gebhart/patrepeval huggingface dataset:
A retroviral Cys-Xaa2-Cys-Xaa4-His-Xaa4-Cys peptide binds metal ions: spectroscopic studies and a proposed three-dimensional structure. (1989)

Retroviral gag gene-encoded core nucleic acid binding proteins contain either one or two sequences of the form Cys-Xaa2-Cys-Xaa4-His-Xaa4-Cys. Previously, one of us has proposed that these sequences form metal-binding domains in analogy with the "zinc finger" domains first observed in transcription factor IIIA. We report that an 18-amino acid peptide derived from the core nucleic acid binding protein from Rauscher murine leukemia virus binds metal ions such as Co2+ and Zn2+. The absorption spectrum of the peptide-Co2+ complex is highly suggestive of tetrahedral coordination involving three cysteinates and one histidine. Titration experiments indicate that the dissociation constant for the peptide-Co2+ complex is 1.0 microM and that Zn2+ binds more tightly than Co2+. A detailed three-dimensional structure for this domain based on conserved substructures in other crystallographically characterized metalloproteins and on a detailed analysis of the Cys-Xaa2-Cys-Xaa4-His-Xaa4-Cys sequences from retroviruses and other related sources is proposed.
2D XFEM-based modeling of retraction and successive resections for preoperative image update (2009)

This paper considers an approach to improving outcomes for neurosurgery patients by enhancing intraoperative navigation and guidance. Currently, intraoperative navigation systems do not accurately account for brain shift or tissue resection. We describe how preoperative images can be incrementally updated to take into account any type of brain tissue deformation that may occur during surgery, and thus to improve the accuracy of image-guided navigation systems. For this purpose, we have developed a non-rigid image registration technique using a biomechanical model, which deforms based on the Finite Element Method (FEM). While the FEM has been used successfully for dealing with deformations such as brain shift, it has difficulty with tissue discontinuities. Here, we describe a novel application of the eXtended Finite Element Method (XFEM) in the field of image-guided surgery in order to model brain deformations that imply tissue discontinuities. In particular, this paper presents a detailed account of the use of XFEM for dealing with retraction and successive resections, and demonstrates the feasibility of the approach by considering 2D examples based on intraoperative MR images. To evaluate our results, we compute the modified Hausdorff distance between Canny edges extracted from images before and after registration. We show that this distance decreases after registration, and thus demonstrate that our approach improves alignment of intraoperative images.
The significance of complement in proliferative vitreoretinopathy. (1991)

Complement is the principal effector arm of antibody-mediated allergic response and plays a central role in the pathogenesis of many immunologic disorders. The possible pathophysiologic importance of complement was examined in the development of proliferative vitreoretinopathy (PVR). Vitreous aspirates from patients with idiopathic PVR (n = 21) and traumatic PVR (n = 15) were examined for total vitreal protein (TVP) and complement components C3, C3d, C4, and C1q-fixed immunoglobulins using enzyme-linked immunosorbent assay (ELISA), sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and western blotting. The TVP, C3 components, and factor C4 were elevated significantly in diseased vitreous. The C3-TVP and C4-TVP ratios showed no difference between traumatic and idiopathic PVR. A C4 index to estimate the rate of intraocular C4 synthesis had a mean value of 3.2 (n = 15). The increased relative amount of C3d reflected complement activation in diseased vitreous. The negative values in normal human serum and plasma and in patient plasma samples (n = 15) indicated a local reaction in the eye. The authors found C1q-fixed immunoglobulin G; this may be the cause of complement activation by the classic pathway. These findings support the opinion that the cause of PVR may be based partly on an autoimmune reaction against ocular structures.
Novel pharmaceutical excipients for colon targeting (1995)

