gebhart/patrepeval huggingface dataset:
Transcription through Intergenic Chromosomal Memory Elements of the Drosophila Bithorax Complex Correlates with an Epigenetic Switch (2002)

The proteins of the trithorax and Polycomb groups maintain the differential expression pattern of homeotic genes established by the early embryonic patterning system during development. These proteins generate stable and heritable chromatin structures by acting via particular chromosomal memory elements. We established a transgenic assay system showing that the Polycomb group response elements bxd and Mcp confer epigenetic inheritance throughout development. With previously published data for the Fab7 cellular memory module, we confirmed the cellular memory function of Polycomb group response elements. In Drosophila melanogaster, several of these memory elements are located in the large intergenic regulatory regions of the homeotic bithorax complex. Using a transgene assay, we showed that transcription through a memory element correlated with the relief of silencing imposed by the Polycomb group proteins and established an epigenetically heritable active chromatin mode. A memory element remodeled by the process of transcription was able to maintain active expression of a reporter gene throughout development. Thus, transcription appears to reset and change epigenetic marks at chromosomal memory elements regulated by the Polycomb and trithorax proteins. Interestingly, in the bithorax complex of D. melanogaster, the segment-specific expression of noncoding intergenic transcripts during embryogenesis seems to fulfill this switching role for memory elements regulating the homeotic genes.
Screening of bacterial strains for pectinolytic activity: characterization of the polygalacturonase produced by Bacillus sp (1999)

One hundred sixty eight bacterial strains, isolated from soil and samples of vegetable in decomposition, were screened for the use of citrus pectin as the sole carbon source. 102 were positive for pectinase depolymerization in assay plates as evidenced by clear hydrolization halos. Among them, 30% presented considerable pectinolytic activity. The cultivation of these strains by submerged and semi-solid fermentation for polygalacturonase production indicated that five strains of Bacillus sp produced high quantities of the enzyme. The physico-chemical characteristics, such as optimum pH of 6.0 - 7.0, optimum temperatures between 45oC and 55oC, stability at temperatures above 40oC and in neutral and alkaline pH, were determined.
Characterization of murine monoclonal antibodies directed against basic fibroblast growth factor (1987)

Monoclonal antibodies (McAbs) were developed that identify the complete (1-146 aa) and the NH2-terminal truncated (des 1-15) form of bovine basic fibroblast growth factor (bFGF). Four McAbs, designated McAbs 6, 8, 38, and 42, bind the complete form of bFGF found in bovine pituitary, brain, and adrenal gland. One of these McAbs, McAbs 42, also binds to the des 1-15 aa form of bFGF found in bovine adrenal gland, kidney, and corpus luteum. None of the McAbs binds bovine-brain-derived acidic FGF (aFGF). McAbs 6, 8, and 38 recognized the same epitope located within the first ten residues of the NH2-terminal of complete bFGF. McAb 42 recognizes a "core" epitope found on both the complete and des 1-15 aa bFGFs. The McAbs are murine IgGs with affinity constants of 10(7)-10(8) liter/M for bovine-pituitary-derived bFGF. McAbs 8 and 42 have been used in a two-site ELISA to detect the complete form of bFGF. The ELISA is sensitive to 38.5 fmole/well of bFGF and is not affected by the presence of calf serum or bovine-brain-derived aFGF. These McAbs should be useful in distinguishing the native and des 1-15 aa forms of bFGF from each other, and from aFGF and other growth factors.
Applications of nucleic acid technology in the CNS (2003)

This review examines applications of nucleic acid technology in the form of catalytic nucleic acids (ribozymes and DNAzymes) and RNA interference (RNAi) in the CNS. The basic mechanism of catalytic nucleic acids and RNAi is reviewed, and potentials and problems highlighted. Recent advances in chemical modifications and delivery techniques are summarized. Applications in the CNS, including their use in primary neuronal cells, organotypic slice culture and the brain in vivo are further discussed.
Sequence homologies in mammalian 5.8S ribosomal RNA (1976)

