gebhart/patrepeval huggingface dataset:
Combined multiplanar optical coherence tomography and confocal scanning ophthalmoscopy (2004)

We demonstrate the clinical application of a multiplanar imaging system that simultaneously acquires en face (C-scan) optical coherence tomography (OCT) and the corresponding confocal ophthalmoscopic images, along with cross-sectional (B-scan) OCT at specifiable locations on the confocal image. The advantages of the simultaneous OCT and confocal acquisition as well as the challenges of interpreting the C-scan OCT images are discussed. Variations in tissue inclination with respect to the coherence wave surface alter the sampling of structures within the depth of the retina, producing novel slice orientations that are often challenging to interpret. We have evaluated for the first time the utility of C-scan OCT for a variety of pathologies, including melanocytoma, diabetic retinopathy, choroidal neovascular membrane, and macular pucker. Several remarkable new aspects of clinical anatomy were revealed using this new technique. The versatility of selective capture of C-scan OCT images and B-scan OCT images at precise points on the confocal image affords the clinician a more complete and interactive tool for 3-D imaging of retinal pathology.
Data‐Driven Shape Analysis and Processing (2016)

Abstract Data‐driven methods serve an increasingly important role in discovering geometric, structural and semantic relationships between shapes. In contrast to traditional approaches that process shapes in isolation of each other, data‐driven methods aggregate information from 3D model collections to improve the analysis, modelling and editing of shapes. Data‐driven methods are also able to learn computational models that reason about properties and relationships of shapes without relying on hard‐coded rules or explicitly programmed instructions. Through reviewing the literature, we provide an overview of the main concepts and components of these methods, as well as discuss their application to classification, segmentation, matching, reconstruction, modelling and exploration, as well as scene analysis and synthesis. We conclude our report with ideas that can inspire future research in data‐driven shape analysis and processing.
Myotonic syndromes (2002)

It now appears likely that myotonic dystrophy is the first instance of a genetic disease in which the harmful effect of a mutation involves the production of a pathogenic RNA. However, the exact mechanism is not understood, and it is unclear whether this RNA-mediated disease process is also responsible for the manifestations of myotonic dystrophy in non-muscle tissues.
Selective induction of p53 and chemosensitivity in RB-deficient cells by E1A mutants unable to bind the RB-related proteins (1997)

The adenovirus E1A oncoprotein renders primary cells sensitive to the induction of apoptosis by diverse stimuli, including many anticancer agents. E1A-expressing cells accumulate p53 protein, and p53 potentiates drug-induced apoptosis. To determine how E1A promotes chemosensitivity, a series of E1A mutants were introduced into primary human and mouse fibroblasts using high-titer recombinant retroviruses, allowing analysis of E1A in genetically normal cells outside the context of adenovirus infection. Mutations that disrupted apoptosis and chemosensitivity separated into two complementation groups, which correlated precisely with the ability of E1A to associate with either the p300/CBP or retinoblastoma protein families. Furthermore, E1A mutants incapable of binding RB, p107, and p130 conferred chemosensitivity to fibroblasts derived from RB-deficient mice, but not fibroblasts from mice lacking p107 or p130. Hence, inactivation of RB, but not p107 or p130, is required for chemosensitivity induced by E1A. Finally, the same E1A functions that promote drug-induced apoptosis also induce p53. Together, these data demonstrate that p53 accumulation and chemosensitivity are linked to E1A's oncogenic potential, and identify a strategy to selectively induce apoptosis in RB-deficient tumor cells.
Molecular alterations of the AKT2 oncogene in ovarian and breast carcinomas (1995)

