bluuebunny/crossref_metadata_2025_split huggingface dataset:
From basic perception deficits to facial affect recognition impairments in schizophrenia
Authors: Marosi Csilla , Fodor Zsuzsanna , Csukly Gábor 
Published: June 2019

AbstractWhile impaired facial emotion recognition and magnocellular deficits in visual perception are core features of schizophrenia, their relationship is still unclear. Our aim was to analyze the oscillatory background of these processes and to investigate the connection between the magnocellular pathway deficit and the abnormal facial affect processing. Thirty-nine subjects with schizophrenia and forty socially matched healthy controls subjects were enrolled. A 128 channel EEG was recorded in three experimental tasks: first, participants viewed magnocellular biased low-spatial frequency (LSF) and parvocellular biased high-spatial frequency (HSF) Gabor-patches, then faces and houses were presented and in the third task a facial affect recognition task was presented with happy, sad and neutral faces. Event-related theta (4–7 Hz) synchronization (ERS) (i.e. an increase in theta power) by magnocellular biased stimuli was decreased in patients relative to controls, while no similar differences were found between groups in the parvocellular biased condition. ERS was significantly lower in patients compared to healthy controls both in the face and in the emotion recognition task. Theta ERS to magnocellular biased stimuli, but not to parvocellular biased stimuli, were correlated with emotion recognition performance. These findings indicate a bottom up disruption of face perception and emotion recognition in schizophrenia.
In-silico Prediction of Synergistic Anti-Cancer Drug Combinations Using Multi-omics Data
Authors: Celebi Remzi , Bear Don’t Walk Oliver , Movva Rajiv , Alpsoy Semih , Dumontier Michel 
Published: June 2019

AbstractChemotherapy is a routine treatment approach for early-stage cancers, but the effectiveness of such treatments is often limited by drug resistance, toxicity, and tumor heterogeneity. Combination chemotherapy, in which two or more drugs are applied simultaneously, offers one promising approach to address these concerns, since two single-target drugs may synergize with one another through interconnected biological processes. However, the identification of effective dual therapies has been particularly challenging; because the search space is large, combination success rates are low. Here, we present our method for DREAM AstraZeneca-Sanger Drug Combination Prediction Challenge to predict synergistic drug combinations. Our approach involves using biologically relevant drug and cell line features with machine learning. Our machine learning model obtained the primary metric = 0.36 and the tie-breaker metric = 0.37 in the extension round of the challenge which was ranked in top 15 out of 76 submissions. Our approach also achieves a mean primary metric of 0.39 with ten repetitions of 10-fold cross-validation. Further, we analyzed our model’s predictions to better understand the molecular processes underlying synergy and discovered that key regulators of tumorigenesis such as TNFA and BRAF are often targets in synergistic interactions, while MYC is often duplicated. Through further analysis of our predictions, we were also ble to gain insight into mechanisms and potential biomarkers of synergistic drug pairs.
The effect of trait anxiety on attentional mechanisms in combined context and cue conditioning and extinction learning
Authors: Stegmann Yannik , Reicherts Philipp , Andreatta Marta , Pauli Paul , Wieser Matthias J. 
Published: June 2019

AbstractSensory processing and attention allocation are shaped by threat, but the role of trait-anxiety in sensory processing as a function of threat predictability remains incompletely understood. Therefore, we measured steady-state visual evoked potentials (ssVEPs) as an index of sensory processing of predictable and unpredictable threat cues in 29 low (LA) and 29 high (HA) trait-anxious participants during a modified NPU-paradigm followed by an extinction phase. Three different contextual cues indicated safety (N), predictable (P) or unpredictable threat (U), while foreground cues signalled shocks in the P-condition only. All participants allocated increased attentional resources to the central P-threat cue, replicating previous findings. Importantly, LA individuals exhibited larger ssVEP amplitudes to contextual threat (U and P) than to contextual safety cues, while HA individuals did not differentiate among contextual cues in general. Further, HA exhibited higher aversive ratings of all contexts compared to LA. These results suggest that high trait-anxious individuals might be worse at discriminating contextual threat stimuli and accordingly overestimate the probability and aversiveness of unpredictable threat. These findings support the notion of aberrant sensory processing of unpredictable threat in anxiety disorders, as this processing pattern is already evident in individuals at risk of these disorders.
Measuring the atomic spin-flip scattering rate by x-ray emission spectroscopy
Authors: Decker Régis , Born Artur , Büchner Robby , Ruotsalainen Kari , Stråhlman Christian , Neppl Stefan , Haverkamp Robert , Pietzsch Annette , Föhlisch Alexander 
Published: June 2019

