bluuebunny/crossref_metadata_2025 huggingface dataset:
Phenex: Ontological Annotation of Phenotypic Diversity
Authors: Balhoff James , Dahdul Wasila , Kothari Cartik , Lapp Hilmar , Lundberg John , Mabee Paula , Midford Peter , Westerfield Monte , Vision Todd
Published: July 2019

Phenotypic differences among species have long been systematically itemized and described by biologists in the process of investigating phylogenetic relationships and trait evolution. Traditionally, these descriptions have been expressed in natural language within the context of individual journal publications or monographs. Thus, this rich store of phenotype data has been largely unavailable for statistical and computational comparisons across studies or integration with other biological knowledge.Here we describe Phenex, a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic similarities and differences using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Phenex can be be configured to load ontologies for different taxonomic groups. The graphical user interface was developed for, and tested by, evolutionary biologists accustomed to working with lists of taxa, characters, character states, and character-by-taxon matrices.Annotation of phenotypic data using ontologies and globally unique taxonomic identifiers will allow biologists to better leverage decades of work in systematics and comparative morphology and contribute to an ever more useful web of linked biological data.
Metabolic constraints on the evolution of genetic codes: Did multiple 'preaerobic' ecosystem transitions entrain richer dialects?
Authors: Wallace Rodrick
Published: July 2019

A mathematical model based on Tlusty's topological deconstruction suggests that multiple punctuated ecosystem shifts in available metabolic free energy, broadly akin to the 'aerobic' transition, enabled a punctuated sequence of increasingly complex genetic codes. These evolved until the ancestor to the present narrow spectrum of nearly maximal codes became locked-in by path dependence.
Detection of Metabolites by Proton Ex Vivo NMR, in Vivo MR Spectroscopy Peaks and Tissue Content Analysis: Biochemical-Magnetic Resonance Correlation: Preliminary Results
Authors: Sharma Rakesh , Rehani Madan , Agrawala Arun
Published: July 2019

*Aim*: Metabolite concentrations by in vivo magnetic resonance spectroscopy and ex vivo NMR spectroscopy were compared with excised normal human tissue relaxation times and tissue homogenate contents.*Hypothesis*: Biochemical analysis combined with NMR and MR spectroscopy defines better tissue analysis.

Materials and Methods:

Metabolites were measured using peak area, amplitude and molecular weights of metabolites in the reference solutions. In normal brain and heart autopsy, muscle and liver biopsy tissue ex vivo NMR peaks and spin-lattice (T1) and spin-spin (T2) relaxation times, were compared with diseased tissue NMR data in meningioma brain, myocardial infarct heart, duchene-muscular-dystrophy muscle and diffused-liver-injury liver after respective in vivo proton MR spectroscopy was done. NMR data was compared with tissue homogenate contents and serum levels of biochemical parameters.*Results*: The quantitation of smaller NMR visible metabolites was feasible for both ex vivo NMR and in vivo MR spectroscopy. Ex vivo H-1 NMR and in vivo MRS metabolite characteristic peaks (disease/normal data represented as fold change), T1 and T2, and metabolites in tissue homogenate and serum indicated muscle fibrosis in DMD, cardiac energy depletion in MI heart, neuronal dysfunction in meningioma brain and carbohydrate-lipid metabolic crisis in DLI liver tissues.*Conclusion*: This preliminary report highlights the biochemical-magnetic resonance correlation as basis of magnetic resonance spectroscopic imaging data interpretation of disease.
Prebiotic Organic Microstructures
Authors: BASSEZ Marie-Paule , TAKANO Yoshinori , KOBAYASHI Kensei
Published: July 2019

Micro- and sub-micrometer spheres, tubules and fiber-filament soft structures have been synthesized in our experiments conducted with 3 MeV proton irradiations of a mixture of simple inorganic constituents, CO, N2 and H2O. We analysed the irradiation products, with scanning electron microscopy (SEM) and atomic force microscopy (AFM). These laboratory organic structures produced wide variety of proteinous and non-proteinous amino acids after HCl hydrolysis. The enantiomer analysis for D-, L- alanine confirmed that the amino acids were abiotically synthesized during the laboratory experiment. Considering hydrothermal activity, the presence of CO2 and H2, of a ferromagnesian silicate mineral environment, of an Earth magnetic field which was much less intense during Archean times than nowadays and consequently of a proton excitation source which was much more abundant, we propose that our laboratory organic microstructures might be synthesized during Archean times. We show similarities in morphology and in formation with some terrestrial Archean microstructures and we suggest that some of the observed Archean carbon spherical and filamentous microstructures might be composed of abiogenic organic molecules. We further propose a search for such prebiotic organic signatures on Mars. This article has been posted on Nature precedings on 21 July 2010 [1]. Extinct radionuclides as source of excitation have been replaced by cosmic radiations which were much more intense 3.5 Ga ago because of a much less intense Earth magnetic field. The new version of the article has been presented at the ORIGINS conference in Montpellier in july 2011 [2] and has since been published in Origins of Life and Evolution of Biospheres 42 (4) 307-316, 2012.DOI: 10.1007/s11084-012-9290-5
Effects of surface passivation on gliding motility assays
Authors: Maloney Andy , Herskowitz Lawrence , Koch Steven
Published: July 2019