Cet article a pour objectif de montrer quels excipients filmogenes recemment synthetises peuvent etre utilises avantageusement pour la vectorisation colique de formes pharmaceutiques ou de systemes a liberation au niveau du colon. Ce concept scientifique, les experiences et les resultats obtenus avec cinq differents types de materiaux degradables au niveau du colon sont discutes. Les materiaux employes initialement etaient des polyisobutylenes azo-reticules de differentes densites de reticulation, puis des copolymeres constitues de diisocyanates et de sucres ou de segment soligosaccharidiques, et des derives polysaccharidiques. Le role joue par les sucres ou les oligosaccharides dans les copolymeres etait celui de sequence biodegradable. L'urethane pouvait etre considere comme l'agent responsable des proprietes filmogenes. Le galactomannane de caroube et le dextran ont ete choisis comme matieres premieres car leurs liaisons glycosidiques en β-1,4 ou α-1,6 sont rapidement biodegradables dans le colon humain. Pour l'emploi recherche, ils doivent cependant etre transformes en derives insolubles dans l'eau et dans les liquides de l'estomac et de l'intestin grele. Ces produits sont, en effet, des galactomannanes de caroube completement substitues ou reticules a mailles larges et des esters de dextran de poids moleculaires varies avec differents types et degres de substitution. Certains produits ne peuvent etre utilises comme excipients pour la vectorisation colique, soit parce qu'ils ne sont pas biodegradables au niveau du colon, soit parce qu'ils ont des proprietes filmogenes insuffisantes. Certains materiaux presentent des proprietes de vectorisation colique excellentes in vivo et semblent egalement convenables in vivo. De ce point de vue, le galactomannane reticule de caroube et les esters de dextran et d'acide laurinique doivent etre particulierement mentionnes
Electron microscopic study of galactose-induced cataract. (1969)

Cataractous lenses induced by galactose feeding were studied electron microscopically. The early changes were increased reactivity of the epithelium, edema of the lens cells, and intercellular cyst formation in the bow and posterior zones. These changes continued with further feeding of galactose until the lens cells became irreversibly damaged. The reactive epithelial cells formed marked cell proliferations.
Peptide loading of empty major histocompatibility complex molecules on RMA‐S cells allows the induction of primary cytotoxic T lymphocyte responses (1991)

The antigen processing-defective mutant cell line RMA-S expresses at the cell surface major histocompatibility complex (MHC) class I molecules devoid of peptide that can be efficiently loaded with exogenous immunogenic peptides. We now report that viral peptide-loaded RMA-S cells, unlike parental RMA cells, can induce primary cytotoxic T lymphocyte (CTL) responses in vitro, in a T helper cell-independent fashion. This was shown for an H-2Kb-binding peptide of Sendai virus nucleoprotein and an H-2Db-binding peptide of adenovirus type 5 E1A protein with responding spleen cells of C57BL/6 mice, the strain of origin of RMA and RMA-S cells. Primary Sendai peptide-induced CTL lyse both peptide-loaded and virus-infected cells. Pre-culture of RMA-S cells at low temperature (22 degrees - 26 degrees C), which increases the amount of empty MHC class I molecules at the cell surface, decreases the peptide concentrations required for the induction of primary CTL responses. Primary peptide-specific CTL responses induced by peptide-loaded RMA-S cells are CD4+ cell- and MHC class II+ cell-independent. CTL response induction is blocked by the presence of anti-CD8 monoclonal antibody during culture. Direct peptide binding studies confirm the efficient loading of empty MHC molecules on RMA-S cells with peptide and show 2.5-fold more peptide bound per RMA-S cell compared to RMA cells. An additional factor explaining the difference in primary response induction between RMA and RMA-S cells is related to the CD8 dependence of these responses. MHC class I molecules occupied with irrelevant peptides (a majority present on RMA, largely absent on RMA-S) may interfere in the interaction of the CD8 molecule with relevant MHC/peptide complexes. The results delineate a novel strategy of peptide based in vitro immunization to elicit CD8+ cytotoxic T cell responses.
Fatty Acyl‐CoA Reductase and Wax Synthase from Euglena gracilis in the Biosynthesis of Medium‐Chain Wax Esters (2010)

