bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optic nerve intraneural stimulation allows selective visual cortex activation
Authors: Gaillet Vivien , Cutrone Annarita , Vagni Paola , Artoni Fiorenzo , Pinto Sandra Alejandra Romero , Di Paola Dario Lipucci , Micera Silvestro , Ghezzi Diego 
Published: May 2018

AbstractRetinal prostheses have been developed to restore a functional form of vision in patients affected by outer retinal layer dystrophies. Other approaches, namely optic nerve, thalamic, and cortical prostheses are under investigation to expand this toolbox both as clinical devices and as tools for fundamental research. Optic nerve stimulation is attractive since it bypasses the entire retinal network and directly activates nerve fibers. At the same time, it still takes advantage of the high-level information processing occurring downstream in the visual cortex. Here we show that a new intraneural electrode array (OpticSELINE) is effective in inducing the activation of the visual cortex upon electrical stimulation of the optic nerve. We also demonstrate that intraneural optic nerve stimulation induces selective cortical activation patterns depending on the stimulating electrode, thus suggesting that the OpticSELINE possesses spatial selectivity in fiber stimulation. In conclusion, the OpticSELINE can be used both as visual prosthesis for blind patients and as tool to further investigate the effect of the electrical stimulation in the visual system.
Structure for Energy Cycle: A unique status of Second Law of Thermodynamics for living systems
Authors: Bai Shu-Nong , Ge Hao , Qian Hong 
Published: May 2018

AbstractDistinguishing things from beings, or matters from lives, is a fundamental question. Extending E. Schrödinger’sneg-entropyand I. Prigogine’sdissipative structure, we propose a chemical kinetic view that the earliest “live” process is essentially a special interaction between a pair of specific components under a corresponding, particular environmental conditions. The interaction exists as an inter-molecular-force-bond complex (IMFBC) that couples two separate chemical processes: One is the spontaneous formation of an IMFBC driven by the decrease of Gibbs free energy as a dissipative process; while the other is the disassembly of the IMFBC driven thermodynamically by free energy input from the environment. The two processes that are coupled by the IMFBC were originated independently and considered non-living on Earth, but the IMFBC coupling of the two can be considered as the earliest form of metabolism: This forms the first landmark on the path from things to a being. The dynamic formation and dissemblance of the IMFBCs, as composite individuals, follows a principle designated as “… structure for energy for structure for energy…”, the cycle continues, shortly “structure for energy cycle”. With additional features derived from an IMFBC, such as multiple intermediates, autocatalytic ability of one individual upon the formation of another, aqueous medium, and mutual beneficial relationship between formation of polypeptides and nucleic acids, etc., the IMFBC-centered “live” process spontaneously evolved into more complex living organisms with the characteristics one currently knows.
matchSCore: Matching Single-Cell Phenotypes Across Tools and Experiments
Authors: Mereu Elisabetta , Iacono Giovanni , Guillaumet-Adkins Amy , Moutinho Catia , Lunazzi Giulia , Santos Catarina P. , Miguel-Escalada Irene , Ferrer Jorge , Real Francisco X. , Gut Ivo , Heyn Holger 
Published: May 2018

AbstractSingle-cell transcriptomics allows the identification of cellular types, subtypes and states through cell clustering. In this process, similar cells are grouped before determining co-expressed marker genes for phenotype inference. The performance of computational tools is directly associated to their marker identification accuracy, but the lack of an optimal solution challenges a systematic method comparison. Moreover, phenotypes from different studies are challenging to integrate, due to varying resolution, methodology and experimental design. In this work we introduce matchSCore (https://github.com/elimereu/matchSCore), an approach to match cell populations fast across tools, experiments and technologies. We compared 14 computational methods and evaluated their accuracy in clustering and gene marker identification in simulated data sets. We further used matchSCore to project cell type identities across mouse and human cell atlas projects. Despite originating from different technologies, cell populations could be matched across data sets, allowing the assignment of clusters to reference maps and their annotation.
Antibiotic-induced dysbiosis predicts mortality in an animal model ofClostridium difficileinfection
Authors: Burdet Charles , Sayah-Jeanne Sakina , Nguyen Thu Thuy , Hugon Perrine , Sablier-Gallis Frédérique , Saint-Lu Nathalie , Corbel Tanguy , Ferreira Stéphanie , Pulse Mark , Weiss William , Andremont Antoine , Mentré France , Gunzburg Jean de 
Published: May 2018

