gebhart/patrepeval huggingface dataset:
Lipid composition of membranes of <i>Escherichia coli</i> by liquid chromatography/tandem mass spectrometry using negative electrospray ionization (2007)

A liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS) method using reversed-phase chromatography was developed for the analysis of phospholipids from bacterial extracts of a wild-type strain of Escherichia coli. Product ion mass spectra from [M--H](-) precursor ions allowed an identification of individual phospholipid species that includes both fatty acid composition and fatty acyl location on the glycerol backbone using diagnostic product ions. Thus, complete assignment, including sn-1/sn-2 fatty acyl position, was achieved for this strain of E. coli. In addition, the phospholipids were quantified relative to one another using an internal standard method.
Control of topography, stress and diffusion at molecule-metal interface (2005)

Transport properties of metal-molecule-metal junctions containing monolayer of conjugated and saturated molecules with characteristic dimensions in the range of 30-300 nm are correlated with microscopic topography, stress and chemical bonding at metal-molecule interfaces. Our statistically significant dataset allows us to conclude that the conductivity of organic molecules ~1.5 nm long is at least 4 orders of magnitude lower than is commonly believed.
Targeting of HIV gp120 by oligonucleotide‐photosensitizer conjugates (1999)

Some guanine-rich oligonucleotides inhibit HIV infectivity through interaction with the gp120 glycoprotein. Besides, photoinactivation of viruses attracts attention for blood decontamination. The feasibility of targeting a red light-absorbing chlorin-type photosensitizer to gp120 through covalent coupling with 8-mer phosphodiester oligodeoxynucleotides is investigated. Some conjugates inhibit binding of antibodies directed to gp120. Inhibition is significantly increased upon red light activation. The activity of the conjugates correlates with their ability to self-associate, a process strongly favored by the propensity of the hydrophobic chlorin moiety to dimerize. Thus, the photosensitizer moiety both promotes structures with a higher affinity for gp120 and, upon light activation, can induce site-directed damages to the protein.
Coupling between two microstrip lines through apertures (1978)

An analysis of coupling between two microstrip transmission lines, coupled together through small apertures in the common ground plane, is presented. The experimental results compare well with theory.
The <i>Saccharomyces cerevisiae SCS2</i> Gene Product, a Homolog of a Synaptobrevin-Associated Protein, Is an Integral Membrane Protein of the Endoplasmic Reticulum and Is Required for Inositol Metabolism (1998)

The Saccharomyces cerevisiae SCS2 gene has been cloned as a suppressor of inositol auxotrophy of CSE1 and hac1/ire15 mutants (J. Nikawa, A. Murakami, E. Esumi, and K. Hosaka, J. Biochem. 118:39-45, 1995) and has homology with a synaptobrevin/VAMP-associated protein, VAP-33, cloned from Aplysia californica (P. A. Skehel, K. C. Martin, E. R. Kandel, and D. Bartsch, Science 269:1580-1583, 1995). In this study we have characterized an SCS2 gene product (Scs2p). The product has a molecular mass of 35 kDa and is C-terminally anchored to the endoplasmic reticulum, with the bulk of the protein located in the cytosol. The disruption of the SCS2 gene causes yeast cells to exhibit inositol auxotrophy at temperatures of above 34 degrees C. Genetic studies reveal that the overexpression of the INO1 gene rescues the inositol auxotrophy of the SCS2 disruption strain. The significant primary structural feature of Scs2p is that the protein contains the 16-amino-acid sequence conserved in yeast and mammalian cells. The sequence is required for normal Scs2p function, because a mutant Scs2p that lacks the sequence does not complement the inositol auxotrophy of the SCS2 disruption strain. Therefore, the Scs2p function might be conserved among eukaryotic cells.
Stem and progenitor cell systems in liver development and regeneration (2014)

