gebhart/patrepeval huggingface dataset:
rVISTA 2.0: evolutionary analysis of transcription factor binding sites (2004)

Identifying and characterizing the transcription factor binding site (TFBS) patterns of cis-regulatory elements represents a challenge, but holds promise to reveal the regulatory language the genome uses to dictate transcriptional dynamics. Several studies have demonstrated that regulatory modules are under positive selection and, therefore, are often conserved between related species. Using this evolutionary principle, we have created a comparative tool, rVISTA, for analyzing the regulatory potential of noncoding sequences. Our ability to experimentally identify functional noncoding sequences is extremely limited, therefore, rVISTA attempts to fill this great gap in genomic analysis by offering a powerful approach for eliminating TFBSs least likely to be biologically relevant. The rVISTA tool combines TFBS predictions, sequence comparisons and cluster analysis to identify noncoding DNA regions that are evolutionarily conserved and present in a specific configuration within genomic sequences. Here, we present the newly developed version 2.0 of the rVISTA tool, which can process alignments generated by both the zPicture and blastz alignment programs or use pre-computed pairwise alignments of several vertebrate genomes available from the ECR Browser and GALA database. The rVISTA web server is closely interconnected with the TRANSFAC database, allowing users to either search for matrices present in the TRANSFAC library collection or search for user-defined consensus sequences. The rVISTA tool is publicly available at http://rvista.dcode.org/.
Visuo-haptic display using head-mounted projector (2002)

Proposes a novel visuo-haptic display using a head-mounted projector (HMP) with X'tal Vision (Crystal Vision) optics. Our goal is to develop a device which enables an observer to touch a virtual object just as it is seen. We describe in detail the design of an HMP with X'tal Vision, which is very suitable for augmented reality. For instance, the HMP makes the occlusion relationship between the virtual and the real environments nearly correct. Accordingly, the user can observe his/her real hand with the virtual objects. Furthermore, the HMP reduces eye fatigue because of the low inconsistency of accommodation and convergence. Therefore, we applied HMP-model 2 to a visuo-haptic display using a camouflage technique. This technique, called optical camouflage, makes an obstacle object, such as a haptic display, become translucent. With this method, a user can observe a stereoscopic virtual object with a nearly correct occlusion relationship between the virtual and the real environments, and he can actually feel the object.
Development of Geminivirus-Based Gene Vectors for Dicotyledonous Plants (1990)

Geminiviruses are small icosahedral plant viruses that contain circular single-stranded DNA as their genome. In tomato golden mosaic virus (TGMV), a geminivirus that infects dicotyledonous hosts, several genes involved in replication, spread of virus or DNA in plants, and possibly insect transmission have been identified. Gene replacement experiments suggest that useful plant gene expression vectors can be constructed from TGMV. Following the integration of stable master copies of vectors based on TGMV DNA into plant chromosomal DNA, heritable gene amplification of a number of bacterial genes has been demonstrated, suggesting exciting possibilities for similar amplification of plant genes in the future.
EphrinA1-targeted nanoshells for photothermal ablation of prostate cancer cells (2008)

Gold-coated silica nanoshells are a class of nanoparticles that can be designed to possess strong absorption of light in the near infrared (NIR) wavelength region. When injected intravenously, these nanoshells have been shown to accumulate in tumors and subsequently mediate photothermal treatment, leading to tumor regression. In this work, we sought to improve their specificity by targeting them to prostate tumor cells. We report selective targeting of PC-3 cells with nanoshells conjugated to ephrinA I, a ligand for EphA2 receptor that is overexpressed on PC-3 cells. We demonstrate selective photo-thermal destruction of these cells upon application of the NIR laser.
Uplink performance of a multicarrier-CDMA mobile radio system concept (2002)

Currently the air interface of future mobile radio systems is the topic of worldwide investigations. In this context CDMA (code division multiple access) seems to be a promising candidate as an element of the air interface of future mobile radio systems. The combination of OFDM (orthogonal frequency division multiplexing) and CDMA for mobile radio transmission has been proposed by several authors for the downlink. So far, the more elaborate uplink of such OFDM-CDMA mobile radio concepts has only been the topic of few publications, since channel estimation and data detection are more complex than in the downlink. The uplink of an OFDM-CDMA mobile radio concept is investigated. A pilot tone based channel estimation technique is proposed and several detection techniques suitable for the approach are described. Simulation results are shown for the case of a single receiver antenna as well as for dual receiver antenna diversity. The simulation results indicate that the proposed concept is well suited for future mobile radio systems.
Domains of human c-myc protein required for autosuppression and cooperation with ras oncogenes are overlapping. (1990)

