gebhart/patrepeval huggingface dataset:
Nucleotide sequence and transcriptional analysis of theE. coli ushA gene, encoding periplasmic UDP-sugar hydrolase (5'-nucleotidase): regulation of theushAgene, and the signal sequence of its encoded protein product (1986)

The DNA sequence of the ushA gene, encoding UDP-sugar hydrolase (5'-nucleotidase), has been determined. The amino-terminal sequence encodes a signal peptide whose predicted processing site is confirmed by N-terminal amino acid analysis of purified mature UshA protein. The signal sequence contains a concentration of rare codons in comparison with the mature sequence. The origins of transcription from the ushA promoter have been determined, using primer extension. Three transcripts, originating within a 6 bp region, were identified and might be related to three overlapping potential -10 hexamers in the ushA promoter region. There was a discernable change in the relative proportion of these transcripts during growth-phase regulation of the ushA gene.
Enzyme-Coated Carbon Nanotubes as Single-Molecule Biosensors (2003)

We demonstrate the use of individual semiconducting single-wall carbon nanotubes as versatile biosensors. Controlled attachment of the redox enzyme glucose oxidase (GOx) to the nanotube sidewall is achieved through a linking molecule and is found to induce a clear change of the conductance. The enzyme-coated tube is found to act as a pH sensor with large and reversible changes in conductance upon changes in pH. Upon addition of glucose, the substrate of GOx, a steplike response can be monitored in real time, indicating that our sensor is also capable of measuring enzymatic activity at the level of a single nanotube. This first demonstration of nanotube-based biosensors provides a new tool for enzymatic studies and opens the way to biomolecular diagnostics.
A framework for automatic landmark identification using a new method of nonrigid correspondence (2000)

A framework for automatic landmark identification is presented based on an algorithm for corresponding the boundaries of two shapes. The auto-landmarking framework employs a binary tree of corresponded pairs of shapes to generate landmarks automatically on each of a set of example shapes. The landmarks are used to train statistical shape models, known as point distribution models. The correspondence algorithm locates a matching pair of sparse polygonal approximations, one for each of a pair of boundaries by minimizing a cost function, using a greedy algorithm. The cost function expresses the dissimilarity in both the shape and representation error (with respect to the defining boundary) of the sparse polygons. Results are presented for three classes of shape which exhibit various types of nonrigid deformation.
Redesigning secondary structure to invert coenzyme specificity in isopropylmalate dehydrogenase. (1996)

Rational engineering of enzymes involves introducing key amino acids guided by a knowledge of protein structure to effect a desirable change in function. To date, all successful attempts to change specificity have been limited to substituting individual amino acids within a protein fold. However, the infant field of protein engineering will only reach maturity when changes in function can be generated by rationally engineering secondary structures. Guided by x-ray crystal structures and molecular modeling, site-directed mutagenesis has been used to systematically invert the coenzyme specificity of Thermus thermophilus isopropylmalate dehydrogenase from a 100-fold preference for NAD to a 1000-fold preference for NADP. The engineered mutant, which is twice as active as wild type, contains four amino acid substitutions and an alpha-helix and loop that replaces the original beta-turn. These results demonstrate that rational engineering of secondary structures to produce enzymes with novel properties is feasible.
Preliminary Classification of Matrix Pores in Mudrocks (2010)

Investigation of pore networks in mudrocks is important because shale gas has become a major exploration target and understanding pore networks of these very fine grained rocks is essential to an understanding of production rates and reserves. However, identifying and characterizing mudrock pores are difficult because of their nanometer to micron scale. With development of argon-milling surface-preparation techniques and use of field-emission scanning-electron microscopes, we can now image pores as small as 5 nanometers (nm). A number of different pore types have been identified, and combinations of pore types that constitute pore networks in different mudrock suites are variable. Basic pore types are divided into those associated with organic matter and those that are not. Pores within organic matter appear to be related to thermal maturation of organic matter. Nonorganic-matter pores can be divided into interparticle and intraparticle types and are strongly affected by mechanical and chemical diagenesis. Interparticle pores occur between grains and crystals, whereas intraparticle pores are found within the boundaries of grains. The latter include dissolution molds in fossils and particles, intercrystalline pores within framboids of pyrite, fluid inclusions in crystals, and pores within phosphate grains. Pore types vary in variety and abundance within differing shale-gas reservoir systems. Mississippian Barnett mudrock pores are dominantly associated with organic matter, Jurassic Haynesville/Bossier mudrocks contain mostly interparticle pores, and Cretaceous Pearsall mudrocks contain primarily intraparticle pores. Mudrock pore networks can be overprinted by fractures, producing a dual pore system.
Measuring Security (2011)

