gebhart/patrepeval huggingface dataset:
Growth of Geobacter sulfurreducens with Acetate in Syntrophic Cooperation with Hydrogen-Oxidizing Anaerobic Partners (1998)

Pure cultures of Geobacter sulfurreducens and other Fe(III)-reducing bacteria accumulated hydrogen to partial pressures of 5 to 70 Pa with acetate, butyrate, benzoate, ethanol, lactate, or glucose as the electron donor if electron release to an acceptor was limiting. G. sulfurreducens coupled acetate oxidation with electron transfer to an anaerobic partner bacterium in the absence of ferric iron or other electron acceptors. Cocultures of G. sulfurreducens and Wolinella succinogenes with nitrate as the electron acceptor degraded acetate efficiently and grew with doubling times of 6 to 8 h. The hydrogen partial pressures in these acetate-degrading cocultures were considerably lower, in the range of 0.02 to 0.04 Pa. From these values and the concentrations of the other reactants, it was calculated that in this cooperation the free energy change available to G. sulfurreducens should be about -53 kJ per mol of acetate oxidized, assuming complete conversion of acetate to CO2 and H2. However, growth yields (18.5 g of dry mass per mol of acetate for the coculture, about 14 g for G. sulfurreducens) indicated considerably higher energy gains. These yield data, measurement of hydrogen production rates, and calculation of the diffusive hydrogen flux indicated that electron transfer in these cocultures may not proceed exclusively via interspecies hydrogen transfer but may also proceed through an alternative carrier system with higher redox potential, e.g., a c-type cytochrome that was found to be excreted by G. sulfurreducens into the culture fluid. Syntrophic acetate degradation was also possible with G. sulfurreducens and Desulfovibrio desulfuricans CSN but only with nitrate as electron acceptor. These cultures produced cell yields of 4.5 g of dry mass per mol of acetate, to which both partners contributed at about equal rates. These results demonstrate that some Fe(III)-reducing bacteria can oxidize organic compounds under Fe(III) limitation with the production of hydrogen, and they provide the first example of rapid acetate oxidation via interspecies electron transfer at moderate temperature.
Translation of human hepatitis C virus RNA in cultured cells is mediated by an internal ribosome-binding mechanism (1993)

The human hepatitis C virus (HCV) contains a long 5' noncoding region (5' NCR). Computer-assisted and biochemical analyses suggest that there is a complex secondary structure in this region that is comparable to the secondary structures that are found in picornaviruses (E.A. Brown, H. Zhang, L.-H. Ping, and S.M. Lemon, Nucleic Acids Res. 20:5041-5045, 1992). Previous in vitro studies suggest that the HCV 5' NCR plays an important role during translation (K. Tsukiyama-Kohara, N. Iizuka, M. Kohara, and A. Nomoto, J. Virol. 66:1476-1483, 1992). Dicistronic and monocistronic expression vectors, in vitro translation, RNA transfections, and deletion mutagenesis studies were utilized to demonstrate unambiguously that the HCV 5' NCR is involved in translational control. Our data strongly support the conclusion that an internal ribosome entry site exists within the 5' noncoding sequences proximal to the initiator AUG. Furthermore, our results suggest that the HCV genome is translated in a cap-independent manner and that the sequences immediately upstream of the initiator AUG are essential for internal ribosome entry site function during translation.
Pituitary Adenylyl Cyclase-Activating Polypeptide Stimulates DNA Synthesis But Delays Maturation of Oligodendrocyte Progenitors (2001)

The neuropeptide pituitary adenylyl cyclase-activating peptide (PACAP) and one of its receptors (PAC(1)) are expressed in embryonic neural tube, where they appear to regulate neurogenesis and patterning. We now show that PAC(1) gene expression is also present in neonatal rats in the ventricular and subventricular zones and in the optic chiasm, areas that are rich in oligodendrocyte (OL) progenitors (OLP). Because actions of PACAP on OLP have not been reported, we examined the effects of PACAP on the proliferation of purified OLP in culture and on myelinogenesis in cerebellar slices. Northern analyses on total RNA from purified glial cell subtypes revealed an abundant 7 kb hybridizing transcript in OLP, which was confirmed to correspond to the PAC(1) receptor by reverse transcription-PCR. The presence of this receptor was also corroborated by radioligand binding and cAMP assay. In cultured OL, receptor density decreased during maturation but was partially counterbalanced by the appearance of sites that bound both PACAP and the related peptide vasoactive intestinal peptide. PACAP increased DNA synthesis in OLP cultures almost twofold and increased the bromodeoxyuridine-labeling index in O4-positive OLP. PACAP treatment also resulted in decreased sulfate incorporation into sulfatide in cultures of differentiating OL. The PACAP effect on sulfatide synthesis was fully reproduced in a cerebellar explant model. These findings indicate that PACAP may act at two stages during OL development to (1) stimulate proliferation and (2) delay maturation and/or myelinogenesis.
Epidermal Growth Factor Receptor in Mice and Men-Any Applications to Clinical Practice? (1997)

