gebhart/patrepeval huggingface dataset:
C-erbB-2 Oncoprotein in Gastric Carcinoma: Correlation with Clinical Stage and Prognosis (2001)

The aim of this study was to investigate the expression of the oncogene c-erbB-2 in gastric tumors. Immunohistochemical study of the expression of c-erbB-2 was performed in formalin-fixed, paraffin-embedded sections from 82 gastric adenocarcinomas using polyclonal antibody. c-erbB-2-positive immunostaining was observed in 37 (45%) tumors. Positive staining was detected in 63% of well differentiated, 46% of moderately differentiated and 80% of papillary adenocarcinomas. In poorly differentiated adenocarcinomas, positivity for c-erbB-2 was observed in 21 %. According to the Lauren classification, a higher frequency of c-erbB-2 positive staining was observed in intestinal type tumors (70%). During the follow-up period 43% of the patients with c-erbB-2 oncoprotein-negative tumors and 45% of the patients with c-erbB-2 oncoprotein-positive tumors died. There was no significant association between c-erbB-2 staining and sex, age, clinical stage, tumor grade, histological type or survival rates. In conclusion, almost half of the gastric cancers were positive for c-erbB-2. Nonetheless, the expression of c-erbB-2 oncoprotein did not play a role in prognosis.
Screening λgt Recombinant Clones by Hybridization to Single Plaques in Situ (1977)

A rapid, direct method for screening single plaques of Agt recombinant phage is described. The method allows at least 10(6) clones to be screened per day and simplifies physical containment of recombinants.
Dihydrolipoamide Dehydrogenase Mutation Alters the NADH Sensitivity of Pyruvate Dehydrogenase Complex of Escherichia coli K-12 (2008)

Under anaerobic growth conditions, an active pyruvate dehydrogenase (PDH) is expected to create a redox imbalance in wild-type Escherichia coli due to increased production of NADH (>2 NADH molecules/glucose molecule) that could lead to growth inhibition. However, the additional NADH produced by PDH can be used for conversion of acetyl coenzyme A into reduced fermentation products, like alcohols, during metabolic engineering of the bacterium. E. coli mutants that produced ethanol as the main fermentation product were recently isolated as derivatives of an ldhA pflB double mutant. In all six mutants tested, the mutation was in the lpd gene encoding dihydrolipoamide dehydrogenase (LPD), a component of PDH. Three of the LPD mutants carried an H322Y mutation (lpd102), while the other mutants carried an E354K mutation (lpd101). Genetic and physiological analysis revealed that the mutation in either allele supported anaerobic growth and homoethanol fermentation in an ldhA pflB double mutant. Enzyme kinetic studies revealed that the LPD(E354K) enzyme was significantly less sensitive to NADH inhibition than the native LPD. This reduced NADH sensitivity of the mutated LPD was translated into lower sensitivity of the appropriate PDH complex to NADH inhibition. The mutated forms of the PDH had a 10-fold-higher K(i) for NADH than the native PDH. The lower sensitivity of PDH to NADH inhibition apparently increased PDH activity in anaerobic E. coli cultures and created the new ethanologenic fermentation pathway in this bacterium. Analogous mutations in the LPD of other bacteria may also significantly influence the growth and physiology of the organisms in a similar fashion.
Aspects of social life in the fat-tailed dwarf lemur (Cheirogaleus medius): Inferences from body weights and trapping data (1999)

Body weight is an important attribute of any animal and influences its biology in many ways. In the case of the fat-tailed dwarf lemur (Cheirogaleus medius), this is of special interest because animals of this species store fat to survive extended torpor phases during the austral winter and, as a result, show extreme seasonal variation in body weight. In this paper, I present field data from a 20-month study at the Forestry Station of Ampijoroa in northwestern Madagascar on body weights of repeatedly trapped individuals combined with trapping results to investigate the general biology and notably the social life of C. medius. The most remarkable physical characteristic of wild C. medius is a dramatic weight-loss in males in September following emergence from torpor. Trapping results showed that adult males emerge from torpor earlier than females and offspring, even though food is still scarce. Early emergence from torpor puts males at an energetic disadvantage and confers no advantage in terms of access to females. Observation data from nightly follows indicate that males patrol their home range, probably to guarantee its integrity for the coming active season and to secure the food supply for their families. The high energetic costs of this strategy is argued to represent a form of paternal investment. Body weight data of repeatedly captured individuals showed that they may reach adult size and sexual maturity at 2 years of age but are not socially mature before the age of 3 years. The data presented may serve as a guide for keeping C. medius at a suitable weight in captivity.
Coordinate regulation of virulence genes in Listeria monocytogenes requires the product of the prfA gene (1992)

