bluuebunny/crossref_metadata_2025_split huggingface dataset:
Progression of Parkinson’s disease pathology is reproduced by intragastric administration of rotenone in mice
Authors: Pan-Montojo Francisco , Anichtchik Oleg , Dening Yanina , Knells Lilla , Pursche Stefan , Jung Roland , Gille Gabriele , Spillantini Maria Grazia , Reichmann Heinz , Funk Richard 
Published: July 2019

AbstractIn Parkinson’s disease patients pathology follows a characteristic pattern involving inter alia the enteric nervous system, the dorsal motor nucleus of the vagus, the intermediolateral nucleus of the spinal cord and the substantia nigra, providing the basis for the neuropathological staging of the disease. Here we report that intragastrically administered rotenone, a commonly used pesticide that inhibits mitochondrial Complex I, is able to reproduce PD pathological staging as found in patients. Our results show that low doses of chronically and intragastrically administered rotenone induce PD pathology in all the above-mentioned nervous system structures in wild-type mice. Interestingly, HPLC analysis showed no rotenone levels in the systemic blood or the central nervous system (CNS) (detection limit [rotenone]<20nM), indicating that rotenone is detoxified by the liver. These alterations are sequential, appearing only in synaptically connected nervous structures, treatment time-dependent and accompanied by inflammatory signs and motor dysfunctions. These results strongly suggest that the local effect of pesticides on the ENS might be sufficient to induce PD progression and to reproduce the neuroanatomical and neurochemical features of PD staging. Thus, providing new insight into how environmental factors could trigger PD and pointing out a transsynaptic mechanism by which PD might propagate to and through the CNS.
Accounting for molecular stochasticity in systematic revisions: species limits and phylogeny of Paroaria
Authors: Dávalos Liliana , Porzecanski Ana 
Published: July 2019

AbstractDifferent frameworks have been proposed for using molecular data in systematic revisions, but there is ongoing debate on their applicability, merits and shortcomings. In this paper we examine the fit between morphological and molecular data in the systematic revision of Paroaria, a group of conspicuous songbirds endemic to South America. We delimited species based on examination of > 600 specimens, and developed distance-gap, and distance- and character-based coalescent simulations to test species limits with molecular data. The morphological and molecular data collected were then analyzed using parsimony, maximum likelihood, and Bayesian phylogenetics. The simulations were better at evaluating the new species limits than using genetic distances. Species diversity within Paroaria had been underestimated by 60%, and the revised genus comprises eight species. Phylogenetic analyses consistently recovered a congruent topology for the most recently derived species in the genus, but the most basal divergences were not resolved with these data. The systematic and phylogenetic hypotheses developed here are relevant to both setting conservation priorities and understanding the biogeography of South America.
Development of a new method to preserve caprine cauda epididymal spermatozoa in-situ at -10 degrees Centigrade
Authors: Datta Uttam , Chandrasekar M , Hembram Manik Lal , Dasgupta Raju 
Published: July 2019

AbstractElectrolyte free mediums prepared with soybean lecithin-glycerol,Coenzyme Q10–glycerol and soybean lecithin-Coenzyme Q10-glycerol were inoculated separately into ligated cauda epididymides, equilibrated 2 h at 5 degree centigrade, wrapped with aluminium foils along with testis and freezed at -10 degree centigrade.Spermatozoan characters were evaluated 7 and 21 days after thawing at 38.5 degree centigrade in a water bath for 5 min. Spermatozoan characters were diminished gradually and significantly (P<0.001, P<0.05) between the mediums and observation days. Soybean lecithin-CoenzymeQ10-glycerol effectively protected spermatozoa against cold shock where spermatozoan progressive motility, livability, hypo-osmotic swelling positivity were 30.2 ± 0.62; 45.2 ± 0.82 and 41.6 ± 0.79 percent respectively on day 21. This new method is better than preservation of in-situ epididymal spermatozoa at 5 degree centigrade for a short duration. Therefore, present method can be adopted effectively in field conditions for transportation of freezed epididymides and for re-utilization of maximum functional gametes by artificial reproductive technologies to conserve valuable animals after postmortem / slaughter.
Cyclin kinase inhibitor p21: a mediator of immune tolerance: direct and indirect evidence
Authors: Khanna Ashwani 
Published: July 2019

