bluuebunny/crossref_metadata_2025_split huggingface dataset:
South Dakota Diversity of Temperature: Pictures from Statistical Analysis
Authors: Shmagin Boris , Todey Dennis 
Published: July 2019

AbstractThe regional diversity of monthly temperature was analyzed based on long-term data obtained for South Dakota (SD) from the High Plains Regional Climate Center. Multidimensional statistical methods were used and the principal results presented as a sequence of 2- and 3-dimensional scatterplot pictures depicting the quantitative results. System hierarchical model of landscape was used for research tasks formulation. Initial matrixes for three research tasks were compiled for the state. The first set of initial matrices of time series {Xt*n}, where t = number of years and n = number of meteorological stations, contains two matrixes: X1(67*29) and X2(33*94). The second set -{Xt*m}, where t = number of years and m = number of months in a year: X3(113*12), X4(110*12), and X5(102*12). The third set - {Xn*m}, where n = number of meteorological stations and m = number of months in a year, contains two matrixes: X6(29*12) and X7(94*12). Statistical analysis allowed us to differentiate weather stations by temporal trends and spatial distribution for the time interval 1932-1998. The most variable stations (Brookings, Camp Crook, and Highmore) were determined; their seasonality was described (the most variable months and correlation among months during the year) and their seasonal regime determined. The average annual and monthly temperature distributions were presented for South Dakota based on 29 and 94 stations for the time intervals 1932-1998 and 1963-1995.
PlnTFDB: Plant Transcription Factor Database – Update
Authors: Riaño-Pachón Diego Mauricio , Guedes Correa Luiz Gustavo , Mueller-Roeber Bernd 
Published: July 2019

AbstractPlnTFDB is a publicly available computational resource comprising putative complete sets of transcription factors from plants. The original database listed the putative complete sets of TFs from five different green plant (viridiplantae) species. Up to date, summer 2007, PlnTFDB have had more than one hundred thousand hits from more than one thousand different clients, showing the importance that this resource had acquired for the plant community. In this first major update, we extended the coverage of the database to additional completed viridiplantae genomes, i.e., the moss Physcomitrella patens and the rice Oryza sativa spp indica. The scope of PlnTFDB was broadened to encompass other eukaryote photosynthetic organisms, such as the rhodophyte algae Galdieria sulphuraria and Cyanidioschyzon merolae, and the diatom Thalassiosira pseudonana. This will allow acquiring a better knowledge of plant evolution and on differentiation events. Moreover, the inclusion of large EST collections (i.e., Hordeum vulgare) have further extended the range of this resource to species whose genome are not yet sequenced but that have, nevertheless, highthroughput EST sequencing projects ongoing.
Current status of herbal and their future perspectives
Authors: Samy Ramar Perumal , Gopalakrishnakone Ponnampalam 
Published: July 2019

AbstractTraditional medicine is the synthesis of therapeutic experience of generations of practicing physicians of indigenous systems of medicine. Throughout the history of mankind, many infectious diseases have been treated with herbals. The traditional medicine is increasingly solicited through the tradipractitioners and herbalists in the treatment of infectious diseases. Among the remedies used, plant drugs constitute an important part. A number of scientific investigations have highlighted the importance and the contribution of many plant families i.e. Asteraceae, Liliaceae, Apocynaceae, Solanaceae, Caesalpinaceae, Rutaceae, Piperaceae, Sapotaceae used as medicinal plants. Medicinal plants play a vital role for the development of new drugs (export and import diverse parts or bioactive compounds in the current market). The bioactive extract should be standardized on the basis of active compound. The bioactive extract should undergo limited safety studies.
Kinase independent inhibition of NFκB transcriptional activity by GRK5 through IκBα stabilization.
Authors: Sorriento Daniela , Ciccarelli Michele , Santulli Gaetano , Campanile Alfonso , Altobelli Giovanna Giuseppina , Cimini Vincenzo , Galasso Gennaro , Astone Dalila , Piscione Federico , Pastore Lucio , Trimarco Bruno , Iaccarino Guido 
Published: July 2019

