gebhart/patrepeval huggingface dataset:
Diabetic retinopathy – An update (2011)

Management of diabetes should involve both systemic and ocular aspects. Control of hyperglycemia, hypertension and dyslipidemia are of major role in the management of diabetic retinopathy. In the ocular part; laser treatment remains the cornerstone of treatment of diabetic macular edema (focal/grid), severe non-proliferative and proliferative diabetic retinopathy (panretinal photocoagulation). There is a strong support to combination therapy. Using one or two intravitreal injections such as anti-VEGF and or steroid to reduce central macular thickness followed by focal or grid laser to give a sustained response may offer an alternative to treatment in diabetic macular edema. Anti-VEGF were found to be effective as an adjunct therapy in proliferative diabetic retinopathy patient who is going to have vitrectomy for vitreous hemorrhage with neovascularization, panretinal photocoagulation, and other ocular surgery such as cases with neovascular glaucoma and cataract with refractory macular edema.
Variable-depth streamer acquisition: Broadband data for imaging and inversion (2013)

ABSTRACT Conventional marine acquisition uses a streamer towed at a constant depth. The resulting receiver ghost notch gives the maximum recoverable frequency. To push this limit, the streamer must be towed at a quite shallow depth, but this compromises the low frequencies. Variable-depth streamer (VDS) acquisition is an acquisition technique aimed at achieving the best possible signal-to-noise ratio at low frequencies by towing the streamer very deeply, but by using a depth profile varying with offset in order not to limit the high-frequency bandwidth by notches as in conventional constant-depth streamer acquisition. The idea is to use notch diversity, each receiver having a different notch, so that the final result, combining different receivers, will have no notches. The key step to process VDS acquisitions is the receiver deghosting. We found that the optimal receiver deghosting, instead of being a preprocessing step, should be done postimaging, by using a dual-input, migration and mirror migration, and a new joint deconvolution algorithm that produces a 3D real amplitude deghosted output. This method can be applied poststack, the inputs being the migration and mirror migration images and the output being the deghosted image. Using a multichannel joint deconvolution, the inputs are the migrated and mirror migrated image gathers and the outputs are the prestack deghosted image gathers. This method preserves the amplitude-versus-offset behavior, as the deghosted output can be seen on synthetic examples to be equal to a reference computed by migrating the data modeled without any reflecting water surface. A real data set was used to illustrate this method, and another one was used to check the possibility of performing prestack elastic inversion on the deghosted gathers.
Dendritic cell infiltration pattern along the colorectal adenoma‐carcinoma sequence (2008)

We have previously reported that the dendritic cell (DC) functional index cytokine interleukin-12 was significantly decreased in colorectal carcinoma (CRC) tissues. In this study, the DC infiltration pattern and the density of mature DCs (mDCs; labeled by anti-CD83 and anti-CD208) and immature DCs (iDCs; labeled by anti-CD1alpha) were characterized using immunohistochemistry (IHC) in tissue samples from 23 patients with CRC, 33 patients with colorectal adenoma (CRA), and 19 healthy controls. In addition, the DC function inhibitor cyclooxygenase-2 (COX-2) and the downstream signal molecule prostaglandin E2 (PGE2) and related receptors EP2/EP4 were measured by quantitative real-time PCR and double immunofluorescence staining. The IHC analyses revealed changed densities of mDCs and iDCs in the tumor microenvironment; in CRA and CRC, the density of mDCs was decreased, but the density of iDCs was gradually increased. Furthermore, the distribution patterns of DCs were also altered. In CRA, mDCs were abundantly distributed in the subepithelial stroma of the adenomatous mass. In CRC, the distribution of mDCs in the tumor stroma was not homogeneous, and mDCs residing in the stroma at invading edges were more frequently found compared with in the intratumoral stroma (P<0.05). Increased iDCs were found in the intratumoral mass in CRC, and some infiltrated into the malignant epithelium. By quantitative real-time PCR, a gradually increased level of COX-2 mRNA was demonstrated in the local tissues along the adenoma-carcinoma sequence, and double immunofluorescence staining showed a colocalization of PGE2 receptors EP2/EP4 with mDCs in the stroma of CRC. In conclusion, our current findings revealed an altered DC infiltration pattern along the adenoma-carcinoma sequence; gradually increased COX-2 expression might contribute to the DC functional defect.
Characteristics of a Serially Transplanted Mouse Mammary Tumor and Its Tissue-Culture-Adapted Derivative (1972)