In this study, we report differences in the observed gliding speed of microtubules dependent on the choice of bovine casein used as a surface passivator. We observed differences in both speed and support of microtubules in each of the assays. Whole casein, comprised of [alpha]~s1~, [alpha]~s2~, [beta], and [kappa] casein, supported motility and averaged speeds of 966 ± 7 nm/s. Alpha casein can be purchased as a combination of s1 and s2 and supported gliding motility and average speeds of 949 ± 4 nm/s. Beta casein did not support motility very well and averaged speeds of 870 ± 30 nm/s. Kappa casein supported motility very poorly and we were unable to obtain an average speed. Finally, we observed that mixing alpha, beta, and kappa casein with the proportions found in bovine whole casein supported motility and averaged speeds of 966 ± 7 nm/s.
Arbuscular mycorrhizal fungus spores host bacteria and their biofilm efficient in nutrient biodynamics and soil-borne plant pathogen suppression
Authors: Cruz Andre , Ishii Takaaki
Published: July 2019

The combination of bacteria and arbuscular mycorrhizal fungi (AMF) would be ideal for nutrient biodvnamics in soils and protection from soil-borne plant pathogens (SBPP). During the process of plant colonization AMF interact with bacteria where spores cytoplasm and hvphae provide specific niches for certain populations of bacteria. The clarification of the relationship AMF-bacteria has great potential for sustainable agriculture. The currently research aimed to isolate and characterize bacteria. Which we have designated most probable endobacteria (MPE) from an AMF spore. Three bacterial strains were taken from about 500 spores by using a 200 &x00B5;m diameter hvpodermic needle. These bacteria were identified by DNA and morphological methods. Antagonism to SBPP (Pythium ultimum NBRC 100123, Fusarium oxyxporum f. sp. lactucae MAFF 744088, Rhizoctonia solani MAFF 237426 and Roselinia necatrix - isolated from a Japanese apricot (Prunus mume) by Dr. Norihiko Kobayashi), P solubilization, ethylene production, nitrogenase activity and stimulation of AMF hyphal growth were evaluated. Here we show that the bacteria strongly functioned on nutrient biodynamics (P solubilization and Nitrogenase activity), ethylene production, protection from SBPP and stimulation of AMF hyphal growth. In addition, fresh samples of spores and hyphae were observed and photographed with a new type of scanning electronic microscope (SEM) (FEI Co., Quanta 250FEG), where the hyphae and spores with bacterial slime could be detected. Our results demonstrated the importance of bacteria associated to AMF for the soil ecology having a substantial mpact on sustainability. More specifically, the methods of extraction by ultra-thin needle reveled species associated to AMF, probably from inside spores. Moreover, the observation of bacterial biofilm showed a physical structure that the bacteria could form surround spores and hyphae to help AMF.
Optimal encoding of interval timing in expert percussionists
Authors: Burr David , Chicchini Guido , Arrighi Roberto , Giusti Marco , Cecchetti Luca
Published: July 2019

We measured temporal reproduction in expert drummers, string-musicians and non-musical subjects. While duration reproduction of the controls showed a characteristic regression to the mean, drummers responded veridically. This behavior is well explained by a model that combines optimally the sensory estimate for duration (more precise in drummers) with a prior, given by the average of the past few trials. These results highlight the efficiency and adaptability of sensori-motor mechanisms estimating temporal duration.
Allele-specific primer based identification of dimeric alpha-amylase inhibitor
Authors: Sharma Pradeep , Sharma Pooja , Saini Manoj , Singh S. S.
Published: July 2019

Wheat is one of the most important staple food crops cultivated over 200 mha in the range of environment throughout the world. Wheat production must continue to increase by 2% annually, more particularly in developing world including south-east Asia. Besides increasing the inherent productivity of wheat, it is important to minimize the losses caused to production by various abiotic and biotic factors. Alpha–amylase inhibitors are attractive candidates for the control of seed weevils as these insects are highly dependent on starch as the energy source. They play an important role in the carbohydrate metabolism of many heterotrophic and autotrophic organisms. In this study, we aimed to make sequence comparison and phylogenetic relationship among dimeric alpha-amylase inhibitor genes. These genes were clustered into two major groups based on phylogenetic analysis. Multiple alignments show at least 24 candidates single nucleotide polymorphisms in inhibitor genes, which could further be exploited for SNPs based haplotype diversity among Indian released wheat genotype. We have detected dimeric alpha-amylase inhibitor genes in cultivated and wild ancestors of wheat using genome specific primers. Genes encoding dimeric alpha-amylase belong to the family of 24 kDa alpha-amylase inhibitors. In this study, specific primer pairs were designed based on SNPs of these genes and chromosome locations of inhibitor genes confirmed by amplification in accession of T. urartu, A. tauschii, and A. speltoides. Results obtained under this study support that inhibitor genes amplified with primer PSWDAIAF1/PSWDAIAF2 and PSWDAIBF1/PSWDAIBF2 is present on genome B. These results further support evidence at molecular level that dimeric alpha-amylase inhibitor in cultivated wheat is encoded by a multigene family.
Attentional control and engagement with digital technology
Authors: Alloway Tracy , Alloway Ross
Published: July 2019