AbstractMembers of the G protein receptor kinase (GRK) family that regulates receptor desensitization and members of the nuclear transcription factors family NF[kappa]B have been recently and convincingly demonstrated to interact, although the effects on transcription and gene expression have not yet been described. Using overexpression, knockdown (small interfering RNA) and mutagenesis experiments, we demonstrate that GRK5 couples to and stabilizes the NF[kappa]B inhibitor I[kappa]B[alpha], and inhibits NF[kappa]B activity. Studies with minigenes suggest that the N-terminal Regulation of G protein Signaling (RGS) homology (RH) domain confers GRK5 such ability. GRK5-RH domain overexpression affects NF[kappa]B dependent phenotypes, such as apoptosis protection, cytokine production and inflammation and tissue regeneration. Our results reveal a novel, unexpected role of GRK5 in NF[kappa]B transcription activity regulation that represents a possible target for diagnostic and therapeutics.
Transient-mediated fate determination in a transcriptional circuit of HIV
Authors: Weinberger Leor , Dar Roy , Simpson Michael 
Published: July 2019

AbstractSteady-state behavior and bistability have been proposed as mechanisms for decision-making in gene circuits. However, transient gene expression has also been proposed to control cell fate with the decision arbitrated by the lifetime of the expression transient. Here, we report that transcriptional positive-feedback plays a critical role in determining HIV infected cell-fate by extending the duration of Tat expression transients far beyond what protein half-life modulation can achieve. To directly quantify feedback strength and its effects on the duration of Tat transcriptional pulses, we exploit the noise inherent to gene-expression and measure shifts in the autocorrelation of expression noise. The results indicate that transcriptional positive-feedback extends the single-cell Tat expression lifetime by ~6-fold for both minimal Tat circuits and full-length, actively-replicating HIV-1. Importantly, artificial weakening of Tat positive-feedback shortened the duration of Tat expression transients and biased the probability in favor of latency. Thus, transcriptional positive-feedback appears to modulate transient expression lifetime and thereby control cell-fate in HIV.
A new dynamic property of human consciousness
Authors: Lee UnCheol , Kim Seunghwan , Noh Gyu-Jeong , Choi Byung-Moon 
Published: July 2019

AbstractAs pointed out by William James, "the consciousness is a dynamic process, not a thing" , during which short term integration is succeeded by another differentiated neural state through the continual interplay between the environment, the body, and the brain itself. Thus, the dynamic structure underlying successive states of the brain is important for understanding human consciousness as a process. In order to investigate the dynamic property of human consciousness, we developed a new method to reconstruct a state space from electroencephalogram(EEG), in which a trajectory, reflecting states of consciousness, is constructed based on the global information integration of the brain. EEGs were obtained from 14 subjects received an intravenous bolus of propopol. Here we show that the degree of human consciousness is directly associated with the information integration capacity of gamma wave, which is significantly higher in the conscious state than in the unconscious state. And we found a new time evolutional property of human consciousness. The conscious state showed a lower dimensional dynamic process which changed to a random-like process after loss of consciousness. This characteristic dynamic property, appeared only in the gamma band, might be used as an indicator to distinguish the conscious and unconscious states and also considered as an important fact for the human consciousness model.
Reciprocal homeostatic reactions to chronic excitatory synaptic receptor inactivation in developing cerebral cortex networks
Authors: Corner Michael 
Published: July 2019

AbstractChronic blockade of actively excitatory glutamatergic synaptic receptors in co-cultured organotypic rodent neocortex explants leads to a compensatory up-regulation of otherwise inactive input channels so as to maintain almost normal levels of ongoing bursts of action potentials. We report here that this homeostatic return of spontaneous (now kainate receptor driven) firing is accompanied by a reciprocal down-regulation of blocked AMPA and NMDA receptors, such that the developing cortical network is protected against becoming hyperactive when those synaptic inputs are again able to transmit normally.
Ecological optimum of ectothermic organisms: static-dynamical approach
Authors: Verbitsky Vladimir , Verbitskaya Tamara 
Published: July 2019

