bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of wheat gene expression related to the oxidative stress response and signal transduction under short-term osmotic stress
Authors: Dudziak Karolina , Zapalska Magdalena , Börner Andreas , Szczerba Hubert , Kowalczyk Krzysztof , Nowak Michał 
Published: February 2019

AbstractWater shortage is a major environmental stress that causes the generation of reactive oxygen species (ROS). The increase in ROS production induces molecular responses, which are key factors in determining the level of plant tolerance to stresses, including drought. The aim of this study was to determine the expression levels of genes encoding MAPKs (MAPK3andMAPK6), antioxidant enzymes (CAT,APXandGPX) and enzymes involved in proline biosynthesis (P5CSandP5CR) inTriticum aestivumL. seedlings in response to short-term drought conditions. A series of wheat intervarietal substitution lines (ISCSLs) obtained by the substitution of single chromosomes from a drought-sensitive cultivar into the genetic background of a drought-tolerant cultivar was used. This source material allowed the chromosomal localization of the genetic elements involved in the response to the analyzed stress factor (drought). The results indicated that the initial plant response to drought stress resulted notably in changes in the expression ofMAPK6andCATand both theP5CSandP5CRgenes. Our results showed that the substitution of chromosomes 3B, 5A, 7B and 7D had the greatest impact on the expression level of all tested genes, which indicates that they contain genetic elements that have a significant function in controlling tolerance to water deficits in the wheat genome.
Crustacean larval factor shares structural characteristics with the insect-specific follicle cell protein
Authors: Ventura Tomer , Nguyen Chan , Fitzgibbon Quinn P. , Abramov Tomer , Smith Gregory G. , Elizur Abigail 
Published: February 2019

AbstractLiterature on the cuticle formation in larval stages of the diverse group of decapod crustaceans is lacking, as opposed to a wealth of knowledge in several insect groups. Here we provide the first glimpse of the cuticular organisation in larvae of the eastern spiny lobster Sagmariasus verreauxi. A bioinformatic approach applied to S. verreauxi transcriptome through metamorphosis identified for the first time a small secreted protein with multiple isoforms that is highly expressed in crustacean larvae. This protein, named crustacean larval factor (Clf) shares structural characteristics with insect follicle cell protein 3 (FCP3), an insect-specific, rapidly evolving protein, with spatial-temporal regulated expression that is restricted to follicular cells during the production of the vitellin coat. Furthermore, we identified the FCP3 domain in additional structural proteins in multiple arthropod groups. Recombinant Clf inhibited in vitro calcium carbonate crystalline precipitation, in keeping with the finding that the spiny lobster larval cuticle is mainly composed of amorphous calcium carbonate. In addition, the recombinant Clf was shown to bind chitosan. Taken together, this research identifies two novel structural domains with lineage-specific expansion across arthropods. In crustaceans, Clf is found predominantly in larvae and the spatial-temporal regulated FCP3 factor occurs as a domain identified in multiple structural proteins across arthropods. Given the shared ten cysteines backbone between the Clf and FCP domains, a shared evolution is suggested and should be further explored.
Silencing of spinal Trpv1 attenuates neuropathic pain in rats by inhibiting CAMKII expression and ERK2 phosphorylation
Authors: Guo Shao-Hui , Lin Jia-Piao , Huang Ling-Er , Yang Yan , Chen Chao-Qin , Li Na-Na , Su Meng-Yun , Zhao Xian , Zhu Sheng-Mei , Yao Yong-Xing 
Published: February 2019

