bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nanofiber fabrication in a temperature and humidity controlled environment for improved fibre consistency
Authors: Hardick Oliver , Stevens Bob , Bracewell Daniel 
Published: July 2019

AbstractTo fabricate nanofibers with reproducible characteristics, an important demand for many applications, the effect of controlled atmospheric conditions on resulting electrospun cellulose acetate (CA) nanofibers was evaluated for temperature ranging 17.5 - 35°C and relative humidity ranging 20% - 70%. With the potential application of nanofibers in many industries, especially membrane and filter fabrication, their reproducible production must be established to ensure commercially viability.Cellulose acetate (CA) solution (0.2 g/ml) in a solvent mixture of acetone/DMF/ethanol (2:2:1) was electrospun into nonwoven fibre mesh with the fibre diameter ranging from 150nm to 1µm.The resulting nanofibers were observed and analyzed by scanning electron microscopy (SEM), showing a correlation of reducing average fibre diameter with increasing atmospheric temperature. A less pronounced correlation was seen with changes in relative humidity regarding fibre diameter, though it was shown that increased humidity reduced the effect of fibre beading yielding a more consistent, and therefore better quality of fibre fabrication.Differential scanning calorimetry (DSC) studies observed lower melt enthalpies for finer CA nanofibers in the first heating cycle confirming the results gained from SEM analysis. From the conditions that were explored in this study the temperature and humidity that gave the most suitable fibre mats for a membrane purpose were 25.0°C and 50%RH due to the highest level of fibre diameter uniformity, the lowest level of beading while maintaining a low fibre diameter for increased surface area and increased pore size homogeneity. This study has highlighted the requirement to control the atmospheric conditions during the electrospinning process in order to fabricate reproducible fibre mats.
Gene therapy of hypoparathyroidism with TheraCyte-encapsulated stem cells
Authors: Choulu Fong , Huang Shun-Chen , Hsieh Kun-Chou , Chi Shun-Yu , Hung Pei-Hua , Wang Feng-Sheng 
Published: July 2019

AbstractThe parathyroid hormone (PTH) (1-34) gene was inserted into a pcDNA3 promoter and E. coli competent cells were used to amplify the cDNA. C3H/10T1/2 stem cells were transfected with PTH (1-34) cDNA using Lipofectamine reagents. After G418 treatment live cells at a density of 4x107 were loaded onto a TheraCyte unit. After parathyroidectomy, rats were either the implanted with 4x107 TheraCyte-encapsulated cells (group A), subcutaneously injected with 4x107 live cells containing PTH (1-34) cDNA (group B) or injected with nothing (group C).Serum levels of calcium, phosphorus and PTH (1-34) were measured at baseline, 1 month, 2 months, 3 months and 4 months after therapy. Immunohistochemical staining and RT-PCR were performed to find PTH (1-34)-positive cells and to detect PTH (1-34) mRNA.Serum calcium and PTH (1-34) levels were significantly higher in group A than in group B or C. PTH (1-34)-positive cells were found in the TheraCyte group 4 months after implantation. PTH (1-34) mRNA was detected in stem cells 48 hr after transfection and also in stem cells after transfection and 72 hr after G418 treatment.Implantation of the TheraCyte-encapsulated stem cells, which were tranfected with PTH (1-34) cDNA can treat hypoparathyroidism.
Production of Transgenic Cloned Miniature Pigs with Membrane-bound Human Fas Ligand (FasL) by Somatic Cell Nuclear Transfer
Authors: Seol Jae Goo , Kim Soo Hyun , Jin Dong-Il , Hong Seung Pyo , Yoo Ji Yeon , Choi Ki Myung , Park Young Chul , Yun Yun Jin , Park Kwang Wook , Heo Jae Young 
Published: July 2019