AbstractBackgroundAntibiotic disruption of the intestinal microbiota favors colonization byClostridium difficile. Using a charcoal-based adsorbent to decrease intestinal antibiotic concentrations, we studied the relationship between antibiotic concentrations in feces and the intensity of dysbiosis, and quantified the link between this intensity and mortality.MethodsWe administered either moxifloxacin (n=70) or clindamycin (n=60) to hamsters by subcutaneous injection from day 1 (D1) to D5, and challenged them with aC. difficiletoxigenic strain at D3. Hamsters received various doses of a charcoal-based adsorbent, DAV131A, to modulate intestinal antibiotic concentrations. Gut dysbiosis was evaluated at D0and D3using diversity indices determined from 16S rRNA gene profiling. Survival was monitored until D16. We analyzed the relationship between fecal antibiotic concentrations and dysbiosis at the time ofC. difficilechallenge and studied their capacity to predict subsequent death of the animals.ResultsIncreasing doses of DAV131A reduced fecal concentrations of both antibiotics, lowered dysbiosis and increased survival from 0% to 100%. Mortality was related to the level of dysbiosis (p<10−5for the change of Shannon index in moxifloxacin-treated animals and p<10−9in clindamycin-treated animals). The Shannon diversity index and unweighted UniFrac distance best predicted death, with areas under the ROC curve of 0.89 [95%CI, 0.82;0.95] and 0.95 [0.90;0.98], respectively.ConclusionsAltogether, moxifloxacin and clindamycin disrupted the diversity of the intestinal microbiota with a dependency to the DAV131A dose; mortality afterC. difficilechallenge was related to the intensity of dysbiosis in a similar manner with the two antibiotics.
Intercellular Signaling Network Underlies Biological Time Across Multiple Temporal Scales
Authors: Millstein Joshua , Summa Keith C. , Yang Xia , Zhu Jun , Mi Huaiyu , Vitaterna Martha H. , Turek Fred W. , Zhang Bin 
Published: May 2018

AbstractMotivationCellular, physiological and molecular processes must be organized and regulated across multiple time domains throughout the lifespan of an organism. The technological revolution in molecular biology has led to the identification of numerous genes implicated in the regulation of diverse temporal biological processes. However, it is natural to question whether there is an underlying regulatory network governing multiple timescales simultaneously.ResultsUsing queries of relevant databases and literature searches, a single dense multiscale temporal regulatory network was identified involving core sets of genes that regulate circadian, cell cycle, and aging processes. The network was highly enriched for genes involved in signal transduction (P = 1.82e-82), with p53 and its regulators such as p300 and CREB binding protein forming key hubs, but also for genes involved in metabolism (P = 6.07e-127) and cellular response to stress (P = 1.56e-93). These results suggest an intertwined molecular signaling network that affects biological time across multiple temporal scales in response to environmental stimuli and available resources.Contactjoshua.millstein@usc.eduSupplementary informationSupplementary data are available online.
High-throughput Analysis of Arabidopsis Stem Vibrations to Identify Mutants with Altered Mechanical Properties
Authors: Nakata Miyuki T. , Takahara Masahiro , Sakamoto Shingo , Yoshida Kouki , Mitsuda Nobutaka 
Published: May 2018

AbstractMechanical properties are rarely used as quantitative indices for the large-scale mutant screening of plants, even in the model plant Arabidopsis thaliana. The mechanical properties of plant stems generally influence their vibrational characteristics. Here, we developed Python-based software, named AraVib, for the high-throughput analysis of free vibrations of plant stems, focusing specifically on Arabidopsis stem vibrations, and its extended version, named AraVibS, to identify mutants with altered mechanical properties. These programs can be used without knowledge of Python and require only an inexpensive handmade setting stand and an iPhone/iPad with a high-speed shooting function for data acquisition. Using our system, we identified an nst1 nst3 double-mutant lacking secondary cell walls in fiber cells and a wrky12 mutant displaying ectopic formation of secondary cell wall compared with wild type by employing only two growth traits (stem height and fresh weight) in addition to videos of stem vibrations. Furthermore, we calculated the logarithmic decrement, the damping ratio, the natural frequency and the stiffness based on the spring-mass-damper model from the video data using AraVib. The stiffness was estimated to be drastically decreased in nst1 nst3, which agreed with previous tensile test results. However, in wrky12, the stiffness was significantly increased. These results demonstrate the effectiveness of our new system. Because our method can be applied in a high-throughput manner, it can be used to screen for mutants with altered mechanical properties.
Self-similarity and multifractality in human brain activity: a wavelet-based analysis of scale-free brain dynamics☆
Authors: La Rocca Daria , Zilber Nicolas , Abry Patrice , van Wassenhove Virginie , Ciuciu Philippe 
Published: May 2018