The KHJJ tumor line, derived from a primary mammary tumor arising in a BALB/c mouse after implantation of a hyperplastic alveolar nodule, has been maintained for over 100 transplant generations. The 25th generation of this tumor was grown and selected in cell culture, producing a new tumor cell line, EMT6. This new line can be grown and studied either as an animal tumor or a cell culture and allows the in vitro assay of cell survival after the treatment of animal tumors in situ. Retrospective examination of tumor specimens throughout the history of the tumor lines suggests that these tumor lines were derived from 2 morphologically distinct subpopulations of a mixed primary tumor. The morphology, latent period, and transplantation characteristics (assayed by TD50) of the 2 lines throughout their histories of serial transplantation are described. The antigenicity, growth patterns, and cell population kinetics (analyzed by the percent-labeled mitosis technique and model-based computer analysis) are described for both tumors. Characteristics of EMT6 cells in culture are compared with those of cells in the tumor.
Monoclonal antibodies recognizing single amino acid substitutions in hemoglobin. (1986)

Four monoclonal antibodies (mAb) to non-human primate hemoglobin referred to as Cap-4, Cap-5, Rh-2, and Rh-4, and two mAb to human hemoglobin, referred to as H-1 and H-3 were isolated and were partially characterized. Binding studies with these mAb on a panel of hemoglobins and isolated alpha and beta globin chains revealed a unique reactivity pattern for each mAb. Amino acid sequence analysis of the antigens used to generate the binding data suggests that the specific recognition of certain hemoglobin antigens by each mAb is controlled by the presence of a particular amino acid at a specific position within the epitope. The use of synthetic peptides as antigens confirmed this observation for five of the mAb. No synthetic peptides were tested with the sixth mAb, Rh-2. The amino acids required for binding of mAb Cap-4, Cap-5, Rh-4, and Rh-2 to hemoglobin are alanine at beta 5, threonine at beta 13, glutamine at beta 125, and leucine at alpha 68. The non-human primate hemoglobin antibodies require a specific amino acid that is not present in human hemoglobin. The amino acid required for binding of Cap-4, Cap-5, and Rh-4 could arise by a single base change in the beta globin gene, whereas the amino acid required for Rh-2 binding would only occur if two base changes occurred. Thus these mAb are candidate probes for a somatic cell mutation assay on the basis of the detection of peripheral blood red cells that possess single amino acid substituted hemoglobin as a result of single base substitutions in the globin genes of precursor cells.
Police and Community Responses to Youth Gangs (2004)

Although there are no national data on youth gangs in Australia there is a perception that youth gangs are an emerging problem. This paper draws largely on overseas attempts to deal with gang related activity and the extent to which they have been successful. The paper discusses the use of police powers in suppressing gangs; the weapons issue; the use of aggressive coercive measures, youth curfews and anti loitering laws; community based responses to youth gangs, including the use of a four step problem solving model; and specific community strategies, including the employment of detached youth and community workers, the provision of specific facilities and services for youth, and community development initiatives. The most successful interventions have some combination of coercive and developmental measures. A key issue for both policy makers and practitioners is the weight given to particular measures within the context of an overall strategy. While for tactical purposes, coercive force may occasionally be necessary, positive approaches to gang issues also require developmental strategies and active community involvement.
SmartV: Intelligent vigilance monitoring based on sensor fusion and driving dynamics (2013)

