gebhart/patrepeval huggingface dataset:
Laminin‐5 γ2‐chain and collagenase‐2 (MMP‐8) in human peri‐implant sulcular fluid (2003)

Laminin-5 (LN-5) is an important epithelial cell-derived structural and adhesive component in hemidesmosomes and basement membranes (BM). In peri-implant tissue, gingival BM underlies the junctional epithelium (JE) and reflects the peri-implant health. Matrix metalloproteinase-8 (MMP-8 or collagenase-2) is one of the key mediators of periodontal tissue destruction. Western immunoblotting with image analysis was used to quantitate the molecular forms of LN-5 gamma2-chain and MMP-8 in peri-implant sulcular fluid (PISF) from healthy and diseased implants. These observations were related to the recorded gingival (GI) and bone resorption (BR) indices of the studied sites. Altogether, 72 PISF samples from osseointegrated dental implants were examined. Significantly elevated levels of fragmented LN-5 gamma2-chain species (45 and 70 kDa) and MMP-8 immunoreactivities were observed in diseased PISF in relation to healthy PISF. The elevated levels of both LN-5 gamma2-chain 45 and 70 kDa fragments and MMP-8 in diseased PISF from peri-mucositis (BR = 0) and peri-implantitis (BR >/= 1) lesions strongly correlated with elevated GI. Low levels - almost comparable to those seen in healthy control PISF - were seen in PISF from peri-implantitis lesions (BR >/= 1) with no GI. Activation of 75 kDa neutrophil (PMN)-type proMMP-8 to 10 kDa lower-molecular-size active forms was especially detected in PISF from peri-implantitis with elevated GI. These cross-sectional findings indicate that elevated MMP-8 and LN-5 gamma2-chain fragment levels in PISF can reflect the active phase of the inflammatory peri-implant disease. Longitudinal studies are required to assess their use, either alone or in combination as molecular biochemical PISF markers, to predict the risk of progression of peri-implantitis, as well as to monitor the impact of treatment of the disease.
Smart E-Beam for Defect Identification & Analysis in the Nanoscale Technology Nodes: Technical Perspectives (2017)

Optical beam has been the veteran inspector of semiconductor wafer production house, ever since the birth of integrated circuit (IC). As technology and market place raise the bar on chip density, Moore’s law stretches to the limit. Due to its inherent physical limitations, the optical method just cannot see the measuring rod of silicon industry getting recalibrated to finer nano-scales. Electron Beam Inspection (EBI), by virtue of its high resolution, has started to rule the nodes at 10 nm and below. As the geometries shrink, defects can reside deep within the structures. EBI can find those tiny defects, which otherwise go scot-free with optical tools. However, EBI suffers the handicap of poor performance and low throughput. It is therefore essential to complement EBI by judiciously crafting out the methods for getting the desired performance, a subject matter to which, this article is committed to. The research torchlights the critical EBI throughput problem to round-up “care-areas”. Such guided and focused inspection augments throughput, thereby positioning EBI as the industrial grade candidate in finer nanometer segment. Besides gearing up to current trends, the smart EBI school of thought is inspirational, to fuel the aspirations for 1 nanometer scale.
Food Components Activating Capsaicin Receptor TRPV1 (2009)

This chapter contains sections titled: Introduction How to Evaluate Activity to TRPV1 Pungency-Related Compounds in Capsium Fruits Ginger Compounds Sansho Compounds Nonpungent Compounds from Foods of Hot Orwarm Nature and Cool or Cold Nature Conclusion References
Inhibition of carcinoma and melanoma cell growth by type 1 transforming growth factor beta is dependent on the presence of polyunsaturated fatty acids. (1990)