Euglena gracilis, a unicellular phytoflagellate, can accumulate a large amount of medium-chain wax esters under anaerobic growth conditions. Here we report the identification and characterization of two genes involved in the biosynthesis of wax esters in E. gracilis. The first gene encodes a fatty acyl-CoA reductase (EgFAR) involved in the conversion of fatty acyl-CoAs to fatty alcohols and the second gene codes for a wax synthase (EgWS) catalyzing esterification of fatty acyl-CoAs and fatty alcohols, yielding wax esters. When expressed in yeast (Saccharomyces cerevisiae), EgFAR converted myristic acid (14:0) and palmitic acid (16:0) to their corresponding alcohols (14:0Alc and 16:0Alc) with myristic acid as the preferred substrate. EgWS utilized a broad range of fatty acyl-CoAs and fatty alcohols as substrates with the preference towards myristic acid and palmitoleyl alcohol. The wax biosynthetic pathway was reconstituted by co-expressing EgFAR and EgWS in yeast. When myristic acid was fed to the yeast, myristyl myristate (14:0-14:0), myristyl palmitoleate (14:0-16:1), myristyl palmitate (14:0-16:0) and palmityl myristate (16:0-14:0) were produced. These results indicate EgFAR and EgWS are likely the two enzymes involved in the biosynthesis of medium-chain wax esters in E. gracilis.
Evidence for two fatty alcohol oxidases in the biosurfactant-producing yeast Candida (Torulopsis) bombicola (1990)

Fatty alcohol oxidase activities in Candida (Torulopsis) bombicola ATCC 22214, which produces large amounts of glycolipids consisting of omega- and (omega-1)-hydroxyfatty acids and a sugar moiety, occurred only in the microsomal fraction whether the cells had grown on n-alkanes, carbohydrates or a mixture of the two. High activities occurred in glucose-grown cells. Aliphatic alcohols from octanol to hexadecanol were oxidized with two maxima in activities for decanol and for tetradecanol. Differences in their pH optima and in temperature stability suggest two separate enzymes are present. Long chain diols, but not omega-hydroxyfatty acids, were also oxidized.
Experimental and Theoretical Studies of the Propargyl-Allenylindium System (2004)

The transient organoindium intermediates formed in the reaction of propargyl bromide with indium in aqueous media and tetrahydrofuran were investigated by NMR spectroscopy and found to be allenylindium(I) and allenylindium(III) dibromide. The influence of solvent and methyl substitution on the propargyl-allenylindium system was also studied. The experimental observations were supported by theoretical calculations using the B3LYP/6-311+G* method.
oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes (2005)

Targeted transcript profiling studies can identify sets of co-expressed genes; however, identification of the underlying functional mechanism(s) is a significant challenge. Established methods for the analysis of gene annotations, particularly those based on the Gene Ontology, can identify functional linkages between genes. Similar methods for the identification of over-represented transcription factor binding sites (TFBSs) have been successful in yeast, but extension to human genomics has largely proved ineffective. Creation of a system for the efficient identification of common regulatory mechanisms in a subset of co-expressed human genes promises to break a roadblock in functional genomics research. We have developed an integrated system that searches for evidence of co-regulation by one or more transcription factors (TFs). oPOSSUM combines a pre-computed database of conserved TFBSs in human and mouse promoters with statistical methods for identification of sites over-represented in a set of co-expressed genes. The algorithm successfully identified mediating TFs in control sets of tissue-specific genes and in sets of co-expressed genes from three transcript profiling studies. Simulation studies indicate that oPOSSUM produces few false positives using empirically defined thresholds and can tolerate up to 50% noise in a set of co-expressed genes.
Identification of Ice Binding Proteins from Chlamydomonas sp. AnF0046 and AnF0048 (2010)

Most of polar algae are known to produce ice binding proteins (IBPs). IBPs are diverse proteins with the capability of inhibiting ice crystal growth against in subzero environments for their survival. Two microalgae, named AnF0046 and AnF0048, were used in this study. To examine thephysiological properties, we carried out a comparative analysis on growth with Chlamydomonas reinhardtii. Growth rate of C. reinhardtii is 1.6 and 1.1 fold higher than those of AnF0046 and AnF0048, respectively. AnF0046 and AnF0048 produced 1.4 and 1.7 fold lower amounts of chlorophylls than that of C. reinhardtii. Extraction of genomic DNA was conducted for confirmation of gene existence related to IBPs. The bands on 1-D gel from either AnF0046 or AnF0048 were comparable with that from C. reinhardtii. To search IBP encoding gene, primers were designed based on IBP isoforms produced by Chlamydomonas sp. CCMP681. The primer designed from isoform1 had the most homologous sequence. A single band at 2.5 kbp was found from overlapping fragments. Forward and reverse sequences, each with 950 bp, were obtained after sequencing. The two Antartic microalgae, AnF0046 and AnF0048, found to have IBP coding genes.
Quantitative Recovery of Biotinylated Proteins from Streptavidin-Based Affinity Chromatography Resins (2008)