Road traffic accidents (RTAs) pose a public health and development challenge and greatly affect the human capital development of every nation. Main causes for a significant percentage of RTAs are recklessness, fatigue or stress, inexperienced driving and driving under the influence of alcohol. Reputed automobile companies and authorities have established standards and/or proactive/reactive solutions over the years to overcome this problem but the rates continue to grow each year. Software solutions that focus on preventing RTAs are difficult to be found in economy class automobiles that are used by the majority of consumers. The limited number of successful applications are either bound to a certain brand/model and/or focus on a specific task. SmartV is smart phone based vigilance monitoring system that focuses on the majority of factors contributing to RTAs. These include DUI (driving under the influence of alcohol), health issues and vehicle defects. The mobile application communicates with a heart rate monitor and a Bluetooth OBDII Adapter. These will continuously monitor the heart rate of the driver and the status of the vehicle respectively. During the course of the drive, the system monitors the behavior of the vehicle for existence of dangerous driving patterns that are defined in Visual Detection of DWI Motorists[8] a study conducted by U.S.A. N.H.T.S.A. The final product is a versatile, non-intrusive, flexible and most importantly an affordable mobile application that captures the vehicle's behavior, the health level of the driver and the status of the vehicle. Real environment operation of SmartV has yielded significant results proving itself to be a successful and an affordable Vigilance Monitoring System for the future.
S2-5: An Anti-HER3 Antibody That Stabilizes the Inactive Conformation Inhibits Both HER2 and Ligand Driven Tumor Growth. (2011)

Abstract Background: HER3 (ErbB3) is a member of the ErbB family of receptor tyrosine kinases (RTK). In normal physiology, ligands (e.g. neuregulin) activate HER3 by promoting dimerization with other RTK's such as HER2 (ErbB2). Inappropriate HER2/HER3 dimerization as a result of HER2 over-expression in cancer results in HER3 mediated activation of the oncogenic PI3K pathway. The HER2− targeted antibody trastuzumab inefficiently inhibits HER2 mediated HER3 activation allowing persistent HER3 signaling that is speculated to limit clinical responses. Consequently, combination of a HER3- targeted agent with trastuzumab may be of clinical benefit. Furthermore, ectopic HER3 activation has recently been implicated in the relief of a feedback loop induced by PI3K inhibitors that may perhaps limit their efficacy in HER2 driven tumors. Since HER3 activation in HER2 driven cancers occurs in a ligand- independent manner, antibodies that primarily inhibit ligand- induced HER3 activation are largely inactive in HER2 driven xenograft models. Results: H3F15, a high affinity (26pM) HER3- targeted fully human IgG1 antibody was selected from the Human Combinatorial Antibody Library (HuCAL) using phage display technology. In a broad range of HER2 amplified breast and gastric cell lines, H3F15 displayed potent inhibition (IC50 &amp;lt;1nM) of HER3/AKT phosphorylation and proliferation. Interestingly, H3F15 also effectively inhibited neuregulin stimulated HER3 phosphorylation and downstream signaling in MCF7 cells indicating that H3F15 inhibits multiple modes of HER3 activation. Determining the H3F15/HER3 crystal structure revealed that H3F15 binds a novel conformational epitope that traps HER3 in the inactive conformation thus preventing its activation by either HER2 or neuregulin. In vivo testing of H3F15 using xenograft tumor models driven by either HER2 (BT474) or HER3 ligands (BxPC3) confirmed that single agent H3F15 (20mg/kg) significantly inhibited tumor growth (83 and 77% inhibition respectively). Furthermore, combinations of H3F15 with either trastuzumab or PI3K- targeted agents were synergistic in a panel of HER2 driven cell lines whilst the in vivo combination of H3F15 (20mg/kg) with trastuzumab (1mg/kg) was sufficient to induce tumor regression. Discussion: H3F15 is a HER3- targeted antagonist IgG1 that stabilizes the inactive form of HER3. This novel mechanism of action enables H3F15 to uniquely inhibit both ligand-induced and HER2−mediated activation of HER3. Thus H3F15 is the first HER3 antibody to display single-agent efficacy in both HER2 and ligand driven xenograft models whilst also inducing tumor regressions in combination with trastuzumab. Based on preclinical data, combining H3F15 with either trastuzumab or PI3K- targeted agents fully inhibits the HER2/HER3 signaling pathway, which may lead to greater and more sustained clinical efficacy in HER2 driven cancers. Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr S2-5.
Microarray-Based Mutation Analysis of 183 Spanish Families with Usher Syndrome (2010)