Amino acids 106 to 143 and 354 to 433 of the human c-myc protein (439 amino acids) were shown to be required for the protein to suppress c-myc gene transcription and were found to exactly overlap with those necessary for c-myc to cooperate with ras oncogenes in the transformation of rat embryo fibroblasts. The essential carboxyl-terminal region harbors structural motifs (a basic region, a helix-loop-helix motif, and a "leucine zipper"), which, in other proteins, can mediate dimerization and sequence-specific DNA binding.
Human Mena+11a Isoform Serves as a Marker of Epithelial Phenotype and Sensitivity to Epidermal Growth Factor Receptor Inhibition in Human Pancreatic Cancer Cell Lines (2008)

Collectively, our data indicate that the hMena(+11a) isoform is associated with an epithelial phenotype and identifies EGFR-dependent cell lines that are sensitive to the EGFR inhibitor erlotinib. The availability of anti-hMena(+11a)-specific probes may offer a new tool in pancreatic cancer management if these results can be verified prospectively in cancer patients.
Border zone neovascularization in cerebral ischemic infarct. (1999)

Immunocytochemical and quantitative studies on vascular reaction (angiogenesis) in cortical border zone of infarct were undertaken. Intensity and temporal profile of angiogenesis was assessed in 60 patients aged between 48 and 69 (younger group), and between 70 and 92 (older group), with cerebral infarct in the area of middle cerebral artery vascularization, who died during the first six weeks following the stroke. We have found that angiogenesis was a multistage process in which four stages were distinguished: phase of primary activation of endothelial cells, two consecutive phases of active angiogenesis and final phase of only sporadic proliferation of vessels. The distinction of phases in a multiphase angiogenic cascade helped us to evaluate the correlation with survival time and the age of patients. The most pronounced intensification of angiogenesis and increased density of CD 31 positive capillaries in penumbra were observed in the second phase, especially in younger patients. The duration of the penumbral neovascularization decreased in the older age patient. Our results indicate that sprouting angiogenesis is a quantitatively significant source of vessels in the cerebral infarct border zone. However, non-therapeutically stimulated angiogenesis developed only 3-4 days after the stroke, that is beyond the period of reversible changes in ischemic penumbra recognized as a "therapeutical window" in the human brain. The angiogenic therapy opens a new way towards the revascularization of ischemic brain infarct.
Scnn1 Sodium Channel Gene Family in Genetically Engineered Mice (2000)

The amiloride-sensitive epithelial sodium channel is the limiting step in salt absorption. In mice, this channel is composed of three subunits (alpha, beta, and gamma), which are encoded by different genes (Scnn1a, Scnn1b, and Scnn1c, respectively). The functions of these genes were recently investigated in transgenic (knockout) experiments, and the absence of any subunit led to perinatal lethality. More defined phenotypes have been obtained by introducing specific mutations or using transgenic rescue experiments. In this report, these approaches are summarized and a current gene-targeting strategy to obtain conditional inactivation of the channel is illustrated. This latter approach will be indispensable for the investigation of channel function in a wide variety of organ systems.
Structure of tRNA pseudouridine synthase TruB and its RNA complex: RNA recognition through a combination of rigid docking and induced fit (2003)

RNA pseudouridine synthase, TruB, catalyzes pseudouridine formation at U55 in tRNA. This posttranscriptional modification is almost universally conserved and occurs in the T arm of most tRNAs. We determined the crystal structure of Escherichia coli TruB apo enzyme, as well as the structure of Thermotoga maritima TruB in complex with RNA. Comparison of the RNA-free and -bound forms of TruB reveals that this enzyme undergoes significant conformational changes on binding to its substrate. These conformational changes include the ordering of the "thumb loop," which binds right into the RNA hairpin loop, and a 10 degree hinge movement of the C-terminal domain. Along with the result of docking experiments performed on apo TruB, we conclude that TruB recognizes its RNA substrate through a combination of rigid docking and induced fit, with TruB first rigidly binding to its target and then maximizing the interaction by induced fit.
Identification of a p53-dependent negative response element in the bcl-2 gene. (1994)

