gebhart/patrepeval huggingface dataset:
Overexpression of MAP2 and NF-H Associated with Dendritic Pathology in the Spinal Cord of Mice Infected with Rabies Virus (2018)

Rabies is a viral infection that targets the nervous system, specifically neurons. The clinical manifestations of the disease are dramatic and their outcome fatal; paradoxically, conventional histopathological descriptions reveal only subtle changes in the affected nervous tissue. Some researchers have considered that the pathophysiology of rabies is based more on biochemical changes than on structural alterations, as is the case with some psychiatric diseases. However, we believe that it has been necessary to resort to other methods that allow us to analyze the effect of the infection on neurons. The Golgi technique is the gold standard for studying the morphology of all the components of a neuron and the cytoskeletal proteins are the structural support of dendrites and axons. We have previously shown, in the mouse cerebral cortex and now with this work in spinal cord, that rabies virus generates remarkable alterations in the morphological pattern of the neurons and that this effect is associated with the increase in the expression of two cytoskeletal proteins (MAP2 and NF-H). It is necessary to deepen the investigation of the pathogenesis of rabies in order to find therapeutic alternatives to a disease to which the World Health Organization classifies as a neglected disease.
Traffic Sign Occlusion Detection Using Mobile Laser Scanning Point Clouds (2017)

For survey and maintenance of traffic signs, this paper presents a novel traffic sign occlusion detection method using 3-D point clouds and trajectory data acquired by a mobile laser scanning system. To produce a maintenance guide, our method aims to obtain the degree of occlusion by analyzing the spatial relationship between traffic signs, surroundings, and drivers on the road. First, a detection method considering both reflectance and geometric features is developed to capture traffic signs. Next, to simulate the driver's view, a trajectory-based method is proposed to determine driver's observation location and the corresponding observed traffic sign. Finally, to determine whether a traffic sign is in occlusion, a hidden point removal algorithm is adopted and carried out. Furthermore, we develop two indices to evaluate the degree of occlusion. The proposed method is tested using two point cloud data sets collected by an RIEGL VMX-450 system along a 23.68-km-long urban road. The obtained results illustrate the feasibility of the proposed occlusion detection method.
Cholesterol inhibits spontaneous action potentials and calcium currents in guinea pig gallbladder smooth muscle (1999)

Elevated cholesterol decreases agonist-induced contractility and enhances stone formation in the gallbladder. The current study was conducted to determine if and how the electrical properties and ionic conductances of gallbladder smooth muscle are altered by elevated cholesterol. Cholesterol was delivered as a complex with cyclodextrin, and effects were evaluated with intracellular recordings from intact gallbladder and whole cell patch-clamp recordings from isolated cells. Cholesterol significantly attenuated the spontaneous action potentials of intact tissue. Furthermore, calcium-dependent action potentials and calcium currents were reduced in the intact tissue and in isolated cells, respectively. However, neither membrane potential hyperpolarizations induced by the ATP-sensitive potassium channel opener, pinacidil, nor voltage-activated outward potassium currents were affected by cholesterol. Hyperpolarizations elicited by calcitonin gene-related peptide were reduced by cholesterol enrichment, indicating potential changes in receptor ligand binding and/or second messenger interactions. These data indicate that excess cholesterol can contribute to gallbladder stasis by affecting calcium channel activity, whereas potassium channels remained unaffected. In addition, cholesterol enrichment may also modulate receptor ligand behavior and/or second messenger interactions.
Efficient Phrase-Based Document Similarity for Clustering (2008)

In this paper, we propose a phrase-based document similarity to compute the pair-wise similarities of documents based on the suffix tree document (STD) model. By mapping each node in the suffix tree of STD model into a unique feature term in the vector space document (VSD) model, the phrase-based document similarity naturally inherits the term tf-idf weighting scheme in computing the document similarity with phrases. We apply the phrase-based document similarity to the group-average Hierarchical Agglomerative Clustering (HAC) algorithm and develop a new document clustering approach. Our evaluation experiments indicate that, the new clustering approach is very effective on clustering the documents of two standard document benchmark corpora OHSUMED and RCV1. The quality of the clustering results significantly surpass the results of traditional single-word \textit{tf-idf} similarity measure in the same HAC algorithm, especially in large document data sets. Furthermore, by studying the property of STD model, we conclude that the feature vector of phrase terms in the STD model can be considered as an expanded feature vector of the traditional single-word terms in the VSD model. This conclusion sufficiently explains why the phrase-based document similarity works much better than the single-word tf-idf similarity measure.
<i>p</i>-Thiophenylalanine-Induced DNA Cleavage and Religation Activity of a Modified Vaccinia Topoisomerase IB (2011)