AbstractBackgroundThe temporal structure of macroscopic brain activity displays both oscillatory and scale-free dynamics. While the functional relevance of neural oscillations has been largely investigated, both the nature and the role of scale-free dynamics in brain processing have been disputed.New MethodHere, we offer a novel method to rigorously enrich the characterization of scale-free brain activity using a robust wavelet-based assessment of self-similarity and multifractality. For this, we analyzed human brain activity recorded with magnetoencephalography (MEG) while participants were at rest or performing a task.ResultsFirst, we report consistent infraslow (from 0.1 to 1.5 Hz) scalefree dynamics (i.e., self-similarity and multifractality) in resting-state and task data. Second, we observed a fronto-occipital gradient of self-similarity reminiscent of the known hierarchy of temporal scales from sensory to higherorder cortices; the anatomical gradient was more pronounced in task than in rest. Third, we observed a significant increase of multifractality during task as compared to rest. Additionally, the decrease in self-similarity and the increase in multifractality from rest to task were negatively correlated in regions involved in the task, suggesting a shift from structured global temporal dynamics in resting-state to locally bursty and non Gaussian scalefree structures during task.Comparison with Existing Method(s)We showed that the wavelet leader based multifractal approach extends power spectrum estimation methods in the way of characterizing finely scale-free brain dynamics.ConclusionsAltogether, our approach provides novel fine-grained characterizations of scale-free dynamics in human brain activity.HighlightsWe estimated scale-free human brain dynamics using wavelet-leader formalism.High-to-low self-similarity defined a fronto-occipital gradient.The gradient was enhanced in task compared to resting-state.Scale-free brain dynamics showed multifractal properties.Self-similarity decreased whereas multifractality increased from rest to task.
Integrative analysis of single cell expression data reveals distinct regulatory states in bidirectional promoters
Authors: Ardakani Fatemeh Behjati , Kattler Kathrin , Nordström Karl , Gasparoni Nina , Gasparoni Gilles , Fuchs Sarah , Sinha Anupam , Barann Matthias , Ebert Peter , Fischer Jonas , Hutter Barbara , Zipprich Gideon , Felder Bärbel , Eils Jürgen , Brors Benedikt , Lengauer Thomas , Manke Thomas , Rosenstiel Philip , Walter Jörn , Schulz Marcel H. 
Published: May 2018

AbstractBackgroundBidirectional promoters (BPs) are prevalent in eukaryotic genomes. However, it is poorly understood how the cell integrates different epigenomic information, such as transcription factor (TF) binding and chromatin marks, to drive gene expression at BPs. Single cell sequencing technologies are revolutionizing the field of genome biology. Therefore, this study focuses on the integration of single cell RNA-seq data with bulk ChIP-seq and other epigenetics data, for which single cell technologies are not yet established, in the context of BPs.ResultsWe performed integrative analyses of novel human single cell RNA-seq (scRNA-seq) data with bulk ChIP-seq and other epigenetics data. scRNA-seq data revealed distinct transcription states of BPs that were previously not recognized. We find associations between these transcription states to distinct patterns in structural gene features, DNA accessibility, histone modification, DNA methylation and TF binding profiles.ConclusionsOur results suggest that a complex interplay of all of these elements is required to achieve BP-specific transcriptional output in this specialized promoter configuration. Further, our study implies that novel statistical methods can be developed to deconvolute masked subpopulations of cells measured with different bulk epigenomic assays using scRNA-seq data.
Coiled Coil-Mediated Assembly of an Icosahedral Protein Cage with Extremely High Thermal and Chemical Stability
Authors: Cristie-David Ajitha S. , Chen Junjie , Nowak Derek B. , Park Sung I. , Banaszak Holl Mark M. , Su Min , Marsh E. Neil G. 
Published: May 2018