AbstractCell-mediated xenograft rejection, including NK cells and CD8+ CTL, is a major obstacle in successful pig-to-human xenotransplantation. Human CD8+ CTL and NK cells display high cytotoxicity for pig cells, mediated at least in part by the Fas/FasL pathway. To prevent cell-mediated xenocytotoxicity, a membrane-bound form of human FasL (mFasL) was generated as an inhibitor for CTL and NK cell cytotoxicity that could not be cleaved by metalloproteinase to produce putative soluble FasL. We produced two healthy transgenic pigs harboring the mFasL gene via somatic cell nuclear transfer (SCNT). In a cytotoxicity assay using transgenic clonal cell lines and transgenic pig ear cells, the rate of CD8+ CTL-mediated cytotoxicity was significantly reduced in transgenic pig&apos;s ear cells compared with that in normal minipig fetal fibroblasts. Our data indicate that grafts of transgenic pigs expressing membrane-bound human FasL control the cellular immune response to xenografts, creating a window of opportunity to facilitate xenograft survival.
'Kuthiru' and 'Orkayama' – Newly Identified Genetic Resources from Kerala, India for Salinity Tolerance in Indica Rice
Authors: Taliyil Vanaja , Mammootty K 
Published: July 2019

AbstractExistence of genetic variability for salt tolerance within species is of paramount importance in crop improvement program. Pokkali land race of Kerala, India is the international donor parent of most of the salinity tolerance breeding programs in rice. Here we report two new genetic resources, ‘Kuthiru’ and ‘Orkayama’ for salinity tolerance, from Kaipad saline tracts of Kerala. They differ in their morphological, physico-chemical characteristics and cooking qualities. Panicles of these cultivars are long with bold grains. Duration of ‘Kuthiru’ is 110 -120 days, and that of ‘Orkayama’ is 135 -140 days. Molecular analysis revealed that the salinity tolerance mechanism of both land races differ from each other. Using these land races for the first time in breeding program, as donors for salinity tolerance, two saline tolerant non-lodging high yielding red rice varieties, ‘Ezhome –1’ and ‘Ezhome -2’ were commercially released for cultivation in Kaipad rice tract of Kerala state, India in 2010.
Annual population rhythm of Anopheles mosquitoes in Indian subcontinent
Authors: Bhardwaj Mohit , Bharadwaj Leena , Trigunayat Kritika , Trigunayat Madan Mohan 
Published: July 2019

AbstractSeveral organisms show a rhythm based behavior in their life. Mosquitoes are surviving successfully since ancient time on earth while lots of biological creatures have been extinct. Thus it is interesting to study their population load. Climatic conditions affect mosquito population significantly so on the basis of malaria cases their population is estimated in present study in Indian geographical scenario. In this study it was found that their annual population load show a scientific rhythm. A schematic wave form representation is also presented here to show mosquito population load. This study will be helpful in malaria vector eradication and health care policies.
EvoIO: Community-driven standards for sustainable interoperability
Authors: Stoltzfus Arlin , Cranston Karen , Lapp Hilmar , McKay Sheldon , Pontelli Enrico , Vos Rutger , Cellinese Nico 
Published: July 2019

AbstractInteroperability is the property that allows systems to work together independent of who created them, or how or for what purpose they were implemented. It is crucial for aggregating data from different online resources and for integrating different kinds of data. Interoperability is based on effective standards that become and remain broadly adopted. We argue that to develop and apply such standards for evolutionary and biodiversity data sustainably, we need a community-driven, open, and participatory approach. With the goal to build such an approach, the EvoIO collaboration emerged in 2009 from several NESCent-sponsored activities. EvoIO aims to be a nucleating center for developing, applying and disseminating interoperability technology that connects and coordinates between stakeholders, developers, and standards bodies.Members of the EvoIO group have harnessed a variety of collaborative events to successfully build an initial stack of interoperability technologies that is owned by the community and open to participation. The stack addresses syntax, semantics, and programmable services, and at present includes the following components: NeXML (http://nexml.org), a NEXUS-inspired XML format that is validatable yet extensible; CDAO (http://www.evolutionaryontology.org), an ontology of comparative data analysis formalizing the semantics of evolutionary data and metadata; and PhyloWS (http://evoinfo.nescent.org/PhyloWS), a web- services interface standard for querying, retrieving, and referencing phylogenetic data on the web. Beyond demonstration prototypes, reference implementations of EvoIO stack technologies are starting to appear in production use. Aside from producing such information artefacts, EvoIO devotes much of its energy to applying principles of communication and organization that result in open and inclusive processes of community science. One of the key tools employed by EvoIO is the hackathon event format. Hackathons are highly collaborative, hands-on working meetings that catalyze practical innovation, train researchers, and foster cohesion as well as a sense of shared ownership in the results. In summary, we find that broad community participation, buy-in, and ownership are critical for developing interoperability in a sustainable fashion, and there are approaches and tools that can foster these effectively.
Top-down and bottom-up informatics: who has the high ground?
Authors: Smith Vincent , Roberts Dave 
Published: July 2019