The epidermal growth factor receptor (EGF-R) is perhaps the best studied member of tyrosine kinase receptors. Its inactivation by homologous recombination results in three different phenotypes ranging from peri-implantation lethality to postnatal lethality. The mildest form of EGF-R inactivation leads to epithelial immaturity and postnatal death due to respiratory failure and necrotizing enterocolitis-like lesions in the intestine. The defects seen in this 'postnatal lethality phenotype' manifest in the classical EGF-responsive organs (skin, intestine) and organs undergoing branching morphogenesis during development (lung, kidney, mammary gland, pancreas and prostate), and thus accord with the concept of EGF family members being important epithelial mitogens. The respiratory failure of the EGF-R (-/-) mice results from impaired branching of the alveolar tree and leads to decreased surface for gas exchange. Overall, the lung phenotype bears similarity to respiratory distress syndrome and bronchopulmonary dysplasia--the most common complications of prematurity in humans. Intestinal changes seen in the EGF-R (-/-) mice vary in severity, the end-point being severe mucosal lesions and necroses. These findings resemble those seen in necrotizing enterocolitis of premature babies, a serious intestinal problem in the neonate. Although deficient EGF-R function is not the reason for these prematurity-associated diseases it may nevertheless exacerbate them. Potential usage of EGF transforming growth factor-alpha in clinical work is discussed.
Molecular cloning and characterization of (R)-3-hydroxybutyrate dehydrogenase from human heart. (1992)

The complete amino acid sequence of human heart (R)-3-hydroxybutyrate dehydrogenase (EC 1.1.1.30) has been deduced from the nucleotide sequence of cDNA clones. This mitochondrial enzyme has an absolute and specific requirement of phosphatidylcholine for enzymic activity (allosteric activator) and is an important prototype of lipid-requiring enzymes. Despite extensive studies, the primary sequence has not been available and is now reported. The mature form of the enzyme consists of 297 amino acids (predicted M(r) of 33,117), does not appear to contain any transmembrane helices, and is homologous with the family of short-chain alcohol dehydrogenases (SC-ADH) (Persson, B., Krook, M., and Jörnvall, H. (1991) Eur. J. Biochem. 200, 537-543) (30% residue identity with human 17 beta-hydroxysteroid dehydrogenase). The first two-thirds of the enzyme includes both putative coenzyme binding and active site conserved residues and exhibits a predicted secondary structure motif (alternating alpha-helices and beta-sheet) characteristic of SC-ADH. Bovine heart peptide sequences (174 residues in nine sequences determined by microsequencing) have extensive homology (89% identical residues) with the deduced human heart sequence. The C-terminal third (Asn-194 to Arg-297) shows little sequence homology with the SC-ADH and likely contains elements that determine the substrate specificity for the enzyme including the phospholipid (phosphatidylcholine) binding site(s). Northern blot analysis identifies a 1.3-kilobase mRNA encoding the enzyme in heart tissue.
A reliable bi-polarity write/erase technology in flash EEPROMs (2002)