Vaccinia DNA topoisomerase IB is the smallest of the type IB topoisomerases. Because of its small size (314 amino acids) and target site specificity (5'(C/T)CCTTp(↓) sites), it constitutes an excellent model for studying the interaction of type IB enzymes with duplex DNA. In this study, p-thiophenylalanine was incorporated into the enzyme active site (position 274) by in vitro translation in the presence of a chemically misacylated tRNA. The modification, which resulted in replacement of the nucleophilic tyrosine OH group with SH, retained DNA topoisomerase activity and did not alter the DNA cleavage site. However, the modified topoisomerase effected relaxation of supercoiled plasmid DNA at a rate about 16-fold slower than the wild-type enzyme. The thiophenylalanine-induced DNA cleavage rate (k(cl) = 1 × 10(-4) s(-1)) was 30 times lower than for the wild-type enzyme (k(cl) = 3 × 10(-3) s(-1)). In contrast, thiophenylalanine-induced DNA religation was faster than that of the wild-type enzyme. We propose that the change in kinetics reflects the difference in bond energies between the O-P and S-P bonds being formed and broken in the reactions catalyzed by the wild-type and modified enzymes. We also studied the effect of adding Mg(2+) and Mn(2+) to the wild-type and modified topoisomerases I. Divalent metal ions such as Mg(2+) and Mn(2+) increased DNA relaxation activity of the wild-type and modified enzymes. However, the pattern of increases failed to support the possibility that metal ion-heteroatom interaction is required for catalysis.
A Study on Communicaton Antenna Isolation (1973)

Abstract : Problems on FAA communication antennas related to isolation are analyzed. The concpet of using progressively phased circular array to achieve high isolation is studied. The method of study is divided into theoretical and experimental. Theoretical study involved using moment method. Symmetrical dipoles were used as elements. Factors analyzed include array radius, antenna size, position accuracy, impedance, radiation pattern, and isolation. The experimental study involved building scale antennas from existing FAA coaxial dipoles and used them as array elements, and simulated matrix feed conditions to study isolation and radiation pattern. An isolation of 55 db was found possible. The concept is shown to provide high isolation in a very limited space. It provides flexibility for beam forming, and azimuth scanning.
Bacterial ghosts as a novel advanced targeting system for drug and DNA delivery (2005)

Although there are powerful drugs against infectious diseases and cancer on the market, delivery systems are needed to decrease serious toxic and noncurative side effects. In order to enhance compliance, several delivery systems such as polymeric micro- and nanoparticles, liposomal systems and erythrocyte ghosts have been developed. Bacterial ghosts representing novel advanced delivery and targeting vehicles suitable for the delivery of hydrophobic or water-soluble drugs, are the main focus of this review. They are useful nonliving carriers, as they can carry different active substances in more than one cellular location separately and simultaneously. Bacterial ghosts combine excellent natural or engineered adhesion properties with versatile carrier functions for drugs, proteins and DNA plasmids or DNA minicircles. The simplicity of both bacterial ghost production and packaging of drugs and/or DNA makes them particularly suitable for the use as a delivery system. Further advantages of bacterial ghost delivery vehicles include high bioavailability and a long shelf life without the need of cold-chain storage due to the possibility to freeze-dry the material.
A co-relational model of data for large shared data banks (2011)

Contrary to popular belief, SQL and noSQL are really just two sides of the same coin.
Membrane Binding of MinE Allows for a Comprehensive Description of Min-Protein Pattern Formation (2013)

The rod-shaped bacterium Escherichia coli selects the cell center as site of division with the help of the proteins MinC, MinD, and MinE. This protein system collectively oscillates between the two cell poles by alternately binding to the membrane in one of the two cell halves. This dynamic behavior, which emerges from the interaction of the ATPase MinD and its activator MinE on the cell membrane, has become a paradigm for protein self-organization. Recently, it has been found that not only the binding of MinD to the membrane, but also interactions of MinE with the membrane contribute to Min-protein self-organization. Here, we show that by accounting for this finding in a computational model, we can comprehensively describe all observed Min-protein patterns in vivo and in vitro. Furthermore, by varying the system's geometry, our computations predict patterns that have not yet been reported. We confirm these predictions experimentally.
Comamonas testosteroni 3-ketosteroid-delta 4(5 alpha)-dehydrogenase: gene and protein characterization (1996)

