bluuebunny/crossref_metadata_2025_split huggingface dataset:
Suppression of cell cycle progression by Jun dimerization protein (JDP2) involves down-regulation of cyclin A2
Authors: Pan Jianzhi , Nakade Koji , Masuzaki Satoko , Hasegawa Hitomi , Huang Yu-Chang , Murata Takehide , Yoshiki Atsushi , Yamaguchi Naoto , Obata Yuichi , Yokoyama Kazunari 
Published: July 2019

AbstractWe report here a novel role for Jun dimerization protein-2 (JDP2) as a regulator of the progression of normal cells through the cell cycle. To determine the role of JDP2 in vivo, we generated Jdp2 knock-out (Jdp2KO) mice by targeting exon 1 to disrupt the site of initiation of transcription. The healing of wounded skin of Jdp2KO mice proceeded more rapidly than that of control mice and more proliferating cells were found at wound margins. Fibroblasts derived from embryos of Jdp2KO mice proliferated more rapidly and formed more colonies than wild-type fibroblasts. JDP2 was recruited to the promoter of the gene for cyclin A2 (ccna2) at a previously unidentified AP-1 site. Cells lacking Jdp2 had elevated levels of cyclin A2 mRNA. Moreover, reintroduction of JDP2 resulted in repression of transcription of ccna2 and of cell cycle progression. Thus, transcription of the gene for cyclin A2 appears to be a direct target of JDP2 in the suppression of cell proliferation.
Persistence of Edge-State in Stacked Graphene and Nano-Graphene Materials
Authors: Harigaya Kikuo 
Published: July 2019

AbstractNano-carbon materials are investigated intensively. In this paper, the edge-state in nanographene materials with zigzag edges is studied theoretically. In particular, while the inter-layer interactions are considered, we prove that edge states exist at the energy of the Dirac point in the doubly stacked nanographene, and in the case of the infinitely-wide lower layer case. This property applies both for the A-B and A-C stackings.
Enzyme activity and dynamics in near-anhydrous conditions
Authors: Lopez Murielle , Kurkal-Siebert Vandana , Dunn Rachel , Tehei Moeava , Finney John , Smith Jeremy , Daniel Roy 
Published: July 2019

AbstractWater is widely assumed to be essential for life 1, although the exact molecular basis of this requirement is unclear 2-4. Water facilitates protein motions 5-9 and although enzyme activity has been demonstrated at low hydrations in organic solvents 10-13, such non-aqueous solvents may allow the necessary motions for catalysis. To examine enzyme function in the absence of solvation and bypass diffusional constraints we have tested the ability of an esterase to catalyse alcoholysis as an anhydrous powder, using a closed reaction system in which the substrates and products of the enzyme reaction are gaseous 14-15, and where the water content can be well defined 16. At hydrations equivalent to 3 (&177;2) molecules of water per molecule of enzyme, activity is observed that is several orders of magnitude greater than non-enzymatic catalysis. Neutron spectroscopy indicates that the fast (&8804;nanosecond) global anharmonic dynamics of the anhydrous functional enzyme are heavily suppressed. The results indicate that neither hydration water nor the solvent-activated fast anharmonic dynamics are required for enzyme function. An implication of these results is that one of the essential requirements of water for life may lie with its role as a diffusion medium rather than any of its more specific properties.
Roman roads: The hierarchical endosymbiosis of cognitive modules
Authors: Wallace Rodrick 
Published: July 2019

AbstractSerial endosymbiosis theory provides a unifying paradigm for examining the interaction of cognitive modules at vastly different scales of biological, social, and cultural organization. A trivial but not unimportant model associates a dual information source with a broad class of cognitive processes, and punctuated phenomena akin to phase transitions in physical systems, and associated coevolutionary processes, emerge as consequences of the homology between information source uncertainty and free energy density. The dynamics, including patterns of punctuation similar to ecosystem resilience transitions, are largely dominated by the availability of 'Roman roads' constituting channels for the transmission of information between modules.
The Role of Neuregulin 1 in Schizophrenia: A Bioinformatics Approach
Authors: Dias Alvaro , Maracaja-Coutinho Vinicius , Lopo Artur 
Published: July 2019