AbstractRecent years have seen the emergence of several major initiatives supporting the development of biodiversity informatics infrastructures. In Europe examples include: EDIT – the European Distributed Institute of Taxonomy; LifeWatch – a biodiversity analytical platform integrating observatories, databases, processing and computational capacity; and SYNTHESYS – funding researcher access to a network of taxonomic collections, laboratories and libraries. These European projects alone represent a spend of approximately 35 Million Euros, with funding contingent on the collaboration of numerous geographically dispersed institutional partners. In this presentation we will review the major informatics products of these initiatives; the different development models used in their construction; and levels of user engagement that provide an indication of their relative success.A key outcome of these initiatives is the bottom-up emergence of Virtual Research Environments (VRE’s) such as the Scratchpad project ("http://scratchpads.eu":http://scratchpads.eu), the EDIT Cyberplatform ("http://wp5.e-taxonomy.eu/":http://wp5.e-taxonomy.eu/), and CATE ("http://www.cate-project.org/":http://www.cate-project.org/). These tools enable real-time collaboration and dissemination of biodiversity information while simultaneously affording new opportunities for data stewardship, curation, and data mining. Although highly experimental, these environments offer an alternative vision for the practice of biodiversity research that challenges the primacy of traditional publishing as the end point in scholarly communication. Inspired by discourses in the 'Free/Open Source Software' and 'Creative Commons' movements, these tools support the notion of 'Open Science' with its advocacy of more open scientific knowledge production and publishing processes. These VRE’s have the potential to be used as instruments of scientific research, blending social and technical solutions to address the challenges that are otherwise insurmountable through individual efforts. The maturity of these tools is dependent upon greater reliability, especially in the data services on which they depend, and through reduced duplication of developer effort. This will deliver an increasing body of users that can have confidence and trust in the systems they use, and who will benefit from the network effects of an enlarged user community. Delivering this requires greater top-down cooperation and integration of our national funding agencies, supporting bottom-up multinational collaborative efforts amongst our research communities.
Biological taxonomy and ontology development: scope and limitations
Authors: Franz Nico , Thau David 
Published: July 2019

