bluuebunny/crossref_metadata_2025_split huggingface dataset:
Water and the Biology of Prions and Plaques
Authors: Steel Graham , Wiggins Phillippa 
Published: July 2019

AbstractThis is an attempt to account for the insolubility and/or aggregation of prions and plaques in terms of a model of water consisting of an equilibrium between high density and low density microdomains. Hydrophobic molecules, including proteins, accumulate selectively into stable populations, enriched in high density water, at charged sites on biopolymers. In enriched high density water, proteins are probably partially unfolded and may precipitate out when released. All extracellular matrices contain such charged polymers. Prions, which have been shown to accumulate in soils and clays containing silicates and aluminates also probably accumulate in extracellular matrices. Release of proteins follows hydrolysis of the charged groups by highly reactive high density water. This is normally a slow process but is greatly accelerated by urea. Plaques may form with age and disease because of accumulation of urea and, perhaps, glucose in the blood. This favours precipitation of proteins emerging from matrices, rather than refolding and solution. Dialysis should, therefore, interfere with plaque formation and impede the development of some age-related diseases.
Characterization of Fut10 and Fut11, Putative Alpha-1-3/4 Fucosyltransferase Genes Important for Vertebrate Development
Authors: Patnaik Santosh 
Published: July 2019

AbstractTwo new, putative alpha-1-3/4 fucosyltransferases ([alpha]1-3/4 Fuc-Ts), Fuc-TX and Fuc-TXI, were identified in the vertebrate genome and transcriptome sequence databases through sequence homology-based queries. These proteins have a significant sequence similarity to only [alpha]1-3/4 Fuc-Ts, and possess peptide motifs that are evolutionarily conserved among the known vertebrate [alpha]1-3/4 Fuc-Ts. However, Fuc-TX and Fuc-TXI lack the HH[R/W][D/E] sequence that determines the specificity for type 1 or 2 substrates among the known vertebrate enzymes, and Fuc-TXI proteins do not possess a transmembrane domain. The Fut10 and Fut11 genes that encode these proteins are expressed ubiquitously in the adult mouse and in the mouse embryo throughout development. Though a Fuc-T activity of the mouse proteins could not be detected, Fuc-TXI, but not Fuc-TX, was found to hydrolyze GDP-fucose. The interaction of Fuc-TXI with GDP-fucose was also confirmed by its binding to GDP-hexanolamine. In zebrafish, Fut11 transcripts could be detected during early embryonic development. A knock-down of Fuc-TXI in zebrafish embryos with Fut11-specific antisense morpholino oligonucleotides resulted in malformations of the posterior trunk and tail.
A new potential radiosensitizer: ammonium persulfate modified WCNTs
Authors: Yang Jian-She , Yu Bo-Zhang , Li Wen-Xin 
Published: July 2019

AbstractRadiotherapy plays a very important role in cancer treatment. Radiosensitizers have been widely used to enhance the radiosensitivity of cancer cells at given radiations. Here we fabricate multi-walled carbon nanotubes with ammonium persulfate, and get very short samples with 30-50 nanometer length. Cell viability assay show that f-WCNTs induce cell death significantly. We hypothesize that free radicals originated from hydroxyl and carbonyl groups on the surface of f-WCNTs lead cell damage.
From antenna to antenna: Lateral shift of olfactory memory in bees
Authors: Rogers Lesley , Vallortigara Giorgio 
Published: July 2019

AbstractHoneybees, _Apis mellifera_, readily learn to associate odours with sugar rewards and we show here that recall of the olfactory memory, as demonstrated by the bee extending its proboscis when presented with the trained odour, involves first the right and then the left antenna. At 1-2 hour after training using both antennae, recall is possible only when the bee uses its right antenna but by 6 hours after training the memory has made a lateral shift and can now be recalled only when the left antenna is in use. Long-term memory one day after training is also accessed only via the left antenna. This time-dependent shift from right to left antenna is seen as side biases in responding to odour presented to the bee's left or right side and hence may be manifested in natural behaviour.
Concurrent Acquisition of a Single Nucleotide Polymorphism in Diverse Influenza H5N1 Clade 2.2 Sub-clades
Authors: Niman Henry , Boynton Bruce 
Published: July 2019