AbstractWhile extensive work has been dedicated to the measurement of the demagnetization time following an ultra-short laser pulse, experimental studies of its underlying microscopic mechanisms are still scarce. In transition metal ferromagnets, one of the main mechanism is the spin-flip of conduction electrons driven by electron-phonon scattering. Here, we present an original experimental method to monitor the electron-phonon mediated spin-flip scattering rate in nickel through the stringent atomic symmetry selection rules of x-ray emission spectroscopy. Increasing the phonon population leads to a waning of the 3d → 2p3/2 decay peak intensity, which reflects an increase of the angular momentum transfer scattering rate attributed to spin-flip. We find a spin relaxation time scale in the order of 50 fs in the 3d-band of nickel at room temperature, while consistantly, no such peak evolution is observed for the diamagnetic counterexample copper, using the same method.
Yeast screening system reveals the inhibitory mechanism of cancer cell proliferation by benzyl isothiocyanate through down-regulation of Mis12
Authors: Abe-Kanoh Naomi , Kunisue Narumi , Myojin Takumi , Chino Ayako , Munemasa Shintaro , Murata Yoshiyuki , Satoh Ayano , Moriya Hisao , Nakamura Yoshimasa 
Published: June 2019

AbstractBenzyl isothiocyanate (BITC) is a naturally-occurring isothiocyanate derived from cruciferous vegetables. BITC has been reported to inhibit the proliferation of various cancer cells, which is believed to be important for the inhibition of tumorigenesis. However, the detailed mechanisms of action remain unclear. In this study, we employed a budding yeast Saccharomyces cerevisiae as a model organism for screening. Twelve genes including MTW1 were identified as the overexpression suppressors for the antiproliferative effect of BITC using the genome-wide multi-copy plasmid collection for S. cerevisiae. Overexpression of the kinetochore protein Mtw1 counteracts the antiproliferative effect of BITC in yeast. The inhibitory effect of BITC on the proliferation of human colon cancer HCT-116 cells was consistently suppressed by the overexpression of Mis12, a human orthologue of Mtw1, and enhanced by the knockdown of Mis12. We also found that BITC increased the phosphorylated and ubiquitinated Mis12 level with consequent reduction of Mis12, suggesting that BITC degrades Mis12 through an ubiquitin-proteasome system. Furthermore, cell cycle analysis showed that the change in the Mis12 level affected the cell cycle distribution and the sensitivity to the BITC-induced apoptosis. These results provide evidence that BITC suppresses cell proliferation through the post-transcriptional regulation of the kinetochore protein Mis12.
Neuropeptide precursors and neuropeptides in the sea cucumber Apostichopus japonicus: a genomic, transcriptomic and proteomic analysis
Authors: Chen Muyan , Talarovicova Alzbeta , Zheng Yingqiu , Storey Kenneth B. , Elphick Maurice R. 
Published: June 2019