The AKT2 gene is one of the human homologues of v-akt, the transduced oncogene of the AKT8 virus, which induces lymphomas in mice. In previous studies, AKT2, which codes for a serine-threonine protein kinase, was shown to be amplified and overexpressed in some human ovarian carcinoma cell lines and amplified in primary tumors of the ovary. To confirm and extend these findings, we conducted a large-scale, multicenter study of AKT2 alterations in ovarian and breast cancer. Southern-blot analysis demonstrated AKT2 amplification in 16 of 132 (12.1%) ovarian carcinomas and in 3 of 106 (2.8%) breast carcinomas. No AKT2 alteration was detected in 24 benign or borderline tumors. Northern-blot analysis revealed overexpression of AKT2 in 3 of 25 fresh ovarian carcinomas which were negative for AKT2 amplification. The difference in the incidence of AKT2 alterations in ovarian and breast cancer suggests a specific role for this gene in ovarian oncogenesis. No significant association was found between AKT2 amplification and amplification of the proto-oncogenes MYC and ERBB2, suggesting that amplification of AKT2 defines an independent subset of breast and ovarian cancers. Ovarian cancer patients with AKT2 alterations appear to have a poor prognosis. Amplification of AKT2 was especially frequent in undifferentiated tumors (4 of 8, p = 0.019), suggesting that AKT2 alterations may be associated with tumor aggressiveness.
Antioxidant Activity, Inhibition of Nitric Oxide Overproduction, and In Vitro Antiproliferative Effect of Maple Sap and Syrup from Acer saccharum (2010)

Antioxidant activity, inhibition of nitric oxide (NO) overproduction, and antiproliferative effect of ethyl acetate extracts of maple sap and syrup from 30 producers were evaluated in regard to the period of harvest in three different regions of Québec, Canada. Oxygen radical absorbance capacity (ORAC) values of maple sap and syrup extracts are, respectively, 12 +/- 6 and 15 +/- 5 micromol of Trolox equivalents (TE)/mg. The antioxidant activity was also confirmed by a cell-based assay. The period of harvest has no statistically significant incidence on the antioxidant activity of both extracts. The antioxidant activity of pure maple syrup was also determined using the ORAC assay. Results indicate that the ORAC value of pure maple syrup (8 +/- 2 micromol of TE/mL) is lower than the ORAC value of blueberry juice (24 +/- 1 micromol of TE/mL) but comparable to the ORAC values of strawberry (10.7 +/- 0.4 micromol of TE/mL) and orange (10.8 +/- 0.5 micromol of TE/mL) juices. Maple sap and syrup extracts showed to significantly inhibit lipopolysaccharide-induced NO overproduction in RAW264.7 murine macrophages. Maple syrup extract was significantly more active than maple sap extract, suggesting that the transformation of maple sap into syrup increases NO inhibition activity. The highest NO inhibition induced by the maple syrup extracts was observed at the end of the season. Moreover, darker maple syrup was found to be more active than clear maple syrup, suggesting that some colored oxidized compounds could be responsible in part for the activity. Finally, maple syrup extracts (50% inhibitory concentration = 42 +/- 6 microg/mL) and pure maple syrup possess a selective in vitro antiproliferative activity against cancer cells.
Genes required for rapid expression of nitrogenase activity in Azotobacter vinelandii (2005)

Rnf proteins are proposed to form membrane-protein complexes involved in the reduction of target proteins such as the transcriptional regulator SoxR or the dinitrogenase reductase component of nitrogenase. In this work, we investigate the role of rnf genes in the nitrogen-fixing bacterium Azotobacter vinelandii. We show that A. vinelandii has two clusters of rnf-like genes: rnf1, whose expression is nif-regulated, and rnf2, which is expressed independently of the nitrogen source in the medium. Deletion of each of these gene clusters produces a time delay in nitrogen-fixing capacity and, consequently, in diazotrophic growth. Deltarnf mutations cause two distinguishable effects on the nitrogenase system: (i), slower nifHDK gene expression and (ii), impairment of nitrogenase function. In these mutants, dinitrogenase reductase activity is lowered, whereas dinitrogenase activity remains essentially unaltered. Further analysis indicates that deltarnf mutants accumulate an inactive and iron-deficient form of NifH because they have lower rates of incorporation of [4Fe-4S] into NifH. Deltarnf mutations also cause a noticeable decrease in aconitase activity; however, they do not produce general oxidative stress or modification of Fe metabolism in A. vinelandii. Our results suggest the existence of a redox regulatory mechanism in A. vinelandii that controls the rate of expression and maturation of nitrogenase by the activity of the Rnf protein complexes. rnf1 plays a major and more specific role in this scheme, but the additive effects of mutations in rnf1 and rnf2 indicate the existence of functional complementation between the two homologous systems.
Phase II Study of Pegylated Arginine Deiminase for Nonresectable and Metastatic Hepatocellular Carcinoma (2010)

