bluuebunny/crossref_metadata_2025_split huggingface dataset:
Solubilization of M2 Transmembrane Peptide of Influenza A in Pure Water: Implications for Emergence of Proteins and Protein-embedded Primeval Membranes in Unsalted Oceans
Authors: Song Jianxing , Miao Linlin 
Published: July 2019

AbstractWe demonstrated that M2 transmembrane peptide, one of the most hydrophobic sequences in nature, can be solublized to at least ~100 µM in unsalted water without any lipid molecules. Strikingly, the M2 peptide also forms a highly-helical conformation in water which remains almost unchanged even at 95 ºC, as characterized by CD spectroscopy. Our result has critical implications in understanding emergence of proteins and protein-embedded primeval membranes in unsalted oceans.
Incidence response to a suddenly increased cancer risk
Authors: Hallberg Örjan 
Published: July 2019

AbstractIncidence rates of several cancers, including melanoma of the skin and breast cancer, have increased since the middle of the 20th century in Western countries. Here, we developed a model for cancer incidence over time, when considering a suddenly increased cancer risk from an environmental change. A two parameter exponential function was used to simulate cancer risk over calendar time since birth, taking into account the time lapse since the environmental change took place. The calculated incidence for all age cohorts over calendar time was used to calculate the age-standardized rates. The best fit between calculated and reported age-standardized rates was sought by parameter variation. The model was tested using reported rates for melanoma and breast cancer. The best fit was obtained when an increased cancer risk took place from 1955 and with the starting age being that of puberty. Age-standardized rates of melanoma and breast cancer were easily modeled and fit well with reported data. In addition, age-specific rates fit well with reported data without further parameter adjustments. The good fit with reported data when using this simple exponential model strongly supports the hypothesis that an environmental change in the mid-20th century was the main cause of the cancer epidemic noted after 1955. Other forms of cancer should be analyzed in a similar manner.
Comparative functional genomics approach for the annotation of proteins in Unclassified Halophilic archaeon DL31
Authors: Sardeshmukh N , Sanmukh S , Nakkeeran E 
Published: July 2019

AbstractThe structure, function and sub-cellular location prediction for the unknown proteins from Unclassified Halophilic archaeon DL31 were carried out for characterization of the proteins in their respective families. The 991 genes for hypothetical proteins in Halophilic archaeon DL31 chromosome were predicted by the application of computational methods and Bioinformatics web tools. The structure predictions for 206 unknown proteins were possible whereas functions were predicted in 825 protein sequences. The function prediction for the proteins were done by using Bioinformatics web tools like CDD-BLAST, INTERPROSCAN and PFAM by searching protein databases for the presence of conserved domains. The Sub-cellular location predictions were done for all the unknown proteins by using CELLO v 2.5 server. While tertiary structures were constructed using PS2 Server- Protein Structure Prediction server. This study revealed structural, functional and Sub-cellular localization of unknown proteins in Unclassified Halophilic archaeon DL31chromosome.
A subset of co-expressed genes in Slug-based cancer mesenchymal transition signature remains coexpressed in normal samples in a tissue-specific manner
Authors: Cheng Weiyi , Anastassiou Dimitris 
Published: July 2019

AbstractA recently identified gene expression signature of EMT markers containing the transcription factor Slug was found present in samples from many publicly available cancer gene expression datasets of multiple cancer types except leukemia. We also found many of these genes co-expressed in human cancer xenografted cells, but not in mouse stroma cells, suggesting that the signature is largely produced by cancer cells undergoing some type of EMT. Here we report that a partial signature consisting of a subset of the co-expressed genes of the full signature, including at least Slug (SNAI2), collagens COL1A1, COL1A2, COL3A1, COL6A3 and genes DCN and LUM, is also present in leukemia, in which case it is also strongly associated with the chemokine CXCL12 (aka SDF1). The same subset of co-expressed genes is also strongly present even in normal samples in a tissue-specific manner, with lowest expression in brain tissues and highest expression in reproductive system tissues. The full signature, with prominent presence of COL11A1, THBS2 and INHBA appears to be triggered in solid cancers particularly when cancer cells encounter adipocytes.
Aluminium - Magnesium Silicate enhances antibacterial activity of Ampicillin trihydrate, against Salmonella gallinarum
Authors: Chikelu Ogechukwu , Ezeibe Madike , Anosa George , Okorie Okechi , Elendu-Eleke Nnenna , Okoroafor Obianuju , Ngene Augustine 
Published: July 2019