The strong interaction between streptavidin and biotin is one of the most commonly exploited tools in chemistry and biology. Methods for the facile derivatization of a variety of molecules (in particular, proteins) with biotin have been introduced, in order to allow their efficient recovery, immobilization and detection with streptavidin-based reagents. However, when desired, the release of biotinylated proteins from the streptavidin-based reagents remains a major problem, due to the extraordinary stability of this complex. This chapter presents a protocol developed in our laboratory for the quantitative elution of biotinylated proteins from streptavidin sepharose, featuring harsh elution conditions and competition with free biotin. The usefulness of the method is shown by the recovery of biotinylated proteins from organ homogenates, obtained from mice perfused with a reactive ester derivative of biotin.
Murine CD146 is widely expressed on endothelial cells and is recognized by the monoclonal antibody ME-9F1 (2008)

The endothelium plays an important role in the exchange of molecules, but also of immune cells between blood and the underlying tissue. The endothelial molecule S-Endo 1 antigen (CD146) is preferentially located at endothelial junctions and has been claimed to support endothelial integrity. In this study we show that the monoclonal antibody ME-9F1 recognizes the extracellular portion of murine CD146. Making use of ME-9F1 we found CD146 highly expressed and widely spread on endothelial cells in the analyzed murine tissues. In contrast to humans that express CD146 also on T cells or follicular dendritic cells, murine CD146 albeit at low levels was only found on a subset of NK1.1+ cells. The antibody against murine CD146 is useful for immunomagnetic sorting of primary endothelial cells not only from the liver but from various other organs. In vitro, no evidence was seen that the formation and integrity of endothelial monolayers or the transendothelial migration of T cells was affected by antibody binding to CD146 or by crosslinking of the antigen. This makes the antibody ME-9F1 an excellent tool especially for the ex vivo isolation of murine endothelial cells intended to be used in functional studies.
Efficiency assessment of the gene trap approach (1998)

The trapping of genes in murine embryonic stem (ES) cells offers three features in one experimental approach: 1) analysis of the expression patterns of unknown genes by using a simple staining method, 2) rapid cloning of unknown genes, and 3) generation of mutant mouse lines. We performed a gene trap screen aimed at the discovery of new genes regulating embryonic development. We have processed 209 gene trap events for expression patterns in chimeric murine embryos. Randomly tested, beta-galactosidase-positive ES cell clones resulted in vivo in 35% gene trap events showing no beta-galactosidase activity, 39% gene trap events with ubiquitous beta-galactosidase activity, and 26% gene trap events showing beta-galactosidase activity restricted to specific cell types or organs. In vitro preselection reduced gene trap events with ubiquitous beta-galactosidase activity to 10% and increased the gene trap events with restricted beta-galactosidase activity to 64%, making the screening procedure for genes expressed in a restricted manner 2.5-fold more efficient. In five of the seven gene trap insertions into genes in which the expression pattern during embryogenesis was known, the beta-galactosidase marker gene reproduced faithfully the expression pattern of the trapped gene. 5'-Rapid amplification of cDNA ends (5'-RACE) of 28 gene trap events revealed 19 novel mouse genes, 8 known mouse genes, and 1 random transsplicing event. Twelve of the 25 mouse lines that crossed to homozygosity showed overt abnormalities. The genomic structure was investigated in four of these gene trap events, which caused obvious abnormalities. In all four cases, the splice-acceptor gene trap construct was inserted into an exon. One of the 13 gene trap events that did not result in overt abnormalities was examined for the presence of wild-type mRNA. Homozygous animals were found to produce normal levels of wild-type mRNA. Evidently, gene trapping does not always provide all three of the features mentioned above. In this paper, we discuss the efficiency of gene trapping and ways in which some problems may be overcome.
Cell Therapy: A Safe and Efficacious Therapeutic Treatment for Alzheimer’s Disease in APP+PS1 Mice (2012)