Comamonas testosteroni delta 4(5 alpha)- and delta1-dehydrogenases [delta4(5alpha)- and delta1DH] are key enzymes in the degradation of steroids having an A:B ring fusion in a trans configuration. We previously reported the isolation of the delta1dh gene (P. Plesiat, M. Grandguillot, S. Harayama, S. Vragar, and Y. Michel Briand, J. Bacteriol. 173:7219-7227, 1991). In this study, the gene encoding delta 4(5 alpha)DH was cloned in Escherichia coli on a 16-kbp BamHI fragment by screening a genomic bank of C. testosteroni ATCC 17410 with a probe derived from delta1dh. Subcloning experiments in plasmid pUC19 mapped delta 4(5 alpha)dh immediately downstream of delta1dh. The enzyme was overexpressed 18-fold in cells of E. coli JM109 carrying a 2.5-kbp cloned fragment (plasmid pXE25). However, much higher levels of enzymatic activity (264-fold) were obtained in Pseudomonas putida KT2440, using pMMB208 as an expression vector. Studies with crude lysates of KT2440 showed that delta4(5alpha)DH exhibits higher specificity and higher activity toward delta l-androstene-3,17-dione than toward the saturated derivative 5 alpha-androstane-3,17-dione. The reaction was found to be irreversible and to use efficiently typical flavoprotein electron acceptors; optimal conditions for the enzyme activity were pH 8 and 40 degrees C. Analysis of the nucleotide sequence of the insert of pXE25 revealed an open reading frame of 1,593 bp preceded by a putative ribosome-binding site and followed by a potential transcription terminator. The amino acid sequence of the deduced peptide showed a typical flavin adenine dinucleotide-binding site in its N-terminal region, confirming the flavoproteinic structure of delta 4(5 alpha)DH. The predicted molecular mass was consistent with that of the enzyme expressed in a T7 polymerase system (60 kDa). Alignment between delta 4(5 alpha)dh and delta1dh indicated that both genes, though coding for functionally related enzymes, do not derive from a common ancestor.
Transfer functions Under no-Analog Conditions: Experiments With Indian Ocean Planktonic Foraminifera (1977)

This paper documents and investigates an important source of inaccuracy when paleoecological equations calibrated on modern biological data are applied downcore: fossil assemblages for which there are no modern analogs. Algebraic experiments with five calibration techniques are used to evaluate the sensitivity of the methods with respect to no-analog conditions. The five techniques are: species regression; principal-components regression [e.g., Imbrie, J., and Kipp, N. G. (1971). In “The Late Cenozoic Ages,” 71–181]; distance-index regression [Hecht, A. D. (1973). Micropaleontology 19 , 68–77]; diversity-index regression (Williams, D. F., and Johnson, W. C. (1975). Quaternary Research 5 , 237–250]; weighted-average method [Jones, J. I. (1964). Unpublished Ph. D. Thesis, Univ. of Wisconsin]. The experiments indicate that the four regression techniques extrapolate under no-analog conditions, yielding erroneous estimates. The weighted-average technique, however, does not extrapolate under no-analog conditions and consequently is more accurate than the other techniques. Methods for recognizing no-analog conditions downcore are discussed, and ways to minimize inaccuracy are suggested. Using several equations based on different calibration techniques is recommended. Divergent estimates suggest that no-analog conditions occur and that estimates are unreliable. The value determined by the weighted-average technique, however, may well be the most accurate.
Substituent Effects on the Ring-Opening Mechanism of Lithium Bromocyclopropylidenoids to Allenes (2008)

