bluuebunny/crossref_metadata_2025_split huggingface dataset:
Jellyfish as vectors of bacterial disease for farmed fish.
Authors: Ferguson Hugh , Delannoy Christian , Nicolson James , Sutherland David , Crumlish Margaret , Hay Steven 
Published: July 2019

AbstractGill diseases are common, especially in intensively reared fish; they result in respiratory distress, as well as impaired osmoregulation and excretion (1). Bacteria and parasites are common causes of gill disease, as is poor water quality, including planktonic blooms. Swarms or blooms of jellyfish are increasingly and especially problematical (2), and can result in high mortality of farmed fish. Small species of jellyfish such as Philalella quadrata (13 mm diameter) are capable of passing through the mesh of sea-cages and of being sucked into the mouth of fish during respiration. Here we show that the initial damage to gills of farmed Atlantic salmon, likely produced by nematocyst-derived toxins from the jellyfish, was compounded by secondary bacterial infection with Tenacibaculum maritimum. We also demonstrate that these filamentous bacteria were present on the mouth of the jellyfish and that their DNA sequences were almost identical to those of bacteria present on the salmon gills. This suggests that the bacterial lesions were not the result of an opportunistic infection of damaged tissue as previously thought. Instead, P. quadrata is probably acting as a vector for this particular bacterial pathogen, and it is the first time that evidence to support such a link has been presented. We could find no prior literature describing the presence of bacteria associated with jellyfish, other than some studies about their decay. We do not know if all jellyfish of this and other species carry similar bacteria in a symbiotic relationship, nor do we know their source, the role that they play under other circumstances, or indeed whether the jellyfish were themselves diseased. The high proteolytic capabilities of T. maritimum mean that partially digested gill tissues were readily available to the jellyfish, which rely heavily on intracellular digestion for their nutrition.
Hematopoietic Cell Types: Prototype for a Revised Cell Ontology
Authors: Masci Anna Maria , Pulendran Bali , Meehan Terrence , Scheuermann Richard , Morel Penelope , Yao Q. Alison , Nijnik Anastasia , Zand Martin , Mungall Christopher , Diehl Alexander , Augustine Alison , Blake Judith , Cowell Lindsay , Gold Elizabeth , Peters Bjoern , Gondré-Lewis Timothy 
Published: July 2019

AbstractThe Cell Ontology (CL) aims for the representation of in vivo and in vitro cell types from all of biology. Although the CL is a reference ontology of the OBO Foundry, it requires extensive revision to bring it up to current standards for biomedical ontologies, both in its structure and its coverage of various subfields of biology. A recent workshop sponsored by NIAID on hematopoietic cell types in the CL addressed both issues. The section of the ontology dealing with hematopoietic cells was extensively revised, and plans were set for structuring these cell type terms as cross-products with logical definitions built from relationships to external ontologies, such as the Protein Ontology and the Gene Ontology. The methods and improvement to the CL in this area represent a paradigm for improvement of the whole of the ontology over time.
Phase organization of circadian oscillators in extended gate and oscillator models
Authors: Zhao Gang 
Published: July 2019

AbstractThe suprachiasmatic nuclei (SCN) control daily oscillations in physiology and behavior. The gate-oscillator model captures function heterogeneity in SCN and has been successful in reproducing many features of SCN. This paper investigates the mechanism of phase organization in the gate-oscillator model and finds that only stable fixed points of the phase transition function are essential to phase organization. Extending the model with a dead zone of the phase transition function and the propagation delay of the gate signal which represents the spatial structure of SCN, the author discusses how the experimentally reported phase distribution, including phase splitting of animals in LL condition, and fixed phase difference between neurons of SCN could be understood in the framework of the gate-oscillator model. The extended model provides two mechanisms for phase splitting and gives a testable prediction that the two clusters of neurons of the phase splitting animal differ in their inherent periods.
Water Quality and Pollution Status of Lararpur Reservoir with Special Reference to Bacterial Contamination
Authors: Pandey Subhash , Singh Sadhna , Pani Subrata , Malhosia Arti 
Published: July 2019