Pegylated ADI is a promising drug that capitalizes on a significant enzymatic deficiency in HCC. It is safe, well tolerated, and may benefit patients with unresectable HCC.
Using Deep Neural Networks for Inverse Problems in Imaging: Beyond Analytical Methods (2018)

Traditionally, analytical methods have been used to solve imaging problems such as image restoration, inpainting, and superresolution (SR). In recent years, the fields of machine and deep learning have gained a lot of momentum in solving such imaging problems, often surpassing the performance provided by analytical approaches. Unlike analytical methods for which the problem is explicitly defined and domain-knowledge carefully engineered into the solution, deep neural networks (DNNs) do not benefit from such prior knowledge and instead make use of large data sets to learn the unknown solution to the inverse problem. In this article, we review deep-learning techniques for solving such inverse problems in imaging. More specifically, we review the popular neural network architectures used for imaging tasks, offering some insight as to how these deep-learning tools can solve the inverse problem. Furthermore, we address some fundamental questions, such as how deeplearning and analytical methods can be combined to provide better solutions to the inverse problem in addition to providing a discussion on the current limitations and future directions of the use of deep learning for solving inverse problem in imaging.
Normal and amblyopic contrast sensitivity function in central and peripheral retinas. (1978)

Contrast sensitivity functions (CSF's) for temporally modulated sine wave gratings were established at a variety of retinal eccentricities in three esotropic amblyopes with acuities in their amblyopic eyes of 20/50, 20/100, and 20/300. CSF's were shown to vary with eccentricity and the degree of amblyopia. In the 20/50 amblyope, reduced CSF's were confined to the higher spatial frequencies and to the central 5 degrees of the retina. Given greater acuity deficits (e.g., 20/100 and 20/300), CSF's were depressed over the entire spatial frequency range tested, with the effects intruding farther into the peripheral retina than for the 20/50 amblyope. In addition, the detection of the temporal as well as the spatial modulation was depressed in the CSF's of the observers with severe amblyopia.
Complete Correction of Hemophilia A with Adeno-Associated Viral Vectors Containing a Full-Size Expression Cassette (2008)

Hemophilia A is caused by a deficiency in the factor VIII (FVIII) gene. Constrained by limited packaging capacity, even the 4.3-kb B domain-deleted FVIII remained a challenge for delivery by a single adeno-associated viral (AAV) vector. Studies have shown that up to a 6.6-kb vector sequence may be packaged into AAV virions, which suggested an alternative strategy for hemophilia A gene therapy. To explore the usefulness of AAV vectors carrying an oversized FVIII gene, we constructed the AAV-FVIII vector under the control of a beta-actin promoter with a cytomegalovirus enhancer (CB) and a bovine growth hormone (bGH) poly(A) sequence. The CB promoter plus bGH signal was shown to be 3- to 5-fold more potent than the mini-transthyretin (TTR) promoter with a synthetic poly(A) sequence for directing FVIII expression in the liver. Despite the 5.75-kb genome size of pAAV-CB-FVIII, sufficient AAV vectors were produced for in vivo testing. Approximately 3- to 5-fold more FVIII secretion was observed in animals receiving AAV-CB-FVIII vectors than in those receiving standard-sized AAV-TTR-FVIII vectors. Both the activated partial thromboplastin time assay and the whole blood thromboelastographic analysis confirmed that AAV-FVIII vectors fully corrected the bleeding phenotype of hemophilia mice. These results suggest that AAV vectors with an oversized genome should be useful for not only hemophilia A gene therapy but also other diseases with large cDNA such as muscular dystrophy and cystic fibrosis.
Immunization with the C‐Domain of α‐Toxin Prevents Lethal Infection, Localizes Tissue Injury, and Promotes Host Response to Challenge withClostridium perfringens (2004)

Clostridium perfringens gas gangrene is characterized by rapid tissue destruction, impaired host response, and, often, death. Phospholipase C (alpha -toxin) is the virulence factor most responsible for these pathologies. The present study investigated the efficacy of active immunization with the C-terminal domain of alpha -toxin (Cpa247-370) in a murine model of gas gangrene. Primary end points of the study were survival, progression of infection, and tissue perfusion. Secondary end points, which were based on findings of histologic evaluation of tissues, included the extent of tissue destruction and microvascular thrombosis, as well as the magnitude of the tissue inflammatory response. Survival among C-domain-immunized animals was significantly greater than that among sham-immunized control animals. Furthermore, immunization with the C-domain localized the infection and prevented ischemia of the feet. Histopathologic findings demonstrated limited muscle necrosis, reduced microvascular thrombosis, and enhanced granulocytic influx in C-domain-immunized mice. We conclude that immunization with the C-domain of phospholipase C is a viable strategy for the prevention of morbidity and mortality associated with C. perfringens gas gangrene.
Expression pattern of two related cystic fibrosis-associated calcium-binding proteins in normal and abnormal tissues (1988)

