gebhart/patrepeval huggingface dataset:
Wound healing: an overview of acute, fibrotic and delayed healing (2004)

Acute wounds normally heal in a very orderly and efficient manner characterized by four distinct, but overlapping phases: hemostasis, inflammation, proliferation and remodeling. Specific biological markers characterize healing of acute wounds. Likewise, unique biologic markers also characterize pathologic responses resulting in fibrosis and chronic non-healing ulcers. This review describes the major biological processes associated with both normal and pathologic healing. The normal healing response begins the moment the tissue is injured. As the blood components spill into the site of injury, the platelets come into contact with exposed collagen and other elements of the extracellular matrix. This contact triggers the platelets to release clotting factors as well as essential growth factors and cytokines such as platelet-derived growth factor (PDGF) and transforming growth factor beta (TGF-beta). Following hemostasis, the neutrophils then enter the wound site and begin the critical task of phagocytosis to remove foreign materials, bacteria and damaged tissue. As part of this inflammatory phase, the macrophages appear and continue the process of phagocytosis as well as releasing more PDGF and TGF beta. Once the wound site is cleaned out, fibroblasts migrate in to begin the proliferative phase and deposit new extracellular matrix. The new collagen matrix then becomes cross-linked and organized during the final remodeling phase. In order for this efficient and highly controlled repair process to take place, there are numerous cell-signaling events that are required. In pathologic conditions such as non-healing pressure ulcers, this efficient and orderly process is lost and the ulcers are locked into a state of chronic inflammation characterized by abundant neutrophil infiltration with associated reactive oxygen species and destructive enzymes. Healing proceeds only after the inflammation is controlled. On the opposite end of the spectrum, fibrosis is characterized by excessive matrix deposition and reduced remodeling. Often fibrotic lesions are associated with increased densities of mast cells. By understanding the functional relationships of these biological processes of normal compared to abnormal wound healing, hopefully new strategies can be designed to treat the pathological conditions.
Fast forensic video event retrieval using geospatial computing (2010)

This paper presents a fast forensic video events analysis and retrieval system in a geospatial framework. Starting from tracking targets and analyzing video streams from distributed camera networks, the system generates video tracking metadata for each video, maps and fuses them in a uniform geospatial coordinate. The combined metadata is saved into spatial database where target trajectories are represented in geometry and geography data type. Powered by spatial functions of database, various video events such as crossing a line, entering an area, loitering and meeting, are detected by executing stored procedures that we have implemented. Geographic information system(GIS) data of Tiger-Line and GeoNames are integrated with this system to provide contextual information for more advanced forensic queries. A semantic data mining system is also attached to generate text descriptions of events and scene contextual information. The NASA World Wind is the geobrowser used to submit queries and visualize result. The main contribution of this system is that it initiates in running video event retrieval using geospatial computing techniques. This interdisciplinary combination makes this system scalable and manageable for large amount of video data from distributed cameras. It also makes the online video search possible by filtering tremendous amount of data efficiently using geospatial index techniques. From the application point of view, it extends the frontier of geospatial application by presenting a forward-looking application model.
Anemia is associated with decreased survival and increased locoregional failure in patients with locally advanced head and neck carcinoma: a secondary analysis of RTOG 85-27 (1998)

Low Hgb levels are associated with a statistically significant reduction in survival and an increase in locoregional failure in this large prospective study of patients with advanced head and neck cancer. Hgb level should be considered as a stratification variable in subsequent studies of head and neck cancer. Strategies to increase Hgb prior to RT in patients with head and neck cancer may lead to improved survival and loco-regional control.
Recognition of DNA Base Pair Mismatches by a Cyclometalated Rh(III) Intercalator (2000)