Abstract
*Background:*
Uncontrolled proliferation of T-cells is considered a barrier to the induction of transplantation tolerance by T regulatory cells. Therefore, cyclin kinase inhibitor p21, one of the most potent inhibitors of cell proliferation, may exert an important role in the induction/generation of T regulatory cells.*Methods:* CD4^+^CD25^+^ and CD4^+^CD25^-^ cells were isolated from normal healthy blood donors (n=6), p21^-/-^ mice (n=9) and wild type mice (n=9). Proliferation with and without cyclosporine was quantified by ^3^H-thymidine uptake assay (expressed as counts per minute) and FoxP3 mRNA was studied by real-time quantitative RT-PCR.

*Results:*
The difference in proliferation (p<0.003) among CD4^+^CD25^+^ (15236 ± 1190) and CD4^+^CD25^-^ (50317 ± 974) T cells were proportionately similar to the difference in proliferation (p<0.001) of lymphocytes from wild type (28206 ± 2812) and p21^-/-^ mice (49624 ± 2164), proliferation of CD4^+^CD25^-^ and p21 deficient cells was resistant to cyclosporine. The number of T regulatory cells in p21^-/-^ mice were significantly (p<0.002) lower (2.6 ± 0.8%) than wild type mice (14.5 ± 1.6%,) and similar to CD4^+^CD25^-^ T cells, CD4^+^25^+^ T cells from p21^-/-^ mice lacked FoxP3 gene expression. T lymphocytes from wild type inhibited the proliferation of T lymphocytes from p21^-/-^ mice similar to the effect of CD4^+^CD25^+^ T cells on the proliferation of CD4^+^CD25^-^ cells.

*Conclusions:*
Presence of the p21 creates a milieu favorable for immune tolerance and consistent with antiproliferative and immunosuppressive effect of CD4^+^CD25^+^ T-regulatory cells. These findings support the notion that p21 could be used clinically in controlling allo-immune activation to achieve prolongation of graft survival.
Transformation of metabolism with age and lifestyle in Antarctic seals: a case study of systems biology approach to cross-species microarray experiment
Authors: Ptitsyn Andrey , Kanatous Shane 
Published: July 2019

Abstract
*Background:*
The metabolic transformation that changes Weddell seal pups born on land into aquatic animals is not only interesting for the study of general biology, but it also provides a model for the acquired and congenital muscle disorders which are associated with oxygen metabolism in skeletal muscle. However, the analysis of gene expression in seals is hampered by the lack of specific microarrays and the very limited annotation of known Weddell seal (Leptonychotes weddellii) genes.*Results:* Muscle samples from newborn, juvenile, and adult Weddell seals were collected during an Antarctic expedition. Extracted RNA was hybridized on Affymetrix Human Expression chips. Preliminary studies showed a detectable signal from at least 7000 probe sets present in all samples and replicates. Relative expression levels for these genes was used for further analysis of the biological pathways implicated in the metabolism transformation which occurs in the transition from newborn, to juvenile, to adult seals. Cytoskeletal remodeling, WNT signaling, FAK signaling, hypoxia-induced HIF1 activation, and insulin regulation were identified as being among the most important biological pathways involved in transformation. *Conclusion:* In spite of certain losses in specificity and sensitivity, the cross-species application of gene expression microarrays is capable of solving challenging puzzles in biology. A Systems Biology approach based on gene interaction patterns can compensate adequately for the lack of species-specific genomics information.
Transcriptomic analysis implicates ribosomal and energy metabolic pathways in antiepileptic drug action in a Drosophila model
Authors: Singh Priyanka , Mohammad Farhan , Sharma Abhay 
Published: July 2019

