bluuebunny/crossref_metadata_2025_split huggingface dataset:
The zero effect: voxel-based lesion symptom mapping of number transcoding errors following stroke
Authors: Haupt Marleen , Gillebert Céline R. , Demeyere Nele 
Published: August 2017

AbstractZero represents a special case in our numerical system because it is not represented on a semantic level. Former research has shown that this can lead to specific impairments when transcoding numerals from dictation to written digits. Even though, number processing is considered to be dominated by the left hemisphere, studies have indicated that both left as well as right hemispheric stroke patients commit errors when transcoding numerals including zeros. Here, for the first time, a large sample of subacute stroke patients (N = 667) was assessed without being preselected based on the location of their lesion, or a specific impairment in transcoding zero. The results show that specific errors in transcoding zeros were common (prevalence = 14.2%) and a voxel-based lesion symptom mapping analysis (n = 153) revealed these to be related to lesions in and around the right putamen. In line with former research, the present study argues that the widespread brain network for number processing also includes subcortical regions, like the putamen with connections to the insular cortex. These play a crucial role in auditory perception as well as attention. If these areas are lesioned, number processing tasks with higher attentional and working memory loads, like transcoding zeros, can be impaired.
The small GTPase, nucleolar GTP-binding protein 1 (NOG1), has a novel role in plant innate immunity
Authors: Lee Seonghee , Senthil-Kumar Muthappa , Kang Miyoung , Rojas Clemencia M. , Tang Yuhong , Oh Sunhee , Choudhury Swarup Roy , Lee Hee-Kyung , Ishiga Yasuhiro , Allen Randy D. , Pandey Sona , Mysore Kirankumar S. 
Published: August 2017

AbstractPlant defense responses at stomata and apoplast are the most important early events during plant-bacteria interactions. The key components for the signaling of stomatal defense and nonhost resistance have not been fully characterized. Here we report the newly identified small GTPase, Nucleolar GTP-binding protein 1 (NOG1), functions for plant immunity against bacterial pathogens. Virus-induced gene silencing of NOG1 compromised nonhost resistance in N. benthamiana and tomato. Comparative genomic analysis showed that two NOG1 copies are present in all known plant species: NOG1-1 and NOG1-2. Gene downregulation and overexpression studies of NOG1-1 and NOG1-2 in Arabidopsis revealed the novel function of these genes in nonhost resistance and stomatal defense against bacterial pathogens, respectively. Specially, NOG1-2 regulates guard cell signaling in response to biotic and abiotic stimuli through jasmonic acid (JA)- and abscisic acid (ABA)-mediated pathways. The results here provide valuable information on the new functional role of small GTPase, NOG1, in guard cell signaling and early plant defense in response to bacterial pathogens.
Association between taste receptor (TAS) genes and the perception of wine characteristics
Authors: Carrai Maura , Campa Daniele , Vodicka Pavel , Flamini Riccardo , Martelli Irene , Slyskova Jana , Jiraskova Katerina , Rejhova Alexandra , Vodenkova Sona , Canzian Federico , Bertelli Alberto , Dalla Vedova Antonio , Bavaresco Luigi , Vodickova Ludmila , Barale Roberto 
Published: August 2017

AbstractSeveral studies have suggested a possible relationship between polymorphic variants of the taste receptors genes and the acceptance, liking and intake of food and beverages. In the last decade investigators have attempted to link the individual ability to taste 6-n-propylthiouracil (PROP) and the sensations, such as astringency and bitterness, elicited by wine or its components, but with contradictory results. We have used the genotype instead of the phenotype (responsiveness to PROP or other tastants), to test the possible relation between genetic variability and the perception of wine characteristic in 528 subjects from Italy and the Czech Republic. We observed several interesting associations, among which the association between several TAS2R38 gene single nucleotide polymorphisms (P = 0.002) and the TAS2R16-rs6466849 polymorphism with wine sourness P = 0.0003). These associations were consistent in both populations, even though the country of origin was an important factor in the two models, thus indicating therefore that genetics alongside cultural factors also play a significant role in the individual liking of wine.
Litter chemistry explains contrasting feeding preferences of bacteria, fungi, and higher plants
Authors: Bonanomi Giuliano , Cesarano Gaspare , Lombardi Nadia , Motti Riccardo , Scala Felice , Mazzoleni Stefano , Incerti Guido 
Published: August 2017