Oligonucleotide products of complete pancreatic or T1 RNase digestion or partial T1 RNase digestion of HeLa cell (human) and MPC-11 cell (mouse) 5.8S rRNA are identical with those obtained from Novikoff hepatoma (rat) 5.8S rRNA except for minor differences at the termini. pCp is the only major 5' terminus of both human and mouse RNAs; both pGp and pCp 5' termini were found in rat 5.8S RNA. Furthermore, HeLa cells contain C-U-U at the 3' end rather than the C-U terminus of mouse and rat. The results indicate that the nucleotide sequence has been highly conserved during the evolution of mammals and suggest that, as reported for 5S rRNA, this sequence is essentially constant throughout the Mammalia.
Human cDNA Encoding a Novel TGF- Superfamily Protein Highly Expressed in Placenta (1997)

Recently, we developed a simple method for detecting a secretory signal sequence encoded by a cDNA fragment. In this study, we used this method to select cDNA clones encoding secretory proteins from a human full-length cDNA library. Full-sequencing analysis of the candidate clones revealed that one clone encoded a novel TGF-beta superfamily protein. The clone encodes a protein of 308 amino acids of which the C-terminal region shows a characteristic feature of TGF-beta superfamily proteins: seven conserved cysteine residues at the C-terminal preceded by a putative processing site composed of a basic amino acid repeat. The corresponding transcripts are highly expressed in the placenta, so the novel protein may play an important role in reproduction.
Survivin Gene Expression in Endometriosis (2002)

Survivin is a novel inhibitor of apoptosis and is expressed during fetal development and in cancer tissues, but its expression has not been reported in normal adult tissues or benign diseases. We investigated survivin gene and protein expression in a tumor-like benign disease, endometriosis, and correlated them with apoptosis and invasive phenotype of endometriotic tissues. Gene expression levels of survivin, matrix metalloproteinase (MMP)-2, MMP-9, and membrane type 1 (MT1)-MMP in 63 pigmented or nonpigmented endometriotic tissues surgically obtained from 35 women with endometriosis were compared with those in normal eutopic endometrium obtained from 12 women without endometriosis. Survivin, MMP-2, MMP-9, and MT1-MMP mRNA expression levels in clinically aggressive pigmented lesions were significantly higher than those in normal eutopic endometrium, and survivin gene expression in pigmented lesions was also higher than that in nonpigmented lesions (P < 0.05). There was a close correlation between survivin and MMP-2, MMP-9, or MT1-MMP gene expression levels in 63 endometriotic tissues examined (P < 0.01). Apoptotic cells detected by the dUTP nick-end labeling were rare in 11 ovarian endometriotic tissues, which showed positive immunohistochemical expression for survivin and MMPs. Our findings suggest that up-regulation of survivin and MMPs may cooperatively contribute to survival and invasion of endometriosis.
Blur image detection using Laplacian operator and Open-CV (2016)

With the increased usage of digital cameras and picture clicking devices, the number of digital images increases rapidly, which in return demand for image quality assessment in terms of blur. Based on the edge type and sharpness analysis using Laplacian operator, an effective representation of blur image detection scheme is proposed in this paper, which can determine that whether the image is blurred or not, and what is the extent of blur through Variance of Laplacian. In this project a simple, reliable and fast algorithm for image noise estimation is presented. Images taken for the testing is assumed to be corrupted by additive zero mean Gaussian noise. To exclude structures or details from contributive to the noise variance estimation, an easy edge detection algorithm inculcating first-order gradients is applied first. Then a Laplacian operator followed by an averaging over the whole image will provide very accurate noise variance estimation. There is only one parameter which is self-determined and adaptive to the image contents. Simulation results show that the proposed algorithm performs well for different types of images over a large range of noise variances. Performance comparisons against alternative approaches are also provided. Results obtain through screenshots of the experiments demonstrate the effectiveness of the proposed scheme.
Increased expression of Borrelia burgdorferi vlsE in response to human endothelial cell membranes (2001)