Previously, our lab was the first to report the use of antigen-sensitized dendritic cells as a vaccine against Alzheimer's disease (AD). In preparation of this vaccine, we sensitized the isolated dendritic cells ex vivo with Aβ peptide, and administered these sensitized dendritic cells as a therapeutic agent. This form of cell therapy has had success in preventing and/or slowing the rate of cognitive decline when administered prior to the appearance of Aβ plaques in PDAPP mice, but has not been tested in 2 × Tg models. Herein, we test the efficacy and safety of this vaccine in halting and reversing Alzheimer's pathology in 9-month-old APP + PS1 mice. The results showed that administration of this vaccine elicits a long-lasting antibody titer, which correlated well with a reduction of Aβ burden upon histological analysis. Cognitive function in transgenic responders to the vaccine was rescued to levels similar to those found in non-transgenic mice, indicating that the vaccine is capable of providing therapeutic benefit in APP+PS1 mice when administered after the onset of AD pathology. The vaccine also shows indications of circumventing past safety problems observed in AD immunotherapy, as Th1 pro-inflammatory cytokines were not elevated after long-term vaccine administration. Moreover, microhemorrhaging and T-cell infiltration into the brain are not observed in any of the treated subjects. All in all, this vaccine has many advantages over contemporary vaccines against Alzheimer's disease, and may lead to a viable treatment for the disease in the future.
Endoscopic Approach to the Infratemporal Fossa (2009)

Endoscopic exposure of the infratemporal fossa is feasible. Using the combination of the endonasal and Caldwell-Luc approaches for direct transmaxillary access significantly extended exposure, allowing safe and effective resection of infratemporal fossa lesions.
DOCK7 is a critical regulator of the RAGE-Cdc42 signaling axis that induces formation of dendritic pseudopodia in human cancer cells (2012)

Cellular migration is a fundamental process linked to cancer metastasis. Growing evidence indicates that the receptor for advanced glycation end products (RAGE) plays a pivotal role in this process. With regard to downstream signal transducers of RAGE, diaphanous-1 and activated small guanine nucleotide triphosphatases, Rac1 and Cdc42, have been identified. To obtain precise insight into the direct downstream signaling mechanism of RAGE, we screened for proteins interacting with the cytoplasmic domain of RAGE employing an immunoprecipitation-liquid chromatography coupled with an electrospray tandem mass spectrometry system. In the present study, we found that the cytoplasmic domain of RAGE interacted with an atypical DOCK180-related guanine nucleotide exchange factor, dedicator of cytokinesis protein 7 (DOCK7). DOCK7 bound to the RAGE cytoplasmic domain and transduced a signal to Cdc42, resulting in the formation of abundant highly branched filopodia-like protrusions, dendritic pseudopodia. Blocking of the function of DOCK7 greatly abrogated the formation of dendritic pseudopodia and suppressed cellular migration. These results indicate that DOCK7 functions as an essential and downstream regulator of RAGE-mediated cellular migration through the formation of dendritic pseudopodia.
Applications of a Fluidic Artificial Hand in the Field of Rehabilitation (2007)

Since the early middle of last century, use of artificial robotic hands in the field of rehabilitation has been associated with prosthetic devices used for the therapy of upper limb deficiency. Artificial manipulators of the last century were used in general for industrial applications or for service tasks of telemanipulation. In the last three decades, service robotics developed very rapidly. In recent years, robotic systems which are able to complete service tasks in direct cooperation with humans became popular [Yuta at al., (2006)]. Modern robotic rehabilitation devices are intelligent systems used for movement assistance, physical support and indoor navigation, physical rehabilitation, vocational rehabilitation, and interactive entertainment [Bien, Stefanov (2004)]. Dextrous manipulation has become the subject of research for many scientists around the world and artificial hands are used in a wide area of applications [Venkataraman, Iberall (1990)]. Investigations of hand construction, artificial design, and manipulation abilities resulted in the development of different hand prototypes for service