The prfA gene of Listeria monocytogenes encodes a protein that activates transcription of the listeriolysin gene (lisA). In order to explore the role of the prfA gene product in the pathogenesis of listerial infection, we constructed a site-directed insertion mutation in prfA by the chromosomal integration of a novel suicide vector containing a portion of the prfA coding region. This mutation not only transcriptionally silenced the listeriolysin (lisA) gene but also abrogated production of specific RNA transcripts corresponding to the phosphatidylinositol-specific phospholipase C (pic) and metalloprotease (mpl) genes, two further virulence gene products expressed only by pathogenic Listeria strains. The strain was also found to be avirulent when tested in a mouse model of listerial infection. The concomitant loss of multiple characteristics such as production of LisA, Pic, Mpl, and loss of virulence in a mouse infection model is the result of a mutation in a single gene and demonstrates that the prfA gene product is a positive regulator of multiple virulence determinants in L. monocytogenes.
Universal molecule injector in liquid helium: Pulsed cryogenic doped helium droplet source (2002)

Progress toward the construction of a universal molecule injector for doping bulk liquid helium is reported. A pulsed valve that operates at cryogenic temperatures, down to 4 K, is demonstrated within the confinement of a cryostat, operating in the vapor above a steady level of liquid He. The insulated valve can be operated at elevated temperatures with preseeded helium gas in supersonic expansion mode, as demonstrated through laser-induced fluorescence spectra of seeded NO2. At cryogenic operating temperatures, the expansion into vapor helium produces a well-collimated liquid helium droplet beam, which is then used to transfer to the liquid impurities produced by laser ablation from a cryogenic rotating target. The operation can be visualized using copper as the ablation target: the droplet beam is imaged via Rayleigh scattering, while the beam past the plasma is imaged by the fluorescence of the entrained Cu atoms. The beam drags along copper ions and electrons, the recombination of which controls the fluorescence yield downstream.
Vision-Based Offline-Online Perception Paradigm for Autonomous Driving (2015)

Autonomous driving is a key factor for future mobility. Properly perceiving the environment of the vehicles is essential for a safe driving, which requires computing accurate geometric and semantic information in real-time. In this paper, we challenge state-of-the-art computer vision algorithms for building a perception system for autonomous driving. An inherent drawback in the computation of visual semantics is the trade-off between accuracy and computational cost. We propose to circumvent this problem by following an offline-online strategy. During the offline stage dense 3D semantic maps are created. In the online stage the current driving area is recognized in the maps via a re-localization process, which allows to retrieve the pre-computed accurate semantics and 3D geometry in real-time. Then, detecting the dynamic obstacles we obtain a rich understanding of the current scene. We evaluate quantitatively our proposal in the KITTI dataset and discuss the related open challenges for the computer vision community.
Regulation of Cell Death Protease Caspase-9 by Phosphorylation (1998)

Caspases are intracellular proteases that function as initiators and effectors of apoptosis. The kinase Akt and p21-Ras, an Akt activator, induced phosphorylation of pro-caspase-9 (pro-Casp9) in cells. Cytochrome c-induced proteolytic processing of pro-Casp9 was defective in cytosolic extracts from cells expressing either active Ras or Akt. Akt phosphorylated recombinant Casp9 in vitro on serine-196 and inhibited its protease activity. Mutant pro-Casp9(Ser196Ala) was resistant to Akt-mediated phosphorylation and inhibition in vitro and in cells, resulting in Akt-resistant induction of apoptosis. Thus, caspases can be directly regulated by protein phosphorylation.
Surfactant Protein D Augments Bacterial Association but Attenuates Major Histocompatibility Complex Class II Presentation of Bacterial Antigens (2006)