Multiple demands comprise the efficiency of attentional control. There is abundant evidence that when an individual attempts two or more attentionally demanding activities at the same time, the allocation of attention to the tasks is limited and performance suffers as a result. Yet, recent technological innovations require many individuals to manage multiple digital technologies simultaneously or to switch attentional control between tasks. The ability to multitask with various digital technologies involves dividing attention, switching between tasks, and keeping track of multiple strands of information in working memory.
Disordered proteins and network disorder in network descriptions of protein structure, dynamics and function. Hypotheses and a comprehensive review
Authors: Csermely Peter , Sandhu Kuljeet Singh , Hazai Eszter , Hoksza Zsolt , Kiss Huba , Miozzo Federico , Veres Daniel , Piazza Francesco , Nussinov Ruth
Published: July 2019

During the last decade, network approaches became a powerful tool to describe protein structure and dynamics. Here we review the links between disordered proteins and the associated networks, and describe the consequences of local, mesoscopic and global network disorder on changes in protein structure and dynamics. We introduce a new classification of protein networks into ‘cumulus-type’, i.e., those similar to puffy (white) clouds, and ‘stratus-type’, i.e., those similar to flat, dense (dark) low-lying clouds, and relate these network types to protein disorder dynamics and to differences in energy transmission processes. In the first class, there is limited overlap between the modules, which implies higher rigidity of the individual units; there the conformational changes can be described by an ‘energy transfer’ mechanism. In the second class, the topology presents a compact structure with significant overlap between the modules; there the conformational changes can be described by ‘multi-trajectories’; that is, multiple highly populated pathways. We further propose that disordered protein regions evolved to help other protein segments reach ‘rarely visited’ but functionally-related states. We also show the role of disorder in ‘spatial games’ of amino acids; highlight the effects of intrinsically disordered proteins (IDPs) on cellular networks and list some possible studies linking protein disorder and protein structure networks.
Hunter-gatherers in a howling wilderness: Neoliberal capitalism as a language that speaks itself
Authors: Wallace Rodrick
Published: July 2019

The 'self-referential' character of evolutionary process noted by Goldenfeld and Woese (2010) can be restated in the context of a generalized Darwinian theory applied to economic process through a 'language' model: The underlying inherited and learned culture of the firm, the short-time cognitive response of the firm to patterns of threat and opportunity that is sculpted by that culture, and the embedding socioeconomic environment, are represented as interacting information sources constrained by the asymptotic limit theorems of information theory. If unregulated, the larger, compound, source that characterizes high probability evolutionary paths of this composite then becomes, literally, a self-dynamic language that speaks itself. Such a structure is, for those enmeshed in it, more akin to a primitive hunter-gatherer society at the mercy of internal ecological dynamics than to, say, a neolithic agricultural community in which a highly ordered, deliberately adapted, ecosystem is consciously farmed so as to match its productivity to human needs.
Generating descriptive text from functional brain images
Authors: Pereira Francisco , Detre Greg , Botvinick Matthew
Published: July 2019

Recent work has shown that it is possible to take brain images of a subject acquired while they saw a scene and reconstruct an approximation of that scene from the images. Here we show that it is also possible to generate text from brain images. We began with images collected as participants read names of objects (e.g., ``Apartment'). Without accessing information about the object viewed for an individual image, we were able to generate from it a collection of semantically pertinent words (e.g., "door," "window"). Across images, the sets of words generated overlapped consistently with those contained in articles about the relevant concepts from the online encyclopedia Wikipedia. The technique described, if developed further, could offer an important new tool in building human computer interfaces for use in clinical settings.
Large sets of edit-metric sequence identification tags to facilitate large-scale multiplexing of reads from massively parallel sequencing
Authors: Faircloth Brant , Glenn Travis
Published: July 2019

Background

Massively parallel DNA sequencing technologies provide exponential increases in the amount of data returned from the sequencing process, relative to traditional (Sanger-based) techniques. Use of unique, synthetic oligonucleotides (identifying sequence tags) on each sample enables the deconvolution of samples pooled prior to massively parallel sequencing. To counteract oligonucleotide synthesis and sequencing errors, sequence tags should be drawn from combinations with sufficient differences and with an appropriate error-correcting code over the alphabet [A,C,G,T]. This method ensures that errors within the tags do not cause sequences to be assigned to the wrong sample while also enabling correction and recovery of incorrectly-sequenced or incorrectly-synthesized tags. The set of available tags should be large, allowing sample multiplexing to scale with rapid changes in sequencing platform output. The set of tags should also account for errors possible during both the oligonucleotide synthesis and sequencing processes. Most tags in current use have been designed to maintain a particular Hamming distance: a scheme that ensures the distance between tag sequences is maintained in the presence of substitutions. However, sequence identification tags conforming to the edit-metric are more appropriate: edit-metric sequence tags are robust to insertions, deletions, and substitution errors.

