bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel alveolar Krebs cycle-triggered CO2 sensing mechanism regulates regional pulmonary ventilation.
Authors: Schulte-Uentrop Leoni , Goetz Alwin , Kiefmann Rainer , Keller Paula , Tritt Oliver , Heckel Kai , Tank Sascha , Kiefmann Martina 
Published: July 2019

AbstractPulmonary perfusion disorders provoke atelectasis in order to minimize ventilation/perfusion mismatch. However, the underlying mechanisms remain unknown. Because intraalveolar CO2 concentration ([CO2]iA) declines as a consequence of poor pulmonary perfusion we postulated the existence a novel alveolar CO2-sensing mechanism which adapts the ventilation to perfusion. Real-time fluorescence imaging of rat lungs revealed that low [CO2]iA decreased cytosolic and increased mitochondrial Ca2+ in alveolar epithelial cells (AEC), leading to reduction of surfactant secretion and alveolar ventilation. Mitochondrial inhibition by ruthenium red or rotenone blocked the hypocapnia-induced responses. In cultured Type 2 AEC hypocapnia decreased cytosolic Ca2+ independently from pH and increased the NADH production, the mitochondrial transmembrane potential, and subsequently the mitochondrial Ca2+ uptake. All responses were completely blocked by the gene knockdown of the NADH producing Krebs cycle enzyme isocitrate dehydrogenase. Furthermore, ligature of the pulmonary artery of rabbits decreased alveolar ventilation, surfactant secretion, and lung compliance. Addition of 5% CO2 to the inspiratory gas inhibited all responses. Accordingly, we provide evidence for a novel CO2-sensing mechanism of AEC regulated by the Krebs cycle activity in terms of a negative feedback loop adapting surfactant secretion and thus regional ventilation to pulmonary perfusion.
Screening of certain Ayurvedic plants extracts against E. turcicum
Authors: Bhati Kaushal Kumar , Prasad R. , Singh Rajesh 
Published: July 2019

AbstractThe use of chemicals against pathogens is environmentally dangerous, so use of natural inhibitors for disease management is needed. In this work we screen botanical extracts from ayurvedic plants for their antifungal properties against economically important plant fungal pathogen. As a test fungal pathogen, we select E. turcicum, a potent fungal pathogen responsible for Northern leaf corn blight of Maize. This fungal pathogen was challenged by the leaf extract prepared from certain Ayurvedic plants and these observations have shown a promising future in biocontrol of fungus by using such environmentally friendly antifungal agents.
Neural Networks, Cell Genome and Interactome Nonlinear Dynamic Models
Authors: Baianu I. 
Published: July 2019

AbstractOperational logic and bioinformatics models of nonlinear dynamics in complex functional systems such as neural networks, genomes and cell interactomes are proposed. Łukasiewicz Algebraic Logic models of genetic networks and signaling pathways in cells are formulated in terms of nonlinear dynamic systems with n-state components that allow for the generalization of previous logical models of both genetic activities and neural networks. An algebraic formulation of variable 'next-state functions' is extended to a Łukasiewicz Topos with an n-valued Łukasiewicz Algebraic Logic subobject classifier description that represents non-random and nonlinear network activities as well as their transformations in developmental processes and carcinogenesis.
Single Cancer Cell Detection by Near Infrared Microspectroscopy, Infrared Chemical Imaging and Fluorescence Microspectroscopy
Authors: Baianu I. , Korban Schuyler , Costescu Doina 
Published: July 2019

AbstractNovel techniques are currently being developed and established for the accurate chemical analysis and detection of single cancer cells, single embryos and single seeds by Fourier Transform Near Infrared (FT-NIR) Microspectroscopy, Fourier Transform Infrared (FT-IR), Fluorescence and High-Resolution NMR (HR-NMR). The first FT-NIR chemical images of biological systems approaching 1micron resolution are here reported. 400 and 500 MHz, H-1 NMR analyses were carried out that allowed the selection of mutagenized embryos. Detailed chemical analyses are being demonstrated to be also possible by FT-NIR Chemical Imaging/ Microspectroscopy of single cancer cells. FT-NIR Microspectroscopy and Chemical Imaging are also shown to be potentially important in Functional Genomics and Proteomics research through the rapid and accurate detection of high-content microarrays (HCMA). Multi-photon (MP), pulsed femtosecond laser NIR Fluorescence Excitation techniques were shown to be capable of Single Molecule Detection (SMD. Thus, MP NIR excitation for Fluorescence Correlation Spectroscopy (FCS) allowed not only single molecule detection, but also molecular dynamics observations and high resolution, submicron imaging of sub-femtoliter volumes inside living cells with 0.25 micron spatial resolution, in both normal and cancer cells, as well as neoplastic tissues. These novel, ultra-sensitive and rapid FT-NIR/FCS analyses have, therefore, substantial potential for numerous applications in important research areas, such as: medicine, medical/cancer research, pharmacology, agricultural biotechnology, food safety, as well as clinical diagnosis of viral diseases and cancers.
RAB family gene expression in breast cancer cells under influence of paclitaxel
Authors: Rzymowska Jolanta , Malewski Tadeusz , Maj Piotr , Wilkolaski Andrzej 
Published: July 2019

