gebhart/patrepeval huggingface dataset:
Nonribosomal Polypeptide Synthesis: The Biosynthesis of a Cyclic Peptide Antibiotic, Gramicidin S (1969)

Peptide antibiotics are produced by a variety of microorganisms in special physiological circumstances (see Gottlieb and Shaw, 1967). Certain structural features of these substances indicate that the biosynthetic mechanisms must differ from those of proteins. For example, residues other than the 20 or so L-α-amino acids found in proteins are frequently present (including D-amino acids, hydroxy acids, and fatty acids), the molecules are often cyclic, and analog-type substitutions of individual residues are very common. Much evidence (well summarized by Katz, 1968) has been accumulated to date proving that ribosomes, transfer RNA (tRNA) and messenger RNA (mRNA) are not required for the formation of the antibiotic polypeptides. We have studied the biosynthesis of the cyclic decapeptide gramicidin S (Fig. 1) in order to gain an insight into the enzymatic mechanisms involved, and to make possible a detailed comparison with protein synthesis as carried out by ribosomes.
Autocrine hepatocyte growth factor/scatter factor-Met signaling induces transformation and the invasive/metastastic phenotype in C127 cells. (1996)

Hepatocyte growth factor/scatter factor (HGF/SF) is a pleiotropic effector of cells expressing the Met tyrosine kinase receptor. C127 is a non-tumorigenic mouse cell line which expresses negligible levels of HGF/SF and Met proteins. In the present report we have generated C127 cells which overexpress HGF/SF and/or Met proteins, and have analysed the effect of HGF/SF-Met signaling in these cells. We show that this signaling pathway stimulates the growth and invasiveness of C127 cells in vitro and that cells overexpressing both HGF/SF and Met proteins (but neither alone) are phenotypically transformed and highly tumorigenic and metastatic in vivo. Our data unequivocally demonstrates the autocrine dependency of HGF/SF-Met-induced transformation and metastasis in this system and supports the theory that the inappropriate expression of HGF/SF and Met proteins could play a role in the development and spread of human tumors. In addition, this system may be useful for identifying metastasis-associated genes that are activated by HGF/SF-Met signaling.
Phosphatidylinositol-3′ Kinase Is Not Required for Mitogenesis or Internalization of the Flt3/Flk2 Receptor Tyrosine Kinase (1996)

Flt3/Flk2 is a receptor tyrosine kinase that is expressed on early hematopoietic progenitor cells. Flt3/Flk2 belongs to a family of receptors, including Kit and colony-stimulating factor-1R, which support growth and differentiation within the hematopoietic system. The Flt3/Flk2 ligand, in combination with other growth factors, stimulates the proliferation of hematopoietic progenitors of both lymphoid and myeloid lineages in vitro. We report that phosphatidylinositol 3'-kinase (PI3K) binds to a unique site in the carboxy tail of murine Flt3/Flk2. In distinction to Kit and colony-stimulating factor-1R, mutant receptors unable to couple to PI3K and expressed in rodent fibroblasts or in the interleukin 3-dependent cell line Ba/F3 provide a mitogenic signal comparable to wild-type receptors. Flt3/Flk2 receptors that do not bind to PI3K also normally down-regulate, a function ascribed to PI3K in the context of other receptor systems. These data point to the existence of other unidentified pathways that, alone or in combination with PI3K, transduce these cellular responses following the activation of Flt3/Flk2.
Breast Cancer (1992)

BREAST cancer is a major public health problem of great interest and importance to physicians in a variety of specialties. Since this topic was last reviewed in the Journal,1 the incidence of the disease has increased dramatically, heightening concern among physicians and women in general. In addition, long-term results are now available from clinical trials initiated in the 1970s and 1980s to evaluate the usefulness of early detection with mammography and physical examination, breast-conserving treatment with limited breast surgery and irradiation, and adjuvant systemic therapy with hormonal therapy and chemotherapy. Furthermore, in the light of newly gained knowledge, new . . .
High Quality ZnSe and ZnS Nanocrystals Formed by Activating Zinc Carboxylate Precursors (2004)

