gebhart/patrepeval huggingface dataset:
The activating form of CD94 receptor complex: CD94 covalently associated with the Kp39 protein that represents the product of the NKG2-C gene (1998)

Inhibitory receptor complexes formed by CD94 and NKG2-A (Kp43) molecules have been implicated in HLA class I recognition by human natural killer (NK) cells. Additional forms of CD94 receptors have recently been described in NK cells characterized by the lack of NKG2-A expression. These CD94 receptors were shown to display activating functions. Immunoprecipitation with anti-CD94 monoclonal antibodies (mAb) led to the identification, in these cells, of a 39-kDa (Kp39) molecule that was originally believed to represent an activating isoform of the CD94 molecules. In the present study we show that the Kp39 molecule is covalently associated with CD94 and displays a protein backbone (26 kDa) similar to that of NKG2-A (Kp43) glycoproteins. Peptide mapping analysis indicates that Kp39 and NKG2-A glycoproteins belong to the same molecular family. A novel NKG2-specific mAb (termed P25) has been generated that specifically reacts with both NKG2-A and NKG2-C molecules, but fails to recognize NKG2-E molecules. Analysis of polyclonal and clonal NK cells shows that P25 mAb reacts with all NKG2-A+ cells and with a fraction of CD94+ cells lacking the expression of NKG2-A. These data indicate that NKG2-C molecules are indeed expressed only in a subset of cells lacking the expression of NKG2-A. The CD94-associated Kp39 molecule can be detected only in NKG2-A- P25+ cells, i.e. cells expressing NKG2-C molecules. Indeed, reverse transcription-polymerase chain reaction analysis performed on a large panel of NK clones indicates that NKG2-A- P25+ NK clones express the NKG2-C transcript. Notably, the cytolytic activity of these clones can be triggered by the P25 mAb in redirected killing analysis. Finally, biochemical analysis of COS7 cells cotransfected with CD94 and NKG2-C demonstrates the identity between Kp39 and NKG2-C molecules. Altogether, our data demonstrate that NKG2-C molecules associate with CD94 to form an activating receptor complex in a subset of human NK cells.
A mobile robot testbed with manipulator for security guard application (2002)

A mobile robot with a manipulator was developed for a security guard service application. The application image is that a robot patrols the building autonomously and checks for emergencies like fire, intruder, etc. On detecting an emergency the robot informs a remote operator who deals with the emergency by remotely operating the robot. The developed robot has the following functions to perform such a security service: autonomous navigation, master-slave manipulation system with force feedback, a remotely operated camera vision system with wide and stereoscopic view modes. The experiments conducted with the robot show that the robot can navigate autonomously in simple environments with a maximum speed of 1 m/s. A remote operator can perform door-opening using the master-slave manipulator and stereo viewing vision systems. This paper describes the various subsystems of the robot and some findings of the experiments.
Proteasomal inhibition causes the formation of protein aggregates containing a wide range of proteins, including nitrated proteins (2003)

Mutations in Cu,Zn-superoxide dismutase (SOD-1) are associated with some familial cases of amyotrophic lateral sclerosis (ALS), but it is not known how they result in cell death. We examined effects of overexpression of wild-type SOD-1 or the G37R or G85R mutations on the accumulation of ubiquitinated and nitrated proteins, and on loss of cell viability induced by the proteasome inhibitor, lactacystin. Wild-type SOD-1 had no effect on proteasomal activity, but the mutants decreased it somewhat. Treatment with lactacystin (1 micro m) caused only limited cell viability loss, even though it induced a marked inhibition of proteasomal activities. However, viability loss due to apoptosis was substantial in response to lactacystin when cells were overexpressing a mutant SOD-1. The frequency of cells showing immunoreactivity against ubiquitinated- or nitrated-proteins was enhanced when wild-type and mutant SOD-1 s were overexpressed. Ubiquitinated or nitrated alpha-tubulin, SOD-1, alpha-synuclein and 68K neurofilaments were observed in the aggregates. Similar aggregates were observed in cells overexpressing mutant parkin (Del3-5, T240R and Q311'X). The nitric oxide synthase inhibitor, l-NAME, decreased viability loss and aggregation, suggesting that nitration of proteins may play an important role in aggregation and in the cell death accompanying it.
Temporal Control of Puffing Activity in Polytene Chromosomes (1974)