AbstractLaharpur dam was constructed in the southwest of Bhopal city, M.P., India with an objective to store water for irrigational purpose. At the time of planning and construction of the reservoir it was in the outskirts of township but now, with the expansion of the city the reservoir has come well within the settlement. The developmental activities and occupancy in the area is exerting pressure on the water body. Surface water in urban water bodies almost always contains some degree of contamination. This is due to exposure to animals, humans, aquatic life, etc. In addition to this, variety of other human activities resulted in increasing the bacterial concentration of reservoir. Many of these bacteria are pathogenic and spread diseases like typhoid, paratyphoid, gastroenteritis etc. Inflow of sewage in the surface water may play an important role in the transmission of pathogenic agents discharged through feces. Some pathogenic bacteria like Actinomyces sp., Aerobacter aerogenes, A. cloacae, Micrococcus sp., Salmonella sp., Staphylococcus aureus, Bacillussp, and Shigella species indicate the higher level of fecal contamination of water. This untreated water poses a serious threat to the health of consumers and therefore, calls for urgent intervention by government.
Inhibition of Acid Phosphatase Enzyme Activity in the Presence of Noncrystalline Calcium Phosphate and Nanocrystalline Calcium Apatite: a Preliminary Study
Authors: Pekounov Yassen 
Published: July 2019

Abstract
Background
Our bones are remodelled repeatedly during life. A new and “healthy” bone tissue replaces the old one. Accordingly, the bone degrading cells, the osteoclasts, prefer old and fatigued bone. The young bone mineral, i.e. calcium apatite, is less crystalline than the mature one. Is it possible that the osteoclasts distinguish between relatively old and new bone via its crystallinity?*Methodology/Principal Findings*Acid phosphatase is an enzyme largely expressed by the osteoclasts during resorption and therefore used as a marker of the cells activity. This study explores whether its enzymatic activity would be decreased in the presence of biomimitetically prepared noncrystalline calcium phosphate and nanocrystalline bone resembling calcium apatite. The results showed that both biomimetic samples decreased significantly the enzyme activity while synthetic calcium phosphate samples did not. Consistent with our hypothesis the noncrystalline calcium phosphate had the greater inhibition effect.

Conclusions/Significance
The in vitro data suggests that the bone-resorbing cells activity could be regulated by the degree of crystallinity of the bone mineral. These findings report that changes in the properties of biogenic inorganic materials induce specific interactions with biomolecules which in turn should define the cell behaviour. These results can establish an interesting mechanism of cell regulation if confirmed in vivo.
Development and Characterization of Eudragit RS 100 Loaded Microsponges and its Colonic Delivery Using Natural Polysaccharides
Authors: Jain Vikas , Singh Ranjit 
Published: July 2019

AbstractIn the present work, paracetamol loaded eudragit based microsponges were prepared using quasi-emulsion solvent diffusion method. The compatibility of the drug with various formulation components was established. Process parameters were analyzed in order to optimize the formulation. Shape and surface morphology of the microsponges were examined using scanning electron microscopy. The colon specific formulations were prepared by compression coating of microsponges with pectin:hydroxypropylmethylcellulose (HPMC) mixture followed by tabletting. The in vitro dissolution studies were done on all formulations and the results were evaluated kinetically and statically. The kinetics of release study showed that the release data followed Higuchi matrix and the main mechanism of drug release from microsponges was diffusion. In vitro studies exhibited that compression coated colon specific tablet formulations started the release the drug at the 6th hour corresponding to the arrival time to proximal colon
Polymerase-endonuclease amplification reaction for large-scale enzymatic production of antisense oligonucleotide
Authors: Wang Xiaolong , Gou Deming 
Published: July 2019

