bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pro-social motive promotes early understanding of false belief
Authors: Matsui Tomoko , Miura Yui 
Published: July 2019

AbstractEver since Premack & Woodruff's classic article^1^, which introduced the term "theory of mind", researchers have claimed that strategic deception is the most natural behavioural consequence of understanding false belief. Here we challenge that claim, and provide evidence for the first time that the earliest manifestation of false belief understanding in human development is found in young children's emerging pro-social behaviours. In a modified false belief task, children were asked either to choose one protagonist they should help to find the object (the pro-social context), or to choose one they need to deceive so that none of the protagonists can find the object (the competitive context). The results show that the pro-social motive, but not the competitive motive, boosts early false belief understanding. This is most clearly contrasted with findings that apes, our closest living relatives, are capable of intentionally manipulating others by concealing information only under competitive motives, not under cooperative alternatives. Thus, the current findings are the strongest to date that sophisticated understanding of others' belief in humans has its unique origin, separate from the primate origin at some point in recent evolution, when cooperative and communicative motives played an essential role for their survival.
Myth about neuronal nitric oxide synthase in the sarcolemma of skeletal muscles
Authors: Buchwalow Igor , Boecker Werner 
Published: July 2019

AbstractIn skeletal muscles, neuronal NO synthase (nNOS, designated also as NOS1) was reported to be restricted to the sarcolemma. With the advent of modern powerful immunocytochemical techniques this commonly accepted view appears to be a delusion and has to be re-evaluated.
Pancreas islets in metabolic signaling - focus on the &946;-cell
Authors: Suckale Jakob , Solimena Michele 
Published: July 2019

AbstractTaken together the Islets of Langerhans form a nutrient sensing network spread throughout the pancreas. They are tightly connected to the source organ - the intestine - and the target organs - liver, muscle, and fat cells. The expression of a unique set of proteins enables [beta] cells, the most frequent islet cell type, to detect elevated blood glucose levels and secrete insulin accordingly. Neighbouring [beta]-cells achieve tighter regulation of glucose-induced insulin secretion by coordination through cell surface proteins. They also adjust their secretory pathway capacity and flow to avoid being damaged. The immediate reaction of the [beta] cell to nutrients is regulated by translational mechanisms, while longer term adaptations involve changes in transcription. Glucose increases protein synthesis in the [beta] cell overall and especially that of some secretory proteins including insulin. This effect may be mediated through recognition of RNA motifs in the untranslated regions of those messengers. Failure of essential molecular components of the nutrient sensing system due to mutation or weakness paired with cellular stress can lead to dysfunctions, which on a larger scale manifest as diseases like diabetes mellitus.
Polymorphisms of the ENPP1 gene are not associated with type 2 diabetes or obesity in the Chinese Han population
Authors: Zhao Teng , Zhang Di , Liu Yun , Zhou Daizhan , Chen Zhuo , Li Sheng , Yu Lan , Liu Simin , Zhang Zuofeng , Feng Guoyin , He Lin , Xu He 
Published: July 2019

Abstract
*Objective:*
Type 2 Diabetes mellitus is a metabolic disorder characterized by chronic hyperglycemia and with a major feature of insulin resistance. Genetic association studies have suggested that ENPP1 might play a potential role in susceptibility to type 2 diabetes and obesity. Our study aimed to examine the association between ENPP1 and type 2 diabetes and obesity.*Design:* Association study between two SNPs, rs1044498 (K121Q) and rs7754561 of ENPP1 and diabetes and obesity in the Chinese Han population.*Subjects:* 1912 unrelated patients (785 male and 1127 female with a mean age 63.8 ± 9 years), 236 IFG/IGT subjects (83 male and 153 female with a mean age 64 ± 9 years) and 2041 controls (635 male and 1406 female with a mean age 58 ± 9 years). *Measurements:* Subjects were genotyped for two SNPs using TaqMan technology on an ABI7900 system and tested by regression analysis.

