0.11° improves SWE simulation by 35%. To varying degrees across models, additional difference arises from spatial and elevational distribution of precipitation, cold biases revealed by topographic correction, uncertainties in the rain-snow partitioning threshold, and high ablation biases. This work reveals both positive and negative contributions to snow bias in climate models and provides guidance for future model development to enhance SWE simulation.
Three port logic gate using forward volume spin wave interference in a thin yttrium iron garnet film
Authors: Goto Taichi , Yoshimoto Takuya , Iwamoto Bungo , Shimada Kei , Ross Caroline A. , Sekiguchi Koji , Granovsky Alexander B. , Nakamura Yuichi , Uchida Hironaga , Inoue Mitsuteru 
Published: November 2019

AbstractWe demonstrate a logic gate based on interference of forward volume spin waves (FVSWs) propagating in a 54 nm thick, 100 μm wide yttrium iron garnet waveguide grown epitaxially on a garnet substrate. Two FVSWs injected by coplanar waveguides were made to interfere constructively and destructively by varying their phase difference, showing an XNOR logic function. The reflected and resonant waves generated at the edges of the waveguide were suppressed using spin wave absorbers. The observed isolation ratio was 19 dB for a magnetic field of ~2.80 kOe ( = 223 kA m−1) applied perpendicular to the film. The wavelength and device length were ~8.9 μm and ~53 μm, respectively. Further, the interference state of the SWs was analyzed using three-dimensional radio frequency simulations.
Symmetrical electrophysiological brain responses to unilateral and bilateral auditory stimuli suggest disrupted spatial processing in schizophrenia
Authors: Sardari Sara , Pourrahimi Ali Mohammad , Talebi Hossein , Mazhari Shahrzad 
Published: November 2019

AbstractResearch has found auditory spatial processing deficits in patients with schizophrenia (SCZ), but no study has examined SCZ patients’ auditory spatial processing at both pre-attentional and attentional stages. To address this gap, we investigated schizophrenics’ brain responses to sounds originating from different locations (right, left, and bilateral sources). The event-related potentials (ERPs) of 25 chronic schizophrenic patients and 25 healthy subjects were compared. Mismatch negativity (MMN) in response to frequency and duration deviants was assessed. Two P3 components (P3a and P3b) were elicited via a frequency discrimination task, and MMN and P3 were recorded through separate monaural and dichotic stimulation paradigms. Our results corroborated the previously published finding that MMN, P3a, and P3b amplitudes are reduced in SCZ patients, but they showed no significant effect of stimulus location on either MMN or P3. These results indicated similarity between the SCZ patients and healthy individuals as regards patterns of ERP responses to stimuli that come from different directions. No evidence of auditory hemispatial bias in the SCZ patients was found, supporting the existence of non-lateralized spatial processing deficits in such patients and suggesting compensatory changes in the hemispheric laterality of patients’ brains.
DeePathology: Deep Multi-Task Learning for Inferring Molecular Pathology from Cancer Transcriptome
Authors: Azarkhalili Behrooz , Saberi Ali , Chitsaz Hamidreza , Sharifi-Zarchi Ali 
Published: November 2019

AbstractDespite great advances, molecular cancer pathology is often limited to the use of a small number of biomarkers rather than the whole transcriptome, partly due to computational challenges. Here, we introduce a novel architecture of Deep Neural Networks (DNNs) that is capable of simultaneous inference of various properties of biological samples, through multi-task and transfer learning. It encodes the whole transcription profile into a strikingly low-dimensional latent vector of size 8, and then recovers mRNA and miRNA expression profiles, tissue and disease type from this vector. This latent space is significantly better than the original gene expression profiles for discriminating samples based on their tissue and disease. We employed this architecture on mRNA transcription profiles of 10750 clinical samples from 34 classes (one healthy and 33 different types of cancer) from 27 tissues. Our method significantly outperforms prior works and classical machine learning approaches in predicting tissue-of-origin, normal or disease state and cancer type of each sample. For tissues with more than one type of cancer, it reaches 99.4% accuracy in identifying the correct cancer subtype. We also show this system is very robust against noise and missing values. Collectively, our results highlight applications of artificial intelligence in molecular cancer pathology and oncological research. DeePathology is freely available at https://github.com/SharifBioinf/DeePathology.