AbstractAccumulating evidence suggests a potential role of transient receptor potential vanilloid 1 (TRPV1) channels in inflammatory and cancer-related pain. However, the role of TRPV1 in the maintenance of neuropathic pain remains elusive. The current study investigated the effects of transient Trpv1 gene silencing using a small interference RNA (siRNA) on neuropathic pain induced by chronic constriction injury (CCI) of the sciatic nerve in rats. Seven days after CCI, the TRPV1 siRNA was intrathecally administered (5 µg/15 µl, once daily for 2 days). TRPV1 and Ca2+/calmodulin-dependent protein kinase II (CAMKII) expression and extracellular signal-regulated kinase (ERK) phosphorylation in the spinal cord were detected using western blotting. The thresholds to mechanical and thermal stimuli were determined before and after intrathecal TRPV1 siRNA administration. TRPV1 and CAMKII expression and ERK2 phosphorylation in the spinal cord were upregulated after CCI. Intrathecal administration of the TRPV1 siRNA not only attenuated behavioural hyperalgesia but also reduced the expression of TRPV1 and CAMKII, as well as ERK2 phosphorylation. Based on these results, silencing of the TRPV1 gene in the spinal cord attenuates the maintenance of neuropathic pain by inhibiting CAMKII/ERK2 activation and suggests that TRPV1 represents a potential target in pain therapy.
Lamellar ordering, droplet formation and phase inversion in exotic active emulsions
Authors: Bonelli F. , Carenza L. N. , Gonnella G. , Marenduzzo D. , Orlandini E. , Tiribocchi A. 
Published: February 2019

AbstractWe study numerically the behaviour of a two-dimensional mixture of a passive isotropic fluid and an active polar gel, in the presence of a surfactant favouring emulsification. Focussing on parameters for which the underlying free energy favours the lamellar phase in the passive limit, we show that the interplay between nonequilibrium and thermodynamic forces creates a range of multifarious exotic emulsions. When the active component is contractile (e.g., an actomyosin solution), moderate activity enhances the efficiency of lamellar ordering, whereas strong activity favours the creation of passive droplets within an active matrix. For extensile activity (occurring, e.g., in microtubule-motor suspensions), instead, we observe an emulsion of spontaneously rotating droplets of different size. By tuning the overall composition, we can create high internal phase emulsions, which undergo sudden phase inversion when activity is switched off. Therefore, we find that activity provides a single control parameter to design composite materials with a strikingly rich range of morphologies.
Deep learning in head & neck cancer outcome prediction
Authors: Diamant André , Chatterjee Avishek , Vallières Martin , Shenouda George , Seuntjens Jan 
Published: February 2019

AbstractTraditional radiomics involves the extraction of quantitative texture features from medical images in an attempt to determine correlations with clinical endpoints. We hypothesize that convolutional neural networks (CNNs) could enhance the performance of traditional radiomics, by detecting image patterns that may not be covered by a traditional radiomic framework. We test this hypothesis by training a CNN to predict treatment outcomes of patients with head and neck squamous cell carcinoma, based solely on their pre-treatment computed tomography image. The training (194 patients) and validation sets (106 patients), which are mutually independent and include 4 institutions, come from The Cancer Imaging Archive. When compared to a traditional radiomic framework applied to the same patient cohort, our method results in a AUC of 0.88 in predicting distant metastasis. When combining our model with the previous model, the AUC improves to 0.92. Our framework yields models that are shown to explicitly recognize traditional radiomic features, be directly visualized and perform accurate outcome prediction.
Axial electrokinetic trapping of anisotropic particles
Authors: Strubbe Filip , Robben Bavo , Puthenparampil George John , Amer Cid Íngrid , Beunis Filip , Neyts Kristiaan 
Published: February 2019

AbstractAnti-Brownian electrokinetic trapping is a method for trapping single particles in liquid based on particle position measurements and the application of feedback voltages. To achieve trapping in the axial direction, information on the axial particle position is required. However, existing strategies for determining the axial position that are based on measuring the size of the first diffraction ring, theory fitting, advanced optical setups or pre-determined axial image stacks are impractical for anisotropic particles. In this work, axial electrokinetic trapping of anisotropic particles is realized in devices with planar, transparent electrodes. The trapping algorithm uses Fourier-Bessel decomposition of standard microscopy images and is learning from the correlation between applied voltages and changes in the particle appearance. No previous knowledge on the particle appearance, theory fitting or advanced optical setup is required. The particle motion in the trap and the influence of screening of the electric field on this motion are analyzed. The axial trapping method opens new possibilities for measuring properties of anisotropic or isotropic particles and forces acting on such particles.
Pressure Reveals Unique Conformational Features in Prion Protein Fibril Diversity
Authors: Torrent Joan , Martin Davy , Noinville Sylvie , Yin Yi , Doumic Marie , Moudjou Mohammed , Béringue Vincent , Rezaei Human 
Published: February 2019