AbstractSynthetic oligonucleotides are contaminated with highly homologous failure sequences. Oligonucleotide synthesis is difficult to scale up because it requires expensive equipments, hazardous chemicals, and tedious purification process. Here we report a novel thermocyclic reaction, polymerase-endonuclease amplification reaction (PEAR), for the amplification of oligonucleotides. A target oligonucleotide and a tandem repeated antisense probe are subjected to repeated cycles of denaturing, annealing, elongation and cleaving, in which thermostable DNA polymerase elongation and strand slipping generate duplex tandem repeats, and thermostable endonuclease (PspGI) cleavage releases monomeric duplex oligonucleotides. Each round of PEAR achieves &gt;100-fold amplification. The product can be used in one more round of PEAR directly, and the process can be further repeated. In addition to avoiding dangerous materials and improved product purity, this reaction is easy to scale up and amenable to full automation, so it has the potential to be a useful tool for large-scale production of antisense oligonucleotide drugs.
Mammalian cells in culture actively export specific microRNAs
Authors: Wang Kai , Zhang Shile , Weber Jessica , Baxter David , Galas David 
Published: July 2019

AbstractThe discovery of microRNAs (miRNAs) as a new class of regulators of gene expression has triggered an explosion of research, but has left many unanswered questions about how this regulation works and how it is integrated with other regulatory mechanisms. A number of miRNAs have been found to be present in blood plasma and other body fluids of humans and mice in surprisingly high concentrations. This observation was unexpected in two respects: first, the fact that these molecules are present at all outside the cell at significant concentrations; and second, that these molecules appear to be stable outside of the cell. In light of this it has been suggested that the biological function of miRNAs may also extend outside of the cell and mediate cell-cell communication^[1-5]^. Such a system would be expected to export specific miRNAs from cells in response to specific biological stimuli. We report here that after serum deprivation several human cell lines tested do export a spectrum of miRNAs into the culture medium. The export response is substantial and prompt. The exported miRNAs are found both within and outside of microvesicles and exosomes. We have identified some candidate protein components of this system outside the cell, and found one exported protein that plays a role in protecting miRNA from degradation. Our results point to a hitherto unrecognized and uncharacterized miRNA trafficking system in mammalian cells that may involve cell-cell communication.
The modulation of alpha-wave amplitude in human EEG by the intention to act with a motor response
Authors: Kirschfeld Kuno 
Published: July 2019

AbstractThe most conspicuous signal in the human EEG is the so-called alpha wave, oscillations in the frequency range of 8 to 12 Hz. Visual stimulation of the retina suppresses the amplitude of alpha waves (Berger effect), and increased attention can reduce them. Here I show that one more parameter significantly affects the amplitudes of alpha waves: the intention to act by a motor response. Together with data from the literature, these results show that alpha waves are not part of the visual processing network but rather part of a long-range neuromodulatory network. The modulation modifies latencies in perception or motor response. The relevant mechanisms are located in early cortical visual areas; their activity may contribute to hemodynamic changes in these areas and thus explain dissociations between Bold signals and spike activities mentioned in the literature.
In silico microRNA identification from paprika (Capsicum annuum) ESTs
Authors: Manila T. M. , Riju A. , Lakshmi Priya Darshini K. , Chandrasekar A. , Eapen S. J. 
Published: July 2019

AbstractA total of 33,311 Expressed Sequence Tags (EST) of paprika were mined from the GenBank EST database. The redundancy of the EST sequences was removed using CAP3 and it resulted 4,541 contigs 8,539 singletons as nonredundant data sets. The microRNAs were predicted using the program miRNAfinder. This program predicted a total of 85 miRNAs miRNAs. Another study was carried out to find the homologes miRNA using blast based tool named “miRseeK’ A total of 13 miRNAs with significant similarity with the plant miRNAs were obtained from paprika ESTs. The targets of the predicted miRNAs were found using the program miRU2. Findings suggest that most miRNAs play an important role in plant development, signal transduction, protein degradation and in response to environmental stress. The miRNAs were found to be perfectly or nearly complementary to its target mRNAs.
Choice reveals that rats are majoritarily resilient to cocaine addiction
Authors: Cantin Lauriane , Lenoir Magalie , Dubreucq Sarah , Serre Fushia , Vouillac Caroline , Ahmed Serge 
Published: July 2019