AbstractDuring 20th century the majority of researchers interpreted ecological optimum as a certain combination of ambient factors which is optimal for growth, existence and reproduction of an organism. However, it was revealed in many species, that the maximum rates of various processes in an organism are achieved at various combinations of values of different factors, and under variable regimes as opposite to constant regimes. One may state that there is no well defined general concept which takes into account a bulk of data that do not conform the traditional definition of ecological optimum. Here, we show that it is necessary to make distinction between concepts of "static" and "dynamic" optima. It is needed for definition of real ecological optimum and creation of optimum conditions for given factor. We show also that it is necessary to take into account so-called delayed effects of factors. Basing on the analysis of responses of zooplankton to various temperatures and phosphoric load, we show that an optimum has "dynamic" characteristics besides previously known "static" ones, like a range of factor values on tolerance curve or a doze of factor. These "dynamic" characteristics are cyclic and stepwise changes of a factor, a directionality of factor's dynamics in case of stepwise changes and additionally, we reveal stimulating and inhibiting delayed effects of factors. Our results allow for a more detailed concept of ecological optimum, and also may stimulate investigations of quantitative contribution of various parameters of environmental factors to an ecological optimum of an organism or population.
Cryopreservation of a whole liver
Authors: Gavish Zohar , Arav Amir , Ben-Haim Menahem 
Published: July 2019

AbstractPreservation of vascularized organs such as the liver is limited to 24hrs. before destructive processes disqualify it for transplantation. This narrow time window prevents surgeons from performing optimal pathogen screening and matching tests which often lead to re-transplantation. Numerous problems are associated with viably freezing and thawing a whole liver: complicated geometry, poor heat transfer, release of latent heat and the difficulty of generating a uniform cooling rate. Our past success led us to apply our novel freezing technique to a larger solid organ, the liver. Whole livers were frozen/thawed using a directional solidification apparatuses; viability was tested by means of integrity and functionality in vitro and in auxiliary liver transplantation. Thawed livers were intact with over 80% viability; histology revealed normal architecture, bile production and blood flow following auxillary transplantation where normal. Our results suggest a novel cryopreservation method and may enable better organ donor-recipient matching in the future
Bio-communication of Plants
Authors: Witzany Guenther 
Published: July 2019

AbstractPlants communicate with a great variety of symbiotic partners, above and below ground. Constant monitoring of signals of biotic origin as well as abiotic environmental influences allows plants to generate appropriate response behavior. These communication processes are primarily sign-mediated interactions and not simply an exchange of information. They involve active coordination and active organization of a great variety of different behavioural patterns – mediated by signs.
Effects of Pre- and Post-natal smoke exposure on airway neural responses
Authors: Wu Zhong.-Xin , Kish Vincent , Batchelor Thomas , Dey Richard 
Published: July 2019

AbstractAbundant epidemiological data shows that maternal smoking during pregnancy or second-hand smoke exposure during neonatal life and infancy increases the incidence of respiratory illnesses later in life. However, underlying mechanisms initiated in early life but affecting adult disease remain undefined. Neurotrophins, including nerve growth factor (NGF) and brain-derived neurotrophic factor (BDNF), are neurotrophic factors essential in promoting and maintaining differentiation, growth, and survival of central and peripheral nervous system. The goal of this proposal is to examine the potential role of neurotrophin release in mediating long-term effects of prenatal and early postnatal smoke exposure. Our studies showed that an initial exposure to smoke during prenatal and early postnatal periods significantly changed lung function, substance P (SP) innervation in trachea and the level of NGF in BAL fluid after re-exposure to smoke on adult (postnatal day (PD) 60). In controls, smoke exposure (PD 28) with a subsequent re-exposure at PD 60 did not affect lung function or SP innervation or NGF levels. PCR array revealed enhanced expression of multiple genes including NGF and its receptor by smoke exposure only during early prenatal periods. These data suggest that a critical period of exposure exists in early periods of development. Increased expression of NGF and its receptor in airway caused by smoke exposure may enhance susceptibility to respiratory illnesses in adult. These findings have obvious and significant implication both for smoking during pregnancy and the effects of second hand tobacco smoke exposure. The study provides evidence that prenatal and early postnatal life are periods of enhanced susceptibility to detrimental effects of cigarette smoke. These effects appear to be mediated through the release of neurotrophic factors like NGF which regulate growth and maturation of the airway during these susceptible periods.
Requirement of Activation for Hepatitis B Virus Infection
Authors: Bruns Michael , Maenz Claudia 
Published: July 2019

