bluuebunny/crossref_metadata_2025_split huggingface dataset:
A test of psbK-psbI and atpF-atpH as potential plant DNA barcodes using the flora of the Kruger National Park (South Africa) as a model system
Authors: Lahaye Renaud , Savolainen Vincent , Duthoit Sylvie , Maurin Olivier , van der Bank Michelle 
Published: July 2019

AbstractA DNA barcode consists of a standardized short sequence of DNA (400-800bp) used to identify the taxonomic species a small organic fragment belongs to. Even though it has been easy to discriminate animal species by using the mitochondrial gene cox1, this is still difficult for plants seeing that the mitochondrial genome is not variable enough on the species level. During the Second International Barcode of Life Conference in Tapei (September 2007), different plastid regions were proposed as potential plant DNA barcodes, such as atpF-atpH and psbK-psbI, but no consensus on which region to use was reached during the meeting. The largest plant DNA barcoding study to date proposed matK as the best candidate and suggested that in combination with trnH-psbA a slight increase in performance could be achieved. However, no study has tested the suitability of the newly proposed psbK-psbI and atpF-atpH for plant barcoding purposes. Four potential DNA barcodes, matK, trnH-psbA, atpF-atpH, and psbK-psbI, were amplified and sequenced for a selective sampling including mainly trees and shrubs of the flora of the Kruger National Park Africa (South Africa). The performance of each region and also each possible combination of these were tested by applying a battery of metrics and statistical tests. Our results confirm that the second half (5’ end) of matK is the best candidate in a single locus barcoding approach reaching 87.5% of species correctly identified. Combining matK with trnH-psbA and psbK-psbI increased only slightly the performance in discriminating species. The results from this study show that the use of a ‘three-region barcode’ does not significantly outperform matK in a single-locus barcoding approach. We therefore argue against the ‘multiple barcode approach’ proposed by the plant working group, and instead propose to keep barcoding plants in line with the approach taken for animals, i.e. using one barcode: cox1 for animals and matK for plants.
Effect of temperature on waterflea Daphnia magna (Crustacea:Cladocera)
Authors: Khan Quddus , Khan Munawer 
Published: July 2019

AbstractAcclimation of the waterflea Daphnia magna Straus (Crustacea: Cladocera) at 2 o to 12 o C above their habitat temperature (16 o C) for 6 months increased the rate of their metabolic activity (respiration and heartbeat rates). Temperature-enhanced activity appeared to be supported by cellular ATP synthesis (increased cytochrome c oxidase and succinic dehydrogenase activities) and hydrolysis (increased ATPases activities), indicating high rate of intermediary metabolism, the substrates for which may come from the stored glycogen and fat in addition to ingested food. Temperature-enhanced activity was associated with loss of body mass and decrease in body size, both of which may result from hyperactivity (causing lack of replenishment of consumed stored glycogen and fat) and loss of body water (due to hyperosmolarity of water because of evaporation). Hyperthermia-caused hypoxia was associated with increase in hemoglobin (Hb) synthesis (a typical daphnid response to hypoxia). These responses to hyperthermic stress started showing up after one month of acclimation at 27 o-29 o C and after 6 months at lower temperature ranges (18 o-20 o C) indicating the possibility of initiation of similar responses in field populations at current expected rise in global temperature due to climate change. Since the thermal stress will continue for generations, the effects observed with D. magna may start showing up in other small aquatic poikilotherms; indicating the speeding up of their life processes and of their gametes, embryos, larvae, and young adults. Such responses can affect aquatic ecosystem dynamics.
HBsAg-vectored DNA vaccines elicit concomitant protective responses to multiple CTL epitopes relevant in human disease.
Authors: Chen Dekun , Gould Allan , Mather Michael , Haigh Oscar , Barnes Melanie , Kattenbelt Jacqueline , Thomson Scott , Tindle Robert 
Published: July 2019

AbstractVaccines capable of controlling neoplastic and infectious diseases which depend on the cellular immune response for their resolution, have proven difficult to develop. We, and others, have previously demonstrated that the potent immunogenicity of hepatitis B surface antigen (HBsAg), the already- licensed human vaccine for hepatitis B infection, may be exploited to deliver foreign antigens for cytotoxic T-lymphocyte (CTL) induction. In this study we demonstrate that recombinant (r) HBsAg DNA delivering a CTL polyepitope appended at the C' terminus elicits concomitant responses to multiple epitopes restricted through a diversity of MHC class I haplotypes, which are relevant in a number of human diseases. We show that the rHBsAg DNA vaccine elicits concomitant protection against neoplastic and infectious disease. These studies vindicate the use of HBsAg as a powerful vector to deliver CTL responses to foreign antigens, and have implications for a multi-disease vaccine applicable to the HLA-polymorphic human population.
GO-WORDS: An Entropic Approach to Semantic Decomposition of Gene Ontology Terms
Authors: Tong Tuanjie , Lee Yugyung , Dinakarpandian Deendayal 
Published: July 2019