*Results:*
By logistic regression analysis, rs1044498 (K121Q) and rs7754561 showed no statistical association with type 2 diabetes, obesity under additive, dominant and recessive models either before or after adjusting for sex and age. Haplotype analysis found a marginal association of haplotype C-G (p=0.05) which was reported in the previous study.*Conclusion:* Our investigation did not replicated the positive association found previously and suggested that the polymorphisms of ENPP1 might not play a major role in the susceptibility to type 2 diabetes or obesity in the Chinese Han population.
Coincidence between transcriptome analyses on different microarray platforms using a parametric framework
Authors: Konishi Tomokazu , Konishi Fumikazu , Takasaki Shigeru , Inoue Kohei , Nakayama Kouji , Konagaya Akihiko 
Published: July 2019

AbstractA parametric framework for the analysis of transcriptome data is demonstrated to yield coincident results when applied to data acquired using two different microarray platforms. Discrepancies among transcriptome studies are frequently reported, casting doubt on the reliability of collected data. The inconsistency among observations can be largely attributed to differences among the analytical frameworks employed for data analysis. The existing frameworks normalizes data against a standard determined from the data to be analyzed. In the present study, a parametric framework based on a strict model for normalization is applied to data acquired using an in-house printed chip and GeneChip. The framework is based on a common statistical characteristic of microarray data, and each data is normalized on the basis of a linear relationship with this model. In the proposed framework, the expressional changes observed and genes selected are coincident between platforms, achieving superior universality of data compared to other methods.
Biodiversity informatics: the challenge of linking data and the role of shared identifiers
Authors: Page Roderic 
Published: July 2019

AbstractA major challenge facing biodiversity informatics is integrating data stored in widely distributed databases. Initial efforts have relied on taxonomic names as the shared identifier linking records in different databases. However, taxonomic names have limitations as identifiers, being neither stable nor globally unique, and the pace of molecular taxonomic and phylogenetic research means that a lot of information in public sequence databases is not linked to formal taxonomic names. This review explores the use of other identifiers, such as specimen codes and GenBank accession numbers, to link otherwise disconnected facts in different databases. The structure of these links can also be exploited using the PageRank algorithm to rank the results of searches on biodiversity databases. The key to rich integration is a commitment to deploy and reuse globally unique, shared identifiers (such as DOIs and LSIDs), and the implementation of services that link those identifiers.
A PI3K-mediated negative feedback regulates Drosophila motor neuron excitability
Authors: Howlett Eric , Lin Curtis , Lavery William , Stern Michael 
Published: July 2019

AbstractNegative feedback can act as a homeostatic mechanism to maintain neuronal activity at a particular specified value. At the Drosophila neuromuscular junction, a mutation in the type II metabotropic glutamate receptor gene (mGluRA) increased motor neuron excitability by disrupting an autocrine, glutamate-mediated negative feedback. We show that mGluRA mutations increase neuronal excitability by preventing PI3 kinase (PI3K) activation and consequently hyperactivating the transcription factor Foxo. Furthermore, glutamate application increases levels of phospho-Akt, a product of PI3K signaling, within motor nerve terminals in an mGluRA-dependent manner. In humans, PI3K and type II mGluRs are implicated in epilepsy, neurofibromatosis, autism, schizophrenia and other neurological disorders; however, neither the link between type II mGluRs and PI3K, nor the role of Foxo in the control of neuronal excitability, had been previously reported. Our work suggests that some of the deficits in these neurological disorders might result from disruption of glutamate-mediated homeostasis of neuronal excitability.
Immunity to self co-generates regulatory T cells
Authors: Dromey James , Lee Bo Han , Young Helen , Mannering Stuart , Jensen Kent , Thearle Daniel , Fourlanos Spiros , Belov Larissa , Harrison Leonard 
Published: July 2019