AbstractAlthough _in vitro_ models of human hepatitis B virus replication are established, so far none could approximate infection efficiency as expected from in vivo observations. Susceptibility for HBV infections has only been reported for primary hepatocytes of human, chimpanzee or Tupaia belangeri and the cell line HepaRG. Here we show that the insusceptible human hepatoma cell line HepG2 can be infected, when the virus was beforehand activated by passage over whole duck liver cell cultures. That suggests an activation step to be performed by specialized liver cells.
Intracellular Regulatory Networks are close to Monotone Systems
Authors: Ma'ayan Avi , Iyengar Ravi , Sontag Eduardo 
Published: July 2019

AbstractSeveral meso-scale biological intracellular regulatory networks that have specified directionality of interactions have been recently assembled from experimental literature. Directed networks where links are characterized as positive or negative can be converted to systems of differential equations and analyzed as dynamical systems. Such analyses have shown that networks containing only sign-consistent loops, such as positive feed-forward and feedback loops function as monotone systems that display well-ordered behavior. Perturbations to monotone systems have unambiguous global effects and a predictability characteristic that confers advantages for robustness and adaptability. We find that three intracellular regulatory networks: bacterial and yeast transcriptional networks and a mammalian signaling network contain far more sign-consistent feedback and feed-forward loops than expected for shuffled networks. Inconsistent loops with negative links can be more easily removed from real regulatory networks as compared to shuffled networks. This topological feature in real networks emerges from the presence of hubs that are enriched for either negative or positive links, and is not due to a preference for double negative links in paths. These observations indicate that intracellular regulatory networks may be close to monotone systems and that this network topology contributes to the dynamic stability.
The Reproducibility of Lists of Differentially Expressed Genes in Microarray Studies
Authors: Shi Leming , Jones Wendell , Jensen Roderick , Harris Stephen , Perkins Roger , Goodsaid Federico , Guo Lei , Croner Lisa , Boysen Cecilie , Fang Hong , Amur Shashi , Bao Wenjun , Barbacioru Catalin , Bertholet Vincent , Cao Xiaoxi Megan , Chu Tzu-Ming , Collins Patrick , Fan Xiao-hui , Frueh Felix , Fuscoe James , Guo Xu , Han Jing , Herman Damir , Hong Huixiao , Kawasaki Ernest , Li Quan-Zhen , Luo Yuling , Ma Yunqing , Mei Nan , Peterson Ron , Puri Raj , Qian Feng , Shippy Richard , Su Zhenqiang , Sun Yongming Andrew , Sun Hongmei , Thorn Brett , Turpaz Yaron , Wang Charles , Wang Sue-Jane , Warrington Janet , Willey James , Wu Jie , Xie Qian , Zhang Liang , Zhang Lu , Zhong Sheng , Wolfinger Russell , Tong Weida 
Published: July 2019

AbstractReproducibility is a fundamental requirement in scientific experiments and clinical contexts. Recent publications raise concerns about the reliability of microarray technology because of the apparent lack of agreement between lists of differentially expressed genes (DEGs). In this study we demonstrate that (1) such discordance may stem from ranking and selecting DEGs solely by statistical significance (P) derived from widely used simple t-tests; (2) when fold change (FC) is used as the ranking criterion, the lists become much more reproducible, especially when fewer genes are selected; and (3) the instability of short DEG lists based on P cutoffs is an expected mathematical consequence of the high variability of the t-values. We recommend the use of FC ranking plus a non-stringent P cutoff as a baseline practice in order to generate more reproducible DEG lists. The FC criterion enhances reproducibility while the P criterion balances sensitivity and specificity.
Swine Influenza A Evolution via Recombination - Genetic Drift Reservoir
Authors: Niman Henry 
Published: July 2019