Recently, we have shown that the p53 tumor suppressor gene product can inhibit expression of the bcl-2 gene. In this report, we explored the molecular basis for p53-mediated down-regulation of bcl-2 gene expression using a cotransfection approach involving p53 expression plasmids and chloramphenicol acetyltransferase (CAT) reporter gene constructs containing regions from the bcl-2 gene. When transfected into a p53-deficient human lung cancer cell line H358, reporter gene constructs containing only the promoter region of bcl-2 and upstream sequences were not suppressed by p53. Inclusion of bcl-2 gene sequences corresponding to the 5' untranslated region in bcl-2/CAT constructs, however, resulted in p53-dependent down-regulation. A 195-base pair segment from the bcl-2 gene 5' untranslated region was found to be capable of conferring p53-dependent repression on a heterologous expression plasmid containing CAT under the control of an SV40 immediate early-region promoter. This p53-negative response element functioned in an orientation-independent manner when placed either upstream or downstream of the SV40-CAT transcription unit. The results demonstrate the existence of a negative response element in the bcl-2 gene through which p53 may either directly or indirectly transcriptionally down-regulate expression of this gene involved in the regulation of programmed cell death.
HLA class I, NKG2D, and natural cytotoxicity receptors regulate multiple myeloma cell recognition by natural killer cells (2004)

The role of natural killer (NK) cells in multiple myeloma is not fully understood. Here, NK susceptibility of myeloma cells derived from distinct disease stages was evaluated in relation to major histocompatibility complex (MHC) class I, MHC class I chain-related protein A (MICA), MHC class I chain-related protein B (MICB), and UL16 binding protein (ULBP) expression. MHC class I molecules were hardly detectable on bone marrow cells of early-stage myeloma, while late-stage pleural effusion-derived cell lines showed a strong MHC class I expression. Conversely, a high MICA level was found on bone marrow myeloma cells, while it was low or not measurable on pleural effusion myeloma cells. The reciprocal surface expression of these molecules on bone marrow- and pleural effusion-derived cell was confirmed at mRNA levels. While bone marrow-derived myeloma cells were readily recognized by NK cells, pleural effusion-derived lines were resistant. NK protection of pleural effusion cells was MHC class I dependent. Receptor blocking experiments demonstrated that natural cytotoxicity receptor (NCR) and NK receptor member D of the lectin-like receptor family (NKG2D) were the key NK activating receptors for bone marrow-derived myeloma cell recognition. In ex vivo experiments patient's autologous fresh NK cells recognized bone marrow-derived myeloma cells. Our data support the hypothesis that NK cell cytotoxicity could sculpture myeloma and represents an important immune effector mechanism in controlling its intramedullary stages.
The Spatial Organization of Proton and Lactate Transport in a Rat Brain Tumor (2011)

Tumors create a heterogeneous acidic microenvironment which assists their growth and which must be taken into account in the design of drugs and their delivery. In addition, the acidic extracellular pH (pHe) is itself exploited in several experimental techniques for drug delivery. The way the acidity is created is not clear. We report here the spatial organization of key proton-handling proteins in C6 gliomas in rat brain. The mean profiles across the tumor rim of the Na+/H+ exchanger NHE1, and the lactate-H+ cotransporter MCT1, both showed peaks. NHE1, which is important for extension and migration of cells in vitro, showed a peak 1.55 times higher than in extratumoural tissue at 0.33 mm from the edge. MCT1 had a broader peak, further into the tumor (maximum 1.76 fold at 1.0 mm from the edge). In contrast, MCT4 and the carbonic anhydrase CAIX, which are associated with hypoxia, were not significantly upregulated in the rim. The spatial distribution of MCT4 was highly correlated with that of CAIX, suggesting that their expression is regulated by the same factors. Since protons extruded by NHE1 diffuse away through extracellular clefts, NHE1 requires a continuous source of intracellular protons. From the stoichiometries of metabolic pathways that produce or consume H+, and the greater availability of glucose compared to oxygen in most parts of a tumor, we support the classic view that most of the net proton efflux from C6 gliomas originates in glycolytic formation of lactate and H+ inside the tumor, but add that some lactate is taken up into cells in the rim on MCT1, and some lactate diffuses away, leaving its associated protons available to re-enter cells for extrusion on NHE1. Therapeutic inhibition of NHE1, MCT1 or CAIX is predicted to affect different parts of a tumor.
Expression of the human cystic fibrosis transmembrane conductance regulator gene in the mouse lung afterin vivointratracheal plasmid-mediated gene transfer (1992)