AbstractThe Gene Ontology (GO) has a large and growing number of terms that constitute its vocabulary. An entropy-based approach is presented to automate the characterization of the compositional semantics of GO terms. The motivation is to extend the machine-readability of GO and to offer insights for the continued maintenance and growth of GO. A proto-type implementation illustrates the benefits of the approach.
Effect of Baicalin on inflammatory mediator levels and microcirculation disturbance in rats with severe acute pancreatitis
Authors: Zhang Xiping , Tian Hua , Wu Chen-Jun , Jiang Xin-Ge , Ye Qian , Chen Li , Cai Yang , Xu Ru-Jun , Xie Qi , Yuan Wenqin 
Published: July 2019

Abstract
Objective:
To investigate the effect of Bacailin on inflammatory mediator levels and microcirculation disturbance in severe acute pancreatitis (SAP) rats and explore its therapeutic mechanism on this disease. Methods: SAP model rats were randomly divided into model control group and Baicalin treated group, 45 rats in each group. The same number of normal rats were included in sham-operated group. These groups were further subdivided into 3 h, 6 h and 12 h subgroups, respectively (15 rats in each subgroup). At 3, 6 and 12 hours after operation, rats were killed to conduct the following experiments: (1) to examine the mortality rates of rats, the ascites volume and pancreatic pathological changes in each group; (2) to determine the contents of amylase, PLA~2~, TXB~2~, PGE~2~, PAF and IL-1[beta]; in blood as well as the changes in blood viscosity.

Results:
(1) Compared to model control group, treatment with Baicalin is able to improve the pathological damage of the pancreas, lower the contents of amylase and multiple inflammatory mediators in blood, decrease the amount of ascitic fluid and reduce the mortality rates of SAP rats; (2) at 3 hours after operation, the low-shear whole blood viscosity in Baicalin treated group was significantly lower than that in model control group;at 12 hours after operation, both the high-shear and low-shear whole blood viscosity in Baicalin treated group were also significantly lower than those in model control group.

Conclusion:
Baicalin, as a new drug, has good prospects in the treatment of SAP since it can exert therapeutic effects on this disease through inhibiting the production of inflammatory mediators, lowering blood viscosity, improving microcirculation and mitigating the pathological damage of the pancreas.
Striatal neuroinflammation promotes parkinsonism in rats
Authors: Choi Dong-Young , Hunter Randy , Liu Mei , Cass Wayne , Pandya Jignesh , Sullivan Patrick , Shin Eun-Joo , Kim Hyoung-Chun , Gash Don , Bing Guoying 
Published: July 2019

AbstractThe specific role of neuroinflammation in the pathogenesis of Parkinson's disease remains to be fully elucidated. By infusing lipopolysaccharide (LPS) into the striatum, we investigated the effect of neuroinflammation on the dopamine nigrostriatal pathway. Here, we report that LPS-induced neuroinflammation in the striatum causes progressive degeneration of the dopamine nigrostriatal system, which is accompanied by motor impairments resembling parkinsonism. Our results indicate that neurodegeneration is associated with defects in the mitochondrial respiratory chain related to extensive S-nitrosylation/nitration of mitochondrial proteins. Mitochondrial injury was prevented by treatment of L-N^6^-(l-iminoethyl)-lysine, an inducible nitric oxide synthase (iNOS) inhibitor, suggesting that iNOS-derived NO is responsible for mitochondrial dysfunction. Furthermore, the nigral dopamine neurons exhibited intracytoplasmic [alpha]-synuclein and ubiquitin accumulation. These results demonstrate that degeneration of nigral dopamine neurons by neuroinflammation is associated with mitochondrial malfunction induced by NO-mediated S-nitrosylation/nitration of mitochondrial proteins.
Far-infrared rays control prostate cancer cells in vitro and in vivo
Authors: Shima Hiroki , Yamamoto Shingo , Qiu Jun , Shincho Mayumi , Hirota Seiichi , Yoshikawa Yoshie , Yoshikawa Reigetsu , Hashimoto-Tamaoki Tomoko 
Published: July 2019