AbstractThe sea cucumber Apostichopus japonicus is a foodstuff with very high economic value in China, Japan and other countries in south-east Asia. It is at the heart of a multibillion-dollar industry and to meet demand for this product, aquaculture methods and facilities have been established. However, there are challenges associated with optimization of reproduction, feeding and growth in non-natural environments. Therefore, we need to learn more about the biology of A. japonicus, including processes such as aestivation, evisceration, regeneration and albinism. One of the major classes of molecules that regulate physiology and behaviour in animals are neuropeptides, and a few bioactive peptides have already been identified in A. japonicus. To facilitate more comprehensive investigations of neuropeptide function in A. japonicus, here we have analysed genomic and transcriptomic sequence data and proteomic data to identify neuropeptide precursors and neuropeptides in this species. We identified 44 transcripts encoding neuropeptide precursors or putative neuropeptide precursors, and in some instances neuropeptides derived from these precursors were confirmed by mass spectrometry. Furthermore, analysis of genomic sequence data enabled identification of the location of neuropeptide precursor genes on genomic scaffolds and linkage groups (chromosomes) and determination of gene structure. Many of the precursors identified contain homologs of neuropeptides that have been identified in other bilaterian animals. Precursors of neuropeptides that have thus far only been identified in echinoderms were identified, including L- and F-type SALMFamides, AN peptides and others. Precursors of several peptides that act as modulators of neuromuscular activity in A. japonicus were also identified. The discovery of a large repertoire of neuropeptide precursors and neuropeptides provides a basis for experimental studies that investigate the physiological roles of neuropeptide signaling systems in A. japonicus. Looking ahead, some of these neuropeptides may have effects that could be harnessed to enable improvements in the aquaculture of this economically important species.
Energy expenditure for isometric contractions of right and left ventricular trabeculae over a wide range of frequencies at body temperature
Authors: Pham Toan , Zgierski-Johnston Callum M. , Tran Kenneth , Taberner Andrew J. , Loiselle Denis S. , Han June-Chiew 
Published: June 2019

AbstractWe studied the energy expenditure of isometric contractions using both right-ventricular (RV) and left-ventricular (LV) trabeculae isolated from the rat heart. The energy expenditure under isometric contraction presents entirely as heat liberation. Preparations were challenged to perform at various rates of energy demand while accounting for their inevitable time-dependent decline of performance. They were electrically stimulated to contract at 37 °C with a frequency order (between 0.1 Hz and 10 Hz) dictated by a fully-balanced Latin-Square experimental design. We measured, simultaneously, their stress production and heat output. As functions of stimulus frequency, active stress and heat were not significantly different between RV and LV trabeculae. However, contraction kinetics, indexed as the maximal rate of rise and fall of twitch, were lower in the LV trabeculae. The ratio of heat to stress was greater in the LV trabeculae, suggesting that the economy of contraction of the LV trabeculae is lower. Their lower economy became more pronounced at high stimulus frequencies. Our results allow us to assess whether slowing of kinetics is a causative mechanism for improvement of economy of contraction.
Dual optical force plate for time resolved measurement of forces and pressure distributions beneath shoes and feet
Authors: Tompkins Christopher G. , Sharp James S. 
Published: June 2019

AbstractFrustrated total internal reflection (FTIR) imaging was used to perform remote optical measurements of the forces/pressures exerted beneath shoes and feet during a number of different training activities including countermovement jumps, jogging and drop jumps. A single camera was used to simultaneously image two acrylic, FTIR waveguide imaging elements from below, at frame rates up to 200 frames per second. The images obtained using the camera were converted into pressure/force maps using a previously developed theory which combines the mechanics of contact of soft objects and the scattering of evanescent waves. The forces obtained from the optical measurements were shown to be in good agreement with measurements obtained from load cells placed beneath the FTIR imaging elements. The ability to produce accurate spatial maps of the force/pressure distribution beneath soft contacting objects such as feet and shoe outsoles at high frame rates has numerous potential applications in sports sciences and medicine.
EEG functional connectivity metrics wPLI and wSMI account for distinct types of brain functional interactions
Authors: Imperatori Laura Sophie , Betta Monica , Cecchetti Luca , Canales-Johnson Andrés , Ricciardi Emiliano , Siclari Francesca , Pietrini Pietro , Chennu Srivas , Bernardi Giulio 
Published: June 2019