Results

We present edittag, a python package containing several tools to facilitate the design of edit-metric-based sequence identification tags, check existing sets of sequence identification tags for conformance to the edit-metric, and apply sequence identification tags to primers and/or adapters. We use edittag to design several large sets of edit-metric sequence tags ranging from four to 10 nucleotides in length and edit distance three to nine. Finally, we test a set of fusion primers designed with the software developed here, demonstrating high levels of successful amplification.

Conclusions

Researchers using sequence identification tags should consider using edit-metric-based sequence tags in place of the more common, Hamming-distance-based alternatives. Edit-metric sequence tags are robust to insertion, deletion, and substitution errors, thus more robust to all forms of error present during the DNA sequencing process. Edittag facilitates the generation and application of these robust sequence tags.
Understanding Genomic Evolution of Olfactory Receptors through Fractal and Mathematical Morphology
Authors: Hassan Sk. Sarif , Pal Choudhury Pabitra , Dayasagar B. S. , Chakraborty Shantanav , Guha Ranita , Goswami Arunava
Published: July 2019

Fractals and Mathematical Morphology are immensely used to study many problems in different branches of science and technology including the domain of Biology. There are many more unrevealed facts and figures of genes and genome in Computational Biology. In this paper, our objective is to explore how the evolutionary network is associated among Human, Chimpanzee and Mouse with regards to their genomic information. We are about to explore their genomic evolution through the quantitative measures of fractals and morphology. We have considered olfactory receptors for our case study. These olfactory receptors do function in different species with subtle differences in the structures of DNA sequences. Those subtle differences can be exposed through intricate details of Fractals and Mathematical Morphology.
Kinetic model based on molecular mechanism for action potential
Authors: Xu Lizhong
Published: July 2019

The Hodgkin-Huxley model for action potentials has been widely used but was not built on a microscopic description of the neuronal membrane. Through molecular dynamics simulations, the molecular mechanism of the channel currents is becoming clear. However, the quantitative link between molecular mechanism and action potential remains to be elucidated. Here, a kinetic model for action potential based on the molecular mechanism of the channel currents is proposed. Using it, the experimental observations about action potential are reproduced quantitatively and explained based on molecular mechanism. We find that the accumulation of Na+ ions near exit of the electivity filter is the dominant event to cause the refractory period of the Na+ channel and the types of the channel currents depend on its rate constants. The channel inductance represents the inertia of the channel to retain a certain ion binding state, the channel resistances include ones against state transition and charge transfer.
An uncultured human-associated bacterium model
Authors: Dinis Jorge , Barton David , Ghadiri Jamsheed , Surendar Deepa , Reddy Kavitha , Velasquez Fernando , Chaffee Carol , Lee Wendy , Gavrilova Helen , Ozuna Hazel , Smits Samuel , Ouverney Cleber
Published: July 2019

The Bacteria Domain experienced an explosion of novel lineages identified within the last decade, especially of lineages made entirely of uncultured members. Since numerous cultivable bacteria have been shown to be instrumental in human development, health, and diseases, it is reasonable to speculate that strains from uncultured groups, which comprise nearly 80% of the human gut and 68% of human oral microbial consortia, participate in similar functions. The study of human-associated uncultured bacteria, however, has many practical limitations, such as access to patient samples, unpredictable microbial composition, and low relative abundance, all of which challenge experimental promptness and reproducibility. We propose that uncultured bacteria from environmental sources can serve as a model to better understand the roles their counterparts play in humans. In this study, we illustrate this concept using an environmental TM7 bacterium with &8805;98.5% 16S rDNA gene homology to a group of TM7 bacteria found in both the human oral cavity and skin. Our TM7 model was readily detectable with molecular techniques as viable cells in sludge and in quantities greater than its human-associated relatives. Our approach circumvents difficulties imposed by sampling humans until either a TM7 strain of interest is cultured or an alternative method is proposed.
Word Activation Forces Map Word Networks
Authors: Guo Jun , Guo Hanliang , Wang Zhanyi
Published: July 2019