AbstractThe looming influenza pandemic has focused attention^1-4^ on the rapid evolution of H5N1 and other human and avian serotypes. The basic tenets of influenza genetics^5^ define gradual changes as drifts caused by point mutations created by a polymerase that lacks a proof reading function. More abrupt changes have been linked to reassortment, which shuffles the eight sub-genomic segments of the influenza genome in dually infected host. The complex evolution of these viruses has created a challenge in vaccine development. Swine influenza isolates from 2003 and 2004 have been identified^6^ that have acquired a human influenza gene, PB1. My analysis of the eight gene segments found large portions of two genes, PB2 and PA, which were identical matches with 1977 swine isolates^7,8^. Additional regions were exact matches with 1998 and 2002 isolates,^9,10^ demonstrating homologous recombination between earlier genomes. The absolute fidelity discounts the role of point mutations in gene drift. Moreover the human PB1 gene represented a reservoir for acquisition of polymorphisms in human seasonal flu. These observations challenge the basic tenets of influenza genetics and provide a method for predicting the changes in seasonal and pandemic influenza, as well as other rapidly evolving genomes.
A Three dimesional stochastic spatio-temporal model of cell spreading
Authors: Xiong Yuguang , Rangamani Padmini , Dubin-Thaler Benjamin , Sheetz Michael , Iyengar Ravi 
Published: July 2019

AbstractCell motility is important for many physiological processes and the underlyingbiochemical reactions motility have been well-characterized. Mathematical models, usingthe biochemical reactions and focused on different types of spreading behavior have beenconstructed and analyzed. In this study, we build on these previous models to develop athree-dimensional stochastic model of isotropic spreading of mammalian fibroblasts. The model is composed of three actin remodeling reactions that occur stochastically in space and time and are regulated by membrane resistance forces. Numerical simulations indicate that the model qualitatively captures the experimentally observed isotropic cell spreading behavior. We analyzed the effects of varying branching reaction rates, membrane resistance forces and capping protein concentrations on the dynamics of isotropic spreading. The simulations allowed us to identify the range within which branching reaction rates and membrane force values cooperate to yield isotropic spreading behavior. The model predicts increasing capping protein concentration would lead to a linear decrease in average peripheral velocity. We tested this prediction experimentally using varying concentrations of a pharmacologic agent (Cytochalasin D)that caps growing actin filaments. We find that the experimental results agree with the numerical simulations. Thus, a spatio-temporally complex model made up of a simple set of stochastic reactions near the cell surface, when constrained by membrane forces, can yield deterministic behavior as characterized by isotropic cell spreading.
Concentrations of Polychlorinated Biphenyls (PCBs), Polychlorinated Dibenzo-p-dioxins and Furans (PCDD/Fs), and Polybrominated Diphenyl Ethers (PBDEs) as Functions of Sample Depth in Killer Whale (Orcinus orca) Blubber
Authors: Ikonomou Michael , Rayne Sierra , Crewe Norman 
Published: July 2019

AbstractConcentrations of polychlorinated biphenyls (PCBs), polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs), and polybrominated diphenyl ethers (PBDEs) were examined as a function of depth in killer whale (Orcinus orca) blubber samples. Lipid-normalized concentrations of PCBs, PCDD/Fs, and PBDEs did not display significant variation with depth in three distinct blubber layers (outer, central, and inner). Significantly more variation in contaminant concentrations were observed with depth on a wet weight basis for the killer whale sample. The current study indicates that non-invasive microdart biopsy sampling methods commonly used for monitoring contaminants in marine mammals yield representative details on contaminant burdens for chlorinated and brominated aromatic compounds in marine mammal blubber, regardless of the quantity and type of blubber sampled, provided that lipid normalization is performed on resulting analytical determinations.