gebhart/patrepeval huggingface dataset:
Molecular Basis of the Pleiotropic Phenotype of Mice Carrying the hypervariable yellow (Ahvy) Mutation at the agouti Locus (1996)

The murine agouti locus regulates a switch in pigment synthesis between eumelanin (black/brown pigment) and phaeomelanin (yellow/red pigment) by hair bulb melanocytes. We recently described a spontaneous mutation, hypervariable yellow (Ahvy) and demonstrated that Ahvy is responsible for the largest range of phenotypes yet identified at the agouti locus, producing mice that are obese with yellow coats to mice that are of normal weight with black coats. Here, we show that agouti expression is altered both temporally and spatially in Ahvy mutants. Agouti expression levels are positively correlated with the degree of yellow pigmentation in individual Ahvy mice, consistent with results from other dominant yellow agouti mutations. Sequencing of 5' RACE and genomic PCR products revealed that Ahvy resulted from the integration of an intracisternal A particle (IAP) in an antisense orientation within the 5' untranslated agouti exon 1C. This retrovirus-like element is responsible for deregulating agouti expression in Ahvy mice; agouti expression is correlated with the methylation state of CpG residues in the IAP long terminal repeat as well as in host genomic DNA. In addition, the data suggest that the variable phenotype of Ahvy offspring is influenced in part by the phenotype of their Ahvy female parent.
Optimization of Bacillus α‐amylase production by Saccharomyces cerevisiae (1991)

Production of Bacillus amyloliquefaciens alpha-amylase by Saccharomyces cerevisiae using the multicopy plasmid pAAH5 and ways of improving the yields of secreted enzyme were studied. In standard non-buffered medium, alpha-amylase was rapidly inactivated but stabilization of the pH at 6 led to stable accumulation of alpha-amylase in the culture medium. Removal of 1100 bp of the upstream sequence of the ADH1 promoter present on pAAH5 resulted in delayed but increased alpha-amylase production: 29-fold in selective medium, two-fold in non-selective medium. With the original ADH1 promoter, accumulation of alpha-amylase in the medium started to level off before the cultures reached stationary phase and was very low when exponentially growing cells were transferred from glucose to ethanol. This coincided with the appearance of a mRNA larger than the alpha-amylase messenger. With the shortened promoter, the normal-size alpha-amylase mRNA was detected under all growth conditions and alpha-amylase was efficiently secreted into the medium also late in stationary phase and after transfer to ethanol. Highest total yields of alpha-amylase were obtained with the short promoter in non-selective glucose-containing medium; this may be explained by the greater final cell density obtained. However, the production of alpha-amylase per cell mass was higher in ethanol-containing selective medium. Seventy to eighty per cent of the alpha-amylase activity was secreted into the medium independent of the total amount produced.
The Relevance of Kindling for Human Epilepsy (2007)

Kindling is one of the most widely used models of seizures and epilepsy, and it has been used in its more than three decade history to provide many key insights into seizures and epilepsy. It remains a mainstay of epilepsy related research, but the question remains how the results from kindling experiments further our understanding of the underlying neurobiology of human epilepsy. In this article we compare the basic features of kindling and human epilepsy, especially human limbic or temporal lobe epilepsy. In this review we focus on a limited number of topics that may show areas in which kindling has been often cited as a tool for better understanding of human epilepsy. These areas include the underlying circuits, the importance of seizure spontaneity, the associated neuropathology, the contribution of genetics, seizure susceptibility, and the underlying pathophysiology of epilepsy. In the course of this article we will show that there are many features that kindling can teach us by direct comparison or implication about human temporal epilepsy. We will also see that not all findings associated with kindling may be applicable to the human condition. Ultimately we wish to encourage critical thinking about kindling and the similarities that it shares and does not share with the human epilepsy so the results from studies using this model are applied rationally to further our insights the mechanisms of human epilepsy.
Distinct Central Amphipathic α-Helices in Apolipoprotein A-I Contribute to the in Vivo Maturation of High Density Lipoprotein by Either Activating Lecithin-Cholesterol Acyltransferase or Binding Lipids (2000)