Words associate with each other in a manner of intricate clusters^1-3^. Yet the brain capably encodes the complex relations into workable networks^4-7^ such that the onset of a word in the brain automatically and selectively activates its associates, facilitating language understanding and generation^8-10^. One believes that the activation strength from one word to another forges and accounts for the latent structures of the word networks. This implies that mapping the word networks from brains to computers^11,12^, which is necessary for various purposes^1,2,13-15^, may be achieved through modeling the activation strengths. However, although a lot of investigations on word activation effects have been carried out^8-10,16-20^, modeling the activation strengths remains open. Consequently, huge labor is required to do the mappings^11,12^. Here we show that our found word activation forces, statistically defined by a formula in the same form of the universal gravitation, capture essential information on the word networks, leading to a superior approach to the mappings. The approach compatibly encodes syntactical and semantic information into sparse coding directed networks, comprehensively highlights the features of individual words. We find that based on the directed networks, sensible word clusters and hierarchies can be efficiently discovered. Our striking results strongly suggest that the word activation forces might reveal the encoding of word networks in the brain.
Scaffolder - Software for Reproducible Genome Scaffolding.
Authors: Barton Michael , Barton Hazel
Published: July 2019

Background:

Assembly of short-read sequencing data can result in a fragmented non-contiguous series of genomic sequences. Therefore a common step in a genome project is to join neighboring sequence regions together and fill gaps in the assembly using additional sequences. This scaffolding step, however, is non-trivial and requires manually editing large blocks of nucleotide sequence. Joining these sequences together also hides the source of each region in the final genome sequence. Taken together, these considerations may make reproducing or editing an existing genome build difficult.

Methods:

The software outlined here, “Scaffolder,” is implemented in the Ruby programming language and can be installed via the RubyGems software management system. Genome scaffolds are defined using YAML - a data format, which is both human and machine-readable. Command line binaries and extensive documentation are available.

Results:

This software allows a genome build to be defined in terms of the constituent sequences using a relatively simple syntax to define the scaffold. This syntax further allows unknown regions to be defined, and adds additional sequences to fill gaps in the scaffold. Defining the genome construction in a file makes the scaffolding process reproducible and easier to edit compared with FASTA nucleotide sequence.

Conclusions:

Scaffolder is easy-to-use genome scaffolding software. This tool promotes reproducibility and continuous development in a genome project. Scaffolder can be found at http://next.gs.
Metabolic Activity of Human Chorionic Gonadotropin (hCG) on Glycemia and Leptinemia in Experimental Animals Fed a Cafeteria Diet
Authors: Belluscio Daniel , Lago Nestor , Klimovsky Ezequiel , Berdeal Maria , Federico Andrea
Published: July 2019

Objectives:

To elucidate the relationship of hCG administration to glycemia, Non Esterified Fatty Acids (NEFA), leptin and adiponectin levels on experimental animals previously submitted to a cafeteria diet, and then to a Low Calorie Diet (LCD). Design: Forty-one rats were selected (21 females, 20 males) and divided into seven (0-6) groups. Animals from groups 1 to 6 were fed a "cafeteria diet" with a mean energy content of 10% protein, 30% carbohydrate and 60% fat. Animals from group 0 were fed the standard laboratory diet. After the fattening period, animals from groups 1 to 6 were submitted to a restricted diet consisting of one-third the average daily intake for rats. hCG was administered for five weeks according to a specific protocol. The effects of hCG treatment were evaluated using analysis of variance (ANOVA).

Results:

These assessments were compared: (1) glycemia, adiponectins, leptins and non-esterified fatty acids (NEFA); (2) weight; (3) formulation effect; and (4) dose effect. Differences in leptins were observed between the Control group and Injectable A (p=0.026), Intrarectal Suspension A (p=0.20), Intrarectal Suspension B (p<0.001), and Intrarectal Suspension C (p<0001) groups. In all cases, the average values were higher for the control group. Significant differences were found in the groups treated with Injectable B, Intrarectal Suspension B (p=0.025) and Intrarectal Suspension C (p=0.037). Groups receiving Intrarectal Suspension B or C showed significantly lower mean leptin values. Differences in glycemia were detected between the Control group and Intrarectal Suspension A (p=0.021) and Intrarectal Suspension B (p=0.020) groups. Groups treated with Intrarectal Suspension A or B showed lower mean blood glucose values.

Conclusions:

Results show the activity of hCG (both urinary and recombinant) on glycemia and leptins levels in experimental animals in different formulations.hCG administration significantly decreased blood sugar and leptin levels, whereas adiponectins were only relatively sensitive to hCG.
Sensory adaptation in the light of information and energy
Authors: Rasumov Nikon , Niven Jeremy , Baker Michael , Laughlin Simon
Published: July 2019

Signal processing in neurons is constrained by internal noise and energy consumption. Neural systems often invest energy in amplifying signals to protect them against internal noise. There is no general expression for the trade-off between energy and information, because it is strongly dependent on the properties of signal, noise and underlying mechanism. We present the first analysis of this energy-information trade-off in a specific system, the R1-6 photoreceptors of the blowfly, Calliphora vicina. These photoreceptors adapt to light level by adjusting their transduction gain (number of light-gated channels opened per photon) and potassium conductance. By combining experimental measures of photoreceptor impedances, transfer functions and signal quality in a basic membrane model we discovered that photoreceptors do not adapt to maximise their sensitivity. Instead, they use a lower sensitivity at which they capture 99% of the information from naturalistic stimuli. This strategy is efficient because it avoids the wasteful amplification of noisy inputs and reduces energy consumption.
Expression cartography of human tissues using self organizing maps
Authors: Wirth Henry , Binder Hans
Published: July 2019

Background:

The availability of parallel, high-throughput microarray and sequencing experiments poses a challenge how to best arrange and to analyze the obtained heap of multidimensional data in a concerted way. Self organizing maps (SOM), a machine learning method, enables the parallel sample- and gene-centered view on the data combined with strong visualization and second-level analysis capabilities. The paper addresses aspects of the method with practical impact in the context of expression analysis of complex data sets.