Abstract*Context:* Notwithstanding the great number of studies on the etiology and pathophysiology of schizophrenia, both issues remain far from being fully understood. Schizophrenia seems to be related to several biochemical abnormalities, which point to a multi-factor etiology and pathophysiology, as well as to the perspective that several etiologically diverse disorders might coexist within this nosographic entity. On the other hand, identical twins reveal a high concordance for schizophrenia. From that standpoint, the perspective that structurally-related proteins may play an important and yet non-deterministic role seems attractive. Among these proteins, it is suggestive that Neuregulin 1 exerts a pivotal role.
Objective:
This paper aims to uncover the most prominent relations that Neuregulin 1 establishes with schizophrenia. *Method:* Several bioinformatical methods are used in order to present: 1. A visual representation of Neuregulin 1’s main molecular pathways, associated with a discussion about their importance to schizophrenia research; 2. A new heatmap of Neuregulin 1 and its receptor’s expression in brain tissues most relevant to the understanding of schizophrenia, created after the development of new R programming scripts (described elsewhere), which facilitate the analysis of gene expression profiles in public datasets; 3. A conceptual map of the literature retrieved using the keywords ‘Neuregulin 1 and human’ in PubMed, followed by a discussion of the most relevant sub-topics.

Results:
Neuregulin 1 polymorphisms affect several brain tissues and contribute to the etiology and pathophysiology of schizophrenia. Suggestively, Neuregulin 1 partially bridges the 'molecular gap' that schizophrenia establishes in relation to bipolar disorder and Alzheimer disease, which involves genes that affect several brain networks, at the same time that they are highly dependent on noxious environmental variables to be triggered.
Application of space technology to the design of sustainable settlements in hot deserts: Bioregenerative life support systems
Authors: Polyakov Yuriy , Musaev Ibrahim , Polyakov Sergey 
Published: July 2019

AbstractWater scarcity in hot deserts, which cover about one-fifth of the Earth’s land area, along with rapid expansion of hot deserts into arable lands is one of the key global environmental problems. This paper proposes and substantiates an interdisciplinary approach to sustainable settlements in hot deserts using the accomplishments in the design of closed bioregenerative life support systems (CBLSS) for beyond-Earth (Lunar, Martian) settlements. Extensive space technology experience in the design of CBLSSes, which simultaneously produce food, water, nutrients, and fertilizers, process wastes, and revitalize air, has been analyzed and systematized with application to hot deserts, which represent extreme habitats with high input of solar energy, poor organic life, and nutrient/mineral-rich soils. A general flow diagram and design principles for hot-desert bioregenerative life support systems (BLSS), which may be considered as solar-powered "bioreactors" with accelerated cycles of carbon and nutrients, are formulated. Research and design guidelines for BLSS solar energy utilization, accelerated food production, water production and recycling, and wastes processing are suggested. Environmental and socioeconomic benefits of building hot-desert BLSSes are discussed.
Evaluation of the Cell Ontology (CL)
Authors: Cowell Lindsay 
Published: July 2019