As an approach to gene therapy for the respiratory manifestations of cystic fibrosis (CF), in vivo plasmid-mediated direct transfer of the normal CF transmembrane conductance regulator (CFTR) gene to the airway epithelium was investigated in mice. To evaluate the feasibility of this strategy, pRSVL, a plasmid composed of a firefly luciferase gene driven by the Rous sarcoma virus long terminal repeat (RSV-LTR), along with cationic liposomes was instilled into the trachea of C57BI/6NCR mice. With administration of 200-400 micrograms plasmid DNA, luciferase expression could be detected in the mouse lung homogenates for at least 4 wk. With this background, a CFTR expression plasmid vector (pRSVCFTR) constructed by replacing the luciferase cDNA from pRSVL with the normal human CFTR cDNA was evaluated in vivo in mice. Intratracheal instillation of pRSVCFTR with cationic liposomes followed by analysis of mouse lung RNA by polymerase chain reaction amplification (after conversion of mRNA to cDNA) using a RSV-LTR specific sense primer and a human CFTR-specific antisense primer demonstrated human CFTR mRNA transcripts from one day to 4 wk after instillation. Further, in vivo evaluation of beta-galactosidase activity after intratracheal administration of an E. coli lacZ gene expression plasmid vector directed by the cytomegalovirus promoter (pCMV beta) demonstrated that the airway epithelium was the major target of transfer and expression of the exogenous gene. These observations demonstrate successful plasmid-mediated gene transfer to the airway epithelium in vivo. This strategy may be feasible as a form of gene therapy to prevent the pulmonary manifestations of CF.
New matrix therapy in chronic corneal ulcers resistant to conventional therapies (2013)

Abstract Purpose To determine the efficacy of a new ophthalmologic solution based on ReGeneraTing Agent technology (RGTA, Cacicol®) in the therapy of chronic corneal ulcers resistant to conventional therapies. Methods This study included 20 patients with chronic corneal ulcers. There were various etiologies:two due to basic chemical burns,two neurotrophic keratitis, one Moreen ulcer, one pseudo‐Mooren, three on IntraCorneal Ring, nine on 9 grafts (one endothelial and 8 penetrating keratoplasties, one post surgery. All patients were previously treated with classical lacrymal substitutes, one with topical ciclosporine, corticoids, and/or A vitamin ocular ointment, and/or one/several amniotic membrane graft. Patients were treated with Cacicol® at a dose regimen of one drop daily every 2 or 3 days for one to three months. The primary outcome measure was healing. The ulcer’s diameter was measured at day 8,then once a month for 3 months. Results Complete healing was observed for 13 patients, i.e. a cure rate of 65 %. For other patients, 6 failures (30%) and one improvement without complete healing (5%) were reported. In the healed group, time of reparation was : 4 in day 8, 4 in one month and 5 in 3 months. Conclusion Cacicol was effective in the treatment of chronic corneal ulcers resistant to conventional therapies. Its efficacy remains to be proven in randomized double‐blind studies.
Acquisition of Brain Na Sensitivity Contributes to Salt-Induced Sympathoexcitation and Cardiac Dysfunction in Mice With Pressure Overload (2009)