The genotyping microarray is a robust, low-cost, rapid technique that is effective for the genetic study of patients with USH. However, it also indicates variants of unclear pathologic nature and detection failures have also been observed. Results must be confirmed by direct sequencing to avoid misdiagnosis, and continuous updates of the microarray should be performed to increase the efficiency and rate of detection of mutations.
Architecture-Based Autonomous Repair Management: An Application to J2EE Clusters (2006)

This paper presents a component-based architecture for autonomous repair management in distributed systems, and a prototype implementation of this architecture, called JADE, which provides repair management for J2EE application server clusters. The JADE architecture features three major elements, which we believe to be of wide relevance for the construction of autonomic distributed systems: (1) a dynamically configurable, component-based structure that exploits the reflective features of the FRACTAL component model; (2) an explicit and configurable feedback control loop structure, that manifests the relationship between the managed system and repair management functions; (3) an original replication structure for the management subsystem itself which makes it fault-tolerant and self-healing.
JAK3 protein tyrosine kinase mediates interleukin-7-induced activation of phosphatidylinositol-3' kinase (1995)

The interleukin-7 (IL-7) receptor is expressed throughout T-cell differentiation and, although lacking a tyrosine kinase domain, mediates tyrosine phosphorylation in T cells. We have identified IL-7-induced activation of three cyoplasmic tyrosine kinases in T cells, Jak1, Jak3, and the src-like kinase p56lck. Many members of the cytokine receptor superfamily activate the Jak protein tyrosine kinase family, with resultant phosphorylation of the Stat transcriptional activator factors. We describe here a novel function of the Jak kinases, because Jak kinase activity is not only required for Stat activation but also for P13 kinase response to IL-7 in human T cells. We show that IL-7 receptor-mediated Jak activation can occur independently of p56lck activity. IL-7-induced P13 kinase activation, mediated by tyrosine phosphorylation of the P13 kinase p85 subunit, is essential to the IL-7 proliferative signal and also occurs in the absence of src family kinase activity. Jak3 is found associated with the p85 subunit of P13 kinase in an IL-7-responsive manner in T cells and appears to regulate IL-7-induced P13 kinase activation by mediating tyrosine phosphorylation of the p85 subunit. Specific inhibition of IL-7-induced Jak kinase activity ablates p85 tyrosine phosphorylation, subsequent P13 kinase activation, and, ultimately, proliferation. The ability to regulate P13 kinase activity indicates a more generalized role for the Jak family than activation of gene transcription via the Stat family in cytokine receptor signal transduction.
A novel class of conformationally restricted oligonucleotide analogues: synthesis of 2′,3′-bridged monomers and RNA-selective hybridisation (1997)

A novel 2′,3′-bicyclic nucleoside 5 has been synthesised and incorporated into oligonucleotide analogues resulting in strong and selective binding to an RNA complement.<br/>
Overexpression of matrix metalloproteinase-7 mRNA in human colon carcinomas (1995)

The findings imply that MMP-7 mRNA is overexpressed in human colorectal carcinomas and that MMP-7 may prove useful as a marker of biologic aggressiveness.
The effect of chymopapain on low back pain. (1992)

One hundred and fifteen patients underwent chymopapain treatment for acute disc protrusion between 1980 and 1988. Sixty-six patients who were treated with single-level injection were reviewed retrospectively with clinical follow-up from 2 to 10 years (mean, 4.6 years). All patients met modified McCulloch criteria (not all patients had leg pain greater than back pain). The presence of pre-existing chronic low back pain (LBP) was recorded in 33 patients and compared to their present low back symptomatology and functional limitations. Patients with pre-existing chronic LBP had a success rate of 52%, whereas patients meeting all the McCulloch criteria without chronic LBP had a success rate of 52%, whereas patients meeting all the McCulloch criteria without chronic LBP had a success rate of 85%. The overall effect of chemonucleolysis on LBP demonstrated no change in 18% and a mild increase in 45% of the patients (even though they had a successful outcome). The pre-existing disc space narrowing and the postoperative change of disc space height of 33 patients assessed on lateral roentgenograms showed no correlation to the clinical response. Temporal sequential computed tomography scan assessment of 56 patients following chemonucleolysis demonstrated little change of disc herniation in the first 3 months, with only a gradual and incomplete resolution in the ensuing 12 months.
Mechanism of phosphate transfer by nucleoside diphosphate kinase: X-ray structures of the phosphohistidine intermediate of the enzymes from Drosophila and Dictyostelium (1995)