The field of computer and communications security begs for a foundational science to guide system design and to reveal the safety, security, and possible fragility of the complex systems we depend on today. To achieve this goal, we must devise suitable metrics for objectively comparing and evaluating the security of system designs and organizations.
Aging and Cancer-Related Loss of Insulin-like Growth Factor 2 Imprinting in the Mouse and Human Prostate (2008)

Loss of imprinting (LOI) is an epigenetic alteration involving loss of parental origin-specific expression at normally imprinted genes. A LOI for Igf2, a paracrine growth factor, is important in cancer progression. Epigenetic modifications may be altered by environmental factors. However, is not known whether changes in imprinting occur with aging in prostate and other tissues susceptible to cancer development. We found a LOI for Igf2 occurs specifically in the mouse prostate associated with increased Igf2 expression during aging. In older animals, expression of the chromatin insulator protein CTCF and its binding to the Igf2-H19 imprint control region was reduced. Forced down-regulation of CTCF leads to Igf2 LOI. We further show that Igf2 LOI occurs with aging in histologically normal human prostate tissues and that this epigenetic alteration was more extensive in men with associated cancer. This finding may contribute to a postulated field of cancer susceptibility that occurs with aging. Moreover, Igf2 LOI may serve as a marker for the presence of prostate cancer.
The Changing Automotive Environment: High-Temperature Electronics (2004)

The underhood automotive environment is harsh and current trends in the automotive electronics industry will be pushing the temperature envelope for electronic components. The desire to place engine control units on the engine and transmission control units either on or in the transmission will push the ambient temperature above 125/spl deg/C. However, extreme cost pressures, increasing reliability demands (10 year/241 350 km) and the cost of field failures (recalls, liability, customer loyalty) will make the shift to higher temperatures occur incrementally. The coolest spots on engine and in the transmission will be used. These large bodies do provide considerable heat sinking to reduce temperature rise due to power dissipation in the control unit. The majority of near term applications will be at 150/spl deg/C or less and these will be worst case temperatures, not nominal. The transition to X-by-wire technology, replacing mechanical and hydraulic systems with electromechanical systems will require more power electronics. Integration of power transistors and smart power devices into the electromechanical actuator will require power devices to operate at 175/spl deg/C to 200/spl deg/C. Hybrid electric vehicles and fuel cell vehicles will also drive the demand for higher temperature power electronics. In the case of hybrid electric and fuel cell vehicles, the high temperature will be due to power dissipation. The alternates to high-temperature devices are thermal management systems which add weight and cost. Finally, the number of sensors in vehicles is increasing as more electrically controlled systems are added. Many of these sensors must work in high-temperature environments. The harshest applications are exhaust gas sensors and cylinder pressure or combustion sensors. High-temperature electronics use in automotive systems will continue to grow, but it will be gradual as cost and reliability issues are addressed. This work examines the motivation for higher temperature operation, the packaging limitations even at 125/spl deg/C with newer package styles and concludes with a review of challenges at both the semiconductor device and packaging level as temperatures push beyond 125/spl deg/C.
Analysis of Sensing margin in Silicon-On-ONO (SOONO) Device for the Capacitor-less RAM Applications (2007)

In this study, we compared sensing margin according to the back gate bias and body doping concentration. We achieved large sensing margin of 62 uA/um at L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">G</sub> = 87 run and demonstrated sensing margin of 45 uA/um with L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">G</sub> = 47 nm that is the smallest device ever reported for the floating body RAM. For the scaling down to the sub 50 nm gate length, we should reduce the body thickness for the SCE with optimum body doping condition . Possibility of scaling down with the capacitor-less RAM is shown to the sub 50 nm from this result.
Transposon-Derived Brucella abortus Rough Mutants Are Attenuated and Exhibit Reduced Intracellular Survival (1998)