The genetic organization of individual bands of polytene chromosomes is an enigma. On the one hand, we have evidence (Rudkin, 1965; Daneholt and Edström, 1967; Mulder et al, 1968; see also Rasch et al., 1971) that an “average” band contains DNA equivalent to 40,000 or so nucleotide pairs. The range is perhaps between 3000 and 100,000 nucleotide pairs (Beermann, 1972). On the other hand, classical (e.g., Painter, 1934; Bridges, 1935, 1936; Mackensen, 1935; Muller and Prokofyeva, 1935) and more modern (e.g., Hochman, 1971; Lefevre, 1971; Lim et al., 1971; Judd et al., 1972; Rayle, 1972) evidence strongly suggests that one band (or band plus adjacent interband(s), if you will: Crick, 1971) corresponds to a unit of genetic function.
Copper, Zinc, Manganese, and Magnesium Status and Complications of Diabetes Mellitus (1991)

Diabetes can alter copper, zinc, magnesium, and lipid peroxidation status. Perturbations in mineral metabolism are more pronounced in diabetic populations with specific complications. It is not known whether differences in trace element status are a consequence of diabetes, or alternatively, whether they contribute to the expression of the disease.
Tracking Genomic Cancer Evolution for Precision Medicine: The Lung TRACERx Study (2014)

The importance of intratumour genetic and functional heterogeneity is increasingly recognised as a driver of cancer progression and survival outcome. Understanding how tumour clonal heterogeneity impacts upon therapeutic outcome, however, is still an area of unmet clinical and scientific need. TRACERx (TRAcking non-small cell lung Cancer Evolution through therapy [Rx]), a prospective study of patients with primary non-small cell lung cancer (NSCLC), aims to define the evolutionary trajectories of lung cancer in both space and time through multiregion and longitudinal tumour sampling and genetic analysis. By following cancers from diagnosis to relapse, tracking the evolutionary trajectories of tumours in relation to therapeutic interventions, and determining the impact of clonal heterogeneity on clinical outcomes, TRACERx may help to identify novel therapeutic targets for NSCLC and may also serve as a model applicable to other cancer types.
Evolutionary Network Design (2008)

Network design is one of the most important and most frequently encountered classes of optimization problems. It is a combinatory field in combinatorial optimization and graph theory. When considering a bicriteria network design (bND) problem with the two conflicting objectives of minimizing cost and maximizing flow. Network design problems where even one flow measure be maximized, are often NP-hard problems. But, in real-life applications, it is often the case that the network to be built is required to optimize multi-criteria simultaneously. Thus the calculation of the multi-criteria network design problems is a difficult task. In this state-of-the-art survey paper, we propose a new multiobjective hybrid genetic algorithm (mo-hGA) hybridized with Fuzzy Logic Control (FLC) and Local Search (LS). Numerical experiments based on the mo-hGA method for designing multiple objective network models show the effectiveness and the efficiency of our approach by comparing with the recent researches.
Cutting Edge: Antigen-Dependent Regulation of Telomerase Activity in Murine T Cells (1998)

Telomeres, structures on the ends of linear chromosomes, function to maintain chromosomal integrity. Telomere shortening occurs with cell division and provides a mechanism for limiting the replicative potential of normal human somatic cells. Telomerase, a ribonucleoprotein enzyme, synthesizes telomeric repeats on chromosomal termini, potentially extending the capacity for cell division. The present study demonstrates that resting T cells express little/no activity, and optimal Ag-specific induction of telomerase activity in vitro requires both TCR and CD28-B7 costimulatory signals. Regulation of telomerase in T cells during in vivo Ag-dependent activation was also assessed by adoptive transfer of TCR transgenic T cells and subsequent Ag challenge. Under these conditions, telomerase was induced in transgenic T cells coincident with a phase of extensive clonal expansion. These findings suggest that telomerase may represent an adoptive response that functions to preserve replicative potential in Ag-reactive lymphocytes.
Design challenges and solutions for ultra-high-density monolithic 3D ICs (2014)

Monolithic 3D ICs (M3D) are an emerging technology that offers an ultra-high-density 3D integration due to the extremely small size of monolithic inter-tier vias. We explore various design styles available in M3D and present design techniques to obtain GDSII-level signoff quality results for each of these styles. We also discuss various challenges facing each style and provide solutions to them.
Medical management of uterine fibroids with medroxyprogesterone acetate (Depo Provera): a pilot study (2004)