The authors describe a technology for scaling down the flash EEPROM cell, which has a conventional self-aligned double poly-Si stacked structure. It is clarified experimentally that a flash memory cell written and erased by Fowler-Nordheim (F-N) tunneling has ten times the retention time of the conventional cell, which is written by channel-hot-electron (CHE) injection and erased by F-N tunneling. This difference of data retentivity between these two write/erase (W/E) technologies is due to decreasing the thin gate oxide leakage current by bi-polarity F-N tunneling stress. This improvement in data retention becomes more pronounced as the gate oxide thickness decreases. Therefore, a bipolarity F-N tunneling WE technology, which enables a flash EEPROM cell to scale down its oxide thickness, shows promise as a key technology for realizing 16 Mb flash EEPROMs and beyond.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
THE RELATION OF INTERLEUKIN-6, TUMOR NECROSIS FACTOR-α, IL-2, AND IL-2 RECEPTOR LEVELS TO CELLULAR REJECTION, ALLOGRAFT DYSFUNCTION, AND CLINICAL EVENTS EARLY AFTER CARDIAC TRANSPLANTATION (1995)

Immunoregulatory cytokines have been implicated in the pathophysiology of graft dysfunction after heart transplantation (HTx). In 15 consecutive patients undergoing HTx we prospectively determined levels of interleukin-6 (IL-6), tumor-necrosis-factor-alpha (TNF-alpha), interleukin-2 (IL-2), and soluble-interleukin-2-receptor (sIL-2-R) at eight points in time during biopsy and right heart catheterization and within 12 hr of echocardiography during the first three months after HTx. Blood was taken from the pulmonary arterial line. IL-6-levels correlated positively with hemodynamic and echocardiographic parameters of pump dysfunction--namely, pulmonary capillary wedge pressure, pulmonary arterial pressure, right atrial pressure, heart rate--and negatively with isovolumic relaxation time and stroke volume independent of the degree of cellular rejection as classified by the ISHLT criteria. A similar pattern was found for TNF-alpha- and sIL-2-R, while IL-2 correlated negatively with left and right heart filling pressures and positively with fractional shortening. In the three patients who died of sepsis or multiorgan failure within the study period IL-6-, TNF-alpha, and sIL-2-R-levels were elevated and IL-2-levels were suppressed compared with the 12 patients with a stable clinical course. IL-6 and sIL-2-R correlated positively while IL-6 and IL-2 correlated negatively. In this pilot study, a cytokine pattern with elevated levels of IL-6, TNF-alpha, and sIL-2-R as well as suppressed levels of IL-2 in the early period after HTx corresponds to impaired hemodynamics independent of cellular rejection and may indicate an unfavorable prognosis. These cytokines may therefore be useful for monitoring and warrant further study.
Quad-Networks: Unsupervised Learning to Rank for Interest Point Detection (2017)

Several machine learning tasks require to represent the data using only a sparse set of interest points. An ideal detector is able to find the corresponding interest points even if the data undergo a transformation typical for a given domain. Since the task is of high practical interest in computer vision, many hand-crafted solutions were proposed. In this paper, we ask a fundamental question: can we learn such detectors from scratch? Since it is often unclear what points are interesting, human labelling cannot be used to find a truly unbiased solution. Therefore, the task requires an unsupervised formulation. We are the first to propose such a formulation: training a neural network to rank points in a transformation-invariant manner. Interest points are then extracted from the top/bottom quantiles of this ranking. We validate our approach on two tasks: standard RGB image interest point detection and challenging cross-modal interest point detection between RGB and depth images. We quantitatively show that our unsupervised method performs better or on-par with baselines.
Molecular cloning and long terminal repeat sequences of human endogenous retrovirus genes related to types A and B retrovirus genes (1986)

By using a DNA fragment primarily encoding the reverse transcriptase (pol) region of the Syrian hamster intracisternal A particle (IAP; type A retrovirus) gene as a probe, human endogenous retrovirus genes, tentatively termed HERV-K genes, were cloned from a fetal human liver gene library. Typical HERV-K genes were 9.1 or 9.4 kilobases in length, having long terminal repeats (LTRs) of ca. 970 base pairs. Many structural features commonly observed on the retrovirus LTRs, such as the TATAA box, polyadenylation signal, and terminal inverted repeats, were present on each LTR, and a lysine (K) tRNA having a CUU anticodon was identified as a presumed primer tRNA. The HERV-K LTR, however, had little sequence homology to either the IAP LTR or other typical oncovirus LTRs. By filter hybridization, the number of HERV-K genes was estimated to be ca. 50 copies per haploid human genome. The cloned mouse mammary tumor virus (type B) gene was found to hybridize with both the HERV-K and IAP genes to essentially the same extent.
A2E, a lipofuscin fluorophore, in human retinal pigmented epithelial cells in culture. (1999)