This paper reports further study of the identity and function of a protein shown to be elevated in serum from cystic fibrosis (CF) patients and clinically normal heterozygotes. Monoclonal antibodies, specifically recognizing the tentatively named cystic fibrosis antigen (CFAg), were produced. Immunoaffinity purification of CFAg from several sources revealed two components: 11 x 10(3) and 14 x 10(3) Mr protein. cDNA clones corresponding to each protein have been isolated. Data-base comparisons of the deduced amino acid sequences suggest that both genes encode related but distinct calcium-binding proteins. We propose the name calgranulin A and B, for the 11 x 10(3) and 14 x 10(3) Mr components, respectively. It is clear from the assignment of the calgranulin genes to chromosome 1 that neither is the product of the mutant CF gene, which maps to chromosome 7. We have used the monoclonal antibodies to study the tissue distribution of the two proteins in a wide-ranging immunohistological survey. Where possible the pattern of expression was confirmed by RNA blot analysis. Strong calgranulin expression in granulocytes was confirmed. In addition to myeloid cells, a restricted subset of normal stratified squamous epithelia were found to be calgranulin-positive. These included tongue, oesophagus and buccal cells, the last of which has been shown to have altered calmodulin activity in CF patients. Using indirect alkaline phosphatase staining, tissue sections of lung, pancreas and skin (normally considered sites where the CF defect is expressed) were not calgranulin-positive. However, by indirect immunofluorescence, nasal polyp sections showed weak patchy calgranulin expression in some epithelial cells, and stronger, higher frequency expression when such cells were briefly cultured.(ABSTRACT TRUNCATED AT 250 WORDS)
Suppression of rat hepatoma cell growth by expression of phosphatidylethanolamine N-methyltransferase-2. (1994)

The expression of rat liver phosphatidylethanolamine N-methyltransferase-2 (PEMT2) in McA-RH7777 rat hepatoma cells resulted in the unexpected inhibition of cell growth. There was a strict correlation (r = 0.973) between the level of expression of the enzyme activity and the generation time for hepatoma cell division. Expression of other foreign proteins via the same vector did not inhibit McA-RH7777 cell growth; thus, retardation of cell division was specific for the methyltransferase. Addition of 1 microM 3-deazaadenosine, which causes inhibition of phosphatidylethanolamine methylation, reversed the PEMT2-mediated inhibition of cell division. Transfection of a line of Chinese hamster ovary cells with PEMT2 had no effect on the division of these cells. Induction of hepatic tumors in rats with N-nitrosodiethylamine coincided with a striking decrease in methyltransferase activity and immunoreactive protein in the tumor nodules. Thus, data from studies in cell culture and intact rats suggest a regulatory role for PEMT2 in hepatocyte cell growth and possibly in the development of liver cancer.
Plasminogen: An Important Hemostatic Parameter in Septic Patients (1997)

Plasminogen or the ratio of plasminogen to antiplasmin are sensitive markers for survival in patients with septicemia.
Catalytic oxidation of methanol over molybdenum oxide–tungsten oxide (1977)

The vapour phase oxidation of methanol to formaldehyde over molybdenum oxide, tungsten oxide and their mixtures has been investigated in an integral flow reactor at atmospheric pressure. The effect of several process variables on the conversion and yield were determined. A high conversion of 95.6% methanol with nearly 95% selectivity was obtained at 430°C. A rate expression has been derived from the kinetics of the reaction.
RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12 (2001)