AbstractHighly pathogenic Influenza A H5N1 was first identified in Guangdong Province in 1996, followed by human cases in Hong Kong in 1997 1,2. The number of confirmed human cases now exceeds 300, and the associated Case Fatality Rate exceeds 60% 3. The genetic diversity of the serotype continues to increase. Four distinct clades or sub-clades have been linked to human cases 4-7. The gradual genetic changes identified in the sub-clades have been attributed to copy errors by viral encoded polymerases that lack an editing function, thereby resulting in antigenic drift 8. We report here the concurrent acquisition of the same polymorphism by multiple, genetically distinct, clade 2.2 sub-clades in Egypt, Russia, and Ghana. These changes are not easily explained by the current theory of “random mutation” through copy error, and are more easily explained by recombination with a common source. This conclusion is supported by additional polymorphisms shared by clade 2.2 isolates in Egypt and Germany.
Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions
Authors: Hucka Michael , Finney Andrew , Hoops Stefan , Keating Sarah , Le Novere Nicolas 
Published: July 2019

AbstractWith the rise of Systems Biology as a new paradigm for understanding biological processes, the development of quantitative models is no longer restricted to a small circle of theoreticians. The dramatic increase in the number of these models precipitates the need to exchange and reuse both existing and newly created models. The Systems Biology Markup Language (SBML) is a free, open, XML-based format for representing quantitative models of biological interest that advocates the consistent specification of such models and thus facilitates both software development and model exchange.Principally oriented towards describing systems of biochemical reactions, such as cell signalling pathways, metabolic networks and gene regulation etc., SBML can also be used to encode any kinetic model. SBML offers mechanisms to describe biological components by means of compartments and reacting species, as well as their dynamic behaviour, using reactions, events and arbitrary mathematical rules. SBML also offers all the housekeeping structures needed to ensure an unambiguous understanding of quantitative descriptions.This specification presents the structures of the language and the rules used to build a valid model. SBML XML Schema and other related documents and software are also available from the SBML project web site, "http://sbml.org/":http://sbml.org/.
Rapid Dissolution of Lignocellulosic Plant Materials in an Ionic Liquid
Authors: Rayne Sierra , Mazza Giuseppe 
Published: July 2019

AbstractConcerns regarding the non-renewable nature of, and pollution from, petroleum derived energy and commercial products has led to the concept of a biomass economy. As part of this vision for a society based on sustainable biomaterials, proposed biorefineries need to tackle the challenges of taking a wide diversity of raw biomass and rapidly and effectively transforming it into functionalizable platform molecules that can be derivatized into industrial and consumer products, or converted into biofuels. A substantial research effort is underway focussed on degrading biomass into smaller constituents using a variety of physical, chemical, and biological processes. One promising technology for the solubilization of biomass is ionic liquids (ILs), which has received considerable attention as a medium for efficient solubilization of a variety of materials. ILs also allow fractional separation when combined with solvent extraction (conventional, and green technologies such as supercritical CO2), precipitation, and adsorption/absorption methods, and to conduct a wide range of chemical reactions using thermal, electrochemical, photochemical, and biocatalytic processes. As a potential pretreatment technology for the biorefineries of the future, we report herein the first rapid dissolution of a range of coniferous and deciduous woods and grassy lignocellulosic plant materials in an IL using microwave radiation.
Meta-Potentiation: Neuro-Astroglial Interactions Supporting Perceptual Consciousness
Authors: Pereira Jr Alfredo , Furlan Fábio Augusto 
Published: July 2019

AbstractConscious perceptual processing involves the sequential activation of cortical networks at several brain locations, and the onset of oscillatory synchrony affecting the same neuronal population. How do the earlier activated circuits sustain their excitation to synchronize with the later ones? We call such a sustaining process "meta-potentiation", and propose that it depends on neuro-astroglial interactions. In our proposed model, attentional cholinergic and stimulus-related glutamatergic inputs to astroglia elicit the release of astroglial glutamate to bind with neuronal NMDA receptors containing the NR2B subunit. Once calcium channels are open, slow inward currents activate the CaM/CaMKII complex to phosphorylate AMPA receptors in a population of neurons connected with the astrocyte, thus amplifying the local excitatory pattern to participate in a larger synchronized assembly that supports consciousness.
Remote estimation of carbon dioxide uptake of terrestrial ecosystems
Authors: Garbulsky Martin F. 
Published: July 2019