AbstractSolutions of different concentrations, of Ampicillin trihydrate (AT) and of a formulation of AT in Aluminium Magnesium Silicate (AMS), were used for sensitivity test on Salmonella gallinarum cultures. Also, S. gallinarum-infected chicks were treated with; 10 mg / Kg (AT), 10 mg / Kg (AT in AMS), 7.5 mg / Kg ( AT), 7.5 mg /Kg (AT in AMS). Mean inhibition area, 28.39 mm produced by AT did not vary significantly (P ) from 26.36 mm produced by AT in AMS. However, 17.5 105 Salmonella gallinarum culture forming units per ml of bile of the untreated chicks and 3.4 105 (80.58 % reduction), 2.5 105 (85.7 % reduction) , 5.4 105 (69.2 % reduction ) and 0.38 105 (97.8 % reduction ) of the respective treated groups, showed AMS significantly (P 0.01) improved AT`s ability to clear the infection, in vivo.
Crosstalk and the spectrum of biological global broadcasts: Toward generalization of the Baars consciousness model across physiological subsystems
Authors: Wallace Rodrick 
Published: July 2019

AbstractOnce cognitive biological phenomena are recognized as necessarily having 'dual' information sources, it is easy to show that the information theory chain rule implies isolating coresident information sources from crosstalk requires more metabolic free energy than permitting correlation. This provides conditions for an evolutionary exaptation leading to dynamic global broadcasts of interacting cognitive biological processes analogous to, but slower than, consciousness, itself included within the paradigm. The argument is closely analogous to the well-studied exaptation of noise to trigger stochastic resonance amplification in physiological systems.
Biodiversity is a cauliflower under the sunlight
Authors: Gatti Cazzolla Roberto 
Published: July 2019

AbstractFor a long time ecologists have questioned the variations of biodiversity across the latitudinal gradient. Recently it has emerged that the changes in [beta]-diversity are caused simply by changes in the sizes of species pools. I combined the species pool size and the fractal nature of ecosystems to clarify some general patterns of this gradient. Considering temperature, humidity and NPP as the main variables of an ecosystem niche and as the axis of the polygon in the Cartesian plane, it is possible to build fractal hypervolumes, whose the fractal dimension rises up to three, moving towards the equator. It follows that the best figure that graphically synthesizes the evolutionary forces that fit this ecosystem hypervolume is the fractal cauliflower.
Clean Coal and Spirulina maxima (Cyanobacteria) Production through Alkaline-Seawater
Authors: Affan Md. Abu , Lee Dae-Won , Park Heung-Sik , Noh Jae-Hoon , Heo Soo-Jin , Oh Chulhong , Jeon Seon-Mi , Son Joo-Won , Son Seung-Gyu , Lee Hyi-Seung , Lee Hyeon Yong , Kang Do-Hyung 
Published: July 2019

AbstractCarbon capture and storage have involved high cost and an earthquake threat. Coal in NaOH-natural seawater (NSW) can produce clean coal, and organic carbon enriched pretreated sweater (PSWS) can be used to grow Spirulina maxima. However, with freshwater shortage, high cost CO2 feedstock incurs S. maxima biomass production, and using PSWS should be considered as an alternative. NaHCO3 and Na2CO3 were used to sediment Mg2+ and Ca2+ of NSW to resolve turbidity and decreasing phosphate solubility. Here, we show that pre-combustion coal and NaOH concentration calculated by our devised formulae for any salinity could dilute volatile matter 19.8 Kg plus CO2 116.50 to 168.89 Kg Ton^-1^ coal in NaOH-NSW by sedimentation Mg2+ and Ca2+ of 99.91% and 32.52%, respectively, and clean coal will be produced. S. maxima biomass production cost was 3.35 times lower in PSWS medium than that of the standard. This method will be used for carbon sequestration and low cost biomass production.
Quantum probabilities in competing lizard communities
Authors: Aerts Diederik , Czachor Marek , D’Hooghe Bart , Kuna Maciej , Sinervo Barry , Sozzo Sandro 
Published: July 2019