AbstractMechanisms of long term action of antiepileptic drugs (AEDs), used in treating epilepsy and many other neurological and psychiatric disorders, are poorly understood. Recently, a novel Drosophila transcriptomic model of locomotor plasticity induced by chronic pentylenetetrazole (PTZ), a chemoconvulsant commonly used to model epileptogenesis and test AEDs in rodents, has been described. In this model, two of the five AEDs tested, sodium valproate (NaVP) and levetiracetam (LEV), not ethosuximide (ETH), gabapentin (GBP) and vigabatrin (VGB), ameliorate development of chronic PTZ induced locomotor alteration. Here, we describe transcriptomic effect of the AEDs in the fly model. Singular treatment with ETH, GBP and VGB in general caused downregulation of genes. In contrast, similar treatment with NaVP and LEV caused upregulation. The GBP and NaVP gene sets showed enrichment of the ribosomal and energy metabolic pathways. The network partners of ETH, VGB and LEV regulated genes in the available interactome map were also found to overrepresent the ribosomal pathway. Unlike PTZ alone, PTZ and LEV combination treatment was found to cause differential regulation of genes that too enriched the ribosomal and energy metabolic pathways. Cumulatively, we provide transcriptomic evidence that suggests involvement of ribosomal and energy metabolic mechanisms in AED action. The Drosophila model provides an excellent opportunity to further understand mechanisms of AED action in molecular details.
Salmonella typhimurium harboring plasmid expressing interleukin-12 induced attenuation of infection and protective immune responses
Authors: Park Yong Keun , Won Suck Yoon , Seung Seok Lee 
Published: July 2019

AbstractIL-12 is known to be an essential cytokine which appears to provide protective immunity against intracellular bacteria, such as Salmonella. In this study, we investigated the possibility of developing a vaccine using IL-12 against virulent Salmonella. We used the host defense system activated by cytokine IL-12. The highly virulent Salmonella strain (Salmonella typhimurium UK-1) was transformed with cytokine-expressing plasmids. These live, wild-type pathogens were used as vaccine strains without undergoing any other biological or genetic attenuating processes. The newly developed strains induced partial protection from infections (30-40%). Of note, the interleukin-12 transformed pathogen was safe upon immunization with low doses (103 CFU), induced IgG responses, and stimulated protective immune responses against Salmonella Typhimurium in mice (80-100%). These results suggest that IL-12 induced attenuation of wild-type Salmonella in the host infection stage and vaccine development using the wild-type strain harboring IL-12 secreting plasmids may be considered as an alternative process for intracellular bacterial vaccine development without the inconvenience of time-consuming attenuation processes.
Rescue with an anti-inflammatory peptide of chickens infected H5N1 avian flu
Authors: Imai Masaki , Okada Alan , Okada Hidechika , Handharyani Ekowati , Tsukamoto Yasuhiro , Adachi Kazuhide , Okada Noriko , Soejoedono Retno Damajanti 
Published: July 2019

AbstractChickens suffering from avian flu caused by H5N1 influenza virus are destined to die within 2 days due to a systemic inflammatory response. Since HVJ infection (1,2) and influenza virus infection (3,4) cause infected cells to activate homologous serum complement, the systemic inflammatory response elicited could be attributed to the unlimited generation of C5a anaphylatoxin of the complement system, which is a causative peptide of serious inflammation. In monkeys inoculated with a lethal dose of LPS (4 mg/kg body weight), inhibition of C5a by an inhibitory peptide termed AcPepA (5) rescued these animals from serious septic shock which would have resulted in death within a day (6). Therefore, we tested whether AcPepA could also have a beneficial effect on chickens with bird flu. On another front, enhanced production of endothelin-1 (ET-1) and the activation of mast cells (MCs) have been implicated in granulocyte sequestration (7). An endothelin receptor derived antisense homology box peptide (8) designated ETR-P1/fl was shown to antagonize endothelin A receptor (ET-A receptor) (9) and reduce such inflammatory responses as endotoxin-shock (10) and hemorrhagic shock (11), thereby suppressing histamine release in the circulation (12). Thus, we also administered ETR-P1/fl to bird flu chickens expecting suppression of a systemic inflammatory response.
Magnetic Resonance imaging (MRI) in detection of Bifidobacterium longum and Clostridium novyi-NT labeled with superparamagnetic iron oxide (SPIO) nanoparticle
Authors: Wang Jianhua , Zhang Xuebin , Zhou Dayong , Wang Qingguo , Li Dan 
Published: July 2019

Abstract*Purpose:* To investigate the MR imaging of Bifidobacterium longum and Clostridium novyi-NT labeling with superparamagnetic iron oxide (SPIO) nanoparticles.
*Materials and methods:*
Tubes containing B. longum-SPIO, Free-SPIO, B. longum and PYG Medium were incubated under anaerobic condition in in vitro experiment. Transmission electron microscope and Prussian blue staining were used to demonstrate intra-bacteria nanoparticles. R~2~^*^ mapping and R~2~ mapping were reconstructed after MR scanning. B. longum-SPIO and C. novyi-NT-SPIO were injected respectively in vivo to show whether it might be traced by MR imaging.