AbstractThe estimation of the carbon balance in ecosystems, regions, and the biosphere is currently one of the main concerns in the study of the ecology of global change. Current remote sensing methodologies for estimating gross primary productivity are not satisfactory because they rely too heavily on (i) the availability of climatic data, (ii) the definition of land-use cover, and (iii) the assumptions of the effects of these two factors on the radiation-use efficiency of vegetation (RUE). A new methodology is urgently needed that will actually assess RUE and overcome the problems associated with the capture of fluctuations in carbon absorption in space and over time. Remote sensing techniques such as the widely used reflectance vegetation indices (e.g., NDVI, EVI) allow green plant biomass and therefore plant photosynthetic capacity to be assessed. Nevertheless, detecting how much of this capacity is actually realized is a much more challenging goal. The Photochemical Reflectance Index (PRI) derived from freely available satellite information (MODIS sensor) presented an exponential relationship with the RUE. Thus, we show that it is possible to estimate RUE in real time and therefore actual carbon uptake at ecosystem, regional, and biosphere levels using the PRI. This conceptual and technological advancement avoids the need to rely on either the sometimes unreliable maximum RUE for each ecosystem, hard-to-obtain climate data, or on imprecise land-use/land-cover data.
An integrated solution for rapid biosensing combining linker free binding, freeze drying and high sensitivity ellipsometric detection
Authors: Yin Yongbai , McKenzie David , Fisher Keith , Guo Chuan , Nosworthy Neil , Bilek Marcela 
Published: July 2019

AbstractA novel integrated biosensor methodology is proposed and demonstrated. The methodology utilizes a nitrogen-containing plasma polymer to achieve linker-free binding of biorecognition molecules that allows the sensor surface to be freeze dried for long shelf life under ambient conditions. The sensor is configured for single wavelength ellipsometric detection providing a low cost, versatile, and rapid sensing and diagnosis platform suitable for a wide range of applications and end-users. The merits of the methodology were demonstrated using three antigen-antibody pairs.
Bacteriophages as a model for studying carbon regulation in aquatic system
Authors: Sanmukh Swapnil , Paunikar Waman , Swaminathan Sandhya , Lokhande Satish 
Published: July 2019

AbstractThe interconversion of carbon in organic, inorganic and refractory carbon is still beyond the grasp of present environmentalists. The bacteria and their phages, being the most abundant constituents of the aquatic environment, represent an ideal model for studing carbon regulation in the aquatic system. The refractory dissolved organic carbon (DOC), a recently coined terminology from the microbe-driven conversion of bioavailable organic carbon into difficult-to-digest refractory DOC by microbial carbon pump (MCP), is suggested to have the potential to revolutionize our view of carbon sequestration. It is estimated that about 95% of organic carbon is in the form of refractory DOC, which is the largest pool of organic matter in the ocean. The refractory DOC is supposed to be the major factor in the global carbon cycle whose source is not yet well understood. A key element of the carbon cycle is the microbial conversion of dissolved organic carbon into inedible forms. The time studies of phage-host interaction under control conditions reveal their impact on the total carbon content of the source and their interconversion among organic, inorganic and other forms of carbon with respect to control source. The TOC- analysis statistics stipulate an increase in inorganic carbon content by 15-25 percent in the sample with phage as compared to the sample without phage. The results signify a 60-70 fold increase in inorganic carbon content in sample with phage, whereas, 50-55 fold in the case of sample without phages as compared with control. This increase in inorganic carbon content may be due to lysis of the host cell releasing its cellular constituents and utilization of carbon constituent for phage assembly and development. It also proves the role of phages in regulating the carbon flow in aquatic systems like oceans, where their concentration outnumbered other species.
PROM Khad an efficient source of P to replace the costly chemical Phosphatic Fertilizer
Authors: Sekhar DMR , Katewa MK , Shaktawat MS 
Published: July 2019