AbstractDespite predictive success, population dynamics and evolutionary game theory still pose fundamental problems. Violation of the competitive exclusion principle in plankton communities provides an example. A promising solution of this ‘paradox of the plankton’ comes from theories involving cyclic competition, an evolutionary analogue of the classical rock-paper-scissors (RPS) game. However, modeling probabilistic RPS structures, one encounters a fundamental difficulty: the pairs rock-scissors, scissors-paper, and paper-rock possess representations in separate Kolmogorovian probability spaces, but a single global probability space for entire triplets does not exist. Populations that take part in cyclic competition should therefore involve probabilistic incompatibilities, analogous to those occurring in quantum mechanics. Here, using experimental data collected from 1990 to 2011 on the RPS cycles of lizards, we show that the incompatibilities are indeed unavoidable, and the data cannot be reconstructed from a single Kolmogorovian probability space. We then prove that the effect is genuinely quantum probabilistic, i.e. all the probabilities can be formulated in terms of a single density matrix and a set of non-commuting projectors. This formal quantum structure is dormant in games where probabilities of strategies do not entangle with probabilities of payoffs, and thus could be overlooked. In more realistic scenarios, involving games ‘with ace in a sleeve’, the non-Kolmogorovian structure can be activated. Surprisingly, lizards occasionally do play such games. In consequence, the formalism of evolutionary games, similarly to quantum mechanics, should begin with density matrix equations. Implications of our finding extend beyond lizard communities, given that RPS games are common in nature and higher dimensional RPS games may be even more common in ecosystems.
Nucleic acid - protein fingerprints. Novel protein classification based on nucleic acid - protein recognition
Authors: Krylov Alexander , Zhdanov Renad 
Published: July 2019

AbstractProtein chemistry uses protein description and classification based on molecular mass and isoelectric point as general features. Enzymes are also compared by enzymatic reaction constants, namely Km and kcat values. Proteins are also studied by binding to different oligonucleotides. Here we suggest a simple experimental method for such a comparison of DNA binding proteins, which we call &quot;nucleic acid-protein fingerprints&quot;. The experimental design of the method is based on an use of short oligonucleotides immobilized inside microarray of hydrogel cells - biochip. As a first stage, we solved a simple experimental task: what is the shortest single strand oligonucleotide to be recognized by protein? We tested binding of oligonucleotides from 2 to 12 bases, and we have obtained unexpected result that tetranucleotide one is long enough for specific protein binding. This 4-mer can contain two universal bases - 5-nitroindole nucleoside analogue (Ni) and only two meaningful bases, like A, G, T and C. The result obtained opens a way for constructing the simplest protein binding microarray. This microarray consists of 16 meaningful dinucleotides, like AA, AG, CT, GG etc. Physical sequences of all the nucleotides were NiNiAA, etc, where Ni is bound to gel through the amino linker. We prepared such an array and tested it for specific binding of several DNA/RNA binding proteins, labeled with fluorescent dyes like Texas Red of Bodipy. We tested RNase A and Binase for binding on the simplest microarray. It contains only 16 units, and there is a significant difference in the binding patterns. The microarray based on 3-mers must contains 64 units and must have much more specificity. The new principle of protein classification based on nucleic acid-protein recognition has been proposed and experimentally proved. Such an experimental approach must lead to a universal classification of specific DNA/RNA binding proteins.
Dispersal of Aedes aegypti: field study in temperate areas and statistical approach
Authors: Bergero Paula , Ruggerio Carlos A. , Lombardo Rubén , Schweigmann Nicolás , Solari Hernán 
Published: July 2019

