gebhart/patrepeval huggingface dataset:
Regulation of selected genome loci using de novo-engineered transcription activator-like effector (TALE)-type transcription factors (2010)

Proteins that can be tailored to bind desired DNA sequences are key tools for molecular biology. Previous studies suggested that DNA-binding specificity of transcription activator-like effectors (TALEs) from the bacterial genus Xanthomonas is defined by repeat-variable diresidues (RVDs) of tandem-arranged 34/35-amino acid repeat units. We have studied chimeras of two TALEs differing in RVDs and non-RVDs and found that, in contrast to the critical contributions by RVDs, non-RVDs had no major effect on the DNA-binding specificity of the chimeras. This finding suggests that one needs only to modify the RVDs to generate designer TALEs (dTALEs) to activate transcription of user-defined target genes. We used the scaffold of the TALE AvrBs3 and changed its RVDs to match either the tomato Bs4, the Arabidopsis EGL3, or the Arabidopsis KNAT1 promoter. All three dTALEs transcriptionally activated the desired promoters in a sequence-specific manner as mutations within the targeted DNA sequences abolished promoter activation. This study is unique in showing that chromosomal loci can be targeted specifically by dTALEs. We also engineered two AvrBs3 derivatives with four additional repeat units activating specifically either the pepper Bs3 or UPA20 promoter. Because AvrBs3 activates both promoters, our data show that addition of repeat units facilitates TALE-specificity fine-tuning. Finally, we demonstrate that the RVD NK mediates specific interaction with G nucleotides that thus far could not be targeted specifically by any known RVD type. In summary, our data demonstrate that the TALE scaffold can be tailored to target user-defined DNA sequences in whole genomes.
Temporally designed treatment of melanoma cells by ATRA and polyI (2012)

In the last three decades, the incidence of melanoma has increased worldwide and no effective treatment modalities have been developed yet. All-trans retinoic acid (ATRA) and polyinosinic:polycytidylic acid (polyI:C) are strong inducers of toll-like receptor 3 (TLR3) and MDA5 expression, and polyI:C-induced TLR3 and MDA5 signaling specifically causes cell death in melanoma cells in vitro. We addressed the question of whether ATRA pretreatment could enhance the efficacy of polyI:C and, if so, would ATRA have any additional effects on this process. We found that the combined treatment of human melanoma cells with ATRA and polyI:C strongly increased the expression of TLR3 and MDA5 in both WM35 and WM983A cells associated with significantly higher mRNA and secreted levels of interferon β (IFNβ), CXCL1, CXCL8/IL-8, CXCL9, and CXCL10 than cells treated with either ATRA or polyI:C. Silencing of MDA5 by siRNA moderately affected IFNβ secretion, whereas TLR3 knockdown interfered with both CXCL chemokine and IFNβ production. Furthermore, the supernatants of ATRA+polyI:C-activated cultures increased the migration of both human monocyte-derived macrophages and CD1a dendritic cells significantly as compared with the supernatants of cells treated with either ATRA or polyI:C, and this effect occurred in a TLR3-dependent manner. In conclusion, consecutive treatment with ATRA and polyI:C results in strong, TLR3/MDA5-mediated chemokine and IFN responses in cultured human melanoma cells, which triggers a functional migratory response in professional antigen-presenting cells. This novel mode of concomitant activation may represent a more efficient treatment option for future melanoma therapy.
Dependence on glucose limitation of the pCO2 influences on CHO cell growth, metabolism and IgG production (2007)