The aim of this study was to determine the effectiveness of medroxyprogesterone acetate (Depo Provera) in the treatment of menorrhagia attributed to uterine fibroids and to determine whether it reduces fibroid volume. Twenty premenopausal women with menorrhagia attributed to uterine fibroids received Depo Provera (150 mg/month) for 6 months. Control of bleeding was assessed by menstrual diary, haematologic parameters (Hb) and uterine and fibroid size measured sonargraphically. Following a period of 6 months after the initiation of Depo Provera, 30% became amenorrhoeic, 70% noticed improvement in their bleeding pattern and 15% had an increase in their haemoglobin levels. The mean uterine and fibroid volume was also reduced by 48% and 33%, respectively. Medical therapy with Depo Provera with symptomatic fibroids causes significant improvement in bleeding pattern as well as a reduction in fibroid volume.
Application of High Amplitude Alternating Magnetic Fields for Heat Induction of Nanoparticles Localized in Cancer (2005)

High-amplitude AMF (up to 1,300 Oe) was well tolerated provided the duty was adjusted to dissipate heat. Results presented suggest that further tissue temperature regulation can be achieved with suitable variations of pulse width for a given amplitude and duty combination. These results suggest that it is possible to apply high-amplitude AMF (> 500 Oe) with pulsing for a time sufficient to treat cancer tissue in which magnetic nanoparticles have been embedded.
Transcripts from the Cellular Homologs of Retroviral Oncogenes: Distribution Among Chicken Tissues (1982)

The oncogenes (v-onc genes) of rapidly transforming retroviruses have homologs (c-onc genes) in the genomes of normal cells. In this study, we characterized and quantitated transcription from four c-onc genes, c-myb, c-myc, c-erb, and c-src, in a variety of chicken cells and tissues. Electrophoretic analysis of polyadenylated RNA, followed by transfer to nitrocellulose and hybridization to cloned onc probes showed that c-myb, c-myc, and c-src each give rise to a single mature transcript, whereas c-erb gives rise to multiple transcripts (B. Vennstrom and J. M. Bishop, Cell, in press) which vary in abundance among different cells and tissues. Transcription from c-myb, c-myc, c-erb, and c-src was quantitated by a "dot-blot" hybridization assay. We found that c-myc, c-erb, and c-src transcription could be detected in nearly all cells and tissues examined, whereas c-myb transcription was detected only in some hemopoietic cells; these cells, however, belong to several different lineages. Thus, in no case was expression of a c-onc gene restricted to a single cell lineage. There appeared to be a correlation between levels of c-myb expression and hemopoietic activity of the tissues and cells examined, which suggests that c-myb may be expressed primarily in immature hemopoietic cells. An examination of c-onc RNA levels in target cells and tissues for viruses carrying the corresponding v-onc genes revealed no obvious correlation, direct or inverse, between susceptibility to transformation by a given v-onc gene and expression of the homologous c-onc gene.
Quantitative Affinity of Genetically Engineered Repeating Polypeptides to Inorganic Surfaces (2008)

Binding kinetics of platinum-, silica-, and gold-binding peptides were investigated using a modified surface plasmon resonance spectroscopy (SPR). Platinum binding septa-peptides, quartz-binding dodecapeptides, and gold-binding 14-aa peptides were originally selected using phage or cell surface display libraries using the mineral or pure forms of these materials. All of the peptides were synthesized singly to investigate their binding kinetics and to assess quantitatively the specific affinity of each to its material of selection. The peptides were also postselection engineered to contain multiple copies of the same original sequences to quantify the effects of repeating units. SPR spectroscopy, normally using gold surfaces, was modified to contain a thin film (a few nm thick) of the material of interest (silica or platinum) on gold to allow the quantitative study of the adsorption kinetics of specific solid-binding peptides. The SPR experiments, carried out at different concentrations, on all three materials substrates, resulted in Langmuir behavior that allowed the determination of the kinetic parameters, including adsorption, desorption, and equilibrium binding constants for each of the solids as well as free energy of adsorption. Furthermore, we also tested multiple repeats of the peptide sequences, specifically three repeats, to see if there is a general trend of increased binding with increased number of binding domains. There was no general trend in the binding strength of the peptides with the increase of the repeat units from one to three, possibly because of the conformational changes between the single and multiple repeat polypeptides. In all cases, however, the binding was strong enough to suggest that these inorganic binding peptides could potentially be used as specific molecular linkers to bind molecular entities to specific solid substrates due to their surface recognition characteristics.
Structural and functional aspects of papain-like cysteine proteinases and their protein inhibitors. (1997)