AbstractWe studied the dispersion of Aedes aegypti during egg laying in natural conditions. Two independent experiments involving mosquitoes dispersing from urbanization towards adjacent un-urbanized areas were carried out and analyzed in statistical terms. We find relations between stochastic variables related to the egg laying mosquito activity (ELMA), useful to assess dispersion probabilities, despite the lack of knowledge of the total number of ovipositions in the zone. We propose to evaluate the activity as minus the logarithm of the fraction of negative ovitraps at different distances from buildings. We also estimate the average number of eggs laid per oviposition using a regression between the ELMA and the number of eggs found. Three zones with different oviposition activity were determined: a corridor surrounding the urbanized area, a second region between 10m and 25m and the third region extending from 30m to 45m from the urbanization. The landscape (plant cover) and the human activity in the area appear to have an influence in the dispersal of Aedes aegypti.
Inter-Tunneling Mechanism of Colliding Population Waves
Authors: Kalmykov Lev , Kalmykov Vyacheslav 
Published: July 2019

AbstractHere we show a new interaction mechanism of colliding population waves. It provides a stable coexistence of two similar but different species competing for the same limiting resource during their asexual propagation in a limited homogeneous environment under constant conditions. The revealed mechanism opens new opportunities in conservation biology.
Effect of 2-H and 18-O water isotopes in kinesin-1 gliding assay
Authors: Maloney Andy , Herskowitz Lawrence , Koch Steven 
Published: July 2019

AbstractWe show here the effects of heavy-hydrogen water (^2^H~2~O) and heavy-oxygen water (H~2~^18^O) on the gliding speed of microtubules on kinesin-1 coated surfaces. Increased fractions of isotopic waters used in the motility solution decreased the gliding speed of microtubules by a maximum of 21% for heavy-hydrogen and 5% for heavy-oxygen water. We discuss possible interpretations of these results and the importance for future studies of water effects on kinesin and microtubules. We also discuss the implication for biomolecular devices incorporating molecular motors.
Aetiology and treatment of epidermal depigmentory disorder in humans
Authors: Sawhney S. S. 
Published: July 2019

AbstractThe epidermal depigmentary trigger in humans at post-natal level may occur with the toxification of skin organ with the endogenously produced melanocytotoxic hydrogen peroxide and subsequent formation of hydrogen peroxide- melanolipoprotein conjugate involving the hydrogen bonding of complementary hydroxyl and carbonyl molecular surfaces of these biosignitures respectively. The condition is multifactorial but reversible. The structural and functional degeneration of melanocytes under the acquired condition never occur. The molecular conjugation theory on the aetiology and line of treatment of the epidermal depigmentary disorder (recoined as hepato-epidermal syndrome HES) has been proposed. The inherent sulfoxides of Allium cepa have been found as the renaturant of HES condition with the capacity to dislodge the denaturant hydrogen peroxide forming stronger hydrogen bonding with hydrogen peroxide than that of carbonyl molecular surface of melanolipoprotein, the epidermal colour determinant. The orally and topically defined plant based combined therapy advances the recovery time of HES condition.
Highly Efficient Gene Expression in B Lymphocytes Mediating by Lentivirus Vector
Authors: Tempaku Akira 
Published: July 2019

AbstractGene transduction and expression efficiencies among several type cell lines were compared by using vesicular stomatitis virus-glycoprotein (VSV-G) pseudotyped human immunodeficiency virus type-1 (HIV-1) based lentivirus vector. Large discrepancies of the efficiencies were shown among them. B lymphocytes showed high susceptibility of gene transduction and expression, while other cell lines marked lower potential. Variable gene transduction strategies have been assessed to apply immunological therapies. This study showed that B lymphocytes had facilities enough to support the gene transduction and expression by lentivirus vector. Our result suggested that the lentivirus vector would be a powerful tool to express exogenous genes in B lymphocytes.
Nitric oxide synthase in skeletal muscle fibres of patients with type 2 diabetes
Authors: Punkt Karla , Kandt Katharina , Oberbach Andreas , Adams Volker , Buchwalow Igor , Blueher Matthias 
Published: July 2019