The O antigen of Brucella abortus has been described as a major virulence determinant based on the attenuated survival of fortuitously isolated rough variants. However, the lack of genetic definition of these mutants and the virulence of naturally occurring rough species, Brucella ovis and Brucella canis, has confused interpretation. To better characterize the role of O antigen in virulence and survival, transposon mutagenesis was used to generate B. abortus rough mutants defective in O-antigen presentation. Sequence analysis of DNA flanking the site of Tn5 insertion was used to verify insertion in genes encoding lipopolysaccharide (LPS) biosynthetic functions. Not surprisingly, each of the rough mutants was attenuated for survival in mice, but unexpected differences among the mutants were observed. In an effort to define the basis for the observed differences, the structure of the rough LPS and the sensitivity of these mutants to individual killing mechanisms were examined in vitro. All of the B. abortus rough mutants exhibited a 4- to 5-log-unit increase, compared to the smooth parental strain, in sensitivity to complement-mediated lysis. Little change was evident in the sensitivity of these organisms to hydrogen peroxide, consistent with an inability of O antigen to exclude relatively small molecules. Sensitivity to polymyxin B, which was employed as a model cationic, amphipathic peptide similar to defensins found in phagocytic cells, revealed survival differences among the rough mutants similar to those observed in the mouse. One mutant in particular exhibited hypersensitivity to polymyxin B and reduced survival in mice. This mutant was characterized by a truncated rough LPS. DNA sequence analysis of this mutant revealed a transposon interruption in the gene encoding phosphomannomutase (pmm), suggesting that this activity may be required for the synthesis of a full-length core polysaccharide in addition to O antigen. B. abortus O antigen appears to be essential for extra- and intracellular survival in mice.
Identification of transcriptome induced in roots of maize seedlings at the late stage of waterlogging (2010)

The late response to waterlogging in maize roots involves a broad spectrum of genes, which are mainly associated with two response processes: defense at the early stage and adaption at the late stage. Signal transduction plays a key role in activating genes related to the tolerance mechanism for survival during prolonged waterlogging. The crosstalk between carbon and amino acid metabolism reveals that amino acid metabolism performs two main roles at the late stage: the regulation of cytoplasmic pH and energy supply through breakdown of the carbon skeleton.
Free radicals, oxidative stress, and antioxidants in human health and disease (1998)

Free radicals and other reactive oxygen species (ROS) are constantly formed in the human body. Free-radical mechanisms have been implicated in the pathology of several human diseases, including cancer, atherosclerosis, malaria, and rheumatoid arthritis and neurodegenerative diseases. For example, the superoxide radical (O<sub>2</sub> <sup>·-</sup>) and hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>) are known to be generated in the brain and nervous system <i>in vivo</i>, and several areas of the human brain are rich in iron, which appears to be easily mobilizable in a form that can stimulate free-radical reactions. Antioxidant defenses to remove O<sub>2</sub> <sup>·-</sup> and H<sub>2</sub>O<sub>2</sub> exist. Superoxide dismutases (SOD) remove O<sub>2</sub> <sup>·-</sup> by greatly accelerating its conversion to H<sub>2</sub>O<sub>2</sub>. Catalases in peroxisomes convert H<sub>2</sub>O<sub>2</sub> into water and O<sub>2</sub> and help to dispose of H<sub>2</sub>O<sub>2</sub> generated by the action of the oxidase enzymes that are located in these organelles. Other important H<sub>2</sub>O<sub>2</sub>-removing enzymes in human cells are the glutathione peroxidases. When produced in excess, ROS can cause tissue injury. However, tissue injury can itself cause ROS generation (e.g., by causing activation of phagocytes or releasing transition metal ions from damaged cells), which may (or may not, depending on the situation) contribute to a worsening of the injury. Assessment of oxidative damage to biomolecules by means of emerging technologies based on products of oxidative damage to DNA (e.g., 8-hydroxydeoxyguanosine), lipids (e.g., isoprostanes), and proteins (altered amino acids) would not only advance our understanding of the underlying mechanisms but also facilitate supplementation and intervention studies designed and conducted to test antioxidant efficacy in human health and disease.
A non-(1–84) circulating parathyroid hormone (PTH) fragment interferes significantly with intact PTH commercial assay measurements in uremic samples (1998)