Recombinant adenoviruses with cDNAs for human apolipoprotein A-I (wild type (wt) apoA-I) and three mutants, referred to as Delta4-5A-I, Delta5-6A-I, and Delta6-7A-I, that have deletions removing regions coding for amino acids 100-143, 122-165, and 144-186, respectively, were created to study structure/function relationships of apoA-I in vivo. All mutants were expressed at lower concentrations than wt apoA-I in plasma of fasting apoA-I-deficient mice. The Delta5-6A-I mutant was found primarily in the lipid-poor high density lipoprotein (HDL) pool and at lower concentrations than Delta4-5A-I and Delta6-7A-I that formed more buoyant HDL(2/3) particles. At an elevated adenovirus dose and earlier blood sampling from fed mice, both Delta5-6A-I and Delta6-7A-I increased HDL-free cholesterol and phospholipid but not cholesteryl ester. In contrast, wt apoA-I and Delta4-5A-I produced significant increases in HDL cholesteryl ester. Further analysis showed that Delta6-7A-I and native apoA-I could bind similar amounts of phospholipid and cholesterol that were reduced slightly for Delta5-6A-I and greatly for Delta4-5A-I. We conclude from these findings that amino acids (aa) 100-143, specifically helix 4 (aa 100-121), contributes to the maturation of HDL through a role in lipid binding and that the downstream sequence (aa 144-186) centered around helix 6 (aa 144-165) is responsible for the activation of lecithin-cholesterol acyltransferase.
Cloning of genes for production of Escherichia coli Shiga-like toxin type II (1987)

Genes controlling production of Shiga-like toxin type II (SLT-II) in Escherichia coli were cloned from the SLT-II-converting bacteriophage 933W and compared with the Shiga-like toxin type I (SLT-I) genes previously isolated and described from phage 933J. Subcloning analysis identified a region within the 4.9-kilobase EcoRI fragment of phage 933W that was associated with SLT-II production. Experiments with E. coli minicells containing these subclones demonstrated that the 4.9-kilobase EcoRI fragment encodes the structural genes for SLT-II. These experiments additionally showed the genetic organization of the SLT-II genes to be the same as that of the SLT-I genes, with the coding sequence for the large A subunit adjacent to that for the smaller B subunit. The mobilities of the SLT-II subunits in sodium dodecyl sulfate-polyacrylamide gels were slightly greater than those determined for the SLT-I subunits. Although apparent processing of the SLT-I subunits was observed with polymyxin B treatment of the labeled minicells, no processing of the SLT-II subunits was detected. Southern blot hybridization studies suggested that the DNA fragment carrying the SLT-II structural genes shares approximately 50 to 60% homology with the DNA of the SLT-I structural genes.
Efficient Compilation of Array Statements for Private Memory Multicomputers (1993)

One of the core constructs of High Performance Fortran (HPF) is the array-slice assignment statement, combined with the rich choice of data distribution options available to the programmer. On a private memory multicomputer, the HPF compiler writer faces the difficult task of automatically generating the necessary communication for assignment statements involving arrays with arbitrary block-cyclic data distributions. In this paper we present a framework for representing array slices and block-cyclic distributions, and we derive efficient algorithms for sending and receiving the necessary data for array-slice assignment statements. The algorithms include a memory-efficient method of managing the layout of the distributed arrays in each processor''s local memory. We also provide a means of converting the user''s TEMPLATE, ALIGN, and DISTRIBUTE statements into a convenient ''array ownership descriptor''. In addition, we present several optimizations for common distributions and easily-recognized communication patterns. The work presented makes minimal assumptions regarding the processor architecture, the communication architecture, or the underlying language being compiled.
Physiology and Genetics of Xylan Degradation by Gastrointestinal Tract Bacteria (1990)