Surfactant protein D (SP-D) is a secreted pattern recognition molecule associated with lung surfactant and mediates the clearance of pathogens in multiple ways. SP-D is an established part of the innate immune system, but it also modulates the adaptive immune response by interacting with both antigen-presenting cells and T cells. In a previous study, antigen presentation by bone marrow-derived dendritic cells was enhanced by SP-D. As dendritic cell function varies depending on the tissue of origin, we extended these studies to antigen-presenting cells isolated from mouse lung. Flow cytometric studies showed that SP-D binds calcium dependently and specifically to lung CD11c-positive cells. Opsonization of fluorescently labeled Escherichia coli by SP-D enhanced uptake by lung dendritic cells. SP-D facilitated the association of E. coli and antigen-presenting cells by increasing the frequency of CD11+ cells associated with E. coli by up to 10-fold. In contrast to the effect on bone marrow-derived dendritic cells, SP-D decreased the antigen presentation of ovalbumin, expressed in E. coli, to ovalbumin-specific major histocompatibility complex class II-specific T-cell hybridomas by 30-50%. The reduction of antigen presentation did not depend on whether the dendritic cells were isolated from the lungs of nonstimulated mice or mice that had been exposed to LPS aerosols. Our results show that SP-D increases the opsonization of pathogens, but decreases the antigen presentation by lung dendritic cells, and thereby, potentially dampens the activation of T cells and an adaptive immune response against bacterial antigens--during both steady-state conditions and inflammation.
Development of a Single Vector System that Enhances Trans-Splicing of SMN2 Transcripts (2008)

RNA modalities are developing as a powerful means to re-direct pathogenic pre-mRNA splicing events. Improving the efficiency of these molecules in vivo is critical as they move towards clinical applications. Spinal muscular atrophy (SMA) is caused by loss of SMN1. A nearly identical copy gene called SMN2 produces low levels of functional protein due to alternative splicing. We previously reported a trans-splicing RNA (tsRNA) that re-directed SMN2 splicing. Now we show that reducing the competition between endogenous splices sites enhanced the efficiency of trans-splicing. A single vector system was developed that expressed the SMN tsRNA and a splice-site blocking antisense (ASO-tsRNA). The ASO-tsRNA vector significantly elevated SMN levels in primary SMA patient fibroblasts, within the central nervous system of SMA mice and increased SMN-dependent in vitro snRNP assembly. These results demonstrate that the ASO-tsRNA strategy provides insight into the trans-splicing mechanism and a means of significantly enhancing trans-splicing activity in vivo.
Evolutionary families of peptidase inhibitors (2004)

The proteins that inhibit peptidases are of great importance in medicine and biotechnology, but there has never been a comprehensive system of classification for them. Some of the terminology currently in use is potentially confusing. In the hope of facilitating the exchange, storage and retrieval of information about this important group of proteins, we now describe a system wherein the inhibitor units of the peptidase inhibitors are assigned to 48 families on the basis of similarities detectable at the level of amino acid sequence. Then, on the basis of three-dimensional structures, 31 of the families are assigned to 26 clans. A simple system of nomenclature is introduced for reference to each clan, family and inhibitor. We briefly discuss the specificities and mechanisms of the interactions of the inhibitors in the various families with their target enzymes. The system of families and clans of inhibitors described has been implemented in the MEROPS peptidase database (http://merops.sanger.ac.uk/), and this will provide a mechanism for updating it as new information becomes available.
Evidence for Sulfur-Based Radicals in Thiolate Compound I Intermediates (1999)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTEvidence for Sulfur-Based Radicals in Thiolate Compound I IntermediatesMichael T. GreenView Author Information Department of Chemistry and Beckman Institute California Institute of Technology 1200 East California, Pasadena, California 91125 Department of Chemistry and James Franck Institute The University of Chicago, Chicago, Illinois 60637 Cite this: J. Am. Chem. Soc. 1999, 121, 34, 7939–7940Publication Date (Web):August 17, 1999Publication History Received10 May 1999Published online17 August 1999Published inissue 1 September 1999https://pubs.acs.org/doi/10.1021/ja991541vhttps://doi.org/10.1021/ja991541vrapid-communicationACS PublicationsCopyright © 1999 American Chemical SocietyRequest reuse permissionsArticle Views821Altmetric-Citations182LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Chemical calculations,Ligands,Pyrroles,Quantum mechanics,Thiolates Get e-Alerts
Lpr and gld: Single Gene Models of Systemic Autoimmunity and Lymphoproliferative Disease (1991)