AbstractWe introduce a new effective method to control hormone refractory prostate cancer cells by using an activated rubber/resin form (RB), far-infrared ray emitter, with or without sodium butyrate (SB). The growth of three human prostate cancer cell lines (Du145, PC-3 and LNCaP) was suppressed in vitro and in vivo by using RB, and the cells were eradicated with RB + 3 mM SB. G1 arrest and apoptotic pathway proteins were induced by RB with intensified expressions of apoptosis - related mRNA on cDNA microarray. RB radiates the infra-red rays of the 4 to 25 [mu]m wavelengths to an object which exert a favorable influence on a cancer control. These results may render us a new therapeutic modality in hormone refractory prostate cancer.
THE EFFECT OF HEPARIN ON THE CELL CYCLE IN HUMAN B-LYMPHOBLASTS: AN IN VITRO STUDY
Authors: Aksoy Ayse , Erduran Erol , Gedik Yusuf 
Published: July 2019

AbstractHeparin has an apoptotic effect in addition to its anticoagulant, anti-inflammatory, antihypertensive, and antiproliferative effects. In this study, we detected the effect of heparin on the cell cycle of lymphoblasts by flow cytometry (FCM) and tried to determine which phase in the cell cycle of lymphoblasts contains heparin-sensitive points. Twelve children with newly diagnosed acute lymphoblastic leukemia (ALL) were included in the study. Lymphoblasts were incubated in different levels of heparin concentrations (0, 10, and 20 U/mL) and the percentages of lymphoblasts at each phase of the cell cycle were simultaneously measured by FCM at 0, 1, and 2 hours (h). The percentages of lymphoblasts at the G2/M and S phases were significantly increased in 20 U/mL heparin concentration compared to 0 U/mL heparin concentration at 1h (from 1.18% to 10.21% and from 1.03% to 13.63%, respectively; p&lt;0.000), indicating an arrest of cell cycle at the G2/M and S phases by heparin. These findings provide new insights into the molecular mechanism of the apoptotic effect of heparin.Keywords: Cell cycle, Heparin, Leukemia
Two cases of mother-infant cannibalism in orangutans
Authors: Dellatore David , Waitt C. , Foitova Ivona 
Published: July 2019

AbstractTwo unrelated female orangutans (Pongo abelii) were observed on different occasions cannibalizing the remains of their infants, a behavior never before reported in apes. Both orangutans are free-ranging ex-captive individuals in an area of forest which also hosts large numbers of visiting tourists. The cannibalism events appear to have been aberrant behavior, perhaps due to stress and the environmental conditions of the area.
Hydrogen sulfide: a neurotransmitter or just a cofactor of the nitrite in the NO production?
Authors: Grossi Loris 
Published: July 2019

AbstractThe hydrogen sulfide has been recently claimed to have an important role in the cardiovascular system, as well in the central nervous system, but its action seems directly connected to the presence of NO/NO-derivatives. We want to report here chemical evidences that suggest for the H2S a role as a cofactor, able to induce NO release from NO-donors, more than a direct neurotransmitter.
Viral organization of human proteins
Authors: Wuchty Stefan 
Published: July 2019

AbstractA compilation of experimentally verified interactions between HIV-1 and human proteins allows insights into the intricate interplay between viral and host proteins on a large scale.We find that HIV-1 predominantly targets rich-clubs, human proteins that are not only well connected but also strongly intertwined among each other. These assemblies of proteins putatively serve as an infection gateway, allowing the virus to take control of the human host by reaching protein pathways and diversified cellular functions in a pronounced and focused way. In particular, HIV-1 utilizes its small number of proteins in a combinatorial manner, exerting a significant influence on pathways that deal with transcriptional, translational and degradation processes. Surprisingly, the small repertoire of HIV proteins also interferes loosely with many signaling and regulation pathways, suggesting that a widespread involvement in such pathways secures the control of the host cell. Such insights offer novel perspectives to investigate the progression of HIV infection and potentially can contribute to our abilities to fight this virus.
Gene and Pathway-Based Analysis: Second Wave of Genome-wide Association Studies
Authors: Peng Gang , Luo Li , Siu Hloicheong , Zhu Yun , Hu Pengfei , Hong Shengjun , Zhao Jinying , Zhou Xiaodong , Reveille John , Jin Li , Amos Christopher , Xiong Momiao 
Published: July 2019