Hemicelluloses or xylans are major components (35%) of plant materials. For ruminant animals, about 50% of the dietary xylans are degraded, but only small amounts of xylans are degraded in the lower gut of nonruminant animals and humans. In the rumen, the major xylanolytic species are Butyrivibrio fibrisolvens and Bacteroides ruminicola. In the human colon, Bacteroides ovatus and Bacteroides fragilis subspecies "a" are major xylanolytic bacteria. Xylans are chemically complex, and their degradation requires multiple enzymes. Expression of these enzymes by gut bacteria varies greatly among species. Butyrivibrio fibrisolvens makes extracellular xylanases but Bacteroides species have cell-bound xylanase activity. Biochemical characterization of xylanolytic enzymes from gut bacteria has not been done. A xylosidase gene has been cloned from B. fibrosolvens 113. The data from DNA hybridizations using a xylanase gene cloned from B. fibrisolvens 49 indicate this gene may be present in other B. fibrisolvens strains. A cloned xylanase from Bact. ruminicola was transferred to and highly expressed in Bact. fragilis and Bact. uniformis. Arabinosidase and xylosidase genes from Bact. ovatus have been cloned and both activities appear to be catalyzed by a single, bifunctional, novel enzyme. Continued research in genetic and biochemical areas will provide knowledge and insights for manipulation of digestion at the gut level and improved understanding of colonic fiber digestion.
Cross wavelet analysis: significance testing and pitfalls (2004)

Abstract. In this paper, we present a detailed evaluation of cross wavelet analysis of bivariate time series. We develop a statistical test for zero wavelet coherency based on Monte Carlo simulations. If at least one of the two processes considered is Gaussian white noise, an approximative formula for the critical value can be utilized. In a second part, typical pitfalls of wavelet cross spectra and wavelet coherency are discussed. The wavelet cross spectrum appears to be not suitable for significance testing the interrelation between two processes. Instead, one should rather apply wavelet coherency. Furthermore we investigate problems due to multiple testing. Based on these results, we show that coherency between ENSO and NAO is an artefact for most of the time from 1900 to 1995. However, during a distinct period from around 1920 to 1940, significant coherency between the two phenomena occurs.
Quantitative phase imaging of live cells using fast Fourier phase microscopy (2007)

Using the decomposition of an image field in two spatial components that can be controllably shifted in phase with respect to each other, a new quantitative-phase microscope has been developed. The new instrument, referred to as the fast Fourier phase microscope (f-FPM), provides a factor of 100 higher acquisition rate compared with our previously reported Fourier phase microscope. The resulting quantitative-phase images are characterized by diffraction limited transverse resolution and path-length stability better than 2 nm at acquisition rates of 10 frames/s or more. These features make the f-FPM particularly appealing for investigating the structure and dynamics of live cells over a broad range of time scales. In addition, we demonstrate the possibility of examining subcellular structures by digitally processing the amplitude and phase information provided by the instrument. Thus we developed software that can emulate phase contrast and differential interference contrast microscopy images by numerically processing FPM images. This approach adds the flexibility of digitally varying the phase shift between the two interfering beams. The images obtained appear as if they were recorded by variable phase contrast or differential interference contrast microscopes that deliver an enhanced view to the subcellular structure when compared with the typical commercial microscope.
Changes in the plasma levels of vitamin K‐dependent proteins C and S and of C4b‐binding protein during pregnancy and oral contraception (1988)

The plasma concentrations of protein S, protein C and C4b-binding protein (C4BP) were analysed during pregnancy, in the postpartum period and in women using oral contraceptives. Free protein S, measured after precipitation of the C4BP-protein S complexes with 5% PEG 6000, was found to be 8.3 mg/l in the control group, which represents 36.3% of the total plasma protein S content (average 23.5 mg/l). The concentration of protein S was significantly decreased during pregnancy, the lowest levels occurring in the second trimester (14.8 mg/l). The values returned to normal within a few days after delivery. The concentration of free protein S was also decreased, down to an average of 3.7 mg/l at delivery, and did not return to normal within the first week postpartum. The mean concentration of protein S in women using oral contraceptives decreased to 17.7 mg/l and the free fraction went down to 6.6 mg/l. Unlike that of protein S, the plasma concentration of protein C increased during pregnancy, reaching a maximum of 135% in the second trimester. Also, it was significantly higher in the postpartum period and in women using oral contraceptives, than in controls. The level of C4BP was increased throughout pregnancy, with a maximum of 143.4% at delivery. These changes in the plasma levels of proteins C and S during pregnancy indicate that the two proteins differ in the regulation of their synthesis. The major decrease in the level of free protein S may predispose to thrombotic episodes during pregnancy, whereas the increased level of protein C may have the reverse effect. These results indicate the importance of taking into account the normal changes in the plasma levels of protein C and S during pregnancy and the use of oral contraceptives, when evaluating patients with increased risk of thromboembolic disease.
Methicillin-resistant Staphylococcus aureus: evaluation of detection techniques on laboratory-passaged organisms. (1999)