We have previously shown that the Nichols assay for intact parathyroid hormone (I-PTH) reacts with a non-(1-84) molecular form of PTH. This form behaves as a carboxy-terminal fragment and accumulates in renal failure, accounting for 40-60% of the measured immunoreactivity. We wanted to see whether this was a common event with other commercial two-site I-PTH assays. We thus compared the ability of three commercial kits [Nichols (NL), Incstar (IT), and Diagnostic System Laboratories (DSL)] to measure I-PTH in 112 renal failure patients and to detect hPTH(1-84) and non-(1-84)PTH on HPLC profiles of serum pools from uremic patients with I-PTH concentrations of 10-100 pmol/L. The behavior of synthetic hPTH(7-84), a fragment possibly related to non-(1-84)PTH was also compared with hPTH(1-84) in the three assays. The I-PTH concentrations measured with the three assays in the 112 uremic samples were highly related (r2 > or = 0.89, P < 0.0001), and the values measured with NL were, on average, 23% higher than IT. Values measured with DSL were 23% and 56% higher than IT for values less than and more than 40 pmol/L, respectively. The three assays detected two HPLC peaks on four different profiles corresponding to hPTH(1-84) and non-(1-84)PTH. This last peak represented 36 +/- 8.4% of the immunoreactivity with NL, 24 +/- 5.5% with IT, and 25 +/- 2.8% with DSL (NL vs IT or DSL: P < 0.05). These differences were confirmed by a 50% lower immunoreactivity to hPTH(7-84) compared with hPTH(1-84) for IT and DSL but not for NL. These results suggest that most of the two-site I-PTH assays would cross-react with non-(1-84)PTH material, thus explaining about one-half of the 2-2.5 x higher I-PTH concentrations reported in uremic patients without bone involvement than in subjects without uremia.
Remarks on Some Nonparametric Estimates of a Density Function (1956)

This note discusses some aspects of the estimation of the density function of a univariate probability distribution. All estimates of the density function satisfying relatively mild conditions are shown to be biased. The asymptotic mean square error of a particular class of estimates is evaluated.
Ribonucleoprotein complexes of hepatitis delta virus (1993)

Human hepatitis delta virus (HDV) is a subviral satellite agent of hepatitis B virus (HBV). The envelope proteins of HDV are provided by the helper virus, HBV, but very little is known about the internal structure of HDV. The particles contain multiple copies of the delta antigen and an unusual RNA genome that is small, about 1,700 nucleotides in length, single stranded, and circular. By using UV cross-linking, equilibrium density centrifugation, and immunoprecipitation, we obtained evidence consistent with the interpretation that delta antigen and genomic RNA form a stable ribonucleoprotein (RNP) complex within the virion. Furthermore, electron-microscopic examination of the purified viral RNP revealed a roughly spherical core-like structure with a diameter of 18.7 +/- 2.5 nm. We also isolated HDV-specific RNP structures from the nuclei of cells undergoing HDV genome replication; both the genome and antigenome (a complement of the genome) of HDV were found to be in such complexes. From the equilibrium density analyses of the viral and nuclear RNPs, we were able to deduce the number of molecules of delta antigen per molecule of HDV RNA. For virions, this number was predominantly ca. 70, which was larger than for the nuclear RNPs, which were more heterogeneous, with an average value of ca. 30.
Aspergillus, 50 years on (1994)