Nearly monodisperse ZnSe and ZnS nanocrystals were formed in noncoordinating solvents using alternative precursors. The parameter window for the growth of high quality zinc chalcogenide nanocrystals was found to be much narrower than that of the corresponding cadmium chalcogenide nanocrystals. In contrast to syntheses performed in coordinating solvents, generic oxygen containing ligands, such as fatty acids, were found to be reasonable ligands for the formation of ZnSe and ZnS nanocrystals. Activation of the zinc precursor (zinc fatty acid salts) by alkylamines was found to be critical for the formation of high quality ZnSe nanocrystals. The photoluminescence (PL) quantum yield (QY) of ZnSe nanocrystals reached as high as 50% with a full width of half-maximum (fwhm) as narrow as 14 nm. The band gap PL of ZnS nanocrystals was always mixed with a deep-trap tail. The PL fwhm of the band gap emission of the ZnS nanocrystals was typically between 10 and 12 nm.
Error analysis of tissue resistivity measurement (2002)

We identified the error sources in a system for measuring tissue resistivity at eight frequencies from 1 Hz to 1 MHz using the four-terminal method. We expressed the measured resistivity with an analytical formula containing all error terms. We conducted practical error measurements with in-vivo and bench-top experiments. We averaged errors at all frequencies for all measurements. The standard deviations of error of the quantization error of the 8-bit digital oscilloscope with voltage averaging, the nonideality of the circuit, the in-vivo motion artifact and electrical interference combined to yield an error of +/- 1.19%. The dimension error in measuring the syringe tube for measuring the reference saline resistivity added +/- 1.32% error. The estimation of the working probe constant by interpolating a set of probe constants measured in reference saline solutions added +/- 0.48% error. The difference in the current magnitudes used during the probe calibration and that during the tissue resistivity measurement caused +/- 0.14% error. Variation of the electrode spacing, alignment, and electrode surface property due to the insertion of electrodes into the tissue caused +/- 0.61% error. We combined the above errors to yield an overall standard deviation error of the measured tissue resistivity of +/- 1.96%.
Regional blood flow during periodic acceleration (2001)

Periodic sinusoidal inertial forces in the spinal axis increase blood flow to tissues. The increased blood flow is reversible and may be caused by vasodilation secondary to local mediator release. These effects may be desirable in clinical conditions of low tissue oxygen delivery and perfusion.
The rand 36‐item health survey 1.0 (1993)

Recently, Ware and Sherbourne published a new short-form health survey, the MOS 36-Item Short-Form Health Survey (SF-36), consisting of 36 items included in long-form measures developed for the Medical Outcomes Study. The SF-36 taps eight health concepts: physical functioning, bodily pain, role limitations due to physical health problems, role limitations due to personal or emotional problems, general mental health, social functioning, energy/fatigue, and general health perceptions. It also includes a single item that provides an indication of perceived change in health. The SF-36 items and scoring rules are distributed by MOS Trust, Inc. Strict adherence to item wording and scoring recommendations is required in order to use the SF-36 trademark. The RAND 36-Item Health Survey 1.0 (distributed by RAND) includes the same items as those in the SF-36, but the recommended scoring algorithm is somewhat different from that of the SF-36. Scoring differences are discussed here and new T-scores are presented for the 8 multi-item scales and two factor analytically-derived physical and mental health composite scores.
DNA topoisomerase I in the mouse central nervous system: Age and sex dependence (2005)

Topoisomerase I (topo I) is a nuclear enzyme responsible for the topological state of DNA and therefore participates in most DNA transactions, particularly in transcription. Topo I, a ubiquitous enzyme, was identified and characterized in various cell types and tissues; however, the characterization of topo I in the intact central nervous system was not performed. Here we investigated, for the first time, the activity, level, and distribution pattern of topo I in the various selected brain regions in the mouse. In the visual cortex, cerebellum, and striatum the activity of topo I was 3-4-fold higher compared to that found in the hippocampus and hypothalamus. Immunohistochemical and immunofluorescence analyses revealed specific distribution patterns of topo I protein in neurons of each of the areas examined. The highest topo I levels were observed in inhibitory neurons. In addition to the expected nuclear localization of this protein, some neurons exhibited significant cytoplasmic content as well. The activity and level of topo I is age- and gender-dependent. It increases from birth to maturity and decreases, more significantly in males, with senescence. These results point to a possible importance and involvement of topo I activity and regulation in various brain functions.
Size effect on the melting temperature of gold particles (1976)