AbstractThe prion protein (PrP) misfolds and assembles into a wide spectrum of self-propagating quaternary structures, designated PrPSc. These various PrP superstructures can be functionally different, conferring clinically distinctive symptomatology, neuropathology and infectious character to the associated prion diseases. However, a satisfying molecular basis of PrP structural diversity is lacking in the literature. To provide mechanistic insights into the etiology of PrP polymorphism, we have engineered a set of 6 variants of the human protein and obtained PrP amyloid fibrils. We show that pressure induces dissociation of the fibrils, albeit with different kinetics. In addition, by focusing on the generic properties of amyloid fibrils, such as the thioflavin T binding capacities and the PK-resistance, we reveal an unprecedented structure-barostability phenomenological relationship. We propose that the structural diversity of PrP fibrils encompass a multiplicity of packing defects (water-excluded cavities) in their hydrophobic cores, and that the resultant sensitivity to pressure should be considered as a general molecular criterion to accurately define fibril morphotypes. We anticipate that our insights into sequence-dependent fibrillation and conformational stability will shed light on the highly-nuanced prion strain phenomenon and open the opportunity to explain different PrP conformations in terms of volumetric physics.
Proton Magnetic Resonance Spectroscopy of the motor cortex reveals long term GABA change following anodal Transcranial Direct Current Stimulation
Authors: Patel Harshal Jayeshkumar , Romanzetti Sandro , Pellicano Antonello , Nitsche Michael A. , Reetz Kathrin , Binkofski Ferdinand 
Published: February 2019

AbstractAnodal transcranial direct current stimulation (tDCS) over the primary motor cortex (M1) has been reported to increase the firing rates of neurons and to modulate the gamma-aminobutyric acid (GABA) concentration. To date, knowledge about the nature and duration of these tDCS induced effects is incomplete. We aimed to investigate long-term effects of anodal tDCS over M1 on GABA dynamics in humans. Repeated magnetic resonance spectroscopy (MRS) was employed to measure relative GABA concentration in M1 for approximately 64 minutes after stimulation. The study was performed on 32 healthy subjects. Either anodal or sham tDCS were applied for 10 minutes with the active electrode over the left M1 and the reference electrode over the right supra-orbital region. Pre and post-tDCS MRS scans were performed to acquire GABA-edited spectra using 3 T Prisma Siemens scanner. GABA signals showed no change over time in the sham tDCS group, whereas anodal tDCS resulted in a significant early decrease within 25 minutes after tDCS and then significant late decrease after 66 minutes which continued until the last test measurements. The late changes in GABA concentration might be related to long-term plasticity mechanism. These results contribute to a better understanding of the neurochemical mechanism underlying long-term cortical plasticity following anodal tDCS.
Sleep deprivation and its effects on communication during individual and collaborative tasks
Authors: Holding Benjamin C. , Sundelin Tina , Lekander Mats , Axelsson John 
Published: February 2019

AbstractSleep loss has been shown to cause impairments in a number of aspects central for successful communication, ranging from poorer linguistic comprehension to alterations in speech prosody. However, the effect of sleep loss on actual communication is unknown. This study investigated how a night of sleep deprivation affected performance during multiple tasks designed to test verbal communication. Healthy participants (N = 183) spent 8–9 hours per night in bed for three nights and were then randomised to either one night of total sleep deprivation or a fourth night with 8–9 hours in bed. The following day, participants completed two tasks together with another participant: a model-building task and a word-description task. Differences in performance of these tasks were assessed alongside speaking duration, speaking volume, and speaking volume consistency. Additionally, participants individually completed a verbal fluency assessment. Performance on the model-building task was worse if the model-builder was sleep deprived, whereas sleep deprivation in the instruction-giver predicted an improvement. Word-description, verbal fluency, speech duration, speaking volume, and speaking volume consistency were not affected. The results suggest that sleep deprivation leads to changes in communicative performance during instructive tasks, while simpler word-description tasks appear resilient.
Highly efficient coherent conformal projection system based on adaptive fiber optics collimator array
Authors: Zhi Dong , Ma Yanxing , Tao Rumao , Zhou Pu , Wang Xiaolin , Chen Zilun , Si Lei 
Published: February 2019