The ring-opening reactions of lithium bromocyclopropylidenoids to allenes have been investigated computationally at the B3LYP/6-31G(d) level of theory. Formally, two pathways can be considered: the reaction may either proceed in a concerted fashion or stepwise with the intermediacy of a free cyclopropylidene. In both cases, the loss of the bromide ion determines the kinetic of the reaction. The stability of the reactive intermediate, i.e., the carbene, is dependent on the substituent. Cyclopropylidenes bearing an electron-donating group (+M) are extremely unstable and ring-open readily to the allene. In contrast, bromocyclopropylidenoids with electron-withdrawing groups are particularly stable species. Here, a high energy barrier needs to be overcome in order to split off bromide and to generate the corresponding carbene or allene. Still, for most of the monosubstituted cyclopropylidenes investigated during this study, the activation energy for the cyclopropylidene to allene rearrangement is lower than the energy required for parent compound (X = H) except for X = -SiH3 and -CF3.
A Hadamard Transform Raman Microprobe (1989)

The design of a Hadamard transform Raman microprobe is presented. The spatially multiplexed imaging system provides true spectroscopic microscopy. Near-diffraction limited resolution, 1.3 µm, is demonstrated with Raman images of polycrystalline materials.
Urea hydrolysis can predict the potential pathogenicity of Vibrio parahaemolyticus strains isolated in the Pacific Northwest (1994)

The ability of some strains of Vibrio parahaemolyticus to hydrolyze urea (uh+) can be used as a marker to predict which strains isolated from molluscan shellfish harvested in the Pacific Northwest are potentially pathogenic. The thermostable direct hemolysin-producing (TDH+) characteristic is a marker that is correlated with potential pathogenicity, and all of the TDH+ strains that we have isolated have been found to be uh+. Most of the uh+ strains belong to somatic antigen groups O3, O4 and O5. TDH+ strains are usually members of groups O4 and O5. The strains most often associated with human illness are members of the uh+, O4 group. The test for urease production is a simple screening test that can be helpful in predicting which strains are potentially pathogenic.
Facile in situ Preparation of o-Azaxylylene from N,O-Diethoxycarbonyl-o-aminobenzyl Alcohol (1998)

Ah& ------o-Azaxylylenes were generated only by gentle refluxing of N.0diethoxycarhonyl-u-aminobenzyl alcohols in o-
Exacerbation of antigen-induced arthritis in urokinase-deficient mice. (1998)

In rheumatoid arthritis, synovial expression of urokinase (uPA) activity is greatly increased (Busso, N., V. Péclat, A. So, and A. -P. Sappino. 1997. Ann. Rheum. Dis. 56:550- 557). We report the same effect in murine antigen-induced arthritis. uPA-mediated plasminogen activation in arthritic joints may have deleterious effects via degradation of cartilage and bone matrix proteins as well as beneficial effects via fibrin degradation. We evaluated these contrasting effects in vivo by analyzing the phenotype of uPA-deficient (uPA-/-) and control mice during antigen-induced arthritis. Joint inflammation was comparable in both groups up to day 3 and subsequently declined in control mice, remaining significantly elevated in uPA-/- mice on days 10 and 30 after arthritis onset. Likewise, synovial thickness was markedly increased in uPA-deficient mice persisting for up to 2 mo, whereas it subsided in control animals. Bone erosion was exacerbated in uPA-/- mice on day 30. By contrast, no difference in articular cartilage proteoglycan content was found between both groups. Significantly increased accumulation of fibrin was observed by day 30 in arthritic joints of uPA-/- mice. We hypothesized that synovial fibrin deposition plays a role in joint inflammation. Accordingly, defibrinogenation of uPA-/- mice by ancrod significantly decreased the sustained joint inflammation. All the above observations were reproducible in plasminogen-deficient (Pln-/-) mice. In conclusion, synovial fibrin deposition plays a role as a nonimmunological mechanism which sustains chronic arthritis.
Serotypes, Virulence Genes, and Intimin Types of Shiga Toxin (Verotoxin)-Producing <i>Escherichia coli</i> Isolates from Healthy Sheep in Spain (2003)