AbstractThe aim of this study was to investigate the role of paclitaxel on RAB family of genes in primary breast cancer cell lines. The cancer breast cells obtained from 40 women during mastectomy were used to address this issue. The group included patients with intraductal breast cancer - lesions in I or II advancement level by TNM classification and G1-G2 by Bloom classification. (tumor dimensions up to 2.0 cm without metastases to lymph nodes). Cytostatic drugs before surgery were not administered to these patients. The cultures were conducted in 25 cm^2^ plastic containers at RPMI medium with addiction of 10% fetal bovine serum (FBS) at the standard conditions. After reaching concentration levels of 10 000/ml of the cells, the cultures were treated with 60 ng/ml and 300 ng/ml doses of paclitaxel. The concentrations were calculated in relation to therapeutic doses of paclitaxel, applied in polytherapy in patients with breast cancer. The cell cultures untreated for cytostatic were used as a control group. Analysis was conducted for RAB family of genes: RAB3D, RAB5B, RAB5C, RAB7, RAB7L1, RAB9P1, RAB10. RAB11A, RAB311B, RAB13, RAB18, RAB22A, RAB23, RAB26, RAB27A, RAB27B, RAB28, RAB30, RAB31, RAB33A, RAB3D6, RAB 38, RABL2B Total RNA was extracted from the harvest control group and the treated cells, and this was followed by cDNA synthesis, which was used for hybridization assays using arrays. A lower dose of paclitaxel (60 ng/ml) treatment resulted in an increase (2-4 fold- statistically significant), whereas a higher dose (300 ng/ml) caused a decrease (2-fold - statistically insignificant) in expression of examined oncogenes, compared to that of the control group.In summary, this data indicates that 60 ng/ml paclitaxel dose induced the RAB gene expression in an up-regulated pathway. A higher concentration of cytostatic (300 ng/ml) is a toxic dose for primary breast cells in vitro.
Identification Of Mitotically Competent SOX2+ Cells In White Matter Of Normal Human Adult Brain
Authors: Oliver-De la Cruz Jorge , Carrion-Navarro Josefa , Gutierrez-Martin Antonio , Escobedo-Lucea Carmen , Garcia-Verdugo Jose Manuel , Ayuso-Sacido Angel 
Published: July 2019

AbstractSOX2 expression is linked to the undifferentiated state of stem cells in mammalian neurogenic niches. While its expression has been reported in the adult human subventricular zone (SVZ), to date it has not been detected in adult human white matter. Here we describe a population of SOX2+ cells from the white matter of the adult human temporal lobe, which proliferate and express glial markers in vitro.
Peduncle inheritance behavior in Antheraea mylitta. D. - An interesting observation
Authors: Rama Rao Mazumdar , Tiwari Santosh Kumar 
Published: July 2019

AbstractIn eco-racial hybridization of Antheraea mylitta D.( Raily X Daba ) the occurrence of long peduncle with two and more rings were found to be an interesting observation against Daba cultivar. Preliminary studies indicate to incorporate the peduncle structure in breeding programs apart from investigating its impact on physiological behavior of the insect.
Inositol-Related Gene Knockouts Mimic Lithium's Effect on Mitochondrial Function
Authors: Toker Lilach , Berry Gerard , Agam Galila , Belmaker RH , Moechars Dieder , Chalifa-Caspi Vered , Bersudsky Yuly , Plaschkes Inbar 
Published: July 2019