Strains of methicillin-resistant Staphylococcus aureus (MRSA) are a major cause of nosocomial infection. This has led to the widespread introduction of screening techniques to identify patients or staff colonised with the organism and prevent the spread of MRSA in the hospital environment. The aim of laboratory techniques for the detection of MRSA screening is the rapid isolation and identification of MRSA, enabling timely implementation of appropriate infection control measures. This study compares commercially available products used by the majority of laboratories during routine screening of samples for MRSA. Several selective media are tested, including mannitol salt agar, Mueller Hinton agar, milk agar and blood agars. The accuracy of combining rapid agglutination from selective media for identification of MRSA is also determined, using six commercially produced kits. Owing to debate concerning the use of enrichment broth, in addition to primary isolation on solid media, four enrichment broths are tested and compared to direct culture techniques. Using a selection of laboratory-passaged MRSA phage types, results demonstrated that mannitol salt agar containing 75 g/L NaCl, without the addition of oxacillin, recovered all 50 MRSA strains and produced the highest isolation rate. Robertson's cooked-meat broth, with 7.5% NaCl, proved the most effective enrichment medium and was more sensitive than direct culture by 3%. Pastorex Staph-plus proved to be the most efficient rapid agglutination kit when testing MRSA colonies removed directly from selective agars.
Magnetic resonance detection and imaging using force microscope techniques (invited) (1994)

We describe the principles and imaging characteristics of a new type of high resolution magnetic resonance microscopy. Magnetic resonance is detected by measuring a small oscillating magnetic force acting between the spins in a sample and a nearby ferromagnetic particle. The oscillating magnetic force is generated by polarizing the spins in the magnetic field and then modulating the sample magnetization using magnetic resonance techniques. The oscillating magnetic force is detected by sensing the angstrom-scale vibration of a micromechanical cantilever on which the sample is mounted. High spatial resolution is achieved as a result of the narrowness of the magnetic resonance spectral response and the large magnetic field gradient generated by the ferromagnetic particle. Electron paramagnetic resonance images are presented that demonstrate axial resolution on the order of 1 μm and lateral resolution on the order of 5 μm. Submicron resolution can be expected with straightforward technical improvements.
Cloning, sequence, and disruption of the Saccharomyces diastaticus DAR1 gene encoding a glycerol-3-phosphate dehydrogenase (1994)

The Saccharomyces diastaticus DAR1 gene was cloned by complementation in an Escherichia coli strain auxogrophic for glycerol-3-phosphate. DAR1 encodes an NADH-dependent dihydroxyacetone phosphate reductase (sn-glycerol-3-phosphate dehydrogenase [G3PDase; EC 1.1.1.8]) homologous to several other eukaryotic G3PDases. DAR1 is distinct from GUT2, which encodes a glucose-repressed mitochondrial G3PDase, but is identical to GPD1 from S. cerevisiae, a close relative of S. diastaticus. The level of DAR1-encoded G3PDase was increased about threefold in a medium of high osmolarity. Disruption of DAR1 in a haploid S. cerevisiae was not lethal but led to a decrease in cytoplasmic NADH-dependent G3PDase activity, an increase in osmotic sensitivity, and a 25% reduction in glycerol secretion from cells grown anaerobically on glucose.
Partial characterization of the major lipooligosaccharide from a strain of Haemophilus ducreyi, the causative agent of chancroid, a genital ulcer disease. (1992)