AbstractCoherent beam combination (CBC) of fiber laser array, which is a promising approach to overcome the power scaling limitations of the single fiber laser and to achieve high-brightness laser with good beam quality, can be employed in coherent conformal projection system (CCPS) for beam projection and free space laser communication system with enormous potential. To date, all the demonstrated CBC system through several kilometers atmospheric turbulence have employed collimated beams, which significantly decrease the final CBC effect because of the inefficient wavefront overlap. On the other hand, focused CCPS has lots of advantages over collimated projection system since the wave front of the projected beam is closer to that of a convergent spherical wave. In this paper, we design and manufacture focused CCPS based on an adaptive fiber optics collimator array for the first time, which is achieved by introducing controllable spherical aberration through the adaptive fiber optics collimator. A CBC system is setup to evaluate and validate its performance. Results show that compared with the collimated CCPS, the energy portion of the central lobe could be increased by a factor of 44%, which agrees well with the theoretical analysis.
Neutron imaging and modelling inclined vortex driven thin films
Authors: Solheim Timothy E. , Salvemini Filomena , Dalziel Stuart B. , Raston Colin L. 
Published: February 2019

AbstractThe vortex fluidic device (VFD) is a thin film microfluidic platform which has a wide range of applications in synthesis and other areas of science, and it is important to understand the nature of the thin film of liquid in its inclined rapidly rotating tube. Neutron imaging has been used to determine the thickness of the film in a quartz tube with its shape modelled mathematically, showing good agreement between the model and experiments. The resultant equations are useful for studying VFD mediated processing in general, for which the optimal tilt angle of the tube is typically 45°. This includes its utility for the intelligent scale-up of organic syntheses, as demonstrated in the present study by the scaling up of an imine and amide synthesis to >1 g/min.
Neuromuscular magnetic stimulation counteracts muscle decline in ALS patients: results of a randomized, double-blind, controlled study
Authors: Musarò Antonio , Dobrowolny Gabriella , Cambieri Chiara , Onesti Emanuela , Ceccanti Marco , Frasca Vittorio , Pisano Annalinda , Cerbelli Bruna , Lepore Elisa , Ruffolo Gabriele , Cifelli Pierangelo , Roseti Cristina , Giordano Carla , Gori Maria Cristina , Palma Eleonora , Inghilleri Maurizio 
Published: February 2019

AbstractThe aim of the study was to verify whether neuromuscular magnetic stimulation (NMMS) improves muscle function in spinal-onset amyotrophic lateral sclerosis (ALS) patients. Twenty-two ALS patients were randomized in two groups to receive, daily for two weeks, NMMS in right or left arm (referred to as real-NMMS, rNMMS), and sham NMMS (sNMMS) in the opposite arm. All the patients underwent a median nerve conduction (compound muscle action potential, CMAP) study and a clinical examination that included a handgrip strength test and an evaluation of upper limb muscle strength by means of the Medical Research Council Muscle Scale (MRC). Muscle biopsy was then performed bilaterally on the flexor carpi radialis muscle to monitor morpho-functional parameters and molecular changes. Patients and physicians who performed examinations were blinded to the side of real intervention. The primary outcome was the change in the muscle strength in upper arms. The secondary outcomes were the change from baseline in the CMAP amplitudes, in the nicotinic ACh currents, in the expression levels of a selected panel of genes involved in muscle growth and atrophy, and in histomorphometric parameters of ALS muscle fibers. The Repeated Measures (RM) ANOVA with a Greenhouse-Geisser correction (sphericity not assumed) showed a significant effect [F(3, 63) = 5.907, p < 0.01] of rNMMS on MRC scale at the flexor carpi radialis muscle, thus demonstrating that the rNMMS significantly improves muscle strength in flexor muscles in the forearm. Secondary outcomes showed that the improvement observed in rNMMS-treated muscles was associated to counteracting muscle atrophy, down-modulating the proteolysis, and increasing the efficacy of nicotinic ACh receptors (AChRs). We did not observe any significant difference in pre- and post-stimulation CMAP amplitudes, evoked by median nerve stimulation. This suggests that the improvement in muscle strength observed in the stimulated arm is unlikely related to reinnervation. The real and sham treatments were well tolerated without evident side effects. Although promising, this is a proof of concept study, without an immediate clinical translation, that requires further clinical validation.
Identifying Windows of Susceptibility by Temporal Gene Analysis
Authors: Bennett Kristin P. , Brown Elisabeth M. , Santos Hannah De los , Poegel Matthew , Kiehl Thomas R. , Patton Evan W. , Norris Spencer , Temple Sally , Erickson John , McGuinness Deborah L. , Boles Nathan C. 
Published: February 2019