Fecal swabs obtained from 1,300 healthy lambs in 93 flocks in Spain in 1997 were examined for Shiga toxin-producing Escherichia coli (STEC). STEC O157:H7 strains were isolated from 5 (0.4%) animals in 4 flocks, and non-O157 STEC strains were isolated from 462 (36%) lambs in 63 flocks. A total of 384 ovine STEC strains were characterized in this study. PCR showed that 213 (55%) strains carried the stx(1) gene, 10 (3%) possessed the stx(2) gene, and 161 (42%) carried both the stx(1) and the stx(2) genes. Enterohemolysin (ehxA) and intimin (eae) virulence genes were detected in 106 (28%) and 23 (6%) of the STEC strains, respectively. The STEC strains belonged to 35 O serogroups and 64 O:H serotypes (including 18 new serotypes). However, 72% were of 1 of the following 12 serotypes: O5:H-, O6:H10, O91:H-, O117:H-, O128:H-, O128:H2, O136:H20, O146:H8, O146:H21, O156:H-, O166:H28, and ONT:H21 (where NT is nontypeable). Although the 384 STEC strains belonged to 95 different seropathotypes (associations between serotypes and virulence genes), 49% of strains belonged to only 11. O91:H- stx(1) stx(2) (54 strains) was the most common seropathotype, followed by O128:H- stx(1) stx(2) (33 strains) and O6:H10 stx(1) (25 strains). Three strains of serotypes O26:H11, O156:H11, and OX177:H11 had intimin type beta1; 5 strains of serotype O157:H7 possessed intimin type gamma1; and 15 strains of serotypes O49:H-, O52:H12, O156:H- (12 strains), and O156:H25 had the new intimin, intimin type zeta. The majority (82%) of ovine STEC strains belonged to serotypes previously found to be associated with human STEC strains, and 51% belonged to serotypes associated with STEC strains isolated from patients with hemolytic-uremic syndrome. Thus, this study confirms that healthy sheep are a major reservoir of STEC strains pathogenic for humans.
Impact of cytomorphological detection of circulating tumor cells in patients with liver cancer (2004)

The clinical impact of circulating tumor cell (CTC) detection is controversial, mainly due to drawbacks of molecular approaches applied to this field. We sought to determine if the specific identification and counting of circulating tumor cells by cytomorphologic analysis has clinical usefulness. Peripheral blood (6 mL), treated using isolation by size of epithelial tumor cells, was obtained from 44 patients with primary liver cancer (PLC) and without metastases, 30 patients with chronic active hepatitis, 39 with liver cirrhosis, and 38 healthy individuals, and followed up for a mean period of 1 year. We searched for β-catenin mutations in 60 single microdissected CTCs. One patient with liver cancer developed extrahepatic metastases during follow-up. CTCs and microemboli were found in 23 of the 44 patients with liver cancer and in none of the patients with chronic active hepatitis, patients with cirrhosis, or healthy subjects. Their presence was significantly associated with tumor diffusion ( P = .0001) and portal tumor thrombosis ( P = .006). Both the presence ( P = .01) and number ( P = .02) of CTCs and microemboli were significantly associated with a shorter survival. β-Catenin mutations were found in 3 of 60 CTCs, arguing against their impact on the initial step of tumor cell invasion. In conclusion, the highly sensitive and specific detection of CTCs and microemboli may have clinical implications for cancer staging and outcome prediction. We also show the feasibility of molecular studies of individual circulating tumor cells, aimed at identifying gene mutations involved in tumor invasion. (Hepatology 2004;39:792-797.)
Detailed Structural Analysis of Lipids Directly on Tissue Specimens Using a MALDI-SpiralTOF-Reflectron TOF Mass Spectrometer (2012)

Direct tissue analysis using a novel tandem time-of-flight (TOF-TOF) mass spectrometer is described. This system consists of a matrix-assisted laser desorption/ionization ion source, a spiral ion trajectory TOF mass spectrometer "SpiralTOF (STOF)", a collision cell, and an offset parabolic reflectron (RTOF). The features of this system are high precursor ion selectivity due to a 17-m flight path length in STOF and elimination of post-source decay (PSD) ions. The acceleration energy is 20 keV, so that high-energy collision-induced dissociation (HE-CID) is possible. Elimination of PSD ions allows observation of the product ions inherent to the HE-CID process. By using this tandem TOF instrument, the product ion spectrum of lipids provided detailed structural information of fatty acid residues.
The Concept of Asphaltenes (1982)

This chapter considers the composition of heavy oils in terms of a map of molecular weight vs. polarity of the various components in the sample. Thus, a clearer understanding of the nature of asphaltenes is obtained. The inter-relationship of polarity and molecular weight in terms of solubility behavior can be better understood and it becomes clear that there is not a specific chemical composition or a specific molecular weight description for asphaltenes. Rather, asphaltenes contain a wide distribution of polarities and molecular weights.