AbstractThe organization of protein molecules into higher-order nanoscale architectures is ubiquitous in Nature and represents an important goal in synthetic biology. Here we describe the symmetry-directed design of a hollow protein cage with dimensions similar to those of many icosahedral viruses. The cage was constructed based on icosahedral symmetry by genetically fusing a trimeric protein (TriEst) to a small pentameric de novo-designed coiled coil domain, separated by a flexible oligo-glycine linker sequence. Screening a small library of designs in which the linker length varied from 2 to 12 residues identified a construct containing 8 glycine residues (Ico8) that formed well-defined cages. Characterization by dynamic light scattering, negative stain and cryo EM, and by atomic force and IR-photo-induced force microscopy established that Ico8 assembles into a flexible hollow cage with comprising 60-subunits with overall icosahedral geometry. Unexpectedly, the cages were found to encapsulate DNA, even though neither protein component binds nucleic acids on its own. Notably, the cages formed by Ico8 proved to be extremely stable towards thermal and chemical denaturation: whereas TriEst was unfolded by heating (Tm ~75 °C) or denatured by 1.5 M guanidine hydrochloride, the Ico8 cages remained folded even at 120 °C or in 8 M guanidine hydrochloride. The encapsulation of DNA and increased stability of the cages are new properties that emerge from the higher order structure of the protein cage, rather than being intrinsic to the components from which it is constructed.
N-linked glycosylation of the antagonist Short gastrulation increases the functional complexity of BMP signals
Authors: Negreiros E. , Herszterg S. , Hwa K. , Câmara A. , Dias W.B. , Carneiro K. , Bier E. , Todeschini A. , Araujo H. 
Published: May 2018

AbstractDisorders of N-linked glycosylation are increasingly reported in the literature. However, targets responsible for the associated developmental and physiological defects are largely unknown. Bone Morphogenetic Proteins (BMPs) act as highly dynamic complexes to regulate several functions during development. The range and strength of BMP activity depend on interactions with glycosylated protein complexes in the extracellular milieu. Here we investigate the role of glycosylation for the function of the conserved extracellular BMP antagonist Short gastrulation (Sog). We identify conserved N-glycosylated sites and describe the effect of mutating these residues on BMP pathway activity in Drosophila. Functional analysis reveals that loss of individual Sog glycosylation sites enhances BMP antagonism and/or increases the spatial range of Sog effects in the tissue. Mechanistically, we provide evidence that N-terminal and stem glycosylation controls extracellular Sog levels and distribution. The identification of similar residues in vertebrate Chordin proteins suggests that N-glycosylation may be an evolutionarily conserved process that adds complexity to the regulation of BMP activity.Summary StatementN-glycosylation restricts the function of Short gastrulation during Drosophila development by controlling the amount of extracellular protein. This adds another layer of complexity to regulation of Bone Morphogenetic Protein signals.
Treatment outcome and prognostic factors of tonsillectomy for palmoplantar pustulosis and pustulotic arthro‐osteitis: A retrospective subjective and objective quantitative analysis of 138 patients
Authors: Takahara Miki , Hirata Yui , Nagato Toshihiro , Kishibe Kan , Katada Akihiko , Hayashi Tatsuya , Kishibe Mari , Ishida‐Yamamoto Akemi , Harabuchi Yasuaki 
Published: May 2018