AbstractDespite great success of GWAS in identification of common genetic variants associated with complex diseases, the current GWAS have focused on single SNP analysis. However, single SNP analysis often identifies a number of the most significant SNPs that account for only a small proportion of the genetic variants and offers limited understanding of complex diseases. To overcome these limitations, we propose gene and pathway-based association analysis as a new paradigm for GWAS. As a proof of concept, we performed a comprehensive gene and pathway-based association analysis for thirteen published GWAS. Our results showed that the proposed new paradigm for GWAS not only identified the genes that include significant SNPs found by single SNP analysis, but also detected new genes in which each single SNP conferred small disease risk, but their joint actions were implicated in the development of diseases. The results also demonstrated that the new paradigm for GWAS was able to identify biologically meaningful pathways associated with the diseases which were confirmed by gene-set rich analysis using gene expression data.
Left Anterior Negativity reflects distinct neural substrate for linguistic rule application
Authors: Lebib Riadh , Krott Andrea 
Published: July 2019

AbstractA critical issue for understanding language processing in the brain is whether linguistic rule application is subserved by a distinct neural substrate. Previous evidence based on electroencephalographic measurements is indirect because studies focus on neural changes after rule violation, which may reflect processes caused by the violation such as error handling. Here we show that correct rule-governed formations are associated with left frontal negative-going activity, providing direct evidence for rule application in the brain.
Sequential Allocation and Balancing Prognostic Factors in a Psychiatric Clinical Trial
Authors: Fossaluza Victor , Diniz Juliana , Pereira Basilio , Miguel Euripedes , Pereira Carlos 
Published: July 2019

AbstractIn controlled clinical trials, each of several prognostic factors should be balanced across the trial arms. Traditional restricted randomization may be proved inadequate especially with small sample sizes. In psychiatric disorders such as obsessive compulsive disorder (OCD), small trials prevail. Therefore, procedures to minimize the chance of imbalance between treatment arms are advisable. This paper describes a minimization procedure specifically designed for a clinical trial that evaluates treatment efficacy for OCD patients. Aitchison's compositional distance was used to calculate vectors for each possibility of allocation in a covariate adaptive method. Two different procedures were designed to allocate patients in small blocks or sequentially one-by-one. Partial results of this allocation procedure as well as simulated ones are shown. In the clinical trial for which this procedure was developed, the balancing between treatment arms was achieved successfully. Simulations of results considering different arrival order of patients showed that most of the patients are allocated in a different treatment arm if arrival order is modified. Results show that a random factor is maintained with the random arrival order of patients. This specific procedure allows the use of a large number of prognostic factors for the allocation decision and was proved adequate for a psychiatric trial design.
Ionic Liquid Mediated Dye Recovery from Aqueous Solution
Authors: Qadri Shahnaz , Ganoe Ashley , Haik Yousef 
Published: July 2019

AbstractWe describe a method to retrieve hazardous dye from aqueous solution that employs magnetic nanoparticles with strong affinity to dyes. Ionic liquids with stronger affinity to the magnetic particles promote up to 99% dye recovery.
An ancient adaptive episode of convergent molecular evolution confounds phylogenetic inference
Authors: Castoe* Todd , de Koning* A.P. Jason , Kim Hyun-Min , Gu Wanjun , Noonan Brice , Jiang Zhi , Parkinson Christopher , Pollock David 
Published: July 2019

AbstractConvergence can mislead phylogenetic inference by mimicking shared ancestry, but has been detected only rarely in molecular evolution. Here, we show that significant convergence occurred in snake and agamid lizard mitochondrial genomes. Most evidence, and most of the mitochondrial genome, supports one phylogenetic tree, but a subset of mostly amino acid-altering mitochondrial sites strongly support a radically different phylogeny. These sites are convergent, probably selected, and overwhelm the signal from other sites. This suggests that convergent molecular evolution can seriously mislead phylogenetics, even with large data sets. Radical phylogenies inconsistent with previous evidence should be treated cautiously.
Mutations in the SC4MOL gene encoding a novel methyl sterol oxidase cause autosomal recessive psoriasisiform dermatitis, microcephaly and developmental delay
Authors: He Miao , Kratz Lisa , Michel Jushua , Vallejo Abbe , Ferris Laura , Kelley Richard , Hoover Jacqueline , Gibson Michael , Vockley Gerard 
Published: July 2019