AbstractAn ontological representation of the entities relevant to biological research is urgently needed. The cell ontology developed by Bard and colleagues (CL) (Bard et al. 2005) makes a significant contribution towards fulfilling this need by providing an ontology of cell types. The CL has already proven useful for data annotation (e.g. Grumbling et al. 2006), although the ontology’s potential utility goes well beyond that specific application. For example, using the number of distinct cell types in an organism as a measure of biological complexity, Vogel and Chothia (2006) compared the proteomes of 38 organisms of varying complexity and identified patterns in the evolution and expansion of protein domain superfamilies. This work has implications for some of the fundamental questions in biology, such as understanding the processes by which physiology becomes more intricate, new cell types arise, and biological complexity increases. While Vogel and Chothia did not yet utilize the CL for this work, they cite Bard et al. (2005) and describe the ontology’s value for improving and extending their analysis. Thus, in addition to its great utility for database annotation, the CL has the potential to play a significant role in basic scientific inquiry.The prospect of using the CL (and other ontologies) for this type of scientific research is extremely exciting but also imposes requirements on the level of formal rigor applied in ontology development, on the adequacy of the ontology as a representation of reality, and on its adherence to community standards of best practice. It is with these things in mind that I examined the CL to determine whether any revision would be required before my research group could use it for scientific research.After carefully evaluating the CL, my overall impression is that it does not possess the rigor and exactness required of a reference ontology. Furthermore, the problems I see are significant enough that it would be difficult for my research group to use the CL as our application ontology. While some of the problems could be resolved by changing a relation or rewriting a definition, others would require careful rethinking of the ontology’s foundation, because they involve the scope and organizing principle of the ontology as a whole.
Evaluation of CD4+ T Cells in HIV Patients Presenting with Malaria at the University of Ilorin Teaching Hospital Nigeria
Authors: Agbede Olajide , Ajiboye Temitope , Kolawole Olatunji , Babatunde Samuel , Odeigha Louis 
Published: July 2019

AbstractCD4 count is an important immunological marker of disease progression in HIV seropositive patients. This study was carried out to determine the effect of malaria or fever of unknown origin on the population of CD4+ T lymphocytes of HIV seropositive patients attending the highly active antiretroviral therapy (HAART) clinic of the University of Ilorin Teaching Hospital, Ilorin, Nigeria. 36 subjects were selected for this study. Ongoing history of fever was used as a case definition for malaria and malaria was confirmed from microscopic examination of thick and thin film of blood sample obtained from the patients during presentation with fever. The CD4 count was evaluated during presentation of fever and post-fever using flow cytometry. There was significant decrease in CD4 count of the patients. However, upon classifying the patients into 2 groups - those that returned to the clinic after a week and those that returned after a month - a significant increase in CD4 count was noticed in the group that returned after a week, while a significant decrease was noticed in the group that returned after a month (at p value of 95%). Further classification of the patients based on presence of malaria parasite, and body temperature resulted in varying effects on CD4 count post-fever (in the general group, 27 were positive for malaria parasites. Of these 27, there was an increase in CD4 count in 9 (33.3%). However in the group that returned after a week, all 6 (100%) that were positive for malaria parasites showed increase in CD4 count. Five (26.3%) of the 19 patients that had body temperature within the range of 35.5-37.4^o^C showed an increase in CD4 count, while 7 (41.2%) the 17 patients that had body temperature of 37.5^o^C and above showed an increase in CD4 count. The results led to the conclusion that while some components of the immune response to malaria could strengthen the immune system of HIV seropositive patients by increasing their CD4 count, other components will suppress their immunity by decreasing their CD4 count, accelerating the progression to AIDS.
Quantification of growth hormone in serum by isotope dilution mass spectrometry
Authors: Arsene Cristian , Henrion André , Diekmann Nina , Manolopoulou Jenny , Bidlingmaier Martin 
Published: July 2019

AbstractInter-assay variation of antibody based routine tests is hampering comparability of measurement results for growth hormone (GH) between different laboratories and decision making in clinical practice. Here it is demonstrated, that quantification of GH by isotope dilution mass spectrometry (IDMS) constitutes a way to precise and reliable results which can be referred to in evaluation of performance of commercial test kits. With the IDMS method developed, tryptic cleavage products YSFLQNPQTSLCFSESIPTPSNR (T6) and LEDGSPR (T12) of GH are quantified by LC/MS-MS using the isotopically labeled forms of the peptides as internal standards. The GH cleavage fragments are obtained by whole-serum tryptic proteolysis and then extracted from the resulting mixture by semi-preparative reversed phase liquid chromatography followed by strong cation-exchange chromatography. Method validation basing on recovery of recombinant 22 kDa GH spiked to blank serum in defined amounts covering the intended concentration range (3-30 µg/L) would yield mean recoveries of 101.6% (100.7%), standard deviations of 2.5% (2.4%) and combined uncertainties (u~c~) of 3.0% (2.5%) if quantifying T6 (T12) as GH derived fragments, while the LOQ were 1.7 µg/L (2.7 µg/L). Potential to acquisition of reference values is exemplified by application to serum materials used in a recent quality assessment exercise for routine laboratories.
Protein Data Integration through Ontologies
Authors: Sidhu Amandeep 
Published: July 2019