Improved serum-free media were developed for the anchorage-dependent growth of A549 human lung carcinoma and B16 mouse melanoma cell lines in vitro. Type 1 transforming growth factor beta (TGF-beta 1) inhibited the growth of A549 or B16 cells under serum-free conditions or in the presence of 10% serum by 15-33%. In contrast, in the presence of micrograms/ml concentrations of polyunsaturated fatty acids (PUFAs), picomolar concentrations of TGF-beta 1 irreversibly inhibited the serum-free growth of A549 or B16 cells by 90-100%. The PUFAs alone had little effect on cell growth. Cell growth inhibition by TGF-beta 1 was not potentiated by saturated fatty acids, monounsaturated fatty acids, or prostaglandins. Inhibition of A549 or B16 cell growth by TGF-beta 1 in the presence of PUFAs was almost completely reversed by the antioxidant vitamin E, suggesting a role for lipid peroxidation in this process. Inhibition of A549 or B16 cell growth by TGF-beta 1 in the presence of 5% fetal calf serum was also potentiated by PUFAs and partially reversed by antioxidants. The presence of retinoic acid was required for maximal PUFA-dependent growth inhibition of A549 or B16 cells by TGF-beta 1 under some, but not all, conditions. These results suggest that inhibition of carcinoma and melanoma cell growth by TGF-beta 1 is mediated, in large part, by PUFAs.
Toward Part-Based Document Image Decoding (2012)

Document image decoding (DID) is a trial to understand the contents of a whole document without any reference information about font, language, etc. Typically, DID approaches assume the correct segmentation of the document and some a priori knowledge about the language or the script. Unfortunately, this assumption will not hold if we deal with various documents, such as documents with various sized fonts, camera-captured documents, free-layout documents, or historical documents. In this paper, we propose a part-based character identification method where no segmentation into characters is necessary and no a priori information about the document is needed. The approach clusters similar key points and groups frequent neighboring key point clusters. Then a second iteration is performed, i.e., the groups are again clustered and optionally pairs frequent group clusters are detected. Our first experimental results on multi font-size documents look already very promising. We could find nearly perfect correspondences between characters and detected group clusters.
Mutations to Amino Acids Located in Predicted Transmembrane Segment 6 (TM6) Modulate the Activity and Substrate Specificity of Human P-glycoprotein (1994)

Site-directed mutagenesis was used to investigate whether amino acids located in the predicted transmembrane segment, TM6 (residues 330-351), of human P-glycoprotein play essential roles in drug transport. Mutant cDNAs were expressed in mouse NIH 3T3 cells and analyzed with respect to their ability to confer resistance to cytotoxic drugs. Four mutations were found to strongly alter the drug resistance profile conferred by P-glycoprotein. Mutation of Val338 to Ala resulted in a mutant P-glycoprotein which conferred enhanced resistance to colchicine and reduced relative resistance to vinblastine. By contrast, mutant Gly341 to Val conferred little resistance to colchicine or doxorubicin, while its ability to confer resistance to vinblastine or actinomycin D was retained. A reduction in the ability of P-glycoprotein to confer resistance to all four drugs was observed for mutant Ala342 to Leu. Mutation of Ser344 to Ala, Thr, Cys, or Tyr resulted in mutant P-glycoproteins which were unable to confer drug resistance. Photolabeling of P-glycoprotein with azidopine in the presence of varying amounts of vinblastine showed that mutation of Ser344 to Tyr required approximately 15-fold more vinblastine to inhibit photolabeling when compared to wild-type enzyme. All of the Ser344 mutants were found to have reduced drug-stimulated ATPase activity relative to wild-type enzyme. These results, together with our previous demonstration that changes to Phe335 affected dissociation of vinblastine, suggest that TM6 may play an important role in drug--protein interaction and coupling of drug binding to ATPase activity.
Ghost imaging with incoherent and partially coherent light radiation (2005)

We theoretically study ghost imaging with incoherent and partially coherent light radiation by using classical optical coherence theory. A Gaussian thin lens equation is derived for the ghost image. The equation depends on both paths. The quality and visibility of the ghost image are influenced by the source's transverse size, coherence width, and object characteristics. The differences between ghost imaging formed with incoherent light radiation and with entangled photon pairs are discussed.
Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units (1968)

Abstract The general conformations of a system of three linked peptide units are studied, and it is found that there are three types of conformations which contain NH…O hydrogen bonding between the first and the third units. One of them is part of a 3 10 ‐helix, while the other two arc nonhelical. The two nonhelical conformations are very similar, and in both the cases the peptide chain turns around, reversing the direction of progress. Such a conformation can therefore occur in the region where a polypeptide chain folds back on itself, as in the cross‐β structure. The method of representing these interesting tripeptide conformations in a (ϕ,ψ) map is described. Examples of such hydrogen‐bonded, nonhelical conformations which occur in peptides and proteins are discussed—e.g., in cyclohexaglyeyl, an open tetrapeptide Gly‐ L ‐Pro‐ L ‐Leu‐Gly, and in parts of the lysozyme chain.
Review on Transdermal Drug Delivery Systems (2014)