Two cyclometalated complexes of Rh(III), rac-[Rh(ppy)2chrysi]+ and rac-[Rh(ppy)2 phi]+, have been synthesized and characterized with respect to their binding to DNA. The structure of rac-[Rh(ppy)2 phi]Cl.H2O.CH2Cl2 has been determined by X-ray diffraction (monoclinic, P2(1)/c, Z = 4, a = 18.447(3) A, b = 9.770(1) A, c = 17.661(3) A, beta = 94.821(11) degrees, V = 3172.0(8) A3) and reveals that the complex is a distorted octahedron with nearly planar ligands, similar in structure to the DNA mismatch recognition agent [Rh(bpy)2chrysi]3+. The 2-phenylpyridyl nitrogen atoms are shown to be in the axial positions, as a result of trans-directing effects. This tendency simplifies the synthesis and purification of such complexes by limiting the number of possible isomers generated. The abilities of [Rh(ppy)2chrysi]+ and [Rh(ppy)2 phi]+ to bind and, with photoactivation, to cleave DNA have been demonstrated in assays on duplex DNA in the absence and presence of a single CC mismatch. [Rh(ppy)2chrysi]+ was shown upon photoactivation to cleave DNA selectively at the base pair mismatch whereas [Rh(ppy)2 phi]+ cleaves B-DNA nonspecifically. The reactivity of [Rh(ppy)2chrysi]+ was also compared to that of the known mismatch recognition agent [Rh(bpy)2chrysi]3+. Competitive photocleavage studies revealed that a 14-fold excess of [Rh(ppy)2chrysi]+ was required to achieve the same level of binding as that of [Rh(bpy)2chrysi]3+. However, the ratio of damage induced by [Rh(bpy)2chrysi]3+ to that induced by [Rh(ppy)2chrysi]+ is considerably greater than this value, indicating that decreased photoefficiency for the cyclometalated complex must contribute to its significantly attenuated photoreactivity. These cyclometalated intercalators provide the starting points for the design of a new family of metal complexes targeted to DNA.
Photoreduction of 4,4'-bipyridine. A time-resolved Raman analysis (1991)

International audience
Methods for comparing a DNA sequence with a protein sequence (1996)

We describe two methods for constructing an optimal global alignment of, and an optimal local alignment between, a DNA sequence and a protein sequence. The alignment model of the methods addresses the problems of frameshifts and introns in the DNA sequence. The methods require computer memory proportional to the sequence lengths, so they can rigorously process very huge sequences. The simplified versions of the methods were implemented as computer programs named NAP and LAP. The experimental results demonstrate that the programs are sensitive and powerful tools for finding genes by DNA-protein sequence homology.
ACC2 gene polymorphisms, metabolic syndrome, and gene-nutrient interactions with dietary fat (2010)

Acetyl-CoA carboxylase β (ACC2) plays a key role in fatty acid synthesis and oxidation pathways. Disturbance of these pathways is associated with impaired insulin responsiveness and metabolic syndrome (MetS). Gene-nutrient interactions may affect MetS risk. This study determined the relationship between ACC2 polymorphisms (rs2075263, rs2268387, rs2284685, rs2284689, rs2300453, rs3742023, rs3742026, rs4766587, and rs6606697) and MetS risk, and whether dietary fatty acids modulate this in the LIPGENE-SU.VI.MAX study of MetS cases and matched controls (n = 1754). Minor A allele carriers of rs4766587 had increased MetS risk (OR 1.29 [CI 1.08, 1.58], P = 0.0064) compared with the GG homozygotes, which may in part be explained by their increased body mass index (BMI), abdominal obesity, and impaired insulin sensitivity (P < 0.05). MetS risk was modulated by dietary fat intake (P = 0.04 for gene-nutrient interaction), where risk conferred by the A allele was exacerbated among individuals with a high-fat intake (>35% energy) (OR 1.62 [CI 1.05, 2.50], P = 0.027), particularly a high intake (>5.5% energy) of n-6 polyunsaturated fat (PUFA) (OR 1.82 [CI 1.14, 2.94], P = 0.01; P = 0.05 for gene-nutrient interaction). Saturated and monounsaturated fat intake did not modulate MetS risk. Importantly, we replicated some of these findings in an independent cohort. In conclusion, the ACC2 rs4766587 polymorphism influences MetS risk, which was modulated by dietary fat, suggesting novel gene-nutrient interactions.
Rheumatoid arthritis patients have elevated antibodies to cross-reactive and non cross-reactive antigens from Proteus microbes. (2007)

The elevated levels of antibodies against Proteus antigenic epitopes (which are cross-reactive or non cross-reactive with human tissue antigens) observed indicates that this enhanced bacterial immune response in RA patients is specifically triggered by Proteus microbes. Furthermore, the correlation of anti-peptide antibody indices with the biochemical markers of disease activity indicates that these antibodies exert damaging cytotoxic effects on joint tissues during the course of the disease.
Depth-resolved image mapping spectrometer (IMS) with structured illumination (2011)