RNA isolated from virulent Borrelia burgdorferi cells incubated with human endothelial or neurological tissue cells was subjected to subtractive hybridization using RNA from the same strain incubated in tissue culture medium alone. This RNA subtractive technique generated specific probes that hybridized to two restriction fragments (8.2 kb and 10 kb respectively) generated by EcoRI digestion of total plasmid DNA. The 10 kb EcoRI fragment localized to lp28-1 and was subsequently identified as the variable membrane protein-like sequence (vls) region, which includes an expression locus (vlsE) and 15 silent cassettes. vlsE encodes a 36 kDa outer surface protein that undergoes antigenic variation during animal infections. Primer extension analysis identified the 5' end of a transcript and a putative promoter for vlsE. Quantitative reverse transcription-polymerase chain reaction (RT-PCR) suggested that the expression of vlsE increased when virulent B. burgdorferi cells were incubated with human tissue cells or purified cell membranes isolated from those same cell lines. A 138 bp region upstream of the vlsE region that was not reported in the genome sequence was sequenced using specific 32P end-labelled primers in a DNA cycle sequencing system at high annealing temperatures. Analysis revealed that it contained a 51 bp inverted repeat, which could form an extremely stable cruciform structure. Southern blots probed with the vlsE promoter/operator region indicated that part or all of this sequence could be found on other B. burgdorferi plasmids.
Molecular association complexes of polymers. Urea and thiourea complexes of high molecular weight poly(ethylene oxide) (1961)

Abstract Complexes have been formed by mixing urea or thiourea with high molecular weight yoly(ethylene oxide) on a hot roll mill and by precipitation of the complex from benzene solution. The most dramatic method of complex formation, however, is observed when finely divided urea or thiourea is suspended in a benzene solution of poly(ethylene oxide). The complex forms quantitatively, abstracting all the polymer from solution. The rate of complex formation from solid urea or thiourea and poly(ethylene oxide) in solution has been observed, the thiourea complex forming more rapidly than that of urea. This process of formation can be followed by microscopic examination of the suspended urea particles. The crystalline complex appears to form in a ratio of 2 moles of urea or thiourea to 1 mole of oxyethylene monomer unit. The urea complex melts at 143°C. in comparison with the melting point of urea, 132°C., and of poly(ethylene oxide), 65°C. The complex with either urea or thiourea shows distinct x‐ray diffraction patterns, and the presence of complex in a poly(ethylene oxide) matrix can be detected both by x‐ray diffraction and by stiffness–temperature measurements. Both complexes are water‐soluble.
Extraction-spectrophotometric determination of hydrazine with 2-hydroxy-1-naphthaldehyde (1987)

An extraction-spectrophotometric method for the determination of hydrazine, based on its reaction with 2-hydroxy-1-naphthaldehyde at 100 °C, is described. Beer's law is obeyed between 35 and 700 ng ml–1 of hydrazine. The molar absorptivity at 412 nm is 27 000 l mol–1 cm–1. The method described has been applied satisfactorily to the determination of hydrazine in feed waters for steam-generating boilers.
Transfer of yeast artificial chromosomes into mammalian cells and comparative study of their integrity (1995)

Yeast artificial chromosomes (YACs) from the CEPH MegaYAC library (Paris, France) ranging in size from 350 to 1600 kb and mapping to the q22.1 and q22.2 regions of human chromosome 21 were transferred into mammalian cells by spheroplast fusion. The integrity of the YACs from two adjacent parts of the region was compared after retrofitting and stable transfer into mammalian cells. We found that large YACs could easily be manipulated to allow transfer of the YAC material into mammalian cells and that the size of the YAC did not appear to be limiting for fusion. However, we show that there was great variability in the integrity of the YACs from the two regions, which was not related to the size of the YACs. Four YACs in region I from sequence-tagged site (STS) G51E05 up to STS LL103 showed, in general, no loss of material and correct gene transfer into mammalian cells. In contrast, the three YACs in the more centromeric region II (from STS G51B09 up to G51E05) frequently showed a loss of human material during handling, retrofitting and transfer. As a YAC from another library covering region II was also found to be unstable, we propose that the integrity of the YACs is highly dependent on the incorporated human chromosomal DNA.
[Mutations in the epidermal growth factor receptor: structure and biological function in human tumors]. (2006)