Recently, small particles have been shown to exhibit a melting temperature which depends on the particle size. The various possible experimental methods have been compared and measurements of the melting points of small gold particles have been made using a scanning electron-diffraction technique. This method was applied to particles having diameters down to 20 \AA{}. Consideration of the size distribution over an entire sample makes it necessary to carry out a careful analysis of the experimental results in order to deduce the melting temperature of particles having a well-defined diameter. The experimental results are quantitatively in good agreement with two phenomenological models. The first model describes the equilibrium condition for a system formed by a solid particle, a liquid particle having the same mass, and their saturating vapor phase. The second model assumes the preexistence of a liquid layer surrounding the solid particle and describes the equilibrium of such a system in the presence of the vapor phase. In order to permit a better comparison between both models, a new expression for the thermodynamic equilibrium condition has been derived in the present work. In the case of the first model, the agreement was obtained using only the physical constants of massive gold. In applying the second model, however, one is compelled to assume the existence of a liquid layer having a thickness of about 6 \AA{}.
Ibudilast attenuates astrocyte apoptosis via cyclic GMP signalling pathway in an in vitro reperfusion model (2001)

We examined the effect of 3-isobutyryl-2-isopropylpyrazolo[1,5-a]pyridine (ibudilast), which has been clinically used for bronchial asthma and cerebrovascular disorders, on cell viability induced in a model of reperfusion injury. Ibudilast at 10 - 100 microM significantly attenuated the H(2)O(2)-induced decrease in cell viability. Ibudilast inhibited the H(2)O(2)-induced cytochrome c release, caspase-3 activation, DNA ladder formation and nuclear condensation, suggesting its anti-apoptotic effect. Phosphodiesterase inhibitors such as theophylline, pentoxyfylline, vinpocetine, dipyridamole and zaprinast, which increased the guanosine-3',5'-cyclic monophosphate (cyclic GMP) level, and dibutyryl cyclic GMP attenuated the H(2)O(2)-induced injury in astrocytes. Ibudilast increased the cyclic GMP level in astrocytes. The cyclic GMP-dependent protein kinase inhibitor KT5823 blocked the protective effects of ibudilast and dipyridamole on the H(2)O(2)-induced decrease in cell viability, while the cyclic AMP-dependent protein kinase inhibitor KT5720, the cyclic AMP antagonist Rp-cyclic AMPS, the mitogen-activated protein/extracellular signal-regulated kinase inhibitor PD98059 and the leukotriene D(4) antagonist LY 171883 did not. KT5823 also blocked the effect of ibudilast on the H(2)O(2)-induced cytochrome c release and caspase-3-like protease activation. These findings suggest that ibudilast prevents the H(2)O(2)-induced delayed apoptosis of astrocytes via a cyclic GMP, but not cyclic AMP, signalling pathway.
DNA microarrays : a practical approach (1999)

DNA microarrays, or biochips, are small glass chips embedded with ordered rows of DNA and by providing a massive parallel platform for data gathering represent a fundamental technical advance in biomedical research. Such biochips enable the use of advanced fabrication, detection, and data mining technologies that allow data gathering at an unprecedented rate. The first chapter is an introduction to the technology of DNA microarrays, emphasizing the methodological fundamentals of biochips. The next two chapters describe the use of confocal scanning in microarray detection and techniques for the efficient cloning and screening of differentially expressed genes. Chapter 4 describes assay optimization for enzymatic assays and chapter 5 antisense scanning arrays. This is followed by a chapter on the manufacture of molecular arrays using ink-jet printing technology. Chapter 7 describes gene expression analysis from cDNA microarrays and then chapter 8 covers the use of expression data in bioinformatics. Chapter 9 describes the use of active microelectronic arrays for DNA hybridization analysis and the last chapter details the use of microarray technology in pharmacogenomics. This book is intended for genomics researchers investigating patterns of gene expression (and the relationship with disease) wanting to take advantage of this powerful new technology.
Re-examining the Size/Charge Paradigm: Differing in Vivo Characteristics of Size- and Charge-Matched Mesoporous Silica Nanoparticles (2013)