Internalized A2E has an affinity for acidic organelles. The membrane damage exhibited by A2E-accumulating RPE is dependent on the concentration of A2E and reflects the ability of this amphiphilic compound to exert detergent-like effects.
Inflammatory Biomarkers Interleukin‐6 and C‐Reactive Protein and Outcomes in Stable Coronary Heart Disease: Experiences From the STABILITY (Stabilization of Atherosclerotic Plaque by Initiation of Darapladib Therapy) Trial (2017)

URL: http://www.clinicaltrials.gov. Unique identifier: NCT00799903.
Channel equalization for block transmission systems (1995)

In a block transmission system the information symbols are arranged in the form of blocks separated by known symbols. Such a system is suitable for communication over time-dispersive channels subject to fast time-variations, e,g., the HF channel. The known reliable receiver for this system is the nonlinear data-directed estimator (NDDE). This paper presents appropriate equalization methods for this system. A nonstationary innovations representation based on Cholesky factorization is used in order to define a noise whitener and a maximum-likelihood block detector. Also block linear equalizers and block decision-feedback equalizers are derived. For each type we give the zero-forcing and the minimum-mean-squared-error versions. Performance evaluations and comparisons are given. We show that they perform better than conventional equalizers. As compared to the NDDE, the derived block decision-feedback equalizers perform better and are much less complex. Whereas the NDDE uses the Levinson algorithm to solve M/2 Toeplitz systems of decreasing order (where M is the number of symbols per block), the derived equalizers need to process only one Toeplitz system. Moreover, the Schur algorithm, proposed for Cholesky factorization allows us to further reduce the complexity.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
ViewCube (2008)

Literally hundreds of thousands of users of 2D computer-aided design (CAD) tools are in the difficult process of transitioning to 3D CAD tools. A common problem for these users is disorientation in the abstract virtual 3D environments that occur while developing new 3D scenes. To help address this problem, we present a novel in-scene 3D widget called the ViewCube as a 3D orientation indicator and controller. The ViewCube is a cube-shaped widget placed in a corner of the window. When acting as an orientation indicator, the ViewCube turns to reflect the current view direction as the user re-orients the scene using other tools. When used as an orientation controller, the ViewCube can be dragged, or the faces, edges, or corners can be clicked on, to easily orient the scene to the corresponding view. We conducted a formal experiment to measure the performance of the ViewCube comparing: (1) ArcBall-style dragging using the ViewCube for manual view switching, (2) clicking on face/edge/corner elements of the ViewCube for automated view switching and (3) clicking on a dedicated row of buttons for automated view switching. The results indicate that users prefer and are almost twice as fast at using the ViewCube with dragging compared to clicking techniques, independent of a number of ViewCube representations that we examined.
Exotic CTR fuels: non-thermal effects and laser fusion applications (1973)

The peculiarities of human leukocyte antigen (HLA) distribution (classes I and II) in young Georgians (72 patients) and Russians (81 patients) with ischaemic heart disease (IHD) were examined by standard tissue-typing methods. The distributions of HLAs in 267 healthy Russian, and 579 healthy Georgian blood donors were taken as controls. The antigens identified as genetic markers of IHD predisposition among Russians were B12 (relative risk, Rr = 2.91), DR1 (Rr = 3.41), and DR4 (Rr = 3.14), for Georgians B21 (Rr = 6.61) was identified. The difference in predisposition markers between these two populations, both belonging to the same race, indicates that IHD predisposition can be linked with different HLAs in different populations.
Style‐Based Motion Synthesis† (2004)

Abstract Representing motions as linear sums of principal components has become a widely accepted animation technique. While powerful, the simplest version of this approach is not particularly well suited to modeling the specific style of an individual whose motion had not yet been recorded when building the database: it would take an expert to adjust the PCA weights to obtain a motion style that is indistinguishable from his. Consequently, when realism is required, the current practice is to perform a full motion capture session each time a new person must be considered. In this paper, we extend the PCA approach so that this requirement can be drastically reduced: for whole classes of cyclic and noncyclic motions such as walking, running or jumping, it is enough to observe the newcomer moving only once at a particular speed or jumping a particular distance using either an optical motion capture system or a simple pair of synchronized video cameras. This one observation is used to compute a set of principal component weights that best approximates the motion and to extrapolate in real‐time realistic animations of the same person walking or running at different speeds, and jumping a different distance.
Atomic Force Microscopy of Long and Short Double-Stranded, Single-Stranded and Triple-Stranded Nucleic Acids (1996)