*Results:*
Magnetosomes in bacteria were observed by electron microscopic and stained by Prussian blue staining. At the same concentration of SPIOs, the R~2~^*^ value of B. longum-SPIO was significantly higher than that of Free-SPIO (P<0.001), however, the R~2~ value was lower comparing with Free-SPIO (P<0.001). After injection with B. longum-SPIO, they could present in tumor and shorten T~2~^*^.*Conclusion:* B. longum and C. novyi-NT could be labeled by SPIO and then traced by MRI.
Gender differences in a Drosophila transcriptomic model of chronic pentylenetetrazole induced behavioral deficit
Authors: Sharma Abhay , Mohammad Farhan , Singh Priyanka 
Published: July 2019

AbstractA male Drosophila model of locomotor deficit induced by chronic pentylenetetrazole (PTZ), a proconvulsant used to model epileptogenesis in rodents, has recently been described. Antiepileptic drugs (AEDs) ameliorate development of this behavioral abnormality. Time-series of microarray profiling of heads of male flies treated with PTZ has shown epileptogenesis-like transcriptomic perturbation in the fly model. Gender differences are known to exist in neurological and psychiatric conditions including epileptogenesis. We describe here the effects of chronic PTZ in Drosophila females, and compare the results with the male model. As in males, chronic PTZ was found found to cause a decreased climbing speed in females. In males, overrepresentation of Wnt, MAPK, TGF-beta, JAK-STAT, Cell communication, and Dorso-Ventral axis formation pathways in downregulated genes was previously described. Of these, female genes showed enrichment only for Dorso-Ventral axis formation. Most significant, ribosomal pathway was uniquely overrepresented in genes downregulated in females. Gender differences thus exist in the Drosophila model. Gender neutral, Dorso-Ventral axis formation may be considered as the candidate causal pathway in chronic pentylenetetrazole induced behavioral deficit. Prior evidence of developmental mechanisms in epileptogenesis underscores the usefulness of fly model. Gender specific pathways may provide a lead for understanding brain dimorphism in neuropsychiatric disorders.
Generation of "backbone" free, low transgene copy plants by launching T-DNA from the Agrobacterium chromosome
Authors: Oltmanns Heiko , Frame Bronwyn , Lee Lan-Ying , Johnson Susan , Li Bo , Wang Kan , Gelvin Stanton 
Published: July 2019

AbstractIn both applied and basic research, Agrobacterium-mediated transformation is commonly used to introduce genes into plants. We investigated the effect of three Agrobacterium tumefaciens strains and five T-DNA origins of replication on transformation frequency, transgene copy number, and the frequency of integration of non-T-DNA portions of the T-DNA-containing vector ("backbone") into the genome of Arabidopsis thaliana and Zea mays. Launching T-DNA from the picA locus of the Agrobacterium chromosome increases the frequency of single transgene integration events and almost eliminates the presence of vector backbone sequences in transgenic plants. Along with novel Agrobacterium strains we have developed, our findings are useful for improving the quality of T-DNA integration events.
Practical experiences in concurrent, collaborative ontology building using Collaborative Protégé
Authors: Schober Daniel , Malone James , Stevens Robert 
Published: July 2019

AbstractCreation of an ontology according to some common plan is best accomplished collaboratively. This is sometimes contradicted by the distribution of the ontology’s developers. An obvious solution therefore is to build collaboration into ontology development tools. Such support necessarily includes both the technical means to perform editing operations upon an ontology, but also support for the communication that makes collaboration such a vital part of much ontology development. To investigate the distributed, collaborative ontology engineering process and the corresponding capabilities of the Collaborative Protege 3 (CP) tool, members of the OntoGenesis network came together and enriched the Ontology of Biomedical Investigations (OBI) with new content. The communications and interactions of the participants with each other, directly or through the tool, were tracked and analyzed. Our initial analysis of the degree to which this new tool fulfills the practical requirements of collaborative ontology engineering suggests the approach is promising. We present some observations and recommendations for CP based upon this experience.
Studies on Regioselective Binding Mode of Steroid Molecules in Homology Modeled Cytochrome P450-2C11
Authors: Ali Hamed , Yamada Morio , Fujita Hukihisa , Akaho Eiichi 
Published: July 2019