Results:

The method was applied to generate a SOM characterizing the whole genome expression profiles of 67 healthy human tissues selected from ten tissue categories (adipose, endocrine, homeostasis, digestion, exocrine, epithelium, sexual reproduction, muscle, immune system and nervous tissues). SOM mapping reduces the dimension of expression data from ten thousands of genes to a few thousands of metagenes where each metagene acts as representative of a minicluster of co-regulated single genes. Tissue-specific and common properties shared between groups of tissues emerge as a handful of localized spots in the tissue maps collecting groups of co-regulated and co-expressed metagenes. The functional context of the spots was discovered using overrepresentation analysis with respect to pre-defined gene sets of known functional impact. We found that tissue related spots typically contain enriched populations of gene sets well corresponding to molecular processes in the respective tissues. Analysis techniques normally used at the gene-level such as two-way hierarchical clustering provide a better signal-to-noise ratio and a better representativeness of the method if applied to the metagenes. Metagene-based clustering analyses aggregate the tissues into essentially three clusters containing nervous, immune system and the remaining tissues.

Conclusions:

The global view on the behavior of a few well-defined modules of correlated and differentially expressed genes is more intuitive and more informative than the separate discovery of the expression levels of hundreds or thousands of individual genes. The metagene approach is less sensitive to a priori selection of genes. It can detect a coordinated expression pattern whose components would not pass single-gene significance thresholds and it is able to extract context-dependent patterns of gene expression in complex data sets.
More damn lies about data access
Authors: Axton Myles
Published: July 2019

More data than we can handle is no excuse to give up our efforts to promote data access, but it may make us think about new ways to make it sustainable.[This draft was written in the hope that participants of the Sage Congress will write an Nature Genetics Editorial in the manner of Tom Sawyer’s white fence (Twain M. 1876). All contributions received by April 10th 2011 will be attributed.]
Hypothesis: Is the Omega-3 PUFA Content of Milk Related to Type 1 Diabetes?
Authors: Arbesman Harvey , Arbesman Marian
Published: July 2019

The incidence of Type 1 Diabetes (T1D) has been increasing over the past 50 years. The geographical variation in the incidence of T1D varies 400 fold from a low rate in China to a very high incidence in Finland, Sardinia and Yemenite Jews in Israel. The reason behind these epidemiologic findings is unclear at this time and further elucidating the factors related to this intriguing epidemiology of T1D can help us better understand certain risk factors, the pathogenesis of the disease, and help reduce the incidence of T1D. We hypothesize that the variation of the omega-3 polyunsaturated fatty acid (PUFA) content of cow’s milk and human breast milk may play a very important role in the development of Type 1 Diabetes in genetically predisposed individuals and may also be an important confounder in many previously published and ongoing studies. Interestingly, the amount of omega 3 fatty acids in cow’s milk and human breast milk has been shown to vary widely depending on the diet of the cows and nursing mothers. This hypothesis could possibly help explain the conflicting results from various studies regarding cow’s milk exposure, breastfeeding and T1D and may also help explain some of the findings related to other environmental risk factors for the development of T1D through the beneficial effects of omega-3 fatty acids on this autoimmune disease.
Up-expression of GAD65 in the Amygdala of the Rat Model of Chroric Immobilization Stress with Elevated Blood Glucose
Authors: Li Xiao-Jing , Zhang Wei , Liang Bing , Zheng Xiang , Zhou Xue
Published: July 2019

It is believed that the hypothalamus is the regulating center for blood glucose levels, but how chronic stress leads to hyperglycemia is not known. In this experiment, we use the chronic immobilization stressed rat as a model, and found that only rats with increased expression of GAD65 in the amygdala have an elevated level of blood glucose. Considering there are fiber tracks between the amygdala and hypothalamus, including GABAergic projections, this result suggests that the changes in GAD65 expression in the amygdala may correlate with the changes in blood glucose levels, and point to the importance of the the amygdala in blood glucose regulation.
Wikis in scholarly publishing
Authors: Mietchen Daniel , Hagedorn Gregor , Förstner Konrad , Kubke M Fabiana , Koltzenburg Claudia , Hahnel Mark , Penev Lyubomir
Published: July 2019