We present a depth-resolved Image Mapping Spectrometer (IMS) which is capable of acquiring 4D (x, y, z, λ) datacubes. Optical sectioning is implemented by structured illumination. The device's spectral imaging performance is demonstrated in a multispectral microsphere and mouse kidney tissue fluorescence imaging experiment. We also compare quantitatively the depth-resolved IMS with a hyperspectral confocal microscope (HCM) in a standard fluorescent bead imaging experiment. The comparison results show that despite the use of a light source with four orders of magnitude lower intensity in the IMS than that in the HCM, the image signal-to-noise ratio acquired by the IMS is 2.6 times higher than that achieved by the equivalent confocal approach.
SERS Microscopy: Nanoparticle Probes and Biomedical Applications (2009)

Surface-enhanced Raman scattering (SERS) microscopy is a novel method of vibrational microspectroscopic imaging for the selective detection of biomolecules in targeted research. This technique combines the advantages of biofunctionalized metal nanoparticles and Raman microspectroscopy for visualizing and quantifying the distribution of target molecules such as proteins in cells and tissues. Advantages of SERS over existing labeling approaches include the tremendous multiplexing capacity, quantification using the characteristic SERS signatures and high photostability. This review summarizes current designs of nanoparticle-based SERS probes and highlights first biomedical applications of SERS microscopy for protein localization ex and in vivo.
Spin-locking versus chemical exchange saturation transfer MRI for investigating chemical exchange process between water and labile metabolite protons (2010)

Chemical exchange saturation transfer (CEST) and spin-locking (SL) experiments were both able to probe the exchange process between protons of nonequivalent chemical environments. To compare the characteristics of the CEST and SL approaches in the study of chemical exchange effects, we performed CEST and SL experiments at varied pH and concentrated metabolite phantoms with exchangeable amide, amine, and hydroxyl protons at 9.4 T. Our results show that: (i) on-resonance SL is most sensitive to chemical exchanges in the intermediate-exchange regime and is able to detect hydroxyl and amine protons on a millimolar concentration scale. Off-resonance SL and CEST approaches are sensitive to slow-exchanging protons when an optimal SL or saturation pulse power matches the exchanging rate, respectively. (ii) Offset frequency-dependent SL and CEST spectra are very similar and can be explained well with an SL model recently developed by Trott and Palmer (J Magn Reson 2002;154:157-160). (iii) The exchange rate and population of metabolite protons can be determined from offset-dependent SL or CEST spectra or from on-resonance SL relaxation dispersion measurements. (iv) The asymmetry of the magnetization transfer ratio (MTR(asym)) is highly dependent on the choice of saturation pulse power. In the intermediate-exchange regime, MTR(asym) becomes complicated and should be interpreted with care.
New advances in microsphere-based single-dose vaccines (1997)

Polymer microspheres have shown great potential as a next generation adjuvant to replace or complement existing aluminum salts for vaccine potentiation. Microsphere-based systems can now be made to deliver subunit protein and peptide antigens in their native form in a continuous or pulsatile fashion for periods of weeks to months with reliable and reproducible kinetics, often obviating the need for booster immunizations in animal models. Microspheres have also shown potential as carriers for oral vaccine delivery due to their protective effects on encapsulated antigens and their ability to be taken up by the Peyer's patches in the intestine. The potency of these optimal depot formulations for antigen may be enhanced by the co-delivery of vaccine adjuvants, including cytokines, that are either entrapped in the polymer matrix or, alternatively, incorporated into the backbone of the polymer itself and released concomitantly with antigen as the polymer degrades. In this article we review the use of polymer microspheres for single-step immunization and discuss future applications for the improvement of vaccines and immunotherapies by utilizing encapsulation technology.
Electronic publishing unleashed (1995)

This book and disk package describes in full detail this multi-platform format that addresses Macintosh, Windows, DOS, and UNIX users. It includes both tutorial and reference information.
Proposal To Change the Genus Designation Serpula to Serpulina gen. nov. Containing the Species Serpulina hyodysenteriae comb. nov. and Serpulina innocens comb. nov. (1992)