AbstractThe weighted Phase Lag Index (wPLI) and the weighted Symbolic Mutual Information (wSMI) represent two robust and widely used methods for MEG/EEG functional connectivity estimation. Interestingly, both methods have been shown to detect relative alterations of brain functional connectivity in conditions associated with changes in the level of consciousness, such as following severe brain injury or under anaesthesia. Despite these promising findings, it was unclear whether wPLI and wSMI may account for distinct or similar types of functional interactions. Using simulated high-density (hd-)EEG data, we demonstrate that, while wPLI has high sensitivity for couplings presenting a mixture of linear and nonlinear interdependencies, only wSMI can detect purely nonlinear interaction dynamics. Moreover, we evaluated the potential impact of these differences on real experimental data by computing wPLI and wSMI connectivity in hd-EEG recordings of 12 healthy adults during wakefulness and deep (N3-)sleep, characterised by different levels of consciousness. In line with the simulation-based findings, this analysis revealed that both methods have different sensitivity for changes in brain connectivity across the two vigilance states. Our results indicate that the conjoint use of wPLI and wSMI may represent a powerful tool to study the functional bases of consciousness in physiological and pathological conditions.
Prophylactic inhibition of soluble epoxide hydrolase delays onset of nephritis and ameliorates kidney damage in NZB/W F1 mice
Authors: Klocke Jan , Ulu Arzu , Wu Kaiyin , Rudolph Birgit , Dragun Duska , Gollasch Maik , Schunck Wolf-Hagen , Hammock Bruce D. , Riemekasten Gabriela , Enghard Philipp 
Published: June 2019

AbstractEpoxy-fatty-acids (EpFAs), cytochrome P450 dependent arachidonic acid derivatives, have been suggested to have anti-inflammatory properties, though their effects on autoimmune diseases like systemic lupus erythematosus (SLE) have yet to be investigated. We assessed the influence of EpFAs and their metabolites in lupus prone NZB/W F1 mice by pharmacological inhibition of soluble epoxide hydrolase (sEH, EPHX2). The sEH inhibitor 1770 was administered to lupus prone NZB/W F1 mice in a prophylactic and a therapeutic setting. Prophylactic inhibition of sEH significantly improved survival and reduced proteinuria. By contrast, sEH inhibitor-treated nephritic mice had no survival benefit; however, histological changes were reduced when compared to controls. In humans, urinary EpFA levels were significantly different in 47 SLE patients when compared to 10 healthy controls. Gene expression of EPHX2 was significantly reduced in the kidneys of both NZB/W F1 mice and lupus nephritis (LN) patients. Correlation of EpFAs with SLE disease activity and reduced renal EPHX gene expression in LN suggest roles for these components in human disease.
Structure-preserving visualisation of high dimensional single-cell datasets
Authors: Szubert Benjamin , Cole Jennifer E. , Monaco Claudia , Drozdov Ignat 
Published: June 2019

AbstractSingle-cell technologies offer an unprecedented opportunity to effectively characterize cellular heterogeneity in health and disease. Nevertheless, visualisation and interpretation of these multi-dimensional datasets remains a challenge. We present a novel framework, ivis, for dimensionality reduction of single-cell expression data. ivis utilizes a siamese neural network architecture that is trained using a novel triplet loss function. Results on simulated and real datasets demonstrate that ivis preserves global data structures in a low-dimensional space, adds new data points to existing embeddings using a parametric mapping function, and scales linearly to hundreds of thousands of cells. ivis is made publicly available through Python and R interfaces on https://github.com/beringresearch/ivis.
Coro2b, a podocyte protein downregulated in human diabetic nephropathy, is involved in the development of protamine sulphate-induced foot process effacement
Authors: Schwarz Angelina , Möller-Hackbarth Katja , Ebarasi Lwaki , Unnersjö Jess David , Zambrano Sonia , Blom Hans , Wernerson Annika , Lal Mark , Patrakka Jaakko 
Published: June 2019