AbstractIn this paper, we consider the challenges of information integration in proteomics from the prospective of researchers using information technology as an integral part of their discovery process. Specifically, data integration, meta-data specification, data provenance and data quality are discussed here. Here we review existing protein data integration methods and propose the use of common vocabulary for protein data integration using ontologies.
Biospheric context of Siberian development
Authors: Alexandrov Georgii , Inoue Gen , Matsunaga Tsuneo 
Published: July 2019

AbstractRecent publications on human appropriation of Net Primary Production (NPP) raise the question of how much of the biosphere’s productivity we can appropriate in a sustainable way. This article brings the issue into the context of Siberian development. In contrast to many other regions of the world, the population density in Siberia is still very low as compared to the NPP supplied by regional ecosystems. Hence, it is not too late to raise the question on how much of the NPP supplied by Siberian ecosystems we can appropriate in a sustainable way.
We Need A Web For Data
Authors: Wilbanks John 
Published: July 2019

AbstractThe Web has many forums for sharing personal data, but not for scientific data and not in a way that allows the data to be accessed by "machines as users." A Web of data could add tremendous value by integrating disparate disciplines or conduct data-driven queries. Doing this is very complex and requires more robust standards than currently exist. The intended user for most data is not a person; it is a software application that can manipulate the data into something useful for humans. Such software could be "search engines, analytic software, visualization tools, database back ends, and more." This need creates a much different requirement for standards than those that were developed for displaying web data to people. Data software needs a much greater understanding of context and that context has to be supplied alongside the data either through direct integration with the data or linking to a description of it in a persistent and accessible location. Data interoperability must be addressed at the beginning of developing systems because it is significantly harder and costlier to make these connections after both systems have separately implemented non-standardized data collections. Data interoperability must address three levels: legal (intellectual property rights), technical (computer languages and formats), and semantic (meaning of the data). The technical level is the furthest along, with the Semantic Web technologies. Getting scientists to agree on the semantic level could be nearly impossible. The legal level has the greatest opportunity by putting the data into the public domain. There are already precedents for this with genome data and the International Visual Observatory. Putting data into the public domain simplifies the implementation of the technical level. Libraries and publishers in the scholarly publishing community should lead the web of data initiative as they can ensure the connection, curation, and preservation needed. The NSF mandated data sharing could result in funding opportunities to build the web of data. But all involved must be in agreement not to replicate the copyright-controlled model that currently exists with books and journals.
Natural Selection of Paths in Networks
Authors: Fernando Chrisantha , Vasas Vera , Szathmáry Eörs , Husbands Philip 
Published: July 2019