AbstractThe subsidy on phosphate fertilizers rose to an unacceptable level while alternate cost effective technologies are available. Fertilizer industry needs to develop innovative products using the recent advances in the agricultural sciences. Manure producing industries to be supplied rock phosphate mineral (at subsidized costs) as being supplied to chemical fertilizers industries suitable to produce PROM Khad (Phosphate Rich Organic Manure).
Deterministic Separation of Cancer Cells from Blood at 10 mL/min
Authors: Loutherback Kevin , D'Silva Joseph , Liu Liyu , Wu Amy , Austin Robert , Sturm James 
Published: July 2019

AbstractCirculating tumor cells (CTCs) and circulating clusters of cancer and stromal cells have been identified in the blood of patients with malignant cancer and can be used as a diagnostic for disease severity, assess the efficacy of different treatment strategies and possibly determine the eventual location of metastatic invasions for possible treatment. There is thus a critical need to isolate, propagate and characterize viable CTCs and clusters. Here, we present a microfluidic device for mL/min flow rate, continuous-flow capture of viable CTCs from blood using deterministic lateral displacement arrays. We show here that a deterministic bump array can be designed such that it will isolate with efficiency greater than 85% CTCs over a large range in sizes from millimeter volume clinical blood samples in minutes, with no effect on cell vitality so that further culturing and analysis of the cells can be carried out.
Some Computational Aspects of Essential Properties of Evolution and Life
Authors: Zenil Hector , Marshall James 
Published: July 2019

AbstractWhile evolution has inspired algorithmic methods of heuristic optimisation, little has been done in the way of using concepts of computation to advance our understanding of salient aspects of biological evolution. We argue that under reasonable assumptions, interesting conclusions can be drawn that are of relevance to behavioural evolution. We will focus on two important features of life--robustness and fitness optimisation--which, we will argue, are related to algorithmic probability and to the thermodynamics of computation, subjects that may be capable of explaining and modelling key features of living organisms, and which can be used in understanding and formulating algorithms of evolutionary computation.
The 'consciousness' of the living state: Extending the Baars global broadcast model across physiological subsystems
Authors: Wallace Rodrick 
Published: July 2019

AbstractFor the broad spectrum of cognitive biological phenomena having 'dual' information sources, isolation from crosstalk between them requires more metabolic free energy than permitting correlation. This allows an evolutionary exaptation leading to dynamic global broadcasts at multiple scales, similar to the well-studied exaptation of noise to trigger stochastic resonance amplification in physiological systems. Entropy gradient models adapted from nonequilibrium thermodynamics lead to an index theorem in which analytic solutions of empirical equations describe different possible topological modes. Not only is the living state characterized by cognition at every scale and level of organization, but by multiple, shifting, tunable, cooperative broadcasts that link selected subsets of those structures to address problems. As for animal consciousness, the 'stream' of cognitive physiological broadcast is constrained by the riverbanks of embedding context, expressed in terms of systematic regularities of an enveloping environmental information source and the limitations imposed by developmental trajectory.
Gender effects on cytidine analogue metabolism and myelodysplastic syndrome treatment outcomes
Authors: Chan Kenneth , Maciejewski Jaroslaw , Ling Yonghua , Radivoyevitch Tomas , Engelke Kory , Saunthararajah Yogen , Sekeres Mikkael , Mahfouz Reda , Jankowska Ania , Ebrahem Quteba , Hu Zhenbo , Terse Pramod , Tiu Ramon , Covey Joseph 
Published: July 2019

AbstractIn vivo, half-lives of cytidine analogues such as 5-azacytidine and decitabine, used to treat myelodysplastic syndromes (MDS), are determined largely by cytidine deaminase (CDA), an enzyme that rapidly metabolizes these drugs into inactive uridine counterparts. Genetic factors influence CDA activity, and hence, could impact 5-azacytidine/decitabine levels and efficacy, a possibility requiring evaluation. Using an HPLC assay, plasma CDA activity was confirmed to be decreased in individuals with the CDA SNP A79C. More interestingly, there was an even larger decrease in females. Explaining the decrease in enzyme activity, liver CDA expression was significantly lower in female versus male mice. As expected, decitabine plasma levels, measured by mass-spectrometry, were significantly higher in females. In mathematical modeling, the detrimental effect of shortening half-life of S-phase specific therapy was amplified in low S-phase fraction disease (e.g., MDS). Accordingly, in multivariate analysis of MDS patients treated with 5-azacytidine/decitabine, overall survival was significantly worse in males.
Schizophrenia is a TH2 dominant autoimmune disease possibly against acetylcholine receptors of CNS
Authors: Hu Wanchung 
Published: July 2019