Scientific research is a process concerned with the creation, collective accumulation, contextualization, updating and maintenance of knowledge. Wikis provide an environment that allows to collectively accumulate, contextualize, update and maintain knowledge in a coherent and transparent fashion. Here, we examine the potential of wikis as platforms for scholarly publishing. In the hope to stimulate further discussion, the article itself was drafted on "Species-ID":http://species-id.net/w/index.php?title=Wikis_in_scholarly_publishing&oldid=3815 - a wiki that hosts a prototype for wiki-based scholarly publishing - where it can be updated, expanded or otherwise improved.
Counting absolute number of molecules using unique molecular identifiers
Authors: Kivioja Teemu , Vähärautio Anna , Karlsson Kasper , Bonke Martin , Linnarsson Sten , Taipale Jussi
Published: July 2019

Advances in molecular biology have made it easy to identify different DNA or RNA species and to copy them. Identification of nucleic acid species can be accomplished by reading the DNA sequence; currently millions of molecules can be sequenced in a single day using massively parallel sequencing. Efficient copying of DNA-molecules of arbitrary sequence was made possible by molecular cloning, and the polymerase chain reaction. Differences in the relative abundance of a large number of different sequences between two or more samples can in turn be measured using microarray hybridization and/or tag sequencing. However, determining the relative abundance of two different species and/or the absolute number of molecules present in a single sample has proven much more challenging. This is because it is hard to detect individual molecules without copying them, and even harder to make defined number of copies of molecules. We show here that this limitation can be overcome by using unique molecular identifiers (umis), which make each molecule in the sample distinct.
Nanoconfinement of spider silk fibrils begets superior strength, extensibility and toughness
Authors: Giesa Tristan , Arslan Melis , Pugno Nicola , Buehler Markus
Published: July 2019

Silk is an exceptionally strong, extensible and tough material made from simple protein building blocks. The molecular structure of dragline spider silk repeat units consists of semi-amorphous and nanocrystalline beta-sheet protein domains. Here we show by a series of computational experiments how the nanoscale properties of silk repeat units are scaled up to create macroscopic silk fibers with outstanding mechanical properties despite the presence of cavities, tears and cracks. We demonstrate that the geometric confinement of silk fibrils to diameters of 50±30 nm width is critical to facilitate a powerful mechanism by which hundreds of thousands of protein domains synergistically resist deformation and failure to provide enhanced strength, extensibility and toughness at the macroscale, closely matching experimentally measured mechanical properties. Through this mechanism silk fibers exploit the full potential of the nanoscale building blocks, regardless of the details of microscopic loading conditions and despite the presence of large defects. Experimental results confirm that silk fibers are composed of silk fibril bundles with diameters in the range of 20-150 nm, in agreement with our predicted length-scale. Our study reveals a general mechanism to map nanoscale properties to the macroscale and provides a potent design strategy towards novel fiber and bulk nanomaterials.
Neem leaf glucosamine stimulates Interleukin-2 (IL-2) in swiss albino mice
Authors: Venugopalan Santhosh Kumar , Viswesharan Navaratnam , Aiyalu Rajasekaran , N K Nair
Published: July 2019

Neem leaf glucosamine-mediated immune stimulation was studied in male swiss albino mice. Mice were treated with three doses of Neem leaf glucosamine (266, 400 and 800 µg/30gm mouse, intraperitoneal injection) one dose per week for four weeks. At doses of 266, 400 and 800 µg/30gm mouse a significant increase in Interleukin-2 in mice serum was observed when compared to the control group and also an increase in relative organ weight of the thymus was observed but there was a mild increase in liver and kidney weights. The immune stimulatory response of Neem leaf glucosamine was also observed in T-lymphocyte proliferation. Overall, Neem leaf glucosamine showed a stimulatory effect on immune functions in mice. The immunostimulatory effect of Neem leaf glucosamine as reported in this study will have special relevance for the prophylactic and potential therapeutic treatment of various infectious diseases and antitumor activity.
Cancer invasion associated gene expression signature is present in differentially expressed genes in the reprogramming of fibroblasts into stem cells
Authors: Cheng Wei-yi , Kim Hoon , Kandel Jessica , Anastassiou Dimitris
Published: July 2019

Tumors become invasive by penetrating adjacent connective tissue, but the underlying biological mechanisms remain obscure. We recently identified a precise gene expression signature of fibroblastic origin associated with cancer invasion, the first step of the metastatic cascade. The signature contains many coordinately overexpressed genes, prominent among which are COL11A1, THBS2 and INHBA. Here we show that there is a striking similarity between the set of expressed genes in this metastasis-associated fibroblastic (MAF) signature and the set of genes that are downregulated when fibroblasts are reprogrammed to induced pluripotent stem cells (iPSCs). Because it is known that fibroblast reprogramming involves a mesenchymal epithelial transition (MET), the above facts suggest that, conversely, the metastasis-associated fibroblasts responsible for the signature may result from stem-like cells undergoing some type of epithelial-mesenchymal transition (EMT). Therefore, we speculate that cancer stem cells (CSCs) undergoing some type of EMT become fibroblastic to obtain motility and invasiveness, reactivating early embryonic developmental pathways, and that these fibroblast-like cells are the main source of the MAF signature that we previously identified.
Genetic Analysis of ABO and Rh Blood Groups in Brahmin Population of Uttar Pradesh, India”
Authors: Rai Vandana
Published: July 2019