AbstractWe present a novel algorithm that exhibits natural selection of paths in a network. If each node and weighted directed edge has a unique identifier, a path in the network is defined as an ordered list of these unique identifiers. We take a population perspective and view each path as a genotype. If each node has a node phenotype then a path phenotype is defined as the list of node phenotypes in order of traversal. We show that given appropriate path traversal, weight change and structural plasticity rules, a path is a unit of evolution because it can exhibit multiplicative growth (i.e. change it’s probability of being traversed), and have variation and heredity. Thus, a unit of evolution need not be a spatially distinct physical individual. The total set of paths in a network consists of all possible paths from the start node to a finish node. Each path phenotype is associated with a reward that determines whether the edges of that path will be multiplicatively strengthened (or weakened). A pair-wise tournament selection algorithm is implemented which compares the reward obtained by two paths. The directed edges of the winning path are strengthened, whilst the directed edges of the losing path are weakened. Edges shared by both paths are not changed (or weakened if diversity is desired). Each time a node is activated there is a probability that the path will mutate, i.e. find an alternative route that bypasses that node. This generates the potential for a novel but correlated path with a novel but correlated phenotype. By this process the more frequently traversed paths are responsible for most of the exploration. Nodes that are inactive for some period of time are lost (which is equivalent to connections to and from them being broken). This network-based natural selection compares favourably with a standard pair-wise tournament-selection based genetic algorithm on a range of combinatorial optimization problems and continuous parametric optimization problems. The network also exhibits memory of past selective environments and can store previously discovered characters for reuse in later optimization tasks. The pathway evolution algorithm has several possible implementations and permits natural selection with unlimited heredity without template replication.
Plasma amino acid profile is altered by visceral fat accumulation and is a predictor of visceral obesity in humans
Authors: Tanaka Takayuki , Ishizaka Yuko , Mitushima Toru , Tani Mizuki , Toda Akiko , Toda Eiichi , Okada Minoru , Yamamoto Hiroshi , Yamakado Minoru 
Published: July 2019

Abstract
Background:
The plasma amino acid profile can be a useful indicator in clinical settings because it changes in response to various metabolic alternations. However, the association between the plasma amino acid profile and body fat accumulation has not been evaluated in humans.

Objective:
This study aimed to relate plasma amino acids to visceral fat accumulation in humans because excess visceral fat raises the odds ratio of developing metabolic syndrome.

Design:
A total of 1,449 subjects (985 males and 464 females) who had undergone a comprehensive health screening were enrolled in this study. The visceral fat area (VFA) was determined in each subject using CT imaging. Subjects were then divided into two groups according to VFA: high-VFA (&8805;100 cm2, n=867) and low-VFA (&lt;100 cm2, n=582). The plasma amino acid profile was analyzed together with other metabolic valuables and then compared between the two groups using uni- and multivariate analyses.

Results:
As the degree of visceral fat accumulation increased, plasma concentrations of several amino acids changed significantly. Glu, Val, Leu, Ile, Tyr, Ala, Phe, Pro, Lys, Orn, Trp, Met, His and alpha-aminobutyric acid (ABA) levels were significantly higher in the high-VFA group compared to the low-VFA group, whereas the levels of Gly, Ser, Gln and Asn were significantly lower. To evaluate the potential of using amino acids as an indicator of VFA, a discriminant analysis was conducted with the multivariate logistic regression analysis &quot;AminoIndex&quot;, and the ROC curve was calculated. The resulting &quot;AminoIndex&quot; exhibited an area under the ROC curve of 0.81 (95% confidence interval; 0.78 to 0.83), with higher sensitivity and specificity by 80% and 65%, respectively.

Conclusions:
The plasma amino acid profile changes depending on visceral fat content and can be used as a marker for diagnosing elevated visceral obesity in humans.
Are men evolutionarily wired to love the &quot;Easy&quot; buttons?
Authors: Trofimova Irina 
Published: July 2019

AbstractMen's drive for group control and power appears to be an evolutionary inheritance, but it is females, and not males, who developed better abilities for prolonged control and group interaction while males have higher rates of ADHD and autism. This contradictory allocation of sex-related abilities describes the observable behavior, but not the internal meaning attribution leading to the motivation of men and women. Our study in Canada, China and Russia shows that men estimate power- and status-related concepts in significantly more positive terms than women, but give significantly more negative estimations to work-related and reality-related concepts. Men also have a consistent tendency to estimate concepts as less real (even "Reality"), less complex (even "Complexity"), less organized (even "Order"), and more stable (even time-related concepts), than women. These results are interpreted in terms of the evolutionary characteristic of the male sex for irrelevance/redundancy pruning of excessive complexity in human activities.