Nucleoside diphosphate kinase (NDP kinase) has a ping-pong mechanism with a phosphohistidine intermediate. Crystals of the enzymes from Dictyostelium discoideum and from Drosophila melanogaster were treated with phosphoramidate, and their X-ray structures were determined at 2.1 and 2.2 A resolution, respectively. The atomic models, refined to R factors below 20%, show no conformation change relative to the free proteins. In both enzymes, the active site histidine was phosphorylated on N delta, and it was the only site of phosphorylation. The phosphate group interacts with the hydroxyl group of Tyr56 and with protein-bound water molecules. Its environment is compared with that of phosphohistidines in succinyl-CoA synthetase and in phosphocarrier proteins. The X-ray structures of phosphorylated NDP kinase and of previously determined complexes with nucleoside diphosphates provide a basis for modeling the Michaelis complex with a nucleoside triphosphate, that of the phosphorylated protein with a nucleoside diphosphate, and the transition state of the phosphate transfer reaction in which the gamma-phosphate is pentacoordinated.
Review on Fatty Acid Desaturases and their Roles in Temperature Acclimatisation (2017)

Carbohydrates and proteins are polymers of polysaccharides and polypeptide residues, respectively. Conversely, lipids are made up of a wide range of compounds with tremendous differences in structures and lack building blocks. Therefore, fatty acids constitute the major components of various lipid classes such as glycerides and sphingolipids. Fatty acids are organic compounds containing a carboxylic acid group mostly at the end of an aliphatic chain and are categorized into saturated and unsaturated. Most fatty acids especially the so-called polyunsaturated fatty acids (PUFAs) and their derivatives play key biological roles in inflammatory response, cell division, control of lipid metabolism, as signaling molecules, supply of energy and protecting the biological membranes structure and function. In this study, a general overview of fatty acids, their biosynthesis mechanisms as well as biological importance have been discussed. Fatty acid desaturase enzymes and their sources have also been reviewed. Recent studies on the functional expression of different types of desaturase enzymes have also been discussed.
Host-Synthesized Secondary Compounds Influence the In Vitro Interactions between Fungal Endophytes of Maize (2007)

Maize produces a suite of allelopathic secondary metabolites, the benzoxazinoids. 2,4-Dihydroxy-7-methoxy-2H-1,4-benzoxazin-3-one and 2,4-dihydroxy-2H-1,4-benzoxazin-3-one reside as glucosides in plant tissue and spontaneously degrade to 6-methoxy-2-benzoxazolinone (MBOA) and 2-benzoxazolinone (BOA) upon plant cell disruption. Several maize-associated fungi in the genus Fusarium can metabolize MBOA and BOA. BOA tolerance levels in 10 species of Fusarium and in the maize endophytes Nigrospora oryzae, Acremonium zeae, and Periconia macrospinosa were characterized. BOA tolerance ranged from 0.25 to 1.10 mg/ml among species. The influence of substrate alteration by one species on the subsequent growth of another species was assessed in the presence and absence of BOA. The colony area of the secondary colonizer in heterospecific interactions was compared to that in autospecific interactions (one isolate follows itself). In the presence of BOA, four of six secondary colonizers had greater growth (facilitation) when primary colonizers had higher BOA tolerance than the secondary colonizer. When the primary colonizer had lower tolerance than the secondary, three of six secondary colonizers were inhibited (competition) and three not significantly affected. In BOA-free medium, the number of isolates that were facilitated or inhibited was the same regardless of the tolerance level of the primary colonizer. Two of six secondary colonizers were facilitated, two inhibited, and two not significantly affected. This study provides some support for facilitation in stressful conditions under the Menge-Sutherland model. The results are not consistent with the corresponding prediction of competition in the absence of stress. The hypothesis drawn from these data is that in the presence of a toxin, fungal species that detoxify their substrate can enhance the colonization rate of less tolerant fungi.