AbstractDisorders of cholesterol biosynthesis have clinical manifestations involving skeleton, eyes, neurologic development, and skin. We describe a patient with congenital cataracts, developmental delay, microcephaly, and low serum cholesterol who developed severe psoriasiform dermatitis and arthralgias beginning at age 3. Her brain MRI indicatedminor gliosis. Quantitative sterol analysis of patient plasma and skin showed marked elevation of 4alpha-methyl- and 4, 4'-dimethylsterols, indicating a deficiency in the first step of sterol C4 demethylation in cholesterol biosynthesis. Molecular studies showed mutations in SC4MOL, a gene predicted to encode a sterol C4 methyl oxidase. Thus, our patient has a previously undescribed inborn error of cholesterol biosynthesis. Cellular studies with patient-derived fibroblasts showed higher mitotic rate than control cells in cholesterol-depleted medium, in which de novo cholesterol biosynthesis was increased with the accumulation of methylsterol. Immunologic analyses showed dysregulation of immune-related receptors in the patient and her father. Inhibition of sterol C4 methyl oxidase in human transformed lymphoblasts or in fresh leukocytes induced activation of cell cycle, and immune receptor dysregulation. These findings suggest that methylsterols influence mitotic capacity and immune function. SC4MOL is situated within the psoriasis susceptibility locus PSORS9, and is likely a genetic risk factor for common psoriasis.
Multifunctional Nanoparticles for Imaging Guided Interventions
Authors: Haik Yousef , al-Ramadi Basel , Issa Bashar , Qadri Shahnaz , Hayek Saleh , Hijaze Hassan 
Published: July 2019

AbstractWe describe multifunctional magnetic nanoparticles (MNPs) encapsulated in thermosensitive, drug-bearing shells and delivered to the tumor site by genetically modified and non-pathogenic strains of bacteria with known affinity to tumors for an effective and minimally invasive protocol for tumor management. The magnetic nanoparticles also serve as a non-invasive imaging contrast agent, heating agent as well as thermometry monitoring agents. We have shown an efficient tumor management on a mouse model utilizing the MNPs. Our studies showed that these novel MNPs significantly reduce the progress of tumor and prolong the animal life and function as an imaging contrast to visually monitor the tumor treatment and evolution.
On the exotic fishes given to... geometry
Authors: Voytekhovsky Yury 
Published: July 2019

AbstractPolyhedral forms are extremely widespread both in animate and inanimate nature. Thus, crystals occur as polyhedra only. Besides, these forms are quite common with various primitive organisms, i.e. icosahedral viruses, radiolaria and algae. Here we discuss the cases of exotic Boxfish and Porcupinefish. The specific morphology of the Boxfish reveals in polygonal osseous blades, covering its body. As for the Porcupinefish, its polyhedral approximation was observed via certain geometrical techniques applied. Namely, their spine bases were considered the Delaunay point (R, r)-systems. Consequently, the respective Dirichlet tiling proved to be quasifullerenes and analogous to the Boxfish morphology. This unexpected geometrical dualism of the two families corroborates their taxonomic affinity within the Tetradontiformes order. The above biometrical method is highly recommended as a means of characterization of the Tetraodontiformes specimens in terms of the Delaunay (R, r)-systems.
PID: The Pathway Interaction Database
Authors: Schaefer Carl , Anthony Kira , Krupa Shiva , Buchoff Jeffrey , Day Matthew , Hannay Timo , Buetow Kenneth 
Published: July 2019

AbstractThe Pathway Interaction Database (PID, "http://pid.nci.nih.gov":http://pid.nci.nih.gov) is a freely available collection of curated and peer-reviewed pathways composed of human molecular signaling and regulatory events and key cellular processes. Created in a collaboration between the U.S. National Cancer Institute and Nature Publishing Group, the database serves as a research tool for the cancer research community and others interested in cellular pathways, such as neuroscientists, developmental biologists, and immunologists. PID offers a range of search features to facilitate pathway exploration. Users can browse the predefined set of pathways or create interaction network maps centered on a single molecule or cellular process of interest. In addition, the batch query tool allows users to upload long list(s) of molecules, such as those derived from microarray experiments, and either overlay these molecules onto predefined pathways or visualize the complete molecular connectivity map. Users can also download molecule lists, citation lists and complete database content in extensible markup language (XML) and Biological Pathways Exchange (BioPAX) Level 2 format. The database is updated with new pathway content every month and supplemented by specially commissioned articles on the practical uses of other relevant online tools.