RegulonDB is a database on mechanisms of transcription regulation and operon organization in Escherichia coli K-12. The current version has considerably increased numbers of regulatory elements such as promoters, binding sites and terminators. The complete repertoire of known and predicted DNA-binding transcriptional regulators can be considered to be included in this version. The database now distinguishes different allosteric conformations of regulatory proteins indicating the one active in binding and regulating the different promoters. A new set of operon predictions has been incorporated. The relational design has been modified accordingly. Furthermore, a major improvement is a graphic display enabling browsing of the database with a Java-based graphic user interface with three zoom-levels connected to properties of each chromosomal element. The purpose of these modifications is to make RegulonDB a useful tool and control set for transcriptome experiments. RegulonDB can be accessed on the web at the URL: http://www.cifn.unam.mx/Computational_Biology/++ +regulondb/
Molecular cloning, purification and in situ localization of human colon kallikrein (1995)

We have cloned and characterized a full-length cDNA encoding tissue kallikrein from a human colon carcinoma cell line (T84). The nucleic acid sequence of the colon kallikrein cDNA is identical to that of renal/pancreatic or tissue kallikrein cDNA. Reverse-transcription PCR followed by Southern-blot analysis using specific oligonucleotide probes showed expression of tissue kallikrein in human colon, pancreas and kidney. Tissue kallikrein mRNA was localized in glandular epithelial cells (goblet cells) in colon by in situ hybridization histochemistry. Human colon kallikrein was purified to apparent homogeneity by DEAE-Sepharose Cl-6B, aprotinin-affinity, and HQ/M perfusion chromatography. The purified colon kallikrein migrated as a broad, 40-45 kDa band in SDS/PAGE and was recognized by antibodies to human tissue kallikrein. The linear displacement curves for the colon kallikrein in an RIA were parallel with the human tissue kallikrein standard curve, indicating their immunological identity. The N-terminal sequence of the purified colon kallikrein matches completely with that of purified urinary or tissue kallikrein. These results indicate that human colon kallikrein is transcribed from the tissue kallikrein gene.
Fate of Triclosan and Evidence for Reductive Dechlorination of Triclocarban in Estuarine Sediments (2008)

The biocides triclosan and triclocarban are wastewater contaminants whose occurrence and fate in estuarine sediments remain unexplored. We examined contaminant profiles in 137Cs/7Be-dated sediment cores taken near wastewater treatment plants in the Chesapeake Bay watershed (CB), Maryland and Jamaica Bay(JB), New York. In JB, biocide occurrences tracked the time course of biocide usage and wastewater treatment strategies employed, first appearing in the 1950s (triclocarban) and 1960s (triclosan), and peaking in the late 1960s and 1970s (24 +/- 0.54 and 0.8 +/- 0.4 mg/kg dry weight, respectively). In CB, where the time of sediment accumulation was not as well constrained by 137Cs depth profiles, triclocarban was only measurable in 137Cs-bearing sediments, peaking at 3.6 +/- 0.6 mg/ kg midway through the core and exceeding 1 mg/kg in recent deposits. In contrast, triclosan concentrations were low or not detectable in the CB core. Analysis of CB sediment by tandem mass spectrometry produced the first evidence for complete sequential dechlorination of triclocarban to the transformation products dichloro-, monochloro-, and unsubstituted carbanilide, which were detected at maxima of 15.5 +/- 1.8, 4.1 +/- 2.4, and 0.5 +/- 0.1 mg/kg, respectively. Concentrations of all carbanilide congeners combined were correlated with heavy metals (R2 > 0.64, P < 0.01), thereby identifying wastewater as the principal pathway of contamination. Environmental persistence over the past 40 years was observed for triclosan and triclocarban in JB, and for triclocarban's diphenylurea backbone in CB sediments.
Use of automated microscopy for the detection of disseminated tumor cells in bone marrow samples (2001)

The use of automated microscopy has reached the maturity necessary for its routine use in the clinical pathology laboratory. In the following study we compared the performance of an automated microscope system (MDS) with manual method for the detection and analysis of disseminated tumor cells present in bone marrow preparations from breast carcinoma patients. The MDS System detected rare disseminated tumor cells among bone marrow mononuclear cells with higher sensitivity than standard manual microscopy. Automated microscopy also proved to be a method of high reproducibility and precision, the advantage of which was clearly illustrated by problems of variability in manual screening. Accumulated results from two pathologists who had screened 120 clinical slides from breast cancer patients both by manual microscopy and by use of the MDS System revealed only two (3.8%) missed by the automatic procedure, whereas as many as 20 out of 52 positive samples (38%) were missed by manual screening.