The combination of nanoparticle (NP) size, charge, and surface chemistry (e.g., extent of modification with polyethylene glycol (PEG)) is accepted as a key determinant of NP/cellular interactions. However, the influence of spatial arrangement and accessibility of the charged molecules on the NP surface vis-à-vis the average surface charge (zeta (ζ) potential) is incompletely understood. Here we demonstrate that two types of mesoporous silica nanoparticles (MSNP) that are matched in terms of primary and hydrodynamic particle size, shape, pore structure, colloidal stability, and ζ potential, but differ in surface chemistry, viz. the spatial arrangement and relative exposure of surface amines, have profoundly different interactions with cells and tissues when evaluated in vitro and in vivo. While both particles are ∼50 nm in diameter, PEGylated, and positively charged (ζ = +40 mV), PEG-PEI (MSNPs modified with exposed polyamines), but not PEG-NMe3+ (MSNP modified with distributed, obstructed amines) rapidly bind serum proteins, diverse cells types in vitro, and endothelial and white blood cells in vivo (ex ovo chick embryo model). This finding helps elucidate the relative role of surface exposure of charged molecules vs ζ potential in otherwise physicochemically matched MSNP and highlights protein corona neutrality as an important design consideration when synthesizing cationic NPs for biological applications.
Opioid responsiveness of cancer pain syndromes caused by neuropathic or nociceptive mechanisms (1994)

We performed a combined analysis of the results from four controlled single-dose relative-potency studies to assess the impact of inferred pain mechanism on the response to an opioid drug. A total of 168 patients received 474 administrations of either morphine or heroin, and we assessed the analgesic response during a 6-hour period with visual analog scales. We summarized this as a total pain relief (TOTPAR) score. Two experienced pain clinicians reviewed information about pain characteristics and designated each case according to the inferred pain mechanism (neuropathic, nociceptive, or mixed) and the degree of confidence in the inferred mechanism (definite versus probable/possible). They grouped the cases as follows: nociceptive pain only (n = 205), neuropathic pain only (n = 49), and mixed (n = 220). We compared pain relief achieved by patients with different mechanisms, with TOTPAR adjusted for significant covariates (duration of prior opioid administration, doses of opioid administered in the previous 48 hours, pain intensity at the start of the study, BUN:creatinine ratio, and dose of administered opioid). The adjusted mean TOTPAR score of the group with any neuropathic pain was significantly lower than that of the group with nociceptive pain only (26.1 versus 20.4, p = 0.02). The score of the group with definite nociceptive pain alone (adjusted mean TOTPAR = 28.0) was significantly higher than scores of the groups with possible/probable nociceptive pain (TOTPAR = 19.9), mixed mechanisms (TOTPAR = 20.2), definite neuropathic pain alone (TOTPAR = 20.6), and possible/probable neuropathic pain alone (TOTPAR = 22.9).(ABSTRACT TRUNCATED AT 250 WORDS)
Carbon Nanotube Fiber Microelectrodes (2003)

Carbon nanotube (CNT) fibers have been used to fabricate microelectrodes with an attractive electrochemical behavior. By combining the advantages of CNT materials and fiber microelectrodes, the new material expands the scope of CNT-based electrochemical devices. The CNT fiber offers a marked decrease in the overvoltage for the NADH, dopamine, and hydrogen peroxide and circumvents NADH surface fouling effects. Heat treatment is shown to be extremely useful for activating the CNT fiber surfaces for electron transfer. SEM imaging and cyclic-voltammetric data indicate that the heat treatment leads to the removal of nonconducting residues and exposure of a "fresh" CNT surface. The new electrode material thus presents new opportunities for a wide range of electrochemical and analytical applications.
Serum chromium and angiographically determined coronary artery disease. (1978)