AbstractLitter decomposition provides a continuous flow of organic carbon and nutrients that affects plant development and the structure of decomposer communities. Aim of this study was to distinguish the feeding preferences of microbes and plants in relation to litter chemistry. We characterized 36 litter types by13C-CPMAS NMR spectroscopy and tested these materials on 6 bacteria, 6 fungi, and 14 target plants. Undecomposed litter acted as a carbon source for most of the saprophytic microbes, although with a large variability across litter types, severely inhibiting root growth. An opposite response was found for aged litter that largely inhibited microbial growth, but had neutral or stimulatory effects on root proliferation.13C-CPMAS NMR revealed that restricted resonance intervals within the alkyl C, methoxyl C,O-alkyl C and di-O-alkyl C spectral regions are crucial for understanding litter effects. Root growth, in contrast to microbes, was negatively affected by labile C sources but positively associated with signals related to plant tissue lignification. Our study showed that plant litter has specific and contrasting effects on bacteria, fungi and higher plants, highlighting that, in order to understand the effects of plant detritus on ecosystem structure and functionality, different microbial food web components should be simultaneously investigated.
Exploring dengue genome to construct a multi-epitope based subunit vaccine by utilizing immunoinformatics approach to battle against dengue infection
Authors: Ali Mudassar , Pandey Rajan Kumar , Khatoon Nazia , Narula Aruna , Mishra Amit , Prajapati Vijay Kumar 
Published: August 2017

AbstractDengue is considered as a major health issue which causes a number of deaths worldwide each year; tropical countries are majorly affected by dengue outbreaks. It is considered as life threatening issue because, since many decades not a single effective approach for treatment and prevention of dengue has been developed. Therefore, to find new preventive measure, we used immunoinformatics approaches to develop a multi-epitope based subunit vaccine for dengue which can generate various immune responses inside the host. Different B-cell, TC cell, and TH cell binding epitopes were predicted for structural and non-structural proteins of dengue virus. Final vaccine constructs consisting of TC and TH cell epitopes and an adjuvant (β-defensin) at N-terminal of the construct. Presence of B-cell and IFN-γ inducing epitopes confirms the humoral and cell mediated immune response developed by designed vaccine. Designed vaccine was not found allergic and was potentially antigenic in nature. Modeling of tertiary structure and the refined model was used for molecular docking with TLR-3 (immune receptor). Molecular docking and dynamics simulation confirms the microscopic interactions between ligand and receptor. In silico cloning approach was used to ensure the expression and translation efficiency of vaccine within an expression vector.
BioFlow: a non-invasive, image-based method to measure speed, pressure and forces inside living cells
Authors: Boquet-Pujadas Aleix , Lecomte Timothée , Manich Maria , Thibeaux Roman , Labruyère Elisabeth , Guillén Nancy , Olivo-Marin Jean-Christophe , Dufour Alexandre C. 
Published: August 2017

AbstractCell motility is governed by a complex molecular machinery that converts physico-chemical cues into whole-cell movement. Understanding the underlying biophysical mechanisms requires the ability to measure physical quantities inside the cell in a simple, reproducible and preferably non-invasive manner. To this end, we developed BioFlow, a computational mechano-imaging method and associated software able to extract intracellular measurements including pressure, forces and velocity everywhere inside freely moving cells in two and three dimensions with high spatial resolution in a non-invasive manner. This is achieved by extracting the motion of intracellular material observed using fluorescence microscopy, while simultaneously inferring the parameters of a given theoretical model of the cell interior. We illustrate the power of BioFlow in the context of amoeboid cell migration, by modelling the intracellular actin bulk flow of the parasite Entamoeba histolytica using fluid dynamics, and report unique experimental measures that complement and extend both theoretical estimations and invasive experimental measures. Thanks to its flexibility, BioFlow is easily adaptable to other theoretical models of the cell, and alleviates the need for complex or invasive experimental conditions, thus constituting a powerful tool-kit for mechano-biology studies. BioFlow is open-source and freely available via the Icy software.
Amoeboid-mesenchymal migration plasticity promotes invasion only in complex heterogeneous microenvironments
Authors: Talkenberger Katrin , Cavalcanti-Adam Elisabetta Ada , Voss-Böhme Anja , Deutsch Andreas 
Published: August 2017