AbstractPustulosis palmaris et plantaris (PPP) and pustulotic arthro‐osteitis (PAO) are tonsil‐related diseases. Treatment outcome of tonsillectomy and prognostic factors influencing the outcome have not been analyzed quantitatively. We evaluated those using the Palmoplantar Pustulosis Area and Severity Index (PPPASI). At 1, 3, 6, 12, 24 and more than 24 months post‐tonsillectomy, 20 (31%), 34 (48%), 70 (60%), 57 (80%), 36 (95%) and 23 (96%) patients realized 80% or more improvement of PPP skin lesions, respectively, and eight (17%), 23 (36%), 30 (50%), 38 (79%), 12 (100%) and four (100%) patients showed 80% or more improvement of PPPASI (i.e. PPPASI% ≥ 80%), respectively. At 1, 3, 6, 12 and more than 12 months post‐tonsillectomy, 19 (73%), 21 (66%), 27 (73%), 19 (79%) and 15 (83%) patients realized a disappearance of PAO‐induced arthralgia, respectively. Kaplan–Meier analysis of 80 patients with PPP revealed that, at 12 and 24 months post‐tonsillectomy, lesions disappeared (i.e. PPPASI = 0) in 38% and 66% of patients, respectively, and lesions improved by 80% or more (i.e. PPPASI% ≥ 80%) in 71% and 95% of patients, respectively. The log–rank test and univariate and multivariate analyses showed that smoking cessation post‐tonsillectomy and PAO were significant predictive factors for the early disappearance of skin lesions. This report is the first demonstrating objective evidence of the great efficacy of tonsillectomy to improve PPP skin lesions. Even post‐tonsillectomy, smoking inhibited the early disappearance of the lesions.
Ringer's lactate versus normal saline in acute pancreatitis: A systematic review and meta‐analysis
Authors: Iqbal Umair , Anwar Hafsa , Scribani Melissa 
Published: May 2018

OBJECTIVEAggressive i.v. hydration with crystalloids is the first step in managing acute pancreatitis (AP) and is associated with improved survival. Guidelines about the choice of crystalloids to use are unclear. This systematic review and meta‐analysis was aimed to discern whether the choice of fluids in managing pancreatitis was associated with patients' outcomes.METHODSA comprehensive literature review was conducted by searching the Embase, MEDLINE, PubMed and Google Scholar databases to December 2017 to identify all studies that compared normal saline (NS) with Ringer's lactate (RL) for managing AP. The characteristics of the participants, outcome measurements (including mortality, the development of systemic inflammatory response syndrome [SIRS] on admission and at 24 h, and pancreatic necrosis) were analyzed.RESULTSFive studies (three randomized controlled trials and two retrospective cohort studies) with 428 patients were included in this analysis. Mortality trended lower in the RL group but this was not statistically significant (pooled odds ratio [OR] 0.61, 95% CI 0.28–1.29, P = 0.20). Patients in the RL group had significantly decreased odds of developing SIRS at 24 h (pooled OR 0.38, 95% CI 0.15–0.98, P = 0.05).CONCLUSIONSRL has anti‐inflammatory effects and is associated with decreased odds of persistent SIRS at 24 h, which is a marker of severe disease in AP patients. Although mortality trended lower in the RL group this did not achieve statistical significance and hence larger randomized controlled trials are needed to evaluate this association.
Clinical significance of calcium‐binding protein S100A8 and S100A9 expression in non‐small cell lung cancer
Authors: Huang He , Huang Qingdong , Tang Tingyu , Gu Liang , Du Jianzong , Li Zhijun , Lu Xiaoling , Zhou Xiaoxi 
Published: May 2018

BackgroundThe purpose of this study was to evaluate the correlation between calcium‐binding protein S100A8 and S100A9 expression in non‐small cell lung cancer (NSCLC) and patients’ clinical features.MethodsFifty‐two NSCLC patients who underwent surgery at Zhejiang Hospital from February 2014 to January 2016 were included in this study. Calcium‐binding protein S100A8 and S100A9 expression patterns in cancer and para‐cancer tissues were examined by immunohistochemistry assay. The correlation between calcium‐binding protein S100A8 and S100A9 expression patterns and NSCLC patients’ clinical characteristics, including age, gender, tumor node metastasis stage, and pathology type, were evaluated.ResultsS100A8 and S100A9 were generally expressed on the cytoplasm and nucleus of NSCLC cells, mainly located in the cytoplasm, stained with brown particles, and distributed evenly. The positive expression rates of S100A8 and S100A9 in cancer tissues were 71.2% and 76.9%, respectively, which were significantly higher than in para‐cancer tissues at 11.5% and 19.2%, respectively, with statistical significance (P < 0.05). S100A8 and S100A9 positive expression was associated with tumor differentiation degree (P < 0.05) but were not correlated with age, gender, smoking history, tumor diameter, pathology type, tumor node metastasis stage, or pleural effusion (Pall > 0.05).ConclusionS100A8 and S100A9 positive expression in cancer tissues was significantly higher than in para‐cancer tissues and was correlated with tumor differentiation, which may be a potential marker for poor prognosis.