AbstractIn this study, we investigated the regioselective binding mode of steroid molecules and structure requirements for steroid molecules for 16[alpha]-hydroxylation by Cytochrome P450-2C11. Docking study by using the homology Cytochrome P450-2C11 indicated that 16[alpha]-hydroxylation is favored with steroidal molecules possessing the following components, 1) a bent A-B ring configuration (5[beta]-reduced), 2) C-3[alpha]-hydroxyl group, 3) C-17[beta]-acetyl group, and 4) methyl group at both the C-18 and C-19. These respective steroid components requirements such as A-B ring configuration and functional groups at C-3 and C-17 were defined as the inhibitory contribution factor. Overall results by rat CYP2C11 revealed that steroidal structure requirements resulted in causing an effective inhibition of [^3^H]progesterone 16[alpha]-hydroxylation by the adult male rat liver microsome. As far as docking of homology modeled CYP2C11 against investigated steroids is concerned, they are docked at the active site superimposed with flurbiprofen. It was also found that the distance between heme iron and C16[alpha]-H was between 4 to 6 Å and that the related angle was in the range of 180±45°.
An OWL-DL Ontology for Classification of Lipids
Authors: Low Hong Sang , Baker Christopher , Garcia Alex , Wenk Markus 
Published: July 2019

AbstractLipids can be systematically classified according to functional properties, structural features, biochemical origin or biological system. However Lipid nomenclature has yet to become a robust research tool since no rigorous definitions exist for membership of specific lipid classes. Lipids need to be defined in a manner that is systematic yet at the same time semantically explicit. We report on the reuse of existing lipid nomenclature, ontology describing chemical structure and the extension of the OWL-DL Lipid Ontology to support the classification of lipid molecules. We applied definitions, DL-axioms, to describe lipids classes and illustrate suitability of the ontology for the classification of Fatty Acyl lipids and Mycolic acids.
MIREOT: the Minimum Information to Reference an External Ontology Term
Authors: Ruttenberg Alan , Courtot Melanie , Gibson Frank , Lister Allyson , Malone James , Schober Daniel , Brinkman Ryan 
Published: July 2019

AbstractWhile the Web Ontology Language (OWL) provides a mechanism to import ontologies, this mechanism is not always suitable. First, given the current state of editing tools and the issues they have working with large ontologies, direct OWL imports have sometimes proven impractical for day-to-day development. Second, ontologies chosen for integration may be under active development and not aligned with the chosen design principles. Importing heterogeneous ontologies in their entirety may lead to inconsistencies or unintended inferences. In this paper we propose a set of guidelines for importing required terms from an external resource into a target ontology. We describe the guidelines, their implementation, present some examples of application, and outline future work and extensions.
Developing Ontology Support for Human Malaria Control Initiatives
Authors: Olawande Daramola , Segun Fatumo 
Published: July 2019

AbstractMalaria is one of the most common infectious diseases and an enormous public health problem in Sub-Sahara Africa, Asia and parts of America. In this paper, we discuss the development of the Human Malaria Control Ontology (HMCO) which contains general information on Malaria and epidemiological information that can help in the formulation of effective malaria control policies. The HMCO is aimed at providing interoperability support for the knowledge management of malaria control initiatives, and serve as an open semantic web infrastructure for malaria research and treatment.
The Baseline for Response Latency Distributions
Authors: Moscoso del Prado Martín Fermín 
Published: July 2019

AbstractResponse latency - the time taken to initiate or complete an action or task - is one of the principal measures used to investigate the mechanisms subserving human and animal cognitive processes. The right tails of response latency distributions have received little attention in experimental psychology. This is because such very long latencies have traditionally been considered irrelevant for psychological processes, instead, they are expected to reflect 'contingent' neural events unrelated to the experimental question. Most current theories predict the right tail of response latency distributions to decrease exponentially. In consequence, current standard practice recommends discarding very long response latencies as 'outliers'. Here, I show that the right tails of response latency distributions always follow a power-law with a slope of exactly two. This entails that the very late responses cannot be considered outliers. Rather they provide crucial information that falsifies most current theories of cognitive processing with respect to their exponential tail predictions. This exponent constitutes a fundamental constant of the cognitive system that groups behavioral measures with a variety of physical phenomena.