The liver comprises two stem/progenitor cell systems: fetal and adult liver stem/progenitor cells. Fetal hepatic progenitor cells, derived from foregut endoderm, differentiate into mature hepatocytes and cholangiocytes during liver development. Adult hepatic progenitor cells contribute to regeneration after severe and chronic liver injuries. However, the characteristics of these somatic hepatic stem/progenitor cells remain unknown. Culture systems that can be used to analyze these cells were recently established and hepatic stem/progenitor cell-specific surface markers including delta-like 1 homolog (DLK), cluster of differentiation (CD) 13, CD133, and LIV2 were identified. Cells purified using antibodies against these markers proliferate for an extended period and differentiate into mature cells both in vitro and in vivo. Methods to force the differentiation of human embryonic stem and induced pluripotent stem (iPS) cells into hepatic progenitor cells have been recently established. We demonstrated that the CD13(+) CD133(+) fraction of human iPS-derived cells contained numerous hepatic progenitor-like cells. These analyses of hepatic stem/progenitor cells derived from somatic tissues and pluripotent stem cells will contribute to the development of new therapies for severe liver diseases.
Aβ‐peptide length aid apolipoprotein E genotype in Alzheimer's disease (1996)

Apolipoprotein E (ApoE) epsilon4 allele, a risk factor for the development of Alzheimer's disease (AD), is associated with increased amyloid deposition. We examined cerebral cortex in 68 AD cases using antibodies to beta-amyloid (Abeta) peptides of different length (Abeta1-40 and Abeta1-42) and found that the increased plaque frequency observed with epsilon4 genotypes may be largely attributed to an increase in Abeta1-40-positive plaques. Indeed, both the number of Abeta1-40-positive plaques, as well as the ratio of Abeta1-40/Abeta1-42-positive plaques, increased with epsilon4 dosage. In contrast, the frequency of Abeta1-42-immunoreactive plaques was similar for epsilon3/epsilon3, epsilon3/epsilon4, and epsilon4/epsilon4 genotypes. ApoE may influence Abeta1 length by facilitating Abeta1-40 deposition onto Abeta1-42-seeded plaques or by modulating the activity of a putative carboxypeptidase that forms Abeta1-40 from Abeta1-42 in situ.
HPLC of small molecules : a practical approach (1986)

Abbreviations Introduction to HPLC of small molecules Amino acids and small peptides Biogenic amines Carbohydrates Lipids Bile acids Steroids Vitamins Nucleotides, nucleosides and bases Porphyrins Bile pigments
Super-resolution from unregistered aliased images (2006)

Aliasing in images is often considered as a nuisance. Artificial low frequency patterns and jagged edges appear when an image is sampled at a too low frequency. However, aliasing also conveys useful information about the high frequency content of the image, which is exploited in super-resolution applications. We use a set of input images of the same scene to extract such high frequency information and create a higher resolution aliasing-free image. Typically, there is a small shift or more complex motion between the different images, such that they contain slightly different information about the scene. Super-resolution image reconstruction can be formulated as a multichannel sampling problem with unknown offsets. This results in a set of equations that are linear in the unknown signal coefficients but nonlinear in the offsets. This thesis concentrates on the computation of these offsets, as they are an essential prerequisite for an accurate high resolution reconstruction. If a part of the image spectra is free of aliasing, the planar shift and rotation parameters can be computed using only this low frequency information. In such a case, the images can be registered pairwise to a reference image. Such a method is not applicable if the images are undersampled by a factor of two or larger. A higher number of images needs to be registered jointly. Two subspace methods are discussed for such highly aliased images. The first approach is based on a Fourier description of the aliased signals as a sum of overlapping parts of the spectrum. It uses a rank condition to find the correct offsets. The second one uses a more general expansion in an arbitrary Hilbert space to compute the signal offsets. The sampled signal is represented as a linear combination of sampled basis functions. The offsets are computed by projecting the signal onto varying subspaces. Under certain conditions, in particular for bandlimited signals, the nonlinear super-resolution equations can be written as a set of polynomial equations. Using Buchberger's algorithm, the solution can then be computed as a Gröbner basis for the corresponding polynomial ideal. After a description of a standard algorithm, adaptations are made for the use with noisy measurements. The techniques presented in this thesis are tested in simulations and practical experiments. The experiments are performed on sets of real images taken with a digital camera. The results show the validity of the algorithms: registration parameters are computed with subpixel precision, and aliasing is accurately removed from the resulting high resolution image. This thesis is produced according to the concepts of reproducible research. All the results and examples used in this thesis are reproducible using the code and data available online.
Lycopene for the prevention of prostate cancer (2009)