The bacterial genus Serpula Stanton et al. 1991 is illegitimate due to the existence of a fungal genus Serpula Pers. ex S. F. Gray. Consequently, a new genus designation, Serpulina, is proposed for this spirochete genus. Serpula hyodysenteriae, the type species, and Serpula innocens Stanton et al. 1991, therefore, become Serpulina hyodysenteriae comb. nov. and Serpulina innocens comb. nov.
Mesenchymal Stem Cells Derived From Human Exocrine Pancreas Express Transcription Factors Implicated in Beta-Cell Development (2008)

Proliferating cells with characteristics of mesenchymal stem cells and endocrine progenitors were isolated from exocrine tissue. Under specific conditions, these cells expressed little insulin. Human pancreatic exocrine tissue might thus be a source of endocrine cell progenitors.
Chronobiological Aspects of Narcolepsy (1994)

The circadian, circasemidian and ultradian features of sleep-wake patterns in narcolepsy are reviewed with respect to the hypotheses that chronobiological disturbances might either be specific to the condition or contribute to its symptomatic profile. The position is taken that, while there are characteristic temporal features associated with the disorder, the chronobiological system is essentially intact, although quantitatively altered. It appears that the fundamental physiopathogenesis involves state boundary control mechanisms, which operate in state transitions, rather than chronobiological mechanisms affecting the timing of the manifestation of symptoms associated with the disease. We review our recent results from sleep-wake schedule studies designed to improve the maintenance of alertness in narcolepsy-cataplexy and report new analyses of subjective sleepiness data. The schedules employed were designed to take preexisting circadian, circasemidian and ultradian sleep-wake patterns of these patients into consideration.
New globoseries glycosphingolipids in human teratocarcinoma reactive with the monoclonal antibody directed to a developmentally regulated antigen, stage-specific embryonic antigen 3. (1983)

Glycolipids in a cultured human teratocarcinoma cell line (2102Ep) were investigated. The major glycolipids in these cells are globoseries glycolipids having the following structures: (formula; see text) Synthesis of these structures by serial addition of galactose, fucose, and N-acetylneuraminic acid to globoside (Gb4) in this teratocarcinoma is obvious, although further elongation of Gb4 in human cells and tissues has not been previously found with the exception of the presence of a small quantity of Forssman glycolipid in some tissues in the human population (Fs+ group) and in some human cancers. The latter four glycolipids (b-e), with the common internal structure R leads to 3GalNAc beta 1 leads to 3Gal alpha 1 leads to 4R', were all reactive to a monoclonal antibody directed to the 4- to 8-cell stage of murine embryos, known as the stage-specific embryonic antigen 3 (SSEA-3 (Shevinsky, L. H., Knowles, B. B., Damjanov, I., and Solter, D. (1982) Cell 30, 697-705]; structure (c) showed the strongest reactivity. These findings, together with the demonstration of the glycolipid nature of SSEA-1 antigen (Kannagi, R., Nudelman, E., Levery, S. B., and Hakomori, S. (1982) J. Biol. Chem. 257, 14865-14874), indicate that cell surface glycolipids play significant roles as differentiation antigens during the course of embryogenesis.
Validation of a Prediction Algorithm for Progression to Advanced Macular Degeneration Subtypes (2013)

The risk prediction model was validated in an independent study of progression from no, early, or intermediate stages to advanced subtypes of AMD and will be useful for research, clinical trials, and personalized medicine.
Delayed Apoptotic Cell Clearance and Lupus-like Autoimmunity in Mice Lacking the c-mer Membrane Tyrosine Kinase (2002)

Mice lacking the membrane tyrosine kinase c-mer have been shown to have altered macro-phage cytokine production and defective phagocytosis of apoptotic cells despite normal phagocytosis of other particles. We show here that c-mer-deficient mice have impaired clearance of infused apoptotic cells and that they develop progressive lupus-like autoimmunity, with antibodies to chromatin, DNA, and IgG. The autoimmunity appears to be driven by endogenous antigens, with little polyclonal B cell activation. These mice should be an excellent model for studying the role of apoptotic debris as an immunogenic stimulus for systemic autoimmunity.
Immunologic Aspects of Mycobacterial Infections (1989)