The epidermal growth factor receptor (EGFR) plays an important role in the regulation of normal cell proliferation, differentiation and survival. For this reason EGFR status is often altered in a range of human tumor types and generally correlates with a poor prognosis. In recent years a number of mutations in the EGFR gene have been noted that lead to the expression of overactive or constitutively active aberrant receptors. These receptors have been shown to participate actively in the process of tumor genesis. This review provides an overview of the structure of these mutations and their biological function in human tumors plus the potentials of anticancer therapy.
Derivation of Histocompatible Stem Cells from Ovarian Tissue (2010)

Somatic cell nuclear transfer, the first established technique for producing patient-specific autologous stem cells, inevitably requires the sacrifice of viable embryos. To circumvent the serious ethical issues associated with this use of embryos, researchers have developed several alternative methods for the production of histocompatible stem cells. In our research, we have used two methods to derive histocompatible stem cells from murine ovarian tissue. First, we have established autologous stem cells by culturing degeneration-fated preantral follicles to produce developmentally competent, mature oocytes and then parthenogenetically activating these mature oocytes to acquire genetic homogeneity. Second, we have used cell-to-cell interactions to derive stem cells from ovarian stromal cells without undertaking genetic modification. We have successfully derived autologous murine stem cells by manipulating primary and early secondary follicles in vitro, and this method has proved successful even for follicles retrieved from aged ovaries. Furthermore, we believe that it will be possible to isolate stem cells directly from non-germline ovarian tissue or to derive stem cells by culturing the ovarian cells with other somatic cells. If achieved, these aims will greatly advance the development of induced pluripotent stem cell technology, as well as tissue-specific stem cell research. In this review, we introduce the relevant technologies for establishing histocompatible stem cells from ovarian tissue cells without undertaking genetic manipulation and review the current limitations of, and future research directions in, stem cell biology.
Macrophage Scavenger Receptor 1 999C&gt;T (R293X) Mutation and Risk of Prostate Cancer (2005)

Our large-scale analysis of case and controls from several countries found no evidence that the 999C>T mutation is associated with increased risk of prostate cancer. The meta-analysis suggests it is unlikely that this mutation confers more than a 2-fold increased risk.
Controlling the Isomerization Rate of an Azo-BF2 Switch Using Aggregation (2017)

A novel visible-light activated azo-BF<sub>2</sub> switch possessing a phenanthridinyl π-system has been synthesized, and its switching properties have been characterized as a function of concentration. The switch self-aggregates through π-π interactions, and the degree of aggregation modulates the Z → E thermal isomerization rate. This property allows for the active tuning of the thermal relaxation half-life of the same switch from seconds to days.
Animating soft substances with implicit surfaces (1995)

published under the name Marie-Paule Gascuel
MDG1/ERdj4, an ER‐resident DnaJ family member, suppresses cell death induced by ER stress (2003)

MDG1/ERdj4 may play roles in stabilizing GRP78/BiP binding to unfolded substrate proteins in a J domain-dependent manner and prevent the accumulation of unfolded proteins in the ER, consequently protecting cells from ER stress.
Adult rat and human bone marrow stromal cells differentiate into neurons (2000)

Bone marrow stromal cells exhibit multiple traits of a stem cell population. They can be greatly expanded in vitro and induced to differentiate into multiple mesenchymal cell types. However, differentiation to non-mesenchymal fates has not been demonstrated. Here, adult rat stromal cells were expanded as undifferentiated cells in culture for more than 20 passages, indicating their proliferative capacity. A simple treatment protocol induced the stromal cells to exhibit a neuronal phenotype, expressing neuron-specific enolase, NeuN, neurofilament-M, and tau. With an optimal differentiation protocol, almost 80% of the cells expressed NSE and NF-M. The refractile cell bodies extended long processes terminating in typical growth cones and filopodia. The differentiating cells expressed nestin, characteristic of neuronal precursor stem cells, at 5 hr, but the trait was undetectable at 6 days. In contrast, expression of trkA, the nerve growth factor receptor, persisted from 5 hr through 6 days. Clonal cell lines, established from single cells, proliferated, yielding both undifferentiated and neuronal cells. Human marrow stromal cells subjected to this protocol also differentiated into neurons. Consequently, adult marrow stromal cells can be induced to overcome their mesenchymal commitment and may constitute an abundant and accessible cellular reservoir for the treatment of a variety of neurologic diseases.
Profile modeling of high density plasma oxide etching (1995)