AbstractAssessing the relative reward value of cocaine and how it changes with repeated use represents a long-standing goal in addiction research. Surprisingly, recent experimental research in rats – the most frequently used animal model in the field – suggests that the reward value of cocaine may in fact be relatively weak at least in the majority of individuals. Here, we provide strong additional evidence that confirms and extends the validity and generality of this research. Specifically, we demonstrate that no matter how heavy is past cocaine self-administration, most rats value cocaine poorly and readily decide to quit when offered the opportunity of making a different choice (i.e., drinking water sweetened with saccharin, an otherwise biologically inessential rewarding behavior). On average, rats estimate that cocaine is worth about 10 times less than the alternative reward. Only a small minority of rats prefer to continue taking cocaine when offered the choice. These findings reveal the existence of a genuine resilience to cocaine addiction in the majority of rats, a phenomenon that has long been suspected, though not firmly demonstrated, in humans. Only a minority would be prone to develop this disorder. We propose that choice should serve as a behavioral screening assay to identify vulnerable individuals, among the resilient majority, in future experimental research on the determinants of cocaine addiction.
Polymorphisms of TSER and MTHFR are associated with prognosis of fluoropyrimidine-based therapy in colorectal cancer patients
Authors: Kim Jong Woo , Lee Jae Ho , Hong Seung Ho , Bae Su Jin , Kwon Young Do , Oh Doyeun , Kim Nam Keun 
Published: July 2019

AbstractThis study was designed to investigate the influence of TSER and MTHFR polymorphisms on the clinical outcomes of patients with colorectal cancer receiving 5-FU-based chemotherapy. Genomic DNA was isolated from 103 frozen or paraffin-embedded tissues of colorectal cancer patients. The genotypes of two common polymorphisms were determined by PCR-RFLP. Patient prognoses were compared with genotype groups and analyzed according to tumor location. Polymorphisms of TSER and MTHFR 677C>T were not significantly associated with clinicopathological factors. There were no differences in prognosis between genotypes or functional groups when the TSER and MTHFR groups were considered separately. However, analysis of combined genotypes of the TSER and the MTHFR 677C>T polymorphisms were associated with the survival rate of colorectal cancer patients who received 5-FU-based chemotherapy (p=0.028). Prognosis of colorectal cancer patients was significantly different between proximal colon and distal colon cancers (p=0.002). However, prognosis did not receive any effect of the combined genotype when analyzed according to tumor location, such as proximal and distal colon cancer. The combined TSER and MTHFR 677C>T genotypes can be prognostic factors in colorectal cancer, where gene-gene interactions between the genotypes may occur.
Frequency-dependent selection predicts patterns of radiations and biodiversity
Authors: Melian Carlos , Alonso David , Vazquez Diego , Regetz James , Allesina Stefano 
Published: July 2019

AbstractMost empirical studies support a decline in speciation rates through time, although evidence for constant speciation rates also exists. Declining rates have been explained by invoking niche-filling processes, whereas constant rates have been attributed to non-adaptive processes such as sexual selection, mutation, and dispersal. Trends in speciation rate and the processes underlying it remain unclear, representing a critical information gap in understanding patterns of global diversity. Here we show that the speciation rate is driven by frequency dependent selection. We used a frequency-dependent and DNA sequence-based model of populations and genetic-distance-based speciation, in the absence of adaptation to ecological niches. We tested the frequency-dependent selection mechanism using cichlid fish and Darwin&apos;s finches, two classic model systems for which speciation rates and richness data exist. Using negative frequency dependent selection, our model both predicts the declining speciation rate found in cichlid fish and explains their species richness. For groups like the Darwin&apos;s finches, in which speciation rates are constant and diversity is lower, the speciation rate is better explained by a model without frequency-dependent selection. Our analysis shows that differences in diversity are driven by larger incipient species abundance (and consequent lower extinction rates) with frequency-dependent selection. These results demonstrate that mutations, genetic-distance-based speciation, sexual and frequency-dependent selection are sufficient not only for promoting rapid proliferation of new species, but also for maintaining the high diversity observed in natural systems.
Repurposing of Meropenem and Nadifloxacin for Treatment of Burn Patients?
Authors: Moloughney Joseph , Thomas Janice , Costa Christie , Bullon Karla , Spencer James , Toney Jeffrey 
Published: July 2019