The first preliminary structure of a surface lipooligosaccharide from Haemophilus ducreyi has been determined. The major oligosaccharide was released by mild acid hydrolysis and analyzed by liquid secondary ion and tandem mass spectrometry. The mass spectral data combined with composition and methylation analysis yielded the most probable structure; Gal1----4GlcNAc1----3Gal1----4Hep1----6Glc1----( Hep1----2Hep1----)3,4Hep1---- KDO, where the reducing terminal 3-deoxy-D-manno-octulosonic acid (or KDO) exists in an anhydro form. This anhydro species results from the elimination of a phosphate from C-4 of KDO during mild acid hydrolysis. The core heptose trisaccharide consists of L-glycero-D-manno-heptose, but analysis of the peracetylated sugars indicated that the 1,4-linked heptose is likely D-glycero-D-manno-heptose. The monoclonal antibody 3F11 generated against Neisseria gonorrhoeae also binds to this lipooligosaccharide and suggests that the terminal trisaccharide is Gal beta 1----4GlcNAc beta 1----3Gal beta 1----, an epitope found in the glycose moiety of the human erythrocyte glycosphingolipid lactoneotetraglycosylceramide. Mass spectrometric and composition analysis of the lipid A moiety shows that it is similar to the lipid A of Haemophilus influenzae strain I-69 Rd-/b+ proposed by Helander et al. (Helander, I. M., Lindner, B., Brade, H., Altmann, K., Lindberg, A. A., Rietschel, E. T., and Zähringer, U. (1988) Eur. J. Biochem. 177, 483-492). Electrospray mass spectrometric analysis of the intact O-deacylated lipooligosaccharides gave an average Mr of 2710, and supported an overall structure consisting of the above nonasaccharide linked directly to a diphosphorylated lipid A moiety through the single KDO which is phosphorylated. This structure should provide a framework to investigate the roles of lipooligosaccharides in the host immunochemical response and pathology of H. ducreyi infection, a leading cause of genital ulcer disease.
Developmental stages of the third molar in Israeli children. (2003)

There was a high correlation between third molar development and chronological age. Agenesis can be determined conclusively if no radiolucent bud is present beyond age 14. The modified 6-stage method allowed more accurate determination of developmental stages.
A point mutation in the human serum albumin gene results in familial dysalbuminaemic hyperthyroxinaemia. (1994)

Using DNA samples obtained from two unrelated patients, diagnosed as having familial dysalbuminaemic hyperthyroxinaemia (FDH), exons 1-14 which span the entire coding region of the human serum albumin (HSA) gene were amplified by the polymerase chain reaction. The sequence of each of the 14 DNA fragments was then determined. In each case a point mutation was identified at nucleotide 653 which causes an Arg to His substitution at amino acid position 218. The substitution was confirmed by amino acid sequencing of a mutant peptide resulting from tryptic digestion of the protein. Abnormal affinity of FDH HSA for a thyroxine (T4) analogue was verified by an adaptation of the procedure used in routine free T4 measurement. The location of the mutation is discussed in relation to other studies on the binding properties of HSA.
Encoding speech using prototype waveforms (1993)

Voiced speech is interpreted as a concentration of slowly evolving pitch-cycle waveforms. This signal can be reconstructed by interpolation from a downsampled sequence of pitch-cycle waveforms with a rate of one prototype waveform per 20-30 ms interval. The prototype waveform is described by a set of linear-prediction (LP) filter coefficients describing the formant structure and a prototype excitation waveform, quantized with analysis-by-synthesis procedures. The speech signal is reconstructed by filtering an excitation signal consisting of the concatenation of (infinitesimal) sections of the instantaneous excitation waveforms. To obtain the correct level of periodicity, the short-term and the long-term correlations between the instantaneous excitation waveforms can be controlled explicitly. Thus, distortions such as noise, reverberation, and buzziness can be prevented. The coding method is easily combined with existing LP-based speech coders, such as CELP, for unvoiced signals. Excellent voiced speech quality is obtained at rates between 3.0 and 4.0 kb/s.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>