AbstractPodocytes have an important role in the pathogenesis of diabetic nephropathy (DN). Podocyte foot process effacement, mediated largely by the actin-based cytoskeleton of foot processes, is commonly detected in DN and is believed to be a key pathogenic event in the development of proteinuria. In this study, we identified coronin 2b (Coro2b), a member of known actin-regulating proteins, the coronins, as a highly podocyte-enriched molecule located at the cytoplasmic side of the apical plasma membrane. Studies in human renal biopsies show that glomerular Coro2b expression is significantly down-regulated in patients with DN. Studies in knockout mice indicate that Coro2b is not required for the development or maintenance of the glomerular filtration barrier. Moreover, inactivation of Coro2b specifically in podocytes does not affect the outcome of nephropathy in a streptozotocin-induced diabetes model. However, Coro2b seems to modulate the reorganization of foot processes under pathological conditions as Coro2b knockout podocytes are partially protected from protamine sulfate perfusion-induced foot process effacement. Taken together, our study suggests a role for Coro2b in the pathogenesis of glomerulopathies. Further studies regarding the involvement of Coro2b in podocyte health and diseases are warranted.
Two-step closure of the Miocene Indian Ocean Gateway to the Mediterranean
Authors: Bialik Or M. , Frank Martin , Betzler Christian , Zammit Ray , Waldmann Nicolas D. 
Published: June 2019

AbstractThe Tethys Ocean was compartmentalized into the Mediterranean Sea and Indian Ocean during the early Miocene, yet the exact nature and timing of this disconnection are not well understood. Here we present two new neodymium isotope records from isolated carbonate platforms on both sides of the closing seaway, Malta (outcrop sampling) and the Maldives (IODP Site U1468), to constrain the evolution of past water mass exchange between the present day Mediterranean Sea and Indian Ocean via the Mesopotamian Seaway. Combining these data with box modeling results indicates that water mass exchange was reduced by ~90% in a first step at ca. 20 Ma. The terminal closure of the seaway then coincided with the sea level drop caused by the onset of permanent glaciation of Antarctica at ca. 13.8 Ma. The termination of meridional water mass exchange through the Tethyan Seaway resulted in a global reorganization of currents, paved the way to the development of upwelling in the Arabian Sea and possibly led to a strengthening of South Asian Monsoon.
Bidirectional regulatory potentials of short-chain fatty acids and their G-protein-coupled receptors in autoimmune neuroinflammation
Authors: Park Jeongho , Wang Qin , Wu Qi , Mao-Draayer Yang , Kim Chang H. 
Published: June 2019

AbstractMicrobial metabolites, produced in the intestine, have significant effects on inflammatory diseases throughout the body. Short-chain fatty acids (SCFAs) have protective effects on experimental autoimmune encephalitis (EAE) responses but the detailed roles of SCFAs and their receptors in regulating autoimmune CNS inflammation have been unclear. SCFAs metabolically regulate T cells and change the phenotype of antigen presenting cells to efficiently induce IL-10+regulatory T cells. In line with the overall protective effect, blood levels of major SCFAs, such as acetate, propionate and butyrate, are significantly decreased in long-term active progressive multiple sclerosis (MS) patients. Importantly, SCFAs can induce CD4+effector T cells, which are highly inflammatory when transferred into mice, suggesting that the direct effect of SCFAs on T cells can even be pro-inflammatory in the CNS. In contrast to the moderate protective effect of SCFAs, mice deficient in GPR41 or GPR43 are more resistant to EAE pathogenesis. Thus, despite the overall protective function of SCFAs, SCFAs and their receptors have the potential to regulate autoimmune CNS inflammation both positively and negatively.
Delimiting a species’ geographic range using posterior sampling and computational geometry
Authors: Keith Jonathan M. , Spring Daniel , Kompas Tom 
Published: June 2019

AbstractAccurate delimitation of the geographic range of a species is important for control of biological invasions, conservation of threatened species, and understanding species range dynamics under environmental change. However, estimating range boundaries is challenging because monitoring methods are imperfect, the area that might contain individuals is often incompletely surveyed, and species may have patchy distributions. In these circumstances, large areas can be surveyed without finding individuals despite occupancy extending beyond surveyed areas, resulting in underestimation of range limits. We developed a delimitation method that can be applied with imperfect survey data and patchy distributions. The approach is to construct polygons indicative of the geographic range of a species. Each polygon is associated with a specific probability such that each interior point of the polygon has at least that posterior probability of being interior to the true boundary according to a Bayesian model. The method uses the posterior distribution of latent quantities derived from an agent-based Bayesian model and calculates the posterior distribution of the range as a derived quantity from Markov chain Monte Carlo samples. An application of this method described here informed the Australian campaign to eradicate red imported fire ants (Solenopsis invicta).