AbstractBipolar-disorder, characterized by switches between depressive and manic mood, is treated by mood-stabilizers, lithium being one of them. Among hypotheses suggested, the inositol-depletion hypothesis proposes that lithium attenuates hyperactivation of phosphatidylinositol signaling linked to neurotransmission-related receptors.Available for us are knockout-mice of two genes (IMPA1 or Slc5a3) each encoding for a protein related to inositol metabolism. We previously characterized these mice as exhibiting lithium-like neurochemical and behavioral phenotype. We performed a DNA-microarray study searching for pathways commonly affected by chronic lithium treatment and by the knockout of each of the genes. Here we show up-regulation of mitochondrial function in the three paradigms studied. To verify this result, the interrelationship between treatment with lithium and rotenone, an inhibitor of mitochondrial function, was studied behaviorally. Lithium and rotenone counteracted each other&apos;s effects in two bipolar-related models. The results support the inositol-depletion hypothesis and suggest amelioration of aberrant mitochondrial function consequent to inositol-depletion.
Paraoxonase 1 Polymorphism p.Q192R in Patients With Dementia
Authors: Krzywkowski Tomasz 
Published: July 2019

AbstractPON1 PCR-RFLP polymorphism frequency and enzyme activity were determined in 223 patients with dementia (94 with AD, 55 with VaD and 74 with MD) and in 100 age and sex matched controls without dementia. I found no statistical significance of genotype frequencies between analyzed groups.Paraoxonase 1 activity was lower in patients carrying the R allele in locus 192 as compared with the R allele non-carriers. The results showed statistically significant association between PON1 polymorphism and enzyme activity and thus can suggest an important relationship between different isoforms of PON1, enzyme activity and dementia.
High-order chromatin architecture determines the landscape of chromosomal alterations in cancer
Authors: Fudenberg Geoffrey , Getz Gad , Meyerson Matthew , Mirny Leonid 
Published: July 2019

AbstractThe rapid growth of cancer genome structural information provides an opportunity for a better understanding of the mutational mechanisms of genomic alterations in cancer and the forces of selection that act upon them. Here we test the evidence for two major forces, spatial chromosome structure and purifying (or negative) selection, that shape the landscape of somatic copy-number alterations (SCNAs) in cancer. Using a maximum likelihood framework we compare SCNA maps and three-dimensional genome architecture as determined by genome-wide chromosome conformation capture (HiC) and described by the proposed fractal-globule (FG) model. This analysis provides evidence that the distribution of chromosomal alterations in cancer is spatially related to three-dimensional genomic architecture and additionally suggests that purifying selection as well as positive selection shapes the landscape of SCNAs during somatic evolution of cancer cells.
The Proteomics World is Flat: Dependence of Regulation upon Abundance
Authors: Good David , Zubarev Roman 
Published: July 2019

AbstractThe long-standing assumption that proteins divide into house-keeping and cell-specific groups was recently struck down after discovering that the vast majority of expressed proteins are shared across cell lines. Here, we tested a related hypothesis that abundant proteins are less regulated than low-abundance ones. Meta-analysis of published data revealed that protein regulation is only weakly dependent upon the protein abundance, thus providing support to cell characterization by the &quot;top&quot; proteome.
Large scale expansion of mobile elements in specific hotspot regions of the German outbreak _Escherichia coli_ O104:H4
Authors: Crossman Lisa 
Published: July 2019

AbstractThe outbreak strain of _E. coli_ O104:H4 has been sequenced by several groups and made available publicly for CrowdSourcing purposes. Genome comparisons of the complete finished sequence of TY2482 (BGI), have been made with the draft assemblies of c22711 (PacBio) and an historical outbreak strain from 2001 (U. Münster & Life Technologies). A plasmid, pTY2, carrying the _agg_ operon specifying the genes for aggregative adherence fimbriae reveals a frameshift in a gene, _aggB_, that may result in altered binding _in vivo_ compared to the unframeshifted state. Comparisons additionally reveal the presence of genomic islands specific to the outbreak strain relative to other sequenced _E. coli_ strains. These regions, and islands shared with the closest previously sequenced relative _E. coli_ 55989 have been analyzed for insertion sequences and transposable elements. Several islands found in the above strains that are not present in other sequenced _E. coli_ are found to harbor a large-scale expansion of mobile elements that are by and large confined to these hotspot or permissive areas of the chromosome. The implication is that these regions are in genomic flux and may represent specific areas of future concern due to the possibility of mobilisation of the associated genomic features likely responsible for the pathogenic features and antibiotic resistance seen in these strains.
Potential Use of Folate-polyethylene glycol (PEG)-Appended Dendrimer (G3) Conjugate with alpha-Cyclodextrin as DNA Carriers to Tumor Cells
Authors: Hirayama Fumitoshi , Uekama Kaneto , Arima Hidetoshi , Motoyama Keiichi , Higashi Taishi , Yoshimitsu Ayumi , Ikeda Haruna , Arizono Masayo , Hattori Kenjiro , Takeuchi Tomoko 
Published: July 2019