This is a protocol for a Cochrane Review (Intervention). The objectives are as follows: Our primary objective is to determine whether lycopene reduces prostate cancer specific mortality. Our secondary objective is to determine the nature of adverse events associated with lycopene use
A normal mitochondrial protein is selectively synthesized and accumulated during heat shock in Tetrahymena thermophila. (1987)

We have identified and purified a 58-kilodalton protein of Tetrahymena thermophila whose synthesis during heat shock parallels that of the major heat shock proteins. This protein, hsp58, was found in both non-heat-shocked as well as heat-shocked cells; however, its concentration in the cell increased approximately two- to threefold during heat shock. The majority of hsp58 in both non-heat-shocked and heat-shocked cells was found by both cell fractionation studies and immunocytochemical techniques to be mitochondrially associated. During heat shock, the additional hsp58 was found to selectively accumulate in mitochondria. Nondenatured hsp58 released from mitochondria of non-heat-shocked or heat-shocked cells sedimented in sucrose gradients as a 20S to 25S complex. We suggest that this protein may play a role in mitochondria analogous to the role the major heat shock proteins play in the nucleus and cytosol.
Fabrication of 3D packaging TSV using DRIE (2008)

3D stacking of die with TSV (through Silicon Via) connection as well as wafer level packaging of CMOS image sensors (CIS) are becoming very hot topics. While TSV of CIS is definitively a back-end technique, 3D stacking of die through TSV can be done with different strategies: from the via first approach, a front-end process, to the via last approach, a back-end process. Each of these different ways of elaborating the vias has its advantages and drawbacks in terms of electrical performances, refilling materials and cost. They have in common the need to etch the vias. In this paper, we will review the DRIE performances for the definition of the different via shapes, depths, and sizes. A very low temperature (< 150 degC) PECVD process has also been characterized and will be presented for the high demanding packaging of CIS.
Novel Diagnostic Algorithm for Identification of Mycobacteria Using Genus-Specific Amplification of the 16S-23S rRNA Gene Spacer and Restriction Endonucleases (2000)

A novel genus-specific PCR for mycobacteria with simple identification to the species level by restriction fragment length polymorphism (RFLP) was established using the 16S-23S ribosomal RNA gene (rDNA) spacer as a target. Panspecificity of primers was demonstrated on the genus level by testing 811 bacterial strains (122 species in 37 genera from 286 reference strains and 525 clinical isolates). All mycobacterial isolates (678 strains among 48 defined species and 5 indeterminate taxons) were amplified by the new primers. Among nonmycobacterial isolates, only Gordonia terrae was amplified. The RFLP scheme devised involves estimation of variable PCR product sizes together with HaeIII and CfoI restriction analysis. It yielded 58 HaeIII patterns, of which 49 (84%) were unique on the species level. Hence, HaeIII digestion together with CfoI results was sufficient for correct identification of 39 of 54 mycobacterial taxons and one of three or four of seven RFLP genotypes found in Mycobacterium intracellulare and Mycobacterium kansasii, respectively. Following a clearly laid out diagnostic algorithm, the remaining unidentified organisms fell into five clusters of closely related species (i.e., the Mycobacterium avium complex or Mycobacterium chelonae-Mycobacterium abscessus) that were successfully separated using additional enzymes (TaqI, MspI, DdeI, or AvaII). Thus, next to slowly growing mycobacteria, all rapidly growing species studied, including M. abscessus, M. chelonae, Mycobacterium farcinogenes, Mycobacterium fortuitum, Mycobacterium peregrinum, and Mycobacterium senegalense (with a very high 16S rDNA sequence similarity) were correctly identified. A high intraspecies sequence stability and the good discriminative power of patterns indicate that this method is very suitable for rapid and cost-effective identification of a wide variety of mycobacterial species without the need for sequencing. Phylogenetically, spacer sequence data stand in good agreement with 16S rDNA sequencing results, as was shown by including strains with unsettled taxonomy. Since this approach recognized significant subspecific genotypes while identification of a broad spectrum of mycobacteria rested on identification of one specific RFLP pattern within a species, this method can be used by both reference (or research) and routine laboratories.
Epilepsy. (1994)