AbstractThe prospects of integrating full-blown biological taxonomies into an ontological reasoning framework are reviewed. We contrast the common usage of a static 'snapshot' hierarchy in ontological representations of taxonomy with a more realistic situation that involves dynamic, piece-meal revisions of particular taxonomic groups and requires alignment with relevant preceding perspectives. Taxonomic practice is characterized by a range of phenomena that are orthogonal to the logical semantic background from which ontological entities and relationships originate, and therefore pose special challenges to ontological representation and reasoning. Among these phenomena are: (1) the notion that there is a single phylogenetic hierarchy in nature which taxonomy can only gradually approximate; (2) the evolvability of taxa which means that taxon-defining features may be lost in subordinate members or independently gained across multiple sections of the tree of life; (3) the hybrid approach of defining taxa both in reference to properties (intensional) and members (ostensive) which undermines the individual/class dichotomy sustaining conventional ontologies; (4) the idiosyncratic yet inferentially valuable usage of Linnaean ranks; (5) the indelible and semantically complex 250-year legacy of nomenclatural and taxonomic changes that characterizes the current system; (6) the insufficient taxonomic exploration of large portions of the tree of life; and the need to use a sophisticated terminology for aligning taxonomic entities in order to integrate both (7) single and (8) multiple hierarchies. We briefly such how such integration may proceed based on an initial expert alignment of concept relationship and subsequent use of first-order logic algorithms to maximize consistency, reveal implied relationships, and ultimately merge taxonomies. In light of the aforementioned obstacles, we suggest that research along the taxonomy/ontology interface should focus on either strictly nomenclatural entities or specialize in ontology-driven methods for producing alignments between multiple taxonomies. We furthermore suggest that the prospects of developing successful ontologies for taxonomy will largely depend on the ability of the taxonomic expert community to present their phylogenies and classifications in a way that is more compatible with ontological reasoning than concurrent practice. Minimally, this means (1) adopting rigorous standards for linking new core taxonomies to relevant peripheral taxonomies through comprehensive alignments so that their ontological/taxonomic connections are transparent; (2) using lineage-specific ontological standards for phenotype-based accounts of taxa while taking into account the phylogenetic contextuality of phenotypic descriptors; (3) presenting all nomenclatural and taxonomic novelties in an explicit, ontology-compatible format, including intensional and ostensive definitions; and (4) offering comprehensive intensional/ostensive alignments to entities in relevant preceding taxonomies.
Shear stress activation of nitric oxide synthase and increased NO levels in human red blood cells
Authors: Ulker Pinar , Yaras Nazmi , Celik-Ozenci Ciler , Meiselman Herbert , Baskurt Oguz 
Published: July 2019

AbstractSince the discovery of nitric oxide (NO) as a vasoactive molecule, red blood cells (RBC) have been considered to participate in NO-mediated control of the circulation. The classical role attributed to RBC was scavenging of NO, thereby impacting the local bioavailability of this important regulator of vascular tone^1^. RBC have been shown to be a source of NO, primarily via its transport bound to haemoglobin^2, 3^. Under specific conditions, haemoglobin plays an active role in converting NO derivatives (e.g., nitrite) to NO^4, 5^, with this NO originating from RBC being an effective modulator of vascular smooth muscle tone^6^. Interestingly, RBC contain a NO synthase (NOS) protein^7^, can actively synthesize NO using L-arginine as a substrate^8^, and can export NO under appropriate conditions^8, 9^. It has been previously hypothesized that RBC NOS may be activated by shear forces acting on the cell^10^, and we have recently shown that RBC NOS phosphorylation can be enhanced by subjecting RBC in suspension to shearing forces^9^: NO concentration in the suspending medium was increased subsequent to flow of RBC suspensions through five [mu]m pores^11^. We have now directly demonstrated increased RBC NOS activity and intracellular NO levels in immobilized RBC exposed to well-defined fluid shear stress. Immunostaining for serine 1177 phosphorylation and the NO-sensitive fluorescent probe diaminofluorescein were employed. Our results suggest that RBC deformation in constricted vessels may increase NO levels and favor vasodilation, thereby providing an important role for RBC in regulating the circulation.
A Target Restricted Assembly Method (TRAM) for Phylogenomics
Authors: Johnson Kevin , Walden Kimberly , Robertson Hugh 
Published: July 2019

AbstractWhile next generation sequencing technology can produce sequences covering the entire genome, assembly and annotation are still prohibitive steps for many phylogenomics applications. Here we describe a method of Target Restricted Assembly (TRAM) of a single lane of Illumina sequences for genes of relevance to phylogeny reconstruction, i.e. single copy protein-coding genes. This method has the potential to produce a data set of hundreds of genes using only one Illumina lane per taxon.
Gene tree reconciliation: new developments in Bayesian concordance analysis with BUCKy
Authors: Ané Cécile , Dewey Colin , Kotha Satish , Larget Bret 
Published: July 2019