The autosomal recessive lpr and gld genes induce in mice multiple autoantibodies and the progressive accumulation of large numbers of non-malignant CD4- CD8- T lymphocytes. The clinical syndromes and immune abnormalities associated with these two nonallelic genes are nearly identical and are also highly dependent on background genes. MRL/lpr mice are particularly severely affected, and they develop a syndrome that is serologically and pathologically similar to human systemic lupus erythematosus (SLE). Abnormal cell marker expression in the aberrant lpr T lymphocytes includes surface antigens normally associated with activated T cells or even with B cells, and it occurs along with enhanced expression of certain oncogenes. The lpr gene results in intrinsic abnormalities of both T and B lymphocytes, yet its location and product are unknown. The gld gene is located on chromosome 1; its product is also unknown. Although many immunological abnormalities are known, the mechanism whereby these two genes induce autoimmunity and lymphoproliferation remains obscure. Further studies of mice bearing these mutant genes are certain to yield insights into systemic autoimmunity and the control of lymphocyte proliferation.
Evaluation of the SBRC 256 x 256 InSb focal plane array and preliminary specifications for the 1024 x 1024 InSb focal plane array (1993)

The evolution of Santa Barbara Research Center (SBRC) InSb focal plane arrays (FPA) for astronomy has been significant since the introduction of the SBRC 58 X 62 array in the mid 1980's. A 256 X 256 array, whose performance is evaluated herein, is currently available from SBRC, and a 1024 X 1024 InSb FPA is under development by the U.S. Naval Observatory (USNO). National Optical Astronomy Observations (NOAO), and SBRC. This represents an increase by a factor of approximately 300 in the number of pixels in less than 10 years, with attendant increase in performance as well. The availability of high performance infrared arrays has opened up the field of infrared astronomy. As this paper shows, the 256 X 256 InSb FPA is a great improvement over its predecessor in all areas of performance. Its most striking improvement is the complete absence of a latent or residual image after exposure to very high fluxes. Because of its low node capacitance, which results in very low read noise, the full well capacity is somewhat compromised.
Pancreatitis-induced Acute Lung Injury (1988)

Cerulein-induced acute pancreatitis in rats is associated with acute lung injury characterized by increased pulmonary microvascular permeability, increased wet lung weights, and histologic features of alveolar capillary endothelial cell and pulmonary parenchymal injury. The alveolar capillary permeability index is increased 1.8-fold after a 3-hour injury (0.30 to 0.54, p less than 0.05). Gravimetric analysis shows a similar 1.5-fold increase in wet lung weights at 3 hours (0.35% vs. 0.51% of total body weight, p less than 0.05). Histologic features assessed by quantitative morphometric analysis include significant intra-alveolar hemorrhage (0.57 +/- 0.08 vs. 0.12 +/- 0.02 RBC/alveolus at 6 hours, p less than 0.001); endothelial cell disruption (28.11% vs. 4.3%, p less than 0.001); and marked, early neutrophil infiltration (7.45 +/- 0.53 vs. 0.83 +/- 0.18 PMN/hpf at 3 hours, p less than 0.001). The cerulein peptide itself, a cholecystokinin (CCK) analog, is naturally occurring and is not toxic and in several in vitro settings including exposure to pulmonary artery endothelial cells, Type II epithelial cells, and an ex vivo perfused lung preparation. The occurrence of this ARDS-like acute lung injury with acute pancreatitis provides an excellent experimental model to investigate mechanisms and mediators involved in the pathogenesis of ARDS.
The Role of CXCR3 in the Induction of Primary Biliary Cirrhosis (2011)