Part 1 Introduction: the early history, A. Roper humble beginnings at Glasgow university, E. Forbes pedigree of the authors, S.D. Martinelli aspergillus nidulans as an experimental organism, S.D. Martinelli. Part 2 Metabolism and its control: carbon metabolism in aspergilli, D.A. Hondmann and J. Visser alcohol metabolism, B. Felenbok and H.M. Sealy-Lewis inorganic nitrogen assimilation - molecular aspects, J.R. Kinghorn and S.E. Unkles control of metabolic flux in the shikimate and quinate pathways, A.R. Hawkins et al the purine degradation pathway, genetics, biochemistry and regulation, C. Scazzocchio the proline utilization pathway, history and beyond, C. Scazzocchio regulation of acetamide utilization, M.J. Hynes sulphur metabolism, A. Paszewski et al. Part 3 Global gene regulation: nitrogen metabolite repression, M.X. Caddick carbon catabolite repression, J.M. Kelly regulation of gene expression by oxygen, phosphorus and pH, H.N. Arst. Part 4 Development, morphology and organelles: genetic regulation of conidiation, W.E. Timberlake and A.J. Clutterbuck sexual sporulation, S.P. Champe et al control of cell growth, J.H. Doonan ribsomes, S.D. Martinelli mitochondria, T.A. Brown. Part 5 Applied aspects: heterologous gene expression and protein secretion in aspergillus, W. Davies economically important organic acid and enzyme products, E.A. Bodie et al penicillin biosynthesis, J.M. Luengo and M.A. Penalva. Part 6 Molecular tools: vectors for genetic manipulation, G. Turner molecular characterization of chromosomes by pulsed field electrophoresis, G.L. Carter et al. Part 7 Further topics: homologous recombination, F. Osman et al translational suppression, S.D. Martinelli phenoloxidases, G.W. Griffith. Part 8 Appendices: linkage map and loci, A.J. Clutterbuck gene symbols, S.D. Martinelli media, S.D. Martinelli source of strains and vectors, S.D. Martinelli.
Granulocyte-colony stimulating factor improves outcome in a mouse model of amyotrophic lateral sclerosis (2008)

Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disease that results in progressive loss of motoneurons, motor weakness and death within 1-5 years after disease onset. Therapeutic options remain limited despite a substantial number of approaches that have been tested clinically. In particular, various neurotrophic factors have been investigated. Failure in these trials has been largely ascribed to problems of insufficient dosing or inability to cross the blood-brain barrier (BBB). We have recently uncovered the neurotrophic properties of the haematopoietic protein granulocyte-colony stimulating factor (G-CSF). The protein is clinically well tolerated and crosses the intact BBB. This study examined the potential role of G-CSF in motoneuron diseases. We investigated the expression of the G-CSF receptor in motoneurons and studied effects of G-CSF in a motoneuron cell line and in the SOD1(G93A) transgenic mouse model. The neurotrophic growth factor was applied both by continuous subcutaneous delivery and CNS-targeted transgenic overexpression. This study shows that given at the stage of the disease where muscle denervation is already evident, G-CSF leads to significant improvement in motor performance, delays the onset of severe motor impairment and prolongs overall survival of SOD1(G93A)tg mice. The G-CSF receptor is expressed by motoneurons and G-CSF protects cultured motoneuronal cells from apoptosis. In ALS mice, G-CSF increased survival of motoneurons and decreased muscular denervation atrophy. We conclude that G-CSF is a novel neurotrophic factor for motoneurons that is an attractive and feasible drug candidate for the treatment of ALS.
Allele C‐specific methylation of the 5‐HT2A receptor gene: Evidence for correlation with its expression and expression of DNA methylase DNMT1 (2005)

Differential DNA methylation has been suggested to contribute to differential activity of alleles C and T and thereby to genetic associations between the C/T(102) polymorphism in the 5-HT2A receptor gene (5HT2AR) and psychiatric disorders. We surveyed methylation in two CpG sites, which are specific to allele C. The majority of allele C-specific CpG sites were methylated in human temporal cortex and peripheral leukocytes and levels of methylation varied between individuals. Levels of methylation in the promoter correlated significantly with the expression of 5HT2AR. Methylation of allele C-specific CpG sites in the first exon correlated significantly with the expression of DNA methylase 1 (DNMT1) but not S-adenosylhomocysteine hydrolase (AHCY). These findings support the hypothesis that allele-specific DNA methylation is involved in regulation of 5HT2AR expression, influencing expression differences between alleles C and T.
Urodynamic and Immunohistochemical Evaluation of Intravesical Botulinum Toxin A Delivery Using Liposomes (2009)

Intravesical lipotoxin administration cleaved SNAP-25, inhibited calcitonin gene-related peptide release from afferent nerve terminals and blocked the acetic acid induced hyperactive bladder. These results support liposomes as an efficient vehicle for delivering botulinum toxin A without injection.