AbstractIncreased understanding of developmental disorders of the brain has shown that genetic mutations, environmental toxins and biological insults typically act during developmental windows of susceptibility. Identifying these vulnerable periods is a necessary and vital step for safeguarding women and their fetuses against disease causing agents during pregnancy and for developing timely interventions and treatments for neurodevelopmental disorders. We analyzed developmental time-course gene expression data derived from human pluripotent stem cells, with disease association, pathway, and protein interaction databases to identify windows of disease susceptibility during development and the time periods for productive interventions. The results are displayed as interactive Susceptibility Windows Ontological Transcriptome (SWOT) Clocks illustrating disease susceptibility over developmental time. Using this method, we determine the likely windows of susceptibility for multiple neurological disorders using known disease associated genes and genes derived from RNA-sequencing studies including autism spectrum disorder, schizophrenia, and Zika virus induced microcephaly. SWOT clocks provide a valuable tool for integrating data from multiple databases in a developmental context with data generated from next-generation sequencing to help identify windows of susceptibility.
Tissue Engineered Neural Constructs Composed of Neural Precursor Cells, Recombinant Spidroin and PRP for Neural Tissue Regeneration
Authors: Baklaushev V. P. , Bogush V. G. , Kalsin V. A. , Sovetnikov N. N. , Samoilova E. M. , Revkova V. A. , Sidoruk K. V. , Konoplyannikov M. A. , Timashev P. S. , Kotova S. L. , Yushkov K. B. , Averyanov A. V. , Troitskiy A. V. , Ahlfors J.-E. 
Published: February 2019

AbstractWe have designed a novel two-component matrix (SPRPix) for the encapsulation of directly reprogrammed human neural precursor cells (drNPC). The matrix is comprised of 1) a solid anisotropic complex scaffold prepared by electrospinning a mixture of recombinant analogues of the spider dragline silk proteins – spidroin 1 (rS1/9) and spidroin 2 (rS2/12) - and polycaprolactone (PCL) (rSS-PCL), and 2) a “liquid matrix” based on platelet-rich plasma (PRP). The combination of PRP and spidroin promoted drNPC proliferation with the formation of neural tissue organoids and dramatically activated neurogenesis. Differentiation of drNPCs generated large numbers of βIII-tubulin and MAP2 positive neurons as well as some GFAP-positive astrocytes, which likely had a neuronal supporting function. Interestingly the SPRPix microfibrils appeared to provide strong guidance cues as the differentiating neurons oriented their processes parallel to them. Implantation of the SPRPix matrix containing human drNPC into the brain and spinal cord of two healthy Rhesus macaque monkeys showed good biocompatibility: no astroglial and microglial reaction was present around the implanted construct. Importantly, the human drNPCs survived for the 3 month study period and differentiated into MAP2 positive neurons. Tissue engineered constructs based on SPRPix exhibits important attributes that warrant further examination in spinal cord injury treatment.