AbstractMuscle-derived nitric oxide (NO) mediates fundamental physiological actions on skeletal muscle including glucose uptake into muscle cells. Recently, we have shown that the altered glucose metabolism in skeletal muscle of patients with type 2 diabetes (T2D) is associated with changes in the metabolic profile of individual muscle fibres, but fibre-type specific changes in NO synthase (NOS) expression in skeletal muscle of T2D patients remain to be elucidated. Here we investigated fibre-type related NOS expression in vastus lateralis muscle of T2D patients compared with healthy individuals with normal glucose tolerance (NGT). Cytophotometrical assay and Western blotting did not reveal any quantitative differences between NOS expression in muscles from NGT and T2D subjects. Positive NOS immunoreactivity in vastus lateralis of T2D patients was found to be associated with fast-oxidative glycolytic (FOG) muscle phenotype. This indicates that NOS expression in T2D patients correlates both with skeletal muscle fibre type distribution and the activity of oxidative and glycolytic enzymes.
A Critical Evaluation of Clinical Trials in Cancer and Pharmacogenomics
Authors: Baianu I. 
Published: July 2019

AbstractA critical overview of recent clinical trials in cancer is presented focused on signaling pathways blockers or inhibitors with a view to developing successful clinical trials employing personalized cancer therapies. Rational, pharmacogenomic strategies in cancer trials should be adopted that include specific molecular targeting based on adequate data for, and detailed modeling of, cancer cell genomes, modifications of cancer signaling pathways and epigenetic mechanisms. Novel translational oncogenomics research is rapidly expanding through the application of highly sensitive and specific advanced technology, research findings and computational tools and complex models to both pharmaceutical and clinical problems. Multiple sample analyses from several recent clinical studies have shown that gene expression data for cancer cells can be employed to distinguish between tumor types as well as to predict outcomes. Potentially important applications of such results are individualized human cancer therapies or, in general, ‘personalized medicine’ that will have to be validated through optimally designed clinical trials in cancer. A Human Cancer Genomes and Epigenetics Project is proposed that can provide the essential data required for the optimal design of clinical trials with the goal of achieving significant improvements of the survival rates of cancer patients participating in clinical trials for advanced cancer stages. The results of such a six-year Human Cancer Genomes and Epigenetics Project should also greatly aid with the accelerated, rational development of effective anti-cancer medicines and the chemoprevention of cancers.
Molecular Models of DNA Structures and Dynamics: Principles, Techniques and Applications
Authors: Baianu I. 
Published: July 2019

AbstractMolecular models of DNA structures are representations of the molecular geometry and topology of Deoxyribonucleic acid (DNA) molecules using one of several means, such as: closely packed spheres (CPK models) made of plastic, metal wires for 'skeletal models', graphic computations and animations by computers, artistic rendering, and so on, with the aim of simplifying and presenting the essential, physical and chemical, properties of DNA molecular structures either in vivo or in vitro. Computer molecular models also allow animations and molecular dynamics simulations that are very important for understanding how DNA functions in vivo.
Structural and Dynamic Studies of Amino Acids, Proteins and Nucleic Acids By Chemical-Hyperspectral Imaging, FT-IR/NIR, Vibro-Rotational Spectroscopy, Plasma, Microwave and Neutron Spectroscopy
Authors: Baianu I. 
Published: July 2019

AbstractA detailed review of structural and dynamic studies of amino acids, proteins and nucleic acids by spectroscopic techniques: microwaves, near infrared, UV, X-rays and neutrons, including also EXAFS, chemical-hyperspectral imaging and fluorescence correlation spectroscopy and FLIM, FRAP imaging with references, instrumentation diagrams and application examples for several related areas.
An insight into the kinships of the fungi
Authors: Datta Riddhi , Sarkar Joy , Acharya Krishnendu 
Published: July 2019

AbstractThe evolutionary origin of fungi is important in determining the phylogenetic relationships between fungi, animals and plants. However, determining the true relationship of fungi has been somewhat difficult owing to their simple morphology and presence of convergent characters. With the advent of newer molecular techniques, analysis of conserved protein sequences, cytochrome systems, mitochondrial and nuclear genetic material and rRNAs are being employed in elucidating phylogenetic kinships among the eukaryotes. These emerging evidences suggest that the derivation of the fungi from plants or algae would require more evolutionary changes than its derivation from protozoa, the unicellular ancestor of the animals. To gain an overview of the current state of the science, we have extensively reviewed the existing literatures and it appeared to us that fungi are more closely related to animals than to plants.