Epilepsy is the most common of chronic neu- rological disorders and it imposes the biggest burden on health care systems. It varies greatly in its clinical features, aetiology, severity, and prognosis and its association with other neurological disabilities. For this rea- son, many different disciplines may be responsible for supplying care, including neurologists, paediatricians, geriatricians, psychiatrists, and specialists in mental handicap, and in all spheres, the professions allied to medicine have an important input.
Circadian Changes in Core Body Temperature, Metabolic Rate and Locomotor Activity in Rats on a High-Protein, Carbohydrate-Free Diet (2009)

Ingestion of a high-protein meal results in body weight loss due to elevated energy expenditure, while also increasing satiety and decreasing subsequent food intake. The present study aimed to clarify the effects of a high-protein, carbohydrate-free diet (HPCFD) on these physiological indicators from a circadian perspective. Rats were given HPCFD or a pair-fed normal protein content diet (20% protein; NPD) for 4 d. The HPCFD group lost more body weight than the NPD group. Oxygen consumption (VO(2)) in the HPCFD group did not change during the experimental period, and tended to be higher during the light (L) phase than in the NPD group. Carbon dioxide production (VCO(2)) during the L phase was higher in the HPCFD group than in the NPD group, where VCO(2) was gradually decreased during the last dark (D) phase and throughout the L phase. The HPCFD group exhibited higher daily core body temperature (T(b)), particularly during the late D phase and throughout the L phase when compared to the NPD group. Locomotor activities during the D phase of the NPD group tended to gradually increase and were thus significantly higher than in the HPCFD group. These results suggest that HPCFD, even if energy intake is insufficient, maintains circadian changes in metabolic rates, resulting in maintenance of elevated daily T(b) and body weight reduction without increasing activity.
Role of misfit dislocations on pseudomorphic high electron mobility transistors (1995)

The relationship between structural defects and device performance of In0.21Ga0.79As/(Al,Ga)As high electron mobility transistors with different In0.21Ga0.79As channel thicknesses (75–300 Å) was analyzed. Using triple axis x-ray diffraction and transmission electron microscopy, we determined that the presence of misfit dislocations along only one of the 〈110〉 directions did not impair device performance. In fact, the sample with the highest cutoff frequency possessed the misfit dislocations along one 〈110〉 direction. However, for thicker samples, with an orthogonal array of misfit dislocations, the device parameters were significantly degraded. We also determined that x-ray diffuse scattering correlates strongly with device performance, making this nondestructive technique useful for device performance evaluation.
Crystal Structures of Two Coronavirus ADP-Ribose-1″-Monophosphatases and Their Complexes with ADP-Ribose: a Systematic Structural Analysis of the Viral ADRP Domain (2008)

The coronaviruses are a large family of plus-strand RNA viruses that cause a wide variety of diseases both in humans and in other organisms. The coronaviruses are composed of three main lineages and have a complex organization of nonstructural proteins (nsp's). In the coronavirus, nsp3 resides a domain with the macroH2A-like fold and ADP-ribose-1"-monophosphatase (ADRP) activity, which is proposed to play a regulatory role in the replication process. However, the significance of this domain for the coronaviruses is still poorly understood due to the lack of structural information from different lineages. We have determined the crystal structures of two viral ADRP domains, from the group I human coronavirus 229E and the group III avian infectious bronchitis virus, as well as their respective complexes with ADP-ribose. The structures were individually solved to elucidate the structural similarities and differences of the ADRP domains among various coronavirus species. The active-site residues responsible for mediating ADRP activity were found to be highly conserved in terms of both sequence alignment and structural superposition, whereas the substrate binding pocket exhibited variations in structure but not in sequence. Together with data from a previous analysis of the ADRP domain from the group II severe acute respiratory syndrome coronavirus and from other related functional studies of ADRP domains, a systematic structural analysis of the coronavirus ADRP domains was realized for the first time to provide a structural basis for the function of this domain in the coronavirus replication process.
Two new mesophases in a chiral compound (1983)