AbstractImmune responses to self are kept in check by tolerance mechanisms, including suppression by regulatory T cells (Tregs). The defective generation of Tregs specific for self-antigens may lead to autoimmune disease. We identified a novel population of human CD4^+^ Tregs, characterized by high surface expression of CD52, which is co-generated in response to autoantigen. Blood CD4^+^CD52^hi^ T cells were generated preferentially in response to low-dose autoantigen and suppressed proliferation and interferon-[gamma] production by other T cells. Depletion of resting CD4^+^CD52^hi^ T cells enhanced the T-cell response to autoantigen. CD4^+^CD52^hi^ Tregs were neither derived from nor distinguished by markers of conventional resting CD4^+^CD25^+^ Tregs. In response to the pancreatic islet autoantigens glutamic acid decarboxylase, the generation of CD4^+^CD52^hi^ Tregs was impaired in individuals with and at-risk for type 1 diabetes, compared to healthy controls and individuals with type 2 diabetes. CD4^+^CD52^hi^ Tregs co-generated to self-antigen may therefore contribute to immune homeostasis and protect against autoimmune disease.
Suggested actions from the Melbourne HVP Information Seminar
Authors: Cotton Richard , Axton Myles , Bankier Agnes , Brais Bernard , Cavedon Lawrence , du Sart Desirée , George Peter , Goldgar David , Harrison Terence , Hibbert Marienne , Hopper John , Macrae Finlay , O’Keefe Christine , Ravine David , Savarirayan Ravi , Sheffield Les , Smith Tim , Stokes Nicola , Sundararajan Vijaya , Thorburn David , Winship Ingrid 
Published: July 2019

AbstractThe Human Variome Project (HVP; www.humanvariomeproject.org) was initiated at a meeting in June 2006 and addressed the problems of collecting genetic information and generated 96 recommendations (http://www.nature.com/ng/journal/v39/n4/full/ng0407-423.html) to overcome these, with the focus on Mendelian disease. A considerable number of projects have been added, to those that have been ongoing for a number of years, since that meeting. Also, a planning meeting is to be held May 25-29, 2008 in Spain (http://www.humanvariomeproject.org/HVP2008/).A dramatic boost has been given to the HVP by the preparedness and action of the International Society for Gastrointestinal Hereditary Tumours (InSiGHT; www.insight-group.org), to, in order to improve their own informatics systems for dealing with inherited colon cancer, set up a pilot system for collection and databasing mutation and phenotype information, i.e. to act as pilot for the HVP. This is then intended to be transferred to other genes and countries. Much relevant activity in this project is being led from and is based in Melbourne.This meeting in Melbourne has been conceived to review the current local situation and plans for the future. We are privileged that Myles Axton, Editor of Nature Genetics, a strong supporter of the HVP (see April 2007 Nature Genetics Editorial) and who has some ideas in the area (see August 2007 Nature Genetics Editorial) agreed to be keynote speaker.We proposed that the output of this meeting be published and, with permission, the abstracts and presentations placed on the website (www.humanvariomeproject.org/?p=Melbourne_Meeting). We also hope it will inform the May HVP Planning Meeting.
Backup machinery of yeast transcriptional regulatory network
Authors: Sengupta Dhriti , Kundu Sudip 
Published: July 2019

AbstractSeveral studies have suggested the existence of backup machinery of transcriptional regulatory networks (TRNs). Here, we have quantified the backup machinery of yeast gene's TRNs under five different conditions in terms of alternate paths and have revealed that a statistically significant (p<0.0001) stronger backup is maintained for endogenous processes (ENPs) than exogenous processes (EXPs). A number of biologically important genes (SUC2, MF(ALPHA)2, CLN2 etc) are observed that maintain a higher backup. Hub and random transcription factor (TF) knockouts in TRNs have showed ENPs are more robust to deletion than EXPs. While higher average connectivity of TFs in EXPs than ENPs can't explain the higher robustness in ENPs, we have found that the later have a densely interconnectedness explaining their specialized architecture that may have evolved due to evolutionary pressure. Some non-hub TFs identified here are more likely to be essential, and if not essential, have a larger impact on fitness.
Experimental and theoretical study of DNA oxidation
Authors: Song Yuanzhi 
Published: July 2019