Recently, transdermal drug delivery system (TDDS) has become a more and more important approach to administering drugs. Based on its advantages, which are not achievable by other modes of administration, many researchers are dedicated to the study of it, and have made great progress.
Platelet factor 4 is chemotactic for neutrophils and monocytes. (1981)

Platelet factor 4 is shown to be a chemotactic protein for human polymorphonuclear leukocytes and monocytes at concentrations found in human serum and reached locally in injured tissue. The maximum chemotactic response to platelet factor 4 nearly equals that achieved with saturating concentrations of the chemotactic activity derived from the fifth component of human complement, C5. Cells desensitized to C5 chemotactic activity retain chemotactic responsiveness to platelet factor 4. Serum contains inhibitory capacity against the chemotactic activity associated with platelet factor 4. Our results suggest that the local release of platelet factor 4 may be an important stimulus attracting inflammatory cells to sites of blood vessel injury.
Structural Basis for FcγRIIa Recognition of Human IgG and Formation of Inflammatory Signaling Complexes (2011)

The interaction of Abs with their specific FcRs is of primary importance in host immune effector systems involved in infection and inflammation, and are the target for immune evasion by pathogens. FcγRIIa is a unique and the most widespread activating FcR in humans that through avid binding of immune complexes potently triggers inflammation. Polymorphisms of FcγRIIa (high responder/low responder [HR/LR]) are linked to susceptibility to infections, autoimmune diseases, and the efficacy of therapeutic Abs. In this article, we define the three-dimensional structure of the complex between the HR (arginine, R134) allele of FcγRIIa (FcγRIIa-HR) and the Fc region of a humanized IgG1 Ab, hu3S193. The structure suggests how the HR/LR polymorphism may influence FcγRIIa interactions with different IgG subclasses and glycoforms. In addition, mutagenesis defined the basis of the epitopes detected by FcR blocking mAbs specific for FcγRIIa (IV.3), FcγRIIb (X63-21), and a pan FcγRII Ab (8.7). The epitopes detected by these Abs are distinct, but all overlap with residues defined by crystallography to contact IgG. Finally, crystal structures of LR (histidine, H134) allele of FcγRIIa and FcγRIIa-HR reveal two distinct receptor dimers that may represent quaternary states on the cell surface. A model is presented whereby a dimer of FcγRIIa-HR binds Ag-Ab complexes in an arrangement that possibly occurs on the cell membrane as part of a larger signaling assembly.
Tear lipid layer structure and stability following expression of the meibomian glands (1995)

In a masked investigation, tear lipid layer structure and non-invasive break-up time (NIBUT) of both eyes of 40 normal subjects were assessed with the Keeler Tearscope after unilateral manual expression of meibomian fluid from the lower lid. The HIRCAL grid (modified keratometer mire) provided the additional measure of tear thinning time (TTT). Twenty untreated normal subjects formed the control group. No difference in lipid layer structure or stability was observed between the right and left eyes of the controls. The NIBUT of the treated eyes was significantly higher than that of the untreated contralateral eyes which was, in turn, greater than that of the control eyes. Lipid layer thickness in the treated eyes was significantly higher than that in the untreated contralateral eyes and the controls but did not differ between the latter two groups. The TTT of the treated eyes was not significantly different from that of the untreated contralateral eyes but both were significantly higher than that of the controls. Unilateral meibomian gland expression results in increased lipid layer thickness and tear stability. A possible reason for the slight increase in tear stability in the untreated contralateral eyes is a complimentary reflex lacrimation induced by mechanical stimulation of the treated eye. Differences between the results of the Tearscope and HIRCAL grid are attributed to differences in the techniques of tear stability measurement.
Sphingosine 1-Phosphate Inhibits Activation of Caspases that Cleave Poly(ADP-ribose) Polymerase and Lamins during Fas- and Ceramide-mediated Apoptosis in Jurkat T Lymphocytes (1998)