Microscopical, miscibility and X-ray studies establish the existence of two new mesophases in the two enantiomers of 1 (methyl)-heptyl terephthalidene bis amino cinnamate. In one of this two mesophases the two enantiomers do not exhibit a total miscibility range; while for the second the untwisted form observed with the racemic mixture has a higher temperature range of stability than the twisted form observed for the pure enantiomers. Information about the structures of the two phases is given and a comparison is made with the S*C and SD phases. Nevertheless the location of these two phases in the sequence of the presently known calamitic mesophases is not yet completely established.
CD8(+) T cell-mediated spontaneous diabetes in neonatal mice (1996)

Transgenic mice that express the influenza virus hemagglutinin (HA) on pancreatic islet beta cells (ins-HA) demonstrate tolerance of HA even after immunization with influenza virus. Surprisingly, when Ins-HA mice were mated with a transgenic mouse expressing a TCR specific for an epitope of HA that is restricted by MHC class I H-2Kd (Clone-4 TCR), the resulting double transgenic (Ins-HA x Clone-4 TCR)F1 neonates developed spontaneous autoimmune diabetes immediately after birth and died within 10 days. This represents a unique situation in which all safeguards within the immune system that normally maintain tolerance of self-antigens in the neonate are insufficient.
Does full-term pregnancy at a young age protect women against breast cancer through hCG? (2000)

Recent studies found that human and animal breast tissues and human breast cell lines contain low levels of receptors that bind hCG and its structural and functional homologue, LH. Those gonadotropins exert numerous anticancer effects in breast cancer models and cells, which might explain decreased breast cancer incidence in women who complete full-term pregnancies at a young age. The new findings also imply that premature chronic elevations of LH levels might contribute to decreased breast cancer incidence in women with early menopause, and elevated LH levels might contribute to a better prognosis after ovariectomy. Those findings predict that breast cancer risk might be reduced by early hCG treatment of women who plan to delay their first pregnancies; prophylactic hCG treatment might help women with family histories of breast cancer or oncogene mutations that predict breast cancer; and better prognoses might result when hCG is administered to breast cancer tissue.
Radar cross section of rectangular flat plates as a function of aspect angle (1966)

An investigation of the scattering from rectangular flat plates has been carried out to determine analytical formulations suitable for the estimation of radar cross section. Simple physical optics theory provides an accurate means of predicting the near-specular values of plate cross section but fails to account for polarization dependence and detailed shape of the cross section vs. angle curve in nonspecular regions. Calculations based upon the geometrical theory of diffraction show excellent agreement with measured data except at edge-on aspects. This correspondence stems, in part, from the fact that the geometrical theory of diffraction is polarization dependent. The paper is concluded with an analytical description of vertical polarization cross section at the edge-on aspect derived on the basis of measurement data.
Die Silicatischen Tonminerale, par K. Jasmund, 1955 (1956)

Sabatier Germain. Die Silicatischen Tonminerale, par K. Jasmund, 1955. In: Bulletin de la Société française de Minéralogie et de Cristallographie, volume 79, 7-9, 1956. pp. 492-493.
The Metropolis Algorithm (2000)

The Metropolis Algorithm has been the most successful and influential of all the members of the computational species that used to be called the "Monte Carlo method". Today, topics related to this algorithm constitute an entire field of computational science supported by a deep theory and having applications ranging from physical simulations to the foundations of computational complexity. Since the rejection method invention (J. von Neumann), it has been developed extensively and applied in a wide variety of settings. The Metropolis Algorithm can be formulated as an instance of the rejection method used for generating steps in a Markov chain.