AbstractThe electrochemical oxidation of DNA and bases at a glassy carbon electrode were investigated using cyclic and square-wave voltammetry analysis. The predicted oxidative potentials for DNA and bases using DFT method (B3LYP) are in agreement with the experimental ones.The DNA oxidation ascribes to N-protonated guanine and adenine. The calculated oxidative peaks indicate that the initial potential of DNA oxidation is around 0.432V for N-protonated guanine and 0.368V (vs.hydrogen standard electrode) at pH 7.00, and DNA as well as bases in acidity solution are more stable than those in alkalescent solution.
Biogeographic relationships among deep-sea hydrothermal vent faunas at global scale
Authors: Bachraty Charleyne , Legendre Pierre , Desbruyères Daniel 
Published: July 2019

AbstractThe discovery of deep-sea hydrothermal vent fauna, kilometers deep in the oceans, is a great achievement of 20th-century marine biology. The deep-sea hydrothermal food web does not directly depend on the sun energy. Vent communities rely primarily on trophic associations between chemoautotrophic bacteria and consumers. A small number of endemic taxa are adapted to this highly toxic environment distributed along ridge crests. Where they appeared and how they dispersed is among the important questions ecologists must answer. Here, by statistical analysis of the most comprehensive data base ever assembled about deep-sea hydrothermal fauna, we delineate six major hydrothermal provinces in the World Ocean, then we identify five significant dispersal flows between adjacent provinces and derive a hypothesis about the center from which that fauna has dispersed to the oceanic ridges of the world. Our data-driven conclusion can be tested by phylogenetic studies and completed by surveys of less explored fields.
Seeing faces: evidence suggesting cortical disinhibition in the genesis of visual hallucinations.
Authors: Iaria Giuseppe , Fox Christopher , Barton Jason 
Published: July 2019

AbstractThe neural mechanisms responsible for triggering visual hallucinations are poorly understood. Here, we report a unique patient whose hallucinations consist exclusively of faces, and which could be reliably precipitated by looking at trees. Using functional Magnetic Resonance Imaging (fMRI), we found that, while face hallucinations was associated with increased neural activity in a number of cortical regions, including low-level visual areas, there was significant decreased activity in the right fusiform face area, a region that is empirically defined by increase activity during veridical perception of faces. These findings indicate key differences in how hallucinatory and veridical perceptions lead to the same phenomenological experience of seeing faces, and are consistent with the hypothesis that hallucinations may be generated by decreased inhibitory inputs to key cortical regions, in contrast to the excitatory synaptic inputs underlying veridical perception.
Integrated disease management using environmental control in tea fields
Authors: Tomihama Tsuyoshi , Toshiyuki Nonaka , Yatsuka Nishi , Kei Arai 
Published: July 2019

AbstractThe occurrence of plant disease depends on interactions between the host plant, a pathogen, and the environment in a dynamic called "the disease triangle". Bacterial shoot blight (BSB) disease, caused by Pseudomonas syringae pv. theae (Pst), is a major bacterial disease of tea plants in Japan and substantially reduces tea productivity. BSB mainly occurs in the low-temperature season, and lesion formation by Pst is enhanced by both low temperature and the presence of ice nucleation-active Xanthomonas campestris (INAX), which catalyses ice formation at -2 to -4^o^C and is frequently co-isolated with Pst from tea plants^5^. Low temperature is thus the most important environmental factor to influence the incident; however, the effects of environmental controls in fields on the occurrence of the disease are poorly understood. Here we show that the natural incidence of BSB in the field is closely related to low temperatures in late autumn. Frost protection in late autumn, which protected tea plants against extremely low temperatures, significantly decreased the incidence of BSB, and frost protection combined with bactericide application held the incident under the economic threshold level. Our data indicate that environmental control in the field based on microbial interactions in the host offers a new strategy for plant disease control using integrated plant disease management based on the disease triangle concept.
Systems biology of energetic and atomic costs in the yeast transcriptome, proteome, and metabolome
Authors: Barton Michael , Papp Balazs , Delneri Daniela , Oliver Stephen , Rattray Magnus , Bergman Casey 
Published: July 2019