Ceramide, a sphingolipid generated by the hydrolysis of membrane-associated sphingomyelin, appears to play a role as a gauge of apoptosis. A further metabolite of ceramide, sphingosine 1-phosphate (SPP), prevents ceramide-mediated apoptosis, and it has been suggested that the balance between intracellular ceramide and SPP levels may determine the cell fate (Cuvillier, O., Pirianov, G, Kleuser, B., Vanek, P. G., Coso, O. A., Gutkind, J. S., and Spiegel, S. (1996) Nature 381, 800-803). Here, we investigated the role of SPP and the protein kinase C activator, phorbol ester 12-O-tetradecanoylphorbol-13-acetate (TPA), in the caspase cascade leading to the proteolysis of poly(ADP-ribose) polymerase (PARP) and lamins. In Jurkat T cells, Fas ligation or addition of exogenous C2-ceramide induced activations of caspase-3/CPP32 and caspase-7/Mch3 followed by PARP cleavage, effects that can be blocked either by SPP or TPA. Furthermore, both SPP and TPA inhibit the activation of caspase-6/Mch2 and subsequent lamin B cleavage. Ceramide, in contrast to Fas ligation, did not induce activation of caspase-8/FLICE and neither SPP nor TPA were able to prevent this activation. Thus, SPP, likely generated via protein kinase C-mediated activation of sphingosine kinase, suppresses the apoptotic pathway downstream of FLICE but upstream of the executioner caspases, caspase-3, -6, and -7.
Triacetyluridine (TAU) decreases depressive symptoms and increases brain pH in bipolar patients. (2008)

Eleven patients with bipolar depression were given doses of up to 18 g per day of triacetyluridine (TAU) over 6 weeks to test the effect of uridine on symptoms of depression via Montgomery-Asberg Depression Rating Scale (MADRS; Asberg, Montgomery, Perris, Schalling, & Sedvall, 1978) scores and on cellular bioenergetics using phosphorus magnetic resonance spectroscopic imaging (31P-MRSI). All patients and comparison participants (n = 9) completed baseline 31P-MRSI scans, and 9 patients completed posttherapy scans. The percentage changes for MADRS scores (Week 2, -23.8; Week 3, -34.9; Week 4, -42.5) and the time effects of TAU on MADRS scores (Week 2, z = -2.07, p = .039; Week 3, z = -4.28, p < .001; Week 4, z = -4.54, p < .001) may reflect TAU effects on early symptom improvement. TAU responders (patients who had a 50% or greater reduction in MADRS scores from baseline at any time) demonstrated a significant difference from nonresponders in pH changes from baseline (effect size = 150). These results suggest that TAU treatment may decrease symptoms of depression and improve mitochondrial functioning.
Appearance-Based QR Code Beautifier (2013)

Quick Response (QR) code is a widely used matrix bar code with the increasing population of smart phones. However, QR code usually consists of random textures which are not suitable for incorporating with other visual designs (e.g. name card and business advertisement poster). In order to overcome the shortcomings of noise-like looks of QR codes, we propose a systematic QR code beautification framework where the visual appearance of QR code is composed of visually meaningful patterns selected by users, and more importantly, the correctness of message decoding is kept intact. Our work makes QR code from machine decodable only (i.e. standardized random texture) to a personalized form with human visual pleasing appearance. We expect the proposed QR code beautifier can inspire more visual-pleasant mobile multimedia applications.
MUC5B Promoter Polymorphism and Interstitial Lung Abnormalities (2013)

The MUC5B promoter polymorphism was found to be associated with interstitial lung disease in the general population. Although this association was more apparent in older persons, it did not appear to be influenced by cigarette smoking. (Funded by the National Institutes of Health and others; ClinicalTrials.gov number, NCT00005121.).
BeeDoctor, a Versatile MLPA-Based Diagnostic Tool for Screening Bee Viruses (2012)