AbstractWe previously reported that polyamidoamine STARBURST dendrimer (generation 3, G3) (dendrimer) conjugate with alpha-cyclodextrin (alpha-CyD) having an average degree of substitution of 2.4 of alpha-CyD (alpha-CDE) provided remarkable aspects as novel carriers for DNA and siRNA. To develop novel alpha-CDE derivatives with tumor cell specificity, we prepared folate-appended alpha-CDEs (Fol-alpha-CDEs) and folate-polyethylene glycol (PEG)-appended alpha-CDEs (Fol-PalphaCs) with the various degrees of substitution of folate (DSF), and evaluated in vitro and in vivo gene transfer activity, cytotoxicity, cellular association and physicochemical properties. In vitro gene transfer activity of Fol-alpha-CDEs (G3, DSF 2, 5 or 7) was lower than that of &x03B1;-CDE (G3) in KB cells, folate receptor (FR)-overexpressing cancer cells. Of the three Fol-PalphaCs (G3, DSF 2, 5 or 7), Fol-PalphaC (G3, DSF 5) had the highest gene transfer activity in KB cells. The activity of Fol-PalphaC (G3, DSF 5) was significantly higher than that of alpha-CDE (G3) in KB cells, but not in A549 cells, FR-negative cells. Negligible cytotoxicity of the pDNA complex with Fol-PalphaC (G3, DSF 5) was observed in KB cells or A549 cells up to a charge ratio of 100/1 (carrier/pDNA). The cellular association of the pDNA complex with Fol-PalphaC (G3, DSF 5) could be mediated by FR on KB cells, resulting in its efficient cellular uptake. Fol-PalphaC (G3, DSF 5) had higher binding affinity with folate binding protein (FBP) than alpha-CDE (G3), although the physicochemical properties of pDNA complex with Fol-PalphaC (G3, DSF 5) were almost comparable to that with alpha-CDE (G3), although the onset charge ratio and the compaction ability of Fol-PalphaC (G3, DSF 5) were slightly different. Fol-PalphaC (G3, DSF 5) tended to show higher gene transfer activity than alpha-CDE (G3) 12 h after intratumoral administration in mice. These results suggest that Fol-PalphaC (G3, DSF 5), not Fol-alpha-CDEs, could be potentially used as a FR-overexpressing cancer cell-selective DNA carrier.
Design and construction of a new Drosophila species, D.synthetica, by synthetic regulatory evolution
Authors: Moreno Eduardo 
Published: July 2019

AbstractHere, I merge the principles of synthetic biology^1,2^ and regulatory evolution^3-11^ to create a new species^12-15^ with a minimal set of known elements. Using preexisting transgenes and recessive mutations of Drosophila melanogaster, a transgenic population arises with small eyes and a different venation pattern that fulfills the criteria of a new species according to Mayr&apos;s &quot;Biological Species Concept&quot;^7,10^. The genetic circuit entails the loss of a non-essential transcription factor and the introduction of cryptic enhancers. Subsequent activation of those enhancers causes hybrid lethality. The transition from &quot;transgenic organisms&quot; towards &quot;synthetic species&quot;, such as Drosophila synthetica, constitutes a safety mechanism to avoid hybridization with wild type populations and preserve natural biodiversity^16-18^. Drosophila synthetica is the first transgenic organism that cannot hybridize with the original wild type population but remains fertile when crossed with other transgenic animals.
Worm-like carbon shell chains produced from wood
Authors: Suzuki Kyoko , Kita Hidetoshi , Saito Yukie , Suzuki Tsutomu , Sato Kazuhisa , Konno Toyohiko 
Published: July 2019

AbstractLarge-scale utilization of wood which command absolute majority in biomass for functional carbon precursors contributes to reduce greenhouse effect. Wood char generally has a limit on material usage because of its non-graphitic structure^1^, so we developed a new functional wood char by iron-, or nickel-catalyzed carbonization, which has a graphite-like structure with mesopores good for electroconductivity and liquid phase adsorption capacity for macro molecules^2-5^. However the fine structure of the wood char is still not clear. Here we report more than 70 wt % of iron-catalyzed wood char is filled with chained carbon shells formed by 3~20 defective stacking layers of carbon hexagonal planes, which look like nanometer-sized worms swarm. We name them &quot;carbon shell chains&quot;. The discussion of the formation mechanism reveals that the wood cell wall plays an important role for their efficient production. They are stable at 1800 &x00BA;C under vacuum, but in air, burn under 600 &x00BA;C, and are perfectly conversed into hydrogen and carbon monoxide in a short time by steam at 900 &x00BA;C. The control of their decomposition will bring out a new talent in the wood char as a big source of supply for nano-graphite or nano-graphene, for which nanometer size and edge effects have recently attracted considerable attention^6^. In addition, a simple and easy preparation of carbon shell chains implies that they may be naturally produced on or in the earth rich in iron, and might be misinterpreted as nano-worms, though most of them may decompose into organic gases.
Control of konzo in the Democratic Republic of Congo
Authors: Bradbury J. Howard , Mandombi Chretienne , Nahimana D , Banea J. P. , Denton Ian , Kuwa N 
Published: July 2019