AbstractDuring tissue invasion individual tumor cells exhibit two interconvertible migration modes, namely mesenchymal and amoeboid migration. The cellular microenvironment triggers the switch between both modes, thereby allowing adaptation to dynamic conditions. It is, however, unclear if this amoeboid-mesenchymal migration plasticity contributes to a more effective tumor invasion. We address this question with a mathematical model, where the amoeboid-mesenchymal migration plasticity is regulated in response to local extracellular matrix resistance. Our numerical analysis reveals that extracellular matrix structure and presence of a chemotactic gradient are key determinants of the model behavior. Only in complex microenvironments, if the extracellular matrix is highly heterogeneous and a chemotactic gradient directs migration, the amoeboid-mesenchymal migration plasticity allows a more widespread invasion compared to the non-switching amoeboid and mesenchymal modes. Importantly, these specific conditions are characteristic for in vivo tumor invasion. Thus, our study suggests that in vitro systems aiming at unraveling the underlying molecular mechanisms of tumor invasion should take into account the complexity of the microenvironment by considering the combined effects of structural heterogeneities and chemical gradients on cell migration.
Dynamic reverse phase transformation induced high-strain-rate superplasticity in low carbon low alloy steels with commercial potential
Authors: Cao Wenquan , Huang Chongxiang , Wang Chang , Dong Han , Weng Yuqing 
Published: August 2017

AbstractSuperplastic materials are capable of exhibiting large tensile elongation at elevated temperature, which is of great industrial significance because it forms the basis of a fabrication method to produce complex shapes. Superplasticity with elongation larger than 500% has been widely realized in many metals and alloys, but seldomly been succeeded in low carbon low alloy steel, even though it is commercially applied in the largest quantity. Here we report ultrahigh superplastic elongation of 900–1200% in the FeMnAl low carbon steels at high strain rate of 10−2–10−3 s−1. Such high-strain-rate superplasticity was attributed to dynamic austenite reverse phase transformation from a heavily cold rolled ferrite to fine-grained ferrite/austenite duplex microstructure and subsequent limited dynamic grain coarsening, under which a large fraction of high angle boundaries can be resulted for superplastic deformation. It is believed that this finding of the low carbon low alloy steel with ultrahigh superplasticity and relative low cost would remarkably promote the application of superplastic forming technique in automobile, aeronautical, astronautical and other fields.
Aspirin metabolite sodium salicylate selectively inhibits transcriptional activity of ATF6α and downstream target genes
Authors: Mügge Fernanda L. B. , Silva Aristóbolo M. 
Published: August 2017

AbstractIn response to ER stress, activating transcription factor 6 (ATF6) traffics from ER to Golgi apparatus where it is activated by cleavage before being translocated as transcription factor to the cell nucleus. In this work we describe ATF6α as a newly target of the aspirin metabolite sodium salicylate (NaSal). NaSal treatment of cells induces increases in ATF6α mRNA and protein levels, but these events are not accompanied by ATF6 activation. Conversely, NaSal inhibited ATF6 transactivating activity elicited by various ER stress-inducing stimuli in different cell types. This resulted in reduced expression of a subset of ATF6α target genes. Mechanistically, exposure of cells to NaSal results in ATF6α trapping at the Golgi apparatus, thus preventing nuclear translocation. This study provides evidence that NaSal compound restrains the activity of ATF6α, thereby preventing activation of a specific subset of ER-stress responsive genes implicated in different cellular responses.
Hypoxia imaging in cells and tumor tissues using a highly selective fluorescent nitroreductase probe
Authors: Yang Dan , Tian Hang Yu , Zang Tie Nan , Li Ming , Zhou Ying , Zhang Jun Feng 
Published: August 2017

AbstractHypoxia is a characteristic of locally advanced solid tumors, resulting from an imbalance between oxygen consumption and supply. In hypoxic solid tumors, an increased expression of nitroreductase (NTR) is detected, therefore, the development of NTR-targeted fluorescent probes to selectively and efficiently detect hypoxia in vivo is of utmost importance. In this study, a probe (1) has been designed and tested for effective optical detection of NTR in vitro and in vivo. The reduction of probe (1), catalyzed by NTR, resulted in changes of the electron-withdrawn nitrogen group into an electron-donation amino group. In addition, breakage of the O-C bond ensured selective fluorescence enhancement. The in vitro response towards exogenous NTR, from rat liver microsomes, resulted in the optical enhancement during the detection process. In vivo imaging of caerorhabditis elegans (C.elegan) further confirmed the detection of NTR by probe (1). Moreover, probe (1) was successfully used for the detection of hypoxia in both HI5 cells, and a murine tumor model, which demonstrates the potential of probe (1) for application in fluorescence bioimaging studies, and tumor hypoxia diagnosis.
Effect of Crystal Orientation on Femtosecond Laser-Induced Thermomechanical Responses and Spallation Behaviors of Copper Films
Authors: Xiong Qi-lin , Li Zhenhuan , Kitamura Takayuki 
Published: August 2017