AbstractThe escalating number of multidrug resistant pathogens has demanded the swift development of new and potent antibiotics (ref. 2). Metallo-[beta]-lactamases (MBLs) continue to evolve, rendering the latest generation of carbapenem antibiotics useless (ref. 8). SPM-1, a recently discovered MBL, was isolated from a juvenile leukemia patient residing in a hospital in San Palo, Brazil just prior to the patient succumbing to septicemia brought on by Pseudomonas aeruginosa expressing SPM-1 (ref. 8). Screening of the Johns Hopkins Compound library of 1,514 FDA or FAD approved drugs (ref. 1) identified a novel SPM-1 inhibitor that is synergistically compatible with meropenem. Using clinically achievable concentrations, meropenem coupled with nadifloxacin inhibits Pseudomonas aeruginosa expressing SPM-1. This shotgun approach to new drug discovery provided a prompt solution to the grave problem of antibiotic resistant pathogens that are thriving in hospitals today.
Cost effective mass multiplication of Gymnema sylvestre in hydroponic system
Authors: Karthic Raju , Seshadri Sundaram 
Published: July 2019

AbstractPresent experiment was designed with an objective to develop a cost efficient mass multiplication method for Gymnema sylvestre using hydroponic system. A plastic tub, with polyethylene cover, containing 1/10 strength of MS salts supplemented with Indole butyric acid (IBA) at different concentrations (0.5, 1.0, 2.5 mg/L) was studied. Medium containing 0.5mg/L of IBA produced highest rooting (66%) with 96 % survival. This protocol will serve as an alternative to the existing in vitro and clonal multiplication protocols.
Aven and Survivin Expression in Egyptian Acute Leukemia and Their Relation to Apoptosis
Authors: Assem Magda , Abedel- ALhameid Thorraya , A-Basset Gihan , Hilal Amany , Kamel Mahmoud , Khalil Iman , Alsharkawey Nahla , Metwally Ayman 
Published: July 2019

Abstract
Background:
Several anti apoptotic signals have been recently identified. Aven and Survivin are broadly expressed and are conserved in mammalian species. Patients and Methods: 39 AML and 25 ALL were tested. Aven and Survivin expression were detected by RT-PCR. DNA fragmentation was carried out daily after treatment..

Results:
Survivin was expressed (P=0.06) more in AML (74%) than in ALL (52%). While, Aven was equally expressed in both leukemias. Patients were categorized into 3 groups based on DNA fragmentation. Absence of Aven significantly (p&x2039;0.001) contributed to DNA fragmentation,but Survivin did not contribute as much. None of the concordant both positive Survivin and Aven were in group III (the good 5 day fragmentation, (P&lt; 0.001). Survivin was statistically related to CD7 expression (P&lt;0.001) in AML only. There was a significant dissociation between Aven and Survivin in AML (p=0.03) and near significant dissociation in ALL (p=0.07). Conclusion: Aven seems to be more important as an inhibitor of apoptosis than survivin in acute leukemia. The presence of both confers a survival disadvantage and a significantly worse DNA fragmentation pattern suggesting a synergistic inhibition of apoptosis. The highly significant relation between CD7 and survivin expression might suggest their involvement in a common signal transduction pathway.
Pandemic (H1N1) 2009 Cluster Analysis: A Preliminary Assessment
Authors: Wick Charles , Stanford Michael , Jabbour Rabih , Deshpande Samir , McCubbin Patrick , Skowronski Evan , Zulich Alan 
Published: July 2019

AbstractPandemic (H1N1) 2009 virus has been causing major concerns around the world because of its epidemic potential, rapid dissemination, rate of mutations, and the number of fatalities. One way to gain an advantage over this virus is to use existing rapid bioinformatics tools to examine easily and inexpensively generated genetic sequencing data. We have used the protein sequences deposited with the National Center for Biotechnology Information (NCBI) for data mining to study the relationship among the Pandemic (H1N1) 2009 proteins. There are 11 proteins in the Pandemic (H1N1) 2009 virus, and analysis of sequences from 65 different locations around the globe has resulted in two major clusters. These clusters illustrate the Pandemic H1N1 2009 virus is already experiencing significant genetic drift and that rapid worldwide travel is affecting the distribution of genetically distinct isolates.