AbstractWhen phylogenetic trees inferred from different genes are incongruent, several methods are available to reconcile gene trees and extract the shared phylogenetic information from the sequence data. Bayesian Concordance Analysis, implemented in BUCKy, aims to extract the vertical signal and to infer clusters of genes that share the same tree topology. The new version of BUCKy includes a quartet-based estimate of the species tree with branch lengths in coalescent units.
Internal conformation of the 'protein folding code' inferred from empirical tertiary structural classifications using Tlusty's topological approach
Authors: Wallace Rodrick 
Published: July 2019

AbstractTlusty's topological arguments regarding the genetic code are applied to the classification of tertiary irregular protein symmetries. The underlying 'protein folding code network' is found to have one major, highly dominant 'spherical' component, a minor attachment handle in the Morse Theory sense, and as many as two or three additional subminor handles.
Generation of directional selectivity by individual thin dendrites in neocortical pyramidal neurons
Authors: Major Guy 
Published: July 2019

AbstractPatterned 2-photon glutamate uncaging and local GABA iontophoresis were used to test, in brain slices, whether basal and oblique dendrites possess the biophysical machinery to contribute to the directional selectivity exhibited by many sensory neocortical neurons. On average, Distal-to-Proximal (DP) sequences of glutamate stimuli along individual dendrites produced ~1.5-fold larger responses than the same stimuli in reverse order (PD). Proximal inhibition consistent with spatially-offset receptive subfields, preceding PD but following DP sequences, enhanced directionality to ~2.1-fold.
Lightning talk: PyPop - a software pipeline for large-scale multilocus population genomics
Authors: Lancaster Alex , Single Richard , Solberg Owen , Nelson Mark , Thomson Glenys 
Published: July 2019

AbstractPyPop (Python for Population Genomics) is an open-source framework for performing large-scale population genetic analyses on multilocus genotype and allele frequency data. It computes tests and measures of Hardy-Weinberg equilibrium (locus-level and individual genotype-level), linkage disequilibrum, and selection, and estimates multi-locus haplotypes. PyPop supplements and extends existing population genetic software incorporating them as modules, modified to accommodate highly polymorphic data, rather than reimplementing them from scratch. It facilitates evolutionary analyses by integrating population genetic statistics within and across populations.Originally developed to analyze the highly polymorphic genetic data of the human leukocyte antigen region of the human genome, PyPop has applicability to any kind of multilocus genetic data. It was the primary platform for evolutionary analysis of data collected for a major NIH-funded collaborative grant that included over 30 laboratories and 200 populations (Lancaster et al., 2007a,b). PyPop has also been successfully used in studies by our group, with collaborators, and in publications by many independent research teams in over 70 peer reviewed papers.PyPop deploys a standard Extensible Markup Language (XML) output format and integrates the results of multiple analyses on various populations that were performed at different times into a common output format that can be read into a spreadsheet. The XML output format allows PyPop to be embedded as part of larger analysis pipelines. It also features an Application Programming Interface (API) allowing functionality to be incorporated into other programs. This lightning talk will focus on recent features of PyPop which include the prefiltering of the input genotype data and the ability to translate arbitrary allele names into full amino acid or nucleotide sequences.All code is made available under the terms of the GNU General Public License (GNU GPL):Homepage: http://www.pypop.org/References:Lancaster, A. K., M. P. Nelson, R. M. Single, D. Meyer, and G. Thomson, 2007a Software framework for the Biostatistics Core of the International Histocompatibility Working Group. In J. A. Hansen, editor, Immunobiology of the Human MHC: Proceedings of the 13th International Histocompatibility Workshop and Conference, volume I. Seattle, WA: IHWG Press, 510-517.Lancaster, A. K., R. M. Single, O. D. Solberg, M. P. Nelson, and G. Thomson, 2007b PyPop update–a software pipeline for large-scale multilocus population genomics. Tissue Antigens 69 Suppl 1:192-7.