AbstractUltrafast thermomechanical responses and spallation behaviours of monocrystal copper films irradiated by femtosecond laser pulse are investigated using molecular dynamics simulation (MDS). Films with 〈100〉, 〈110〉 and 〈111〉 crystal orientations along the thickness direction were studied. The results show that the crystal orientation has a significant effect on femtosecond laser-induced thermomechanical responses and spallation behaviors of monocrystal copper films. The discrepancy between normal stresses in copper films with different crystal orientation leads to distinct differences in lattice temperature. Moreover, the copper films with different crystal orientations present distinct spallation behaviors, including structural melting (atomic splashing) and fracture. The melting depth of 〈100〉 copper film is lower than that of 〈110〉 and 〈111〉 copper films for the same laser intensity. The dislocations and slip bands are formed and propagate from the solid-liquid interface of 〈110〉 and 〈111〉 copper films, while these phenomena do not appear in 〈100〉 copper film. Additionally, numerous slip bands are generated in the non-irradiated surface region of copper films due to reflection of mechanical stress. These slip bands can finally evolve into cracks (nanovoids) with time, which further result in the fracture of the entire films.
Coherent Raman Imaging of Live Muscle Sarcomeres Assisted by SFG Microscopy
Authors: Kim Hyunmin , Kim Do-Young , Joo Kyung-Il , Kim Jung-Hye , Jeong Soon Moon , Lee Eun Seong , Hahm Jeong-Hoon , Kim Kyuhyung , Moon Dae Woon 
Published: August 2017

AbstractIn this study, we used spectrally focused coherent anti-Stokes Raman scattering (spCARS) microscopy assisted by sum-frequency generation (SFG) to monitor the variations in the structural morphology and molecular vibrations of a live muscle of Caenorhabditis elegans. The subunits of the muscle sarcomeres, such as the M-line, myosin, dense body, and α-actinin, were alternatively observed using spCARS microscopy for different sample orientations, with the guidance of a myosin positional marker captured by SFG microscopy. Interestingly enough, the beam polarization dependence of the spCARS contrasts for two parallel subunits (dense body and myosin) showed a ~90° phase difference. The chemically sensitive spCARS spectra induced by the time-varying overlap of two pulses allowed (after a robust subtraction of the non-resonant background using a modified Kramers–Krönig transformation method) high-fidelity detection of various genetically modified muscle sarcomeres tuned to the C-H vibration (2800–3100 cm−1). Conversely, SFG image mapping assisted by phase-retrieved spCARS spectra also facilitated label-free monitoring of the changes in the muscle content of C. elegans that are associated with aging, based on the hypothesis that the C-H vibrational modes could serve as qualitative chemical markers sensitive to the amount and/or structural modulation of the muscle.
A prospective multicenter study on genome wide associations to ranibizumab treatment outcome for age-related macular degeneration
Authors: Yamashiro Kenji , Mori Keisuke , Honda Shigeru , Kano Mariko , Yanagi Yasuo , Obana Akira , Sakurada Yoichi , Sato Taku , Nagai Yoshimi , Hikichi Taiichi , Kataoka Yasushi , Hara Chikako , Koyama Yasurou , Koizumi Hideki , Yoshikawa Munemitsu , Miyake Masahiro , Nakata Isao , Tsuchihashi Takashi , Horie-Inoue Kuniko , Matsumiya Wataru , Ogasawara Masashi , Obata Ryo , Yoneyama Seigo , Matsumoto Hidetaka , Ohnaka Masayuki , Kitamei Hirokuni , Sayanagi Kaori , Ooto Sotaro , Tamura Hiroshi , Oishi Akio , Kabasawa Sho , Ueyama Kazuhiro , Miki Akiko , Kondo Naoshi , Bessho Hiroaki , Saito Masaaki , Takahashi Hidenori , Tan Xue , Azuma Keiko , Kikushima Wataru , Mukai Ryo , Ohira Akihiro , Gomi Fumi , Miyata Kazunori , Takahashi Kanji , Kishi Shoji , Iijima Hiroyuki , Sekiryu Tetsuju , Iida Tomohiro , Awata Takuya , Inoue Satoshi , Yamada Ryo , Matsuda Fumihiko , Tsujikawa Akitaka , Negi Akira , Yoneya Shin , Iwata Takeshi , Yoshimura Nagahisa 
Published: August 2017