CXCR3 might contribute to the development of PBC in murine model. Knockout of CXCR3 might delay and alleviate the PBC disease progression, but could not entirely block the disease development.
Precerebellin is a cerebellum-specific protein with similarity to the globular domain of complement C1q B chain. (1991)

The cerebellum contains a hexadecapeptide, termed cerebellin, that is conserved in sequence from human to chicken. Three independent, overlapping cDNA clones have been isolated from a human cerebellum cDNA library that encode the cerebellin sequence. The longest clone codes for a protein of 193 amino acids that we term precerebellin. This protein has a significant similarity (31.3% identity, 52.2% similarity) to the globular (non-collagen-like) region of the B chain of human complement component C1q. The region of relatedness extends over approximately 145 amino acids located in the carboxyl terminus of both proteins. Unlike C1q B chain, no collagen-like motifs are present in the amino-terminal regions of precerebellin. The amino terminus of precerebellin contains three possible N-linked glycosylation sites. Although hydrophobic amino acids are clustered at the amino terminus, they do not conform to the classical signal-peptide motif, and no other obvious membrane-spanning domains are predicted from the cDNA sequence. The cDNA predicts that the cerebellin peptide is flanked by Val-Arg and Glu-Pro residues. Therefore, cerebellin is not liberated from precerebellin by the classical dibasic amino acid proteolytic-cleavage mechanism seen in many neuropeptide precursors. In Northern (RNA) blots, precerebellin transcripts, with four distinct sizes (1.8, 2.3, 2.7, and 3.0 kilobases), are abundant in cerebellum. These transcripts are present at either very low or undetectable levels in other brain areas and extraneural structures. A similar pattern of cerebellin precursor transcripts are seen in rat, mouse, and human cerebellum. Furthermore, a partial genomic fragment from mouse shows the same bands in Northern blots as the human cDNA clone. During rat development, precerebellin transcripts mirror the level of cerebellin peptide. Low levels of precerebellin mRNA are seen at birth. Levels increase modestly from postpartum day 1 to 8, then increase more dramatically between day 5 and 15, and eventually reach peak values between day 21 and 56. Because cerebellin-like immunoreactivity is associated with Purkinje cell postsynaptic structures, these data raise interesting possibilities concerning the function of the cerebellin precursor in synaptic physiology.
Infectivity and neutralization of Cryptosporidium parvum sporozoites (1987)

Cryptosporidiosis, a diarrheal disease of calves and humans caused by the coccidian parasite Cryptosporidium parvum, is terminated in hosts with normal immune systems. To assess the mechanisms of immunity in cryptosporidiosis, it is necessary to isolate and quantitate sporozoites, the infective stage of Cryptosporidium spp. Here we report the (i) separation of infective C. parvum oocysts from calf feces by ether extraction, sieving, and hypochlorite treatment; (ii) separation of viable C. parvum sporozoites from intact and excysted oocysts by anion-exchange chromatography; and (iii) quantitation of sporozoite infectivity in vivo by direct intraintestinal injection of isolated sporozoites in 7-day-old BALB/c mice. When isolated sporozoites were incubated with heat-inactivated immune bovine serum, 25 times the 50% infective dose for 7-day-old mice was completely neutralized. Sporozoites incubated with preimmune bovine serum were infectious for 7-day-old mice.
Detecting Changes in 3D Structure of a Scene from Multi-view Images Captured by a Vehicle-Mounted Camera (2013)

This paper proposes a method for detecting temporal changes of the three-dimensional structure of an outdoor scene from its multi-view images captured at two separate times. For the images, we consider those captured by a camera mounted on a vehicle running in a city street. The method estimates scene structures probabilistically, not deterministically, and based on their estimates, it evaluates the probability of structural changes in the scene, where the inputs are the similarity of the local image patches among the multi-view images. The aim of the probabilistic treatment is to maximize the accuracy of change detection, behind which there is our conjecture that although it is difficult to estimate the scene structures deterministically, it should be easier to detect their changes. The proposed method is compared with the methods that use multi-view stereo (MVS) to reconstruct the scene structures of the two time points and then differentiate them to detect changes. The experimental results show that the proposed method outperforms such MVS-based methods.