Cysteine proteinases are widely distributed among living organisms. According to the most recent classifications (Rawlings and Barrett, 1993, 1994), they can be subdivided on the basis of sequence homology into 14 or even 20 different families, the most important being the papain and the calpain families. The papain-like cysteine proteinases are the most abundant among the cysteine proteinases. The family consists of papain and related plant proteinases such as chymopapain, caricain, bromelain, actinidin, ficin, and aleurain, and the lysosomal cathepsins B, H, L, S, C and K. Most of these enzymes are relatively small proteins with Mr values in the range 20000-35000 (reviewed in Brocklehurst et al., 1987; Polgar, 1989; Rawlings and Barrett, 1994; Berti and Storer, 1995), with the exception of cathepsin C, which is an oligomeric enzyme with Mr approximately 200000 (Metrione et al., 1970; Dolenc et al., 1995). A number of cysteine proteinases are located within lysosomes. Four of them, cathepsins B, C, H and L, are ubiquitous in lysosomes of animals, whereas cathepsin S has a more restricted localisation (Barrett and Kirschke, 1981; Kirschke and Wiederanders, 1994). The enzymes, except cathepsin C, are endopeptidases (reviewed in Kirschke et al., 1995), although cathepsin B was found also to be a dipeptidyl carboxypeptidase (Aronson and Barrett, 1978) and cathepsin H also an aminopeptidase (Koga et al., 1992). Cathepsin C is a dipeptidyl aminopeptidase, but at higher pH it exhibits also dipeptidyl transferase activity (reviewed in Kirschke et al., 1995). Among the lysosomal cysteine proteinases, cathepsin L was found to be the most active in degradation of protein substrates, such as collagen, elastin and azocasein (Barrett and Kirschke, 1981; Maciewicz et al., 1987; Mason et al., 1989), arid cathepsin B the most abundant (Kirschke and Barrett, 1981). All the enzymes are optimally active at slightly acidic pH, although their pH optima for degradation of synthetic substrates vary from 5.5 for cathepsin L to 6.8 for cathepsin H (reviewed in Kirschke et al., 1995). Several other lysosomal cysteine proteinases, such as cathepsins N, T and K, are known, although their properties are less well characterised (reviewed in Kirschke et al., 1995). In particular cathepsin K has attracted recent interest (Bromme et al., 1996; Shi et al., 1995; Bossard et al., 1996; Drake et al., 1996) and was found to be expressed specifically in osteoclasts (Drake et al., 1996) with properties similar to cathepsin L (Bossard et al., 1996).
Interaction of CED-4 with CED-3 and CED-9: A Molecular Framework for Cell Death (1997)

Previous genetic studies of the nematode Caenorhabditis elegans identified three important components of the cell death machinery. CED-3 and CED-4 function to kill cells, whereas CED-9 protects cells from death. Here CED-9 and its mammalian homolog Bcl-xL (a member of the Bcl-2 family of cell death regulators) were both found to interact with and inhibit the function of CED-4. In addition, analysis revealed that CED-4 can simultaneously interact with CED-3 and its mammalian counterparts interleukin-1beta-converting enzyme (ICE) and FLICE. Thus, CED-4 plays a central role in the cell death pathway, biochemically linking CED-9 and the Bcl-2 family to CED-3 and the ICE family of pro-apoptotic cysteine proteases.
Clusterin Interacts with Paclitaxel and Confer Paclitaxel Resistance in Ovarian Cancer (2008)