Human aortas sampled from populations where there is little advanced atheromatous plaque formation contain higher concentrations of chromium than do aortas from populations in which atheromatosis is prevalent. In the present study serum cholesterol, triacylglycerols, and chromium (Cr3+) concentrations were measured in 32 subjects in whom coronary artery disease was assessed by cineangiography. The distribution of subjects with diseased and normal arteries overlapped below 5.50 microgram of chromium per liter. Only subjects free of coronary artery disease had chromium concentrations greater than or equal to 5.50 microgram/liter. The role of chromium was assessed in the context of the selected risk factors: cholesterol, triacylglycerols, and systolic and diastolic blood pressure. The group with coronary artery disease had significantly lower serum chromium concentrations than did the group with normally patent arteries.
DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs (2002)

Although the information of cDNAs is indispensable for analyzing gene function, most of the cDNA sequences stored in current databases are imperfect in the sense that they lack the precise information of 5' end termini. To overcome this difficulty, we have developed the oligo-capping method to obtain full-length cDNAs, the information of which has been partly deposited in public databases. In this study, we further constructed human cDNA libraries enriched in clones containing the cap structure to systematically explore the 5' end structure of expressed genes. Of approximately 217 402 5' end sequences obtained, 111 382 have been matched to cDNA sequences of known genes (7889 genes) and are presented in our new database, DataBase of Transcriptional Start Sites (DBTSS; http://elmo.ims.u-tokyo.ac.jp/dbtss/). Sequence comparison between our entries and those of a reference sequence database, RefSeq, revealed that 4683 (34%) of RefSeq sequences should be extended towards the 5' ends. We also mapped each sequence on the human draft genome sequence to identify its transcriptional start site, which provides us with more detailed information on distribution patterns of transcriptional start sites and adjacent regulatory regions.
Identification and analysis of a new tobacco-specific N-nitrosamine, 4-(methylnitrosamino)-4-(3-pyridyl)-1-butanol (1987)

A new tobacco-specific N-nitrosamine, 4-(methylnitrosamino)-4-(3-pyridyl)-1-butanol (iso-NNAL) was isolated from snuff tobacco. Structural characterization of this N-nitrosamine was confirmed by mass spectral analysis. Five popular US brands of moist snuff and three popular US brands of dry snuff tobacco were analyzed for moisture, nicotine and tobacco-specific N-nitrosamines. The moisture content varied from 20 to 53% in moist snuff and from 4.7 to 5.6% in dry snuff. The nicotine levels in these samples varied from 0.6 to 3.2%. The newly identified iso-NNAL was present in concentrations ranging from 0.07 to 2.5 p.p.m. whereas other tobacco-specific N-nitrosamines, N-nitrosonornicotine, N-nitrosoanatabine, N-nitrosoanabasine and 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone were found to range from 0.1 to 178 p.p.m. Iso-NNAL was not detected in mainstream and sidestream smoke of cigarettes. Iso-NNAL is genotoxic in primary rat hepatocytes; its tumorigenic properties are currently being tested in mice and rats.
Population Dynamics, Labour and Small-Holder Farmers' Productivity in Southeast Nigeria (2012)

The study analyzed the population dynamics, labour use and food productivity of small holder farmers in Southeastern Nigeria.  A total of 120 farmer respondents involved in Cassava-based mixed cropping randomly selected (40 each), from three out of the six States that made up the Southeast geo-political zones, was used for the study.  Both primary and secondary sources of data were used.  Simple statistical tools, gross and net margins as well as regression analysis were used to analyze the data collected.  The result of the analysis revealed that farming though profitable is still at subsistence level with a net margin of N28,360 ($US180.64) per hectare, about 46% of the farmers could not afford or access the use of fertilizers and modern inputs required for agricultural intensification prevalent in the area..  The tenure arrangement was by inheritance (64%), which caused much land fragmentations and pressure on limited arable land.  Labour had the highest average factor cost (40.86%), due to high cost of hired labour. The regression result showed that farm size (X 2 ) and fertilizer application (X 4 ), are significant (P=0.01), and positively correlated with crop production.  Conversely, population density (X 1 ) and cropping density (X 3 ) and labour X 7 ) were significant (P=0.01), but negatively correlated with crop output.  To ensure higher productivity and net profit, the study recommends that farmers should be provided with required farm inputs at affordable prices by government and land use act decree of 1978 should be reviewed to make land available to genuine farmers for commercial and mechanized farming.  Birth control should be encouraged. Key words: Population, Labour, Productivity, Small-holder farmers