AbstractWe conducted a genome-wide association study (GWAS) on the outcome of anti-VEGF treatment for exudative age-related macular degeneration (AMD) in a prospective cohort. Four hundred and sixty-one treatment-naïve AMD patients were recruited at 13 clinical centers and all patients were treated with 3 monthly injections of ranibizumab followed by pro re nata regimen treatment for one year. Genomic DNA was collected from all patients for a 2-stage GWAS on achieving dry macula after the initial treatment, the requirement for an additional treatment, and visual acuity changes during the 12-month observation period. In addition, we evaluated 9 single-nucleotide polymorphisms (SNPs) in 8 previously reported AMD-related genes for their associations with treatment outcome. The discovery stage with 256 patients evaluated 8,480,849 SNPs, but no SNPs showed genome-wide level significance in association with treatment outcomes. Although SNPs with P-values of <5 × 10−6 were evaluated in replication samples of 205 patients, no SNP was significantly associated with treatment outcomes. Among AMD-susceptibility genes, rs10490924 in ARMS2/HTRA1 was significantly associated with additional treatment requirement in the discovery stage (P = 0.0023), and pooled analysis with the replication stage further confirmed this association (P = 0.0013). ARMS2/HTRA1 polymorphism might be able to predict the frequency of injection after initial ranibizumab treatment.
Pancreatic islet macroencapsulation using microwell porous membranes
Authors: Skrzypek Katarzyna , Groot Nibbelink Milou , van Lente Jéré , Buitinga Mijke , Engelse Marten A. , de Koning Eelco J. P. , Karperien Marcel , van Apeldoorn Aart , Stamatialis Dimitrios 
Published: August 2017

AbstractAllogeneic islet transplantation into the liver in combination with immune suppressive drug therapy is widely regarded as a potential cure for type 1 diabetes. However, the intrahepatic system is suboptimal as the concentration of drugs and nutrients there is higher compared to pancreas, which negatively affects islet function. Islet encapsulation within semipermeable membranes is a promising strategy that allows for the islet transplantation outside the suboptimal liver portal system and provides environment, where islets can perform their endocrine function. In this study, we develop a macroencapsulation device based on thin microwell membranes. The islets are seeded in separate microwells to avoid aggregation, whereas the membrane porosity is tailored to achieve sufficient transport of nutrients, glucose and insulin. The non-degradable, microwell membranes are composed of poly (ether sulfone)/polyvinylpyrrolidone and manufactured via phase separation micro molding. Our results show that the device prevents aggregation and preserves the islet’s native morphology. Moreover, the encapsulated islets maintain their glucose responsiveness and function after 7 days of culture (stimulation index above 2 for high glucose stimulation), demonstrating the potential of this novel device for islet transplantation.
Choroid Plexitis and Ependymitis by Magnetic Resonance Imaging are Biomarkers of Neuronal Damage and Inflammation in HIV-negative Cryptococcal Meningoencephalitis
Authors: Hammoud Dima A. , Mahdi Eman , Panackal Anil A. , Wakim Paul , Sheikh Virginia , Sereti Irini , Bielakova Bibi , Bennett John E. , Williamson Peter R. 
Published: August 2017

AbstractCNS cryptococcal meningoencephalitis in both HIV positive (HIV+) and HIV negative (HIV−) subjects is associated with high morbidity and mortality despite optimal antifungal therapy. We thus conducted a detailed analysis of the MR imaging findings in 45 HIV− and 11 HIV+ patients to identify imaging findings associated with refractory disease. Ventricular abnormalities, namely ependymitis and choroid plexitis were seen in HIV− but not in HIV+ subjects. We then correlated the imaging findings in a subset of HIV− subjects (n = 17) to CSF levels of neurofilament light chain (NFL), reflective of axonal damage and sCD27, known to best predict the presence of intrathecal T-cell mediated inflammation. We found that ependymitis on brain MRI was the best predictor of higher log(sCD27) levels and choroid plexitis was the best predictor of higher log(NFL) levels. The availability of predictive imaging biomarkers of inflammation and neurological damage in HIV− subjects with CNS cryptococcosis may help gauge disease severity and guide the therapeutic approach in those patients.