Atomic force microscopy (AFM, also called scanning force microscopy) is proving to be a useful technique for imaging DNA. Thus it is important to push the limits of AFM imaging in order to explore both what types of DNA can be reliably imaged and identified and also what substrates and methods of sample preparation are suitable. The following advances in AFM of DNA are presented here. (i) DNA molecules as short as 25 bases can be seen by AFM. The short single-stranded DNAs imaged here (25 and 50 bases long) appeared globular in the AFM, perhaps because they are all capable of intramolecular base pairing and because the DNAs were in a Mg(ll) buffer, which facilitates intramolecular cross-bridging. (ii) AFM images in air of short double-stranded DNA molecules, 100-200 bp, gave lengths consistent with A-DNA. (iii) AFM images of poly (A) show both short bent lumpy molecules with an apparent persistence length of 40 nm and long straight molecules with an apparent persistence length of 600 nm. For comparison, the apparent persistence length for double-stranded DNA from phX-174 under the same conditions was 80 nm. (iv) Structures believed to be triple- stranded DNA were seen in samples of poly(dA.poly(dT) and poly (dG).poly(dC). These structures were twice as high as double-stranded DNA and the same width. (v) Entire molecules of lambda DNA, approx. 16 micron long, were imaged clearly in overlapping scans. (vi) Plasmid DNA was imaged on oxidized silicon, although less clearly than on mica.
The derivation and potential use of human embryonic stem cells (2002)

Human embryonic stem cells lines can be derived from human blastocysts at high efficiency (>50%) by immunosurgical isolation of the inner cell mass and culture on embryonic fibroblast cell lines. These cells will spontaneously differentiate into all the primary embryonic lineages in vitro and in vivo, but they are unable to form an integrated embryo or body plan by themselves or when combined with trophectoderm cells. They may be directed into a number of specific cell types and this enrichment process requires specific growth factors, cell-surface molecules, matrix molecules and secreted products of other cell types. Embryonic stem (ES) cells are immortal and represent a major potential for cell therapies for regenerative medicine. Their use in transplantation may depend on the formation of a large bank of suitable human leucocyte antigen (HLA) types or the genetic erasure of their HLA expression. Successful transplantation may also require induction of tolerance in recipients and ongoing immune suppression. Although it is possible to customize ES cells by therapeutic cloning or cytoplasmic transfer, it would appear unlikely that these strategies will be used extensively for producing ES cells compatible for transplantation. Embryonic stem cell research may deliver a new pathway for regenerative medicine.
High Incidence of Sudden Death with Conduction System and Myocardial Disease Due to Lamins A and C Gene Mutation (2000)

We studied 54 living relatives from a large French kindred, among which 17 members presented with a cardiomyopathy transmitted on an autosomal dominant mode. Five of these individuals had clinical manifestations of muscle disease phenotypically consistent with Emery-Dreifuss muscular dystrophy. Genetic analysis of this kindred had demonstrated a nonsense mutation in the LMNA gene located on chromosome 1q11-q23. This gene encodes lamins A and C, proteins of the nuclear lamina located on the inner face of the nuclear envelope. We retrospectively determined the cause of death of 15 deceased family members, 8 of whom had died suddenly, 2 as a first and single manifestation of the disease. The six other cases had histories of arrhythmias and left ventricular dysfunction before dying suddenly, and three of them died despite the prior implantation of a permanent pacemaker. The mean age of onset of cardiac symptoms among affected living family members was 33 years (range 15-47 years), and the first symptoms were due to marked atrioventricular conduction defects or sinus dysfunction, requiring the implantation of permanent pacemakers in seven cases. Myocardial dysfunction accompanied by ventricular arrhythmias developed rapidly in the course of the disease and resulted in severe dilated cardiomyopathy requiring cardiac transplantation in three cases. In conclusion, in patients presenting a life-threatening familial or sporadic cardiac restricted phenotype similar to that described here, mutations in the lamins A and C gene should be looked for. In the genotypically affected individuals, cardiological and electrophysiological follow-up should be performed to prevent sudden death that could occur rapidly in the evolution of such disease.