The long-term decline of managed honeybee hives in the world has drawn significant attention to the scientific community and bee-keeping industry. A high pathogen load is believed to play a crucial role in this phenomenon, with the bee viruses being key players. Most of the currently characterized honeybee viruses (around twenty) are positive stranded RNA viruses. Techniques based on RNA signatures are widely used to determine the viral load in honeybee colonies. High throughput screening for viral loads necessitates the development of a multiplex polymerase chain reaction approach in which different viruses can be targeted simultaneously. A new multiparameter assay, called "BeeDoctor", was developed based on multiplex-ligation probe dependent amplification (MLPA) technology. This assay detects 10 honeybee viruses in one reaction. "BeeDoctor" is also able to screen selectively for either the positive strand of the targeted RNA bee viruses or the negative strand, which is indicative for active viral replication. Due to its sensitivity and specificity, the MLPA assay is a useful tool for rapid diagnosis, pathogen characterization, and epidemiology of viruses in honeybee populations. "BeeDoctor" was used for screening 363 samples from apiaries located throughout Flanders; the northern half of Belgium. Using the "BeeDoctor", virus infections were detected in almost eighty percent of the colonies, with deformed wing virus by far the most frequently detected virus and multiple virus infections were found in 26 percent of the colonies.
Type 1 von Willebrand disease mutation Cys1149Arg causes intracellular retention and degradation of heterodimers: a possible general mechanism for dominant mutations of oligomeric proteins (2001)

Some families affected by von Willebrand disease type 1 show high penetrance with exceptionally low von Willebrand factor (VWF) levels. Previously, a mutation associated with this dominant phenotype, Cys1149Arg, was found to decrease the secretion of coexpressed normal VWF, and the mutation was proposed to cause intracellular retention of pro-VWF heterodimers. To demonstrate heterodimer formation, a model was developed in which subunits could be distinguished immunologically and by size. Recombinant VWF lacking domain A1 (dA1), A3 (dA3), or both (dA13) was secreted efficiently as a full range of multimers. Cotransfection of Cys1149Arg and dA13 resulted in the secretion of multimeric VWF containing about 250 kd (Cys1149Arg) and about 210 kd (dA13). Cell lysates contained pro-VWF forms of Cys1149Arg and dA13. Immunoprecipitation with an antidomain A1 antibody recovered both subunits in heterodimers, and subunit ratios were consistent with random dimerization. Similar results were obtained for cotransfection of Cys1149Arg and dA1. Normal VWF has a Cys1149-Cys1169 intrachain bond. When cotransfected with normal VWF, Cys1149Arg or the double mutant Cys1149Arg+Cys1169Ser caused a similar decrease in VWF secretion, suggesting that an unpaired Cys1169 does not explain the intracellular retention of Cys1149Arg. VWF Cys1149Arg was not secreted from BHK cells but was degraded intracellularly within about 4 hours, and the proteasome inhibitor lactacystin delayed its clearance more than 16 hours. Thus, dominant von Willebrand disease type 1 may be caused by heterodimerization of mutant and normal subunits in the endoplasmic reticulum followed by proteasomal degradation in the cytoplasm. A similar dominant negative mechanism could cause quantitative deficiencies of other multisubunit proteins.
Engineered Yeasts as Reporter Systems for Odorant Detection (2003)

The functional expression of olfactory receptors (ORs) is a primary requirement to utilize olfactory detection systems. We have taken advantage of the functional similarities between signal transduction cascades in the budding yeast Saccharomyces cerevisiae and mammalian cells. The yeast pheromone response pathway has been adapted to allow ligand-dependent signaling of heterologous expressed G-protein coupled receptors (GPCRs) via mammalian or chimeric yeast/mammalian Galpha proteins. Two different strategies are reported here which offer a positive screen for functional pairs. The OR and Galpha protein are introduced into the modified yeast cells such that they hijack the pheromone response pathway usually resulting in cell cycle arrest. The first strategy utilizes ligand-induced expression of a FUS1-HIS3 reporter gene to permit growth on a selective medium lacking histidine; the second to induce ligand-dependent expression of a FUSI-Hph reporter gene, conferring resistance to hygromycin. Validation of the systems was performed using the rat 17 receptor response to a range of aldehyde odorants previously characterized as functional ligands. Of these only heptanal produced a positive growth response in the concentration range 5 x 10(-8) to 5 x 10(-6) M. Induction conditions appear to be critical for functional expression, and the solvents of odorants have a toxic effect for the highest odorant concentrations. The preference of rat 17 receptor for the ligand heptanal in yeast has to be compared to concurrent results obtained with mammalian expression systems.