Optimal debulking followed by chemotherapy is the standard treatment of managing late-stage ovarian cancer, but chemoresistance is still a major problem. In this study, we compared expression profiles of primary tumor tissue from five long-term (>8 years) and five short-term (<2 years) ovarian cancer survivors and identified clusterin as one of the genes that were significantly up-regulated in short-term survivors. We then evaluated the prognostic significance of clusterin and its possible correlation with chemoresistance in ovarian cancer by immunohistostaining of clusterin in 62 tumor samples from patients with stage III, high-grade serous ovarian cancer. After adjusting for debulking status and age, Cox regression analyses showed that high levels of clusterin expression correlate with poor survival (hazard ratio, 1.07; 95% confidence interval, 1.002-1.443; P = .04). We also investigated clusterin in paclitaxel resistance by modulating the endogenous clusterin expression in ovarian cancer cells and treating the cells with purified clusterin. Results indicate that high-clusterin-expressing ovarian cancer cells are more resistant to paclitaxel. Moreover, exposing ovarian cancer cells to exogenous clusterin increases cells' resistance to paclitaxel. Finally, using size exclusion chromatography and fluorescently labeled paclitaxel, we demonstrated that clusterin binds to paclitaxel. In summary, our findings suggest that high levels of clusterin expression increase paclitaxel resistance in ovarian cancer cells by physically binding to paclitaxel, which may prevent paclitaxel from interacting with microtubules to induce apoptosis. Thus, clusterin is a potential therapeutic target for enhancing chemoresponsiveness in patients with a high-level clusterin expression.
ErbB-2 Amplification Inhibits Down-regulation and Induces Constitutive Activation of Both ErbB-2 and Epidermal Growth Factor Receptors (1999)

ErbB-2/HER2 is an important signaling partner for the epidermal growth factor receptor (EGFR). Overexpression of erbB-2 is also associated with poor prognosis in breast cancer. To investigate how erbB-2 amplification affects its interactions with the EGFR, we used a human mammary epithelial cell system in which erbB-2 expression was increased 7-20-fold by gene transfection. We found that amplification of erbB-2 caused constitutive activation of erbB-2 as well as ligand-independent activation of the EGFR. Overexpression of erbB-2 strongly inhibited erbB-2 down-regulation following transactivation by EGFR. Significantly, down-regulation of activated EGFR was also inhibited by erbB-2 amplification, resulting in enhanced ligand-dependent activation of the EGFR. The rate of EGFR endocytosis was not affected by erbB-2 overexpression, but the rate of lysosomal targeting was significantly reduced. In addition, erbB-2 overexpression promoted rapid recycling of activated EGFR back to the cell surface and decreased ligand dissociation from the EGFR. Our data suggest that overexpression of erbB-2 inhibits both its down-regulation and that of the EGFR. The net effect is increased signaling through the EGFR system.
Ethanol production potential from AFEX™ and steam-exploded sugarcane residues for sugarcane biorefineries (2018)

AFEX™ proved to be a more effective pretreatment method for sugarcane residues relative to StEx due to the higher fermentable sugar recovery and enzymatic hydrolysate fermentability after high solids loading enzymatic hydrolysis and fermentation by <i>S. cerevisiae</i> 424A (LNH-ST). The identification of auxiliary enzyme activities, adequate process integration and the use of robust xylose-fermenting ethanologens were identified as opportunities to further improve ethanol yields from AFEX™- and StEx-treated sugarcane residues.
Combine user defined region-of-interest and spatial layout for image retrieval (2002)

Content-based image retrieval (CBIR) is one of the most active research areas. Many visual feature representations have been explored and many systems built. However, in most of current systems, only the global features such as overall color histogram and texture moments are used which ignore the actual composition of the image in terms of internal objects. Although relevance feedback was proposed (Rui and Huang 1998) to incrementally supply more information, this may fail due to the lack of higher-level information about what exactly was of interest. Since automatic segmentation of the region-of-interest (ROI) is not always reliable, human assistance is necessary. In this paper, a novel approach combining a user defined region-of-interest and spatial layout is proposed for CBIR. Better capture of the image object is achieved by the user rather than the computer. Therefore, more accurate relevance feedback is achieved and thus lends to a more powerful search engine.
Relationship between CDKs and CKIs in regulation of cell cycle progression of human gastric cancer cells (2000)

Western blotting showed that p21~(waf1/cip1) was up-regulated by ATRA in gastric cancer cells, which resulted in a decreased CDK_(2) activity, as revealed by immunoprecipitation assay. However, p16~(ink4), which specifically inhibited cyclin D_(1)/CDK_(4) complexes, was down-regulated by ATRA both at mRNA and protein levels. By accompanying with another inhibitor p21~(waf1/cip1), it let to the increase of CDK_(4) activity after treatment of ATRA for 12 h, and the decrease after 24 h.