In animal models of salt-sensitive hypertension, high salt augments sympathetic outflow via central mechanisms. It is not known, however, whether pressure overload affects salt sensitivity, thereby modifying central sympathetic outflow and cardiac function. We induced left ventricular hypertrophy with aortic banding in mice. Four weeks after aortic banding (AB-4), the left ventricle wall thickness was increased without changing the percentage fractional shortening. AB-4 mice were then fed either a high-salt (8%) diet or regular-salt diet for additional 4 weeks. Cardiac dysfunction, wall thickness, and 24-hour urinary catecholamine excretion were increased with high-salt diet compared with regular-salt diet. We then examined brain Na sensitivity. Intracerebroventricular infusion of high-Na (0.2 mol/L) artificial cerebrospinal fluid into AB-4 mice and mice Sham-4 increased urinary catecholamine excretion, arterial pressure, and heart rate more in AB-4 mice than in Sham-4 mice. Intracerebroventricular infusion of an epithelial Na channel blocker (benzamil) into mice with high-salt diet significantly decreased urinary catecholamine excretion and improved cardiac function. Infusion of either an angiotensin II type 1 receptor blocker or a Rho-kinase inhibitor also attenuated the salt-induced sympathetic hyperactivation and cardiac dysfunction in mice with high-salt diet. The levels of angiotensin II type 1 receptor and phosphorylated moesin, a substrate of Rho-kinase, were significantly greater in AB-4 mice than in Sham-4 mice. These results suggest that mice with pressure overload acquire brain Na sensitivity because of the activation of epithelial Na channel via Rho-kinase and angiotensin II, and this mechanism contributes to salt-induced sympathetic hyperactivation, further pressure overload, and cardiac dysfunction.
Human peripheral blood contains two distinct lineages of dendritic cells (1999)

Human peripheral blood contains two populations of dendritic cells (DC) but their developmental relationship has not been established. Freshly isolated CD11c– DC possessed a lymphoid morphology, lacked myeloid markers but expressed lymphoid markers (CD4+ CD10+) whilst the CD11c+ DC were monocytoid in appearance and expressed myeloid markers. Although both populations were allostimulatory, only the CD11c+ DC were able to take up antigen. Irrespective of the culture conditions the CD11c– cells developed into CD11c– CD13– CD33– CD4+ CD1a– CD83+/– DC. In contrast, cultured CD11c+ cells developed the phenotype CD11c+ CD13+ CD33+/– CD4– CD1a+ CD83+ CD9+. Only the CD11c+ DC expressed macrophage colony-stimulating factor (M-CSF) receptor and gave rise to CD14+, esterase+, phagocytic macrophages when cultured in M-CSF. These data suggest that these two populations of DC represent distinct lineages of antigen-presenting DC.
DNA Methylation Is the Primary Silencing Mechanism for a Set of Germ Line- and Tumor-Specific Genes with a CpG-Rich Promoter (1999)

A subset of male germ line-specific genes, the MAGE-type genes, are activated in many human tumors, where they produce tumor-specific antigens recognized by cytolytic T lymphocytes. Previous studies on gene MAGE-A1 indicated that transcription factors regulating its expression are present in all tumor cell lines whether or not they express the gene. The analysis of two CpG sites located in the promoter showed a strong correlation between expression and demethylation. It was also shown that MAGE-A1 transcription was induced in cell cultures treated with demethylating agent 5'-aza-2'-deoxycytidine. We have now analyzed all of the CpG sites within the 5' region of MAGE-A1 and show that for all of them, demethylation correlates with the transcription of the gene. We also show that the induction of MAGE-A1 with 5'-aza-2'-deoxycytidine is stable and that in all the cell clones it correlates with demethylation, indicating that demethylation is necessary and sufficient to produce expression. Conversely, transfection experiments with in vitro-methylated MAGE-A1 sequences indicated that heavy methylation suffices to stably repress the gene in cells containing the transcription factors required for expression. Most MAGE-type genes were found to have promoters with a high CpG content. Remarkably, although CpG-rich promoters are classically unmethylated in all normal tissues, those of MAGE-A1 and LAGE-1 were highly methylated in somatic tissues. In contrast, they were largely unmethylated in male germ cells. We conclude that MAGE-type genes belong to a unique subset of germ line-specific genes that use DNA methylation as a primary silencing mechanism.
Trace eyeblink conditioning requires the hippocampus but not autophosphorylation of αCaMKII in mice (2005)

Little is known about signaling mechanisms underlying temporal associative learning. Here, we show that mice with a targeted point mutation that prevents autophosphorylation of alphaCaMKII (alphaCaMKII(T286A)) learn trace eyeblink conditioning normally. This forms a sharp contrast to the severely impaired spatial learning in the water maze and contextual fear conditioning observed in alphaCaMKII(T286A) mutants. Importantly, hippocampal lesions impaired trace eyeblink conditioning in alphaCaMKII(T286A) mice, suggesting a potential role of hippocampal alphaCaMKII-independent mechanisms. These results indicate that hippocampal signaling mechanisms that underlie temporal associative learning as assessed by trace eyeblink conditioning may differ from those of spatial and contextual learning.