Immunosuppressive mechanisms loom as important factors in depression of delayed-type hypersensitivity responses during active tuberculosis. Nonspecific suppression may be mediated by circulating immune complexes containing mycobacterial polysaccharides such as D-arabino-D-galactan. The mechanism of suppression involves activation of monocyte production of immunosuppressive prostaglandin E2. Peripheral blood mononuclear cells from patients with tuberculosis include increased numbers of monocytes that suppress the response to tuberculin purified protein derivative (PPD). Antigen-specific suppression is associated with monocyte activation by a number of criteria, including decreased surface expression of HLA-DR determinants and increased production of interleukin 1 (IL-1). The increased production of IL-1 is associated with--and may have a causal relation to--immunosuppression. A second parallel regulatory mechanism involves PPD-specific suppression by Fc gamma receptor-bearing lymphocytes. The consequence of these immunosuppressive circuits is depression of tuberculin-induced blastogenesis, production of IL-2, and generation of IL-2 receptors. These findings suggest that natural infection with Mycobacterium tuberculosis may result in immunosuppression. Studies of potentially protective antigens in experimental systems must be designed to assess and avoid activation of suppressor circuits.
A highly immunogenic region of a human polymorphic epithelial mucin expressed by carcinomas is made up of tandem repeats. (1988)

The nucleotide sequences of partial cDNA clones coding for the core protein of a human polymorphic epithelial mucin were determined, and a large domain was found to consist of a 60-base pair tandem repeat sequence. The cDNA clones were originally selected (Gendler, S. J., Burchell, J. M., Duhig, T., Lamport, D., White, R., Parker, M., and Taylor-Papadimitriou, J. (1987) Proc. Natl. Acad. Sci. U. S. A. 84, 6060-6064) using three monoclonal antibodies which show differential reactivity with the mucin produced by normal and malignant breast. Two of the epitopes are exposed in the normally processed and cancer-associated mucin, while one epitope is unmasked only in the cancer-associated mucin (Burchell, J. M., Durbin, H., and Taylor-Papadimitriou, J. (1983) J. Immunol. 131, 508-513; Burchell, J., Gendler, S., Taylor-Papadimitriou, J., Girling, A., Lewis, A., Millis, R., and Lamport, D. (1987) Cancer Res. 47, 5476-5482). We show here that all three antibodies react with a synthetic peptide with an amino acid sequence corresponding to that predicted by the tandem repeat. Identification of the epitopes preferentially expressed on the cancer-associated mucin should allow a directed approach to the development of tumor-specific antibodies using synthetic peptides as immunogens.
Mouse Mesenchymal Stem Cells Suppress Antigen-Specific TH Cell Immunity Independent of Indoleamine 2,3-Dioxygenase 1 (IDO1) (2009)

Due to their immunosuppressive properties, human mesenchymal stem cells (hMSC) represent a promising tool for cell-based therapies of autoimmune diseases such as multiple sclerosis (MS). Mouse MSC (mMSC) have been used extensively to characterize and optimize route of administration, motility, cellular targets, and immunosuppressive mechanisms in mouse models of autoimmune diseases, such as experimental autoimmune encephalomyelitis (EAE). Tryptophan (trp) catabolism by indolamine-2,3-dioxygenase 1 (IDO1) is a chief endogenous metabolic pathway that tightly regulates unwanted immune responses through depletion of trp and generation of immunosuppressive kynurenines (kyn). IDO1 activity contributes to the immunosuppressive phenotype of hMSC. Here, we demonstrate that although IDO1 is inducible in bone marrow-derived mMSC by proinflammatory stimuli such as interferon-g (IFN-g) and ligands of toll-like receptors (TLR), it does not lead to catabolism of trp in vitro. This failure to catabolize trp is not due to defective TLR signaling as demonstrated by induction of interleukin 6 (IL-6) by TLR activation. While mMSC suppressed the activation of antigen-specific myelin oligodendrocyte glycoprotein (MOG)-reactive T-cell receptor (TCR) transgenic T-helper (TH) cells in co-culture, neither pharmacologic inhibition nor genetic ablation of IDO1 reversed this suppressive effect. Finally, systemic administration of both, IDO1-proficient and phenotypically identical IDO1-deficient mMSC, equally resulted in amelioration of EAE. mMSC, unlike hMSC, do not display IDO1-mediated suppression of antigen-specific T-cell responses.