AbstractSchizophrenia is a very common psychiatric disorder. However, its etiology and pathogenesis is still unknown. Current theory saying that neurotransmitter imbalance such as serotonin or dopamine only provides limited effectiveness in schizophrenia treatment by drugs changing serotonin and dopamine concentration. Despite of such treatment, majority of schizophrenia patients still have very poor prognosis. Thus, the neurotransmitter imbalance theory is not correct. Here, I propose that schizophrenia is actually a TH2 dominant autoimmune disorder. The candidate of autoantigen could be acetylcholine receptors of CNS. My theory can explain the positive as well as negative symptoms of schizophrenia. By microarray analysis of PBMCS, one-tenth of the total 519 significantly expressed genes are immune-related genes. Among them, TH2 related genes are significantly up-regulated including IL-4, histidine decarboxylase, aldehyde dehydrogenase, CCR9, IgE Fc receptor, GATA2, serotonin receptor, phospholipase A2, and prostaglandin D2 synthase. Besides, TH1 and TH17 related genes are down-regulated including CXCL5, cathepsin C, and neutrophil related S100 binding proteins. The new theory sheds a light to better control this detrimental illness. Anti-inflammatory agents could be used to manage schizophrenia in the near future.
Colour reverse learning and animal personalities: the advantage of behavioural diversity assessed with agent-based simulations
Authors: Dyer Adrian , Dorin Alan , Reinhardt Verena , Rosa Marcello 
Published: July 2019

AbstractForaging bees use colour cues to help identify rewarding from unrewarding flowers, but as conditions change, bees may require behavioural flexibility to reverse their learnt preferences. Perceptually similar colours are learnt slowly by honeybees and thus potentially pose a difficult task to reverse-learn. Free-flying honeybees (N = 32) were trained to learn a fine colour discrimination task that could be resolved at ca. 70% accuracy following extended differential conditioning, and were then tested for their ability to reverse-learn this visual problem multiple times. Subsequent analyses identified three different strategies: ‘Deliberative-decisive’ bees that could, after several flower visits, decisively make a large change to learnt preferences; ‘Fickle- circumspect’ bees that changed their preferences by a small amount every time they encountered evidence in their environment; and ‘Stay’ bees that did not change from their initially learnt preference. The next aim was to determine if there was any advantage to a colony in maintaining bees with a variety of decision-making strategies. To understand the potential benefits of the observed behavioural diversity agent-based computer simulations were conducted by systematically varying parameters for flower reward switch oscillation frequency, flower handling time, and fraction of defective ‘target’ stimuli. These simulations revealed that when there is a relatively high frequency of reward reversals, fickle-circumspect bees are more efficient at nectar collection. However, as the reward reversal frequency decreases the performance of deliberative-decisive bees becomes most efficient. These findings show there to be an evolutionary benefit for honeybee colonies with individuals exhibiting these different strategies for managing resource change. The strategies have similarities to some complex decision-making processes observed in humans, and algorithms implemented in artificial intelligence systems.
A database of orthologous exons in primates for comparative analysis of RNA-seq data
Authors: Blekhman Ran 
Published: July 2019

AbstractRNA-seq technology facilitates the study of gene expression at the level of individual exons and transcripts. Moreover, RNA-seq enables unbiased comparative analysis of expression levels across species. Such analyses typically start by mapping sequenced reads to the appropriate reference genome before comparing expression levels across species. However, this comparison requires prior knowledge of orthology at the exon level. With this in mind, I constructed a database of orthologous exons across three primate species (human, chimpanzee, and rhesus macaque). The database facilitates cross-species comparative analysis of exon- and transcript-level regulation. A web application allowing for an easy database query: http://giladlab.uchicago.edu/orthoExon/