Abstract
Background:
Every protein has a variable atomic and energetic cost to the cell based on the synthesis of its constituent amino acids. Quantifying the cost of amino acid synthesis is challenging, however natural selection is expected to favour the use of proteins whose constituents are cheaper to produce in terms of energetic and atomic cost.

Results:
We develop a systems biology approach to estimate the cost of amino acid synthesis based on genome-scale metabolic models, and directly investigate the effects of the cost of amino acid synthesis on transcriptomic, proteomic and metabolomic data in Saccharomyces cerevisiae. We used our two new and six previously reported measures of amino acid cost in conjunction with codon usage bias, tRNA gene number and atomic composition to identify the factors that predict transcript, protein and free amino acid levels in the yeast cell. While most previously reported cost measures are highly correlated, we find that our systems approach to formulating the cost of amino acid synthesis produces a novel measure of cost, which explains similar levels of variation in gene expression. Regardless of the measure used, the cost of amino acid synthesis is weakly associated with transcript and protein levels, independent of codon usage bias. In contrast, energetic costs explain a large proportion of variation in levels of free amino acids.

Conclusions:
In the economy of the yeast cell, the cost of amino acid synthesis correlates with transcript and protein levels to a lesser degree than translational optimisation, whereas atomic and energetic cost plays a much larger role in explaining levels in free amino acids. However, as there appears to be no single currency to compute the cost of amino acid synthesis, a systems approach is necessary to uncover the full effects of amino acid biosynthetic cost in complex biological systems that vary with cellular and environmental conditions.
Tautomeric Equilibria Studies by Mass Spectrometry
Authors: Allegretti Patricia , Schiavonni Mercedes , Castro Eduardo , Furlong Jorge 
Published: July 2019

AbstractTautomerism in organic chemistry has been extensively studied in condensed phase by spectrometric methods, mainly by IR and NMR techniques. Mass spectrometry studies start 40 years ago but just recently it has been recognized the importance of the mass spectral data for the study of tautomerism in the gas phase.Mass spectrometry can provide valuable information in regard to tautomeric equilibria when studying mass spectra among the members of different families of organic compounds.The relevance of the mass spectral data resides on several facts but there are two that are of key importance:1-	Mass spectral fragmentation assignments should be tautomer specific since the corresponding abundances ratios are supposed to be correlated to the keto/enol contents.2-	Ionization in the ion source is supposed to have no effect on the position of the equilibrium so that the results reflect the tautomers content in the gas phase previous to ionization.Some of the carbonylic compounds do not exhibit noticeable tautomerism so the fragment abundances assigned to the enol form is very low or not measurable. Since enolization is more noticeable in the case of thio-derivatives (which correlates adequately with the oxygenated analogues), the study of their mass spectra is an interesting choice to reach some degree of generalization. In addition, experimental findings are supported by semiempirical theoretical calculations, which probed to be adequate not only for supporting tendency correlations among the members of a compound family but also to calculate heats of tautomerization in gas phase.Reports using mass spectrometry for tautomerism are becoming less common. One of the reasons is that now it would appear that the interpretation of MS results is not as straightforward as it was once believed, even though in a recent review it was written that: “Mass spectrometry is the most informative and practical method for studying and identifying tautomers in the gas phase” [1]. In fact, mass spectrometry seems to be very informative for studying and identifying tautomers, because in this case external factors like solvents, intermolecular interactions, etc., can be excluded by transferring the tautomeric system into gas phase, where the process becomes truly unimolecular [1].This review covers the study of Tautomerism by Mass Spectrometry in the last four decades.