A series of glycoprotein and glycolipids on the red blood cell surface constitute blood group antigens. These are A, B, AB and O in ABO blood group system and Rh in rhesus blood group system. These antigens are genetically controlled. Certain diseases have been shown to be associated with certain blood groups. In the present study an attempt is made to study the distribution of ABO and Rh. (D) blood group systems among the Brahmin caste population of Uttar Pradesh State. A total of 200 unrelated Brahmin individuals from Uttar Pradesh were studied for the phenotype and allele frequency distribution of ABO and Rh (D) blood groups. The order of occurrence of ABO phenotypes is B>O>A>AB. The corresponding allele frequencies of O, A, and B alleles are found to be 0.5790, 0.1510 and 0.2697 respectively. The allele frequency of D (0.735) is more than d (0.265). The present study was compared with the other studies reported to understand the affinity between them.
Tuning and regulating the repertoire of glycan determinants
Authors: Wallace Rodrick , Wallace Deborah
Published: July 2019

We apply Tlusty's information-theoretic index theorem analysis of the genetic code to the glycome, using a cognitive paradigm by which external information sources constrain and tune the glycan code error network, in the context of available metabolic energy. The model suggests spontaneous symmetry breaking of the glycan code as a function of metabolic energy intensity, an effect that may be currently present, or embedded in evolutionary trajectory, recording large-scale ecosystem resilience shifts in energy availability such as the aerobic transition. Once focused on a subset of the glycan error code network however, the glycan production machinery must then be regulated by an elaborate cognitive process to ensure that what is produced matches what has been chosen for production. Index theorem methods emerge in a highly natural manner for this composite system whose failures will be represented by a spectrum of glycan disorders.
Information homeostasis as a fundamental principle governing the cell division and death
Authors: Kumar Arvind , Singh Harinder
Published: July 2019

To express genetic information with minimal error is one of the key functions of a cell. Here we propose an information theory based phenomenological model for the expression of genetic information. Based on the model we propose, the concept of "information homeostasis" ensures that genetic information is expressed with minimal error. We suggest that together with energy homeostasis, information homeostasis is a fundamental working principle of a biological cell. This model proposes a novel explanation of why a cell divides and why it stops to divide and thus provides novel insight into oncogenesis and various neuro-degenerative diseases. Moreover, the model suggests a theoretical framework to understand cell division and death, beyond specific biochemical pathways.
Consciousness and subjective time: a plausible auditory approach
Authors: Ehsani Sepehr
Published: July 2019

The perception of time is an indispensable facet of human consciousness, and may in fact be dynamically present in primates and other species, albeit with different manifestations. Moreover, contrary to the physical measures of time, cognitive temporal perception may be subjectively affected by both internal and environmental cues. Here we review the evidence for the potential role of the auditory system in shaping the cortical measures of time, and propose possible auditory methods for studying this aspect of consciousness.
Molecular evolution of RRM-containing proteins and glycine-rich RNA-binding proteins in plants
Authors: Gomez-Porras Judith , Lewinski Martin , Riaño-Pachón Diego Mauricio , Staiger Dorothee
Published: July 2019

Background:

In angiosperms, RNA-binding proteins with an RNA recognition motif (RRM)-type RNA interaction domain play an important role in developmental and environmental responses. Despite their pivotal role, a comprehensive analysis of their number and diversity has only been performed in Arabidopsis so far.

Results:

Here we present a detailed phylogenetic analysis of RRM-containing proteins in plants, the red algae Cyanidioschyzon merolae and cyanobacteria. We identified two major events during the diversification of the RRM in plants, one at the emergence of green plants, and the other at the water-to-land transition. We focused on proteins that combine a single RRM with a glycine-rich stretch, known as glycine-rich RNA-binding proteins (GRPs). We found that GRPs are present in cyanobacteria, however plant and cyanobacterial GRPs are not of monophyletic origin. We provide evidence that plant GRPs form a polyphyletic group.*Conclusion:*Our work provides insights into the origin of GRPs in plants. We determined that the RRM from plants and cyanobacteria do not have a common origin. We could also determine that the acquisition of the glycine-rich stretch has happened at least on three separate occasions during the evolution of GRPs. One event led to the emergence of cyanobacterial GRPs, while later acquisition events led to the emergence of GRPs in the green lineage. No GRPs were found in red or marine green algae. We found a subgroup of GRPs exclusive to land plants, and its appearance may be linked to challenges related to the water-to-land transition.
On the social induction of Alzheimer's disease: An index theorem aging model for amyloid formation
Authors: Wallace Rodrick , Wallace Deborah
Published: July 2019

The central 'risk factor' for Alzheimer's disease (AD) is age. From first principles, we construct a mathematical model of protein folding and its in vivo regulation that gives this result in a natural manner. We extend the basic approach using topological information theory methods, and examine a case history of socially-induced premature aging in the United States.