AbstractKonzo is an upper motor neuron disease that causes irreversible paralysis of the legs mainly in children and young women^1,2^, due to consumption of large amounts of cyanogens from poorly processed cassava, the staple food of tropical Africa^3^. Konzo occurs in the Democratic Republic of Congo (DRC),Mozambique, Tanzania, Cameroon, Central African Republic and Angola. In March 2010 the wetting method, which removes cyanogens from cassava flour^4,5,6^, was taught to and used by the mothers of Kay Kalenge village. This reduced the total cyanide content of cassava flour to the FAO/WHO limit of 10ppm^7^. Cyanogen intake of school children, monitored by urinary thiocyanate analyses, decreased from mean values of 332 to 130 &x03BC;mole/L. The percentage of urine samples that exceeded the danger level of about 350 &x03BC;mole/L decreased from 26 in March 2010 to zero by May 2011. In 2009 there were many new cases of konzo, but none in 2010-2011. Konzo was first identified in1938 in Popokabaka area^8^ and it has now been prevented for the first time in the same area. This methodology is being used in three villages in Boko area and we believe it is the way to control konzo in tropical Africa.
The Starving Cell: Metabolic Syndrome as an Adaptive Process
Authors: Golomb Beatrice 
Published: July 2019

AbstractMetabolic syndrome (MetS) is commonly presumed to stem from obesity, with both propelled by energy surfeit: positive balance of calories consumed to energy expended. A complementary thesis is proposed: that episodes of cell energy deficit (not expressly calorie deficit) drive MetS – the “Starving Cell.”Risk factors for MetS include hypoxemia from sleep apnea, severe calorie debt, mitochondrial dysfunction, oxidative stress; and sleep restriction, illness, surgery, trauma, cold. Each fosters inadequate cell energy, hampering production or boosting demand. MetS factors support energy: glucose, triglycerides, abdominal/visceral fat – and blood pressure, sustaining perfusion. Additional energy-supportive adaptations co-occur in MetS: e.g. increased free fatty acids and deposition of metabolically active ectopic fat. Indeed, increased appetite/calories and reduced activity – features of the energy surfeit model – also arise as adaptations to cell energy deprivation. Among persons who are overweight, the risk for MetS remains determined by energy deprivation contributors.The Thrifty Gene hypothesis, and MetS promotion by fetal energy deprivation, prefigure the Starving Cell thesis. However, evidence is vastly more comprehensive in connecting cell energy deprivations to MetS elements: generalizing the sources of energy deficit that dispose to MetS; the populations vulnerable to their impact; and the forms of adaptation implemented to protect energy. This clarifies why MetS factors cohere; and why other energy-supportive adaptations attend them. It explains bidirectional MetS associations; and why MetS factors appear “paradoxically” protective in some populations. It generates predictions, and suggests approaches to MetS mitigation that complement and modify existing approaches, and may augment their efficacy.
The Five Stars of Online Journal Articles – an article evaluation framework
Authors: Shotton David 
Published: July 2019

AbstractI propose five factors – peer review, open access, enriched content, available datasets and machine-readable metadata – as the Five Stars of Online Journal Articles, a constellation of five independent criteria within a multi-dimensional publishing universe against which online journal articles can be evaluated, to see how well they match up to current visions for research communications. Achievement along each of these publishing axes can vary, analogous to the different stars within the constellation shining with varying luminosities. I suggest a five-point scale for each by which a journal article can be evaluated, and a diagrammatic representation for such evaluations. While the criteria adopted for these scales are somewhat arbitrary, and while the rating of a particular article on each axis may involve elements of subjective judgment, these Five Stars of Online Journal Articles provide a conceptual framework by which to judge the degree to which any article achieves or falls short of the ideal, which should be useful to authors, editors and publishers. I exemplify such evaluations using my own recent publications of relevance to semantic publishing.