The mechanisms of the oxide etching process are studied using the overhang test structures etched on the Applied Materials inductively coupled plasma oxide etcher. The results from the overhang test structures clearly show many details of the surface interactions that etched trenches would not show. Together with results obtained with standard trench structures etched with the same process, a new model for oxide etching is developed to explain the observed profiles and trends. The two neutral, simultaneous deposition and etching model contains several key features. Components controlling the deposition behavior are: (1) polymer chemical vapor deposition, (2) ion enhanced deposition, and (3) angle dependent polymer sputtering. The etch rate is simulated with a saturation model, where the rate can be ion or neutral flux limited. The model is incorporated into the profile simulator SPEEDIE and the simulations are run with one set of parameters. The simulation results show good agreement with the scanning electron microscopy experiment results for both profile and lag trends.
Recovering consistent video depth maps via bundle optimization (2008)

This paper presents a novel method for reconstructing high-quality video depth maps. A bundle optimization model is proposed to address the key issues, including image noise and occlusions, in stereo reconstruction. Our method not only uses the color constancy constraint, but also explicitly incorporates the geometric coherence constraint associating multiple frames in a video, thus can naturally maintain the temporal coherence of the recovered video depths without introducing over-smoothing artifact. To make the inference problem tractable, we introduce an iterative optimization scheme by first initializing disparity maps using segmentation prior and then refining the disparities by means of bundle optimization. Unlike previous work estimating complex visibility parameters, our approach implicitly models the probabilistic visibility in a statistical way. The effectiveness of our automatic method is demonstrated using challenging video examples.
Figure-ground discrimination: a combinatorial optimization approach (1993)

The figure-ground discrimination problem is considered from a combinatorial optimization perspective. A mathematical model encoding the figure-ground discrimination problem that makes explicit a definition of shape based on cocircularity, smoothness, proximity, and contrast is presented. This model consists of building a cost function on the basis of image element interactions. This cost function fits the constraints of an interacting spin system that, in turn, is a well suited physical model that solves hard combinatorial optimization problems. Two combinatorial optimization methods for solving the figure-ground problem, namely mean field annealing, which combines mean field approximation theory and annealing, and microcanonical annealing, are discussed. Mean field annealing may be viewed as a deterministic approximation of stochastic methods such as simulated annealing. The theoretical bases of these methods are described, and the computational models are derived. The efficiencies of mean field annealing, simulated annealing, and microcanonical annealing algorithms are compared. Within the framework of such a comparison, the figure-ground problem may be viewed as a benchmark.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Investigations on Electric Field Distributions in a Microwave Discharge in Hydrogen (2000)

Introduction Microwave discharges play an important role in plasma sources for industrial applications like surface modification and thin film deposition. The electric field distribution in the plasma determines the electron density and energy distribution and the homogeneity of the discharge. The typical amplitude of the electric field is of the order of 100 V/cm. Up to now, this low field strength was not within the reach of laser spectroscopic techniques for electric field measurements. Recently, we have developed a novel technique in atomic hydrogen that allows the measurement of low electric fields down to 5 V/cm. The electric field is determined from the Stark splitting of high Rydberg states. (typically n = 14 20). Here, this technique is applied to a pulsed microwave discharge at 2.45 GHz in hydrogen with a 10 % argon admixture. The spatial and temporal field distribution is investigated in a commercial plasma source (SLAN). For the first time, we can measure both the microwave field and the microfield, originating from the plasma charges by a laser spectroscopic technique with high spatial and temporal resolution.