The culture levels of glucose and CO(2) have been reported to independently have important influences on mammalian cell processes. In this work the combined effects of glucose limitation and CO(2) partial pressure (pCO(2)) on monoclonal antibody (IgG) producing Chinese Hamster Ovary cells were investigated in a perfusion reactor operated with controlled cell specific medium feed rate, pH and osmolality. Under high glucose conditions (14.3 +/- 0.8 mM), the apparent growth rate decreased (from 0.021 to 0.009 h(-1)) as the pCO(2) increased to approximately 220 mmHg, while the cell specific IgG productivity was almost unchanged. The lactate yield from glucose was not affected by pCO(2) up to approximately 220 mmHg and glucose was mainly converted to lactate. A feed medium modification from high (33 mM) to low (6 mM) glucose resulted in <0.1 mM glucose in the culture. As a result of apparently shifting metabolism towards the conversion of pyruvate to CO(2), both the ratio of lactate to glucose and the alanine production rate were lowered (1.51-1.14 and 17.7-0.56 nmol/10(6) cells h, respectively). Interestingly, when the pCO(2) was increased to approximately 140 mmHg, limiting glucose resulted in 1.7-fold higher growth rates, compared to high glucose conditions. However, at approximately 220 mmHg pCO(2) this beneficial effect of glucose limitation on these CHO cells was lost as the growth rate dropped dramatically to 0.008 h(-1) and the IgG productivity was lowered by 15% (P < 0.01) relative to the high glucose condition. The IgG galactosylation increased under glucose- limited compared to high-glucose conditions.
Atrial Natriuretic Peptides During Experimental Atrial Tachycardia: (2004)

Elevated levels of ANPs during chronic atrial tachycardia are related to a high ventricular rate rather than a high atrial rate alone. Rather than atrial tachycardia, the atrial hemodynamic burden is an important determinant of the sustained ANP response.
Caspase-dependent immunogenicity of doxorubicin-induced tumor cell death (2005)

Systemic anticancer chemotherapy is immunosuppressive and mostly induces nonimmunogenic tumor cell death. Here, we show that even in the absence of any adjuvant, tumor cells dying in response to anthracyclins can elicit an effective antitumor immune response that suppresses the growth of inoculated tumors or leads to the regression of established neoplasia. Although both antracyclins and mitomycin C induced apoptosis with caspase activation, only anthracyclin-induced immunogenic cell death was immunogenic. Caspase inhibition by Z-VAD-fmk or transfection with the baculovirus inhibitor p35 did not inhibit doxorubicin (DX)-induced cell death, yet suppressed the immunogenicity of dying tumor cells in several rodent models of neoplasia. Depletion of dendritic cells (DCs) or CD8+T cells abolished the immune response against DX-treated apoptotic tumor cells in vivo. Caspase inhibition suppressed the capacity of DX-killed cells to be phagocytosed by DCs, yet had no effect on their capacity to elicit DC maturation. Freshly excised tumors became immunogenic upon DX treatment in vitro, and intratumoral inoculation of DX could trigger the regression of established tumors in immunocompetent mice. These results delineate a procedure for the generation of cancer vaccines and the stimulation of anti-neoplastic immune responses in vivo.
High-k titanium silicate dielectric thin films grown by pulsed-laser deposition (2002)

We report the pulsed-laser deposition of high-k titanium silicate thin films. The titanium silicate films were deposited by laser ablating a (Ti, Si) target in an oxygen pressure of 70 mTorr. The deposited films were found to exhibit nanocrystalline structure with a grain size of about 3.5 nm as deduced from x-ray diffraction measurements. Fourier transform infrared spectroscopy confirmed the existence of Ti–O–Si bonds in the films. The binding energies of [Ti 2p3/2 (458.6 eV), Si 2p (102.3 eV), O 1s (531.8 eV)] as measured by means of x-ray photoelectron spectroscopy provided evidence of titanium silicate. On the other hand, the average dielectric constant of the pulse laser deposited titanium silicate thin films were found to be about 11 in the frequency range of 100 kHz to 13 MHz.
Real-time Visual Processing For Autonomous Driving (2005)

This paper describes a visual processing algorithm that supports autonomous road following. The algorithm requires that lane markings be present and attempts to track the lane markings on both lane boundaries. The algorithm has been used as part of a complete system to drive an autonomous vehicle, the High Mobility Multipurpose Wheeled Vehicle (HMMWV).
The Role of Adoptively Transferred CD8 T Cells and Host Cells in the Control of the Growth of the EG7 Thymoma: Factors That Determine the Relative Effectiveness and Homing Properties of Tc1 and Tc2 Effectors (2001)

We had previously examined the factors that regulate the response of OVA-specific TCR-transgenic CD8 T cells to the B16 OVA melanoma, growing as lung metastases. We examine here whether the same parameters operate for EG7, growing intradermally. Tc1 or Tc2 CD8 effector cells from OT-1 mice were injected either mixed with the tumor or i.v. at day 0 or 7. Tc2 were one-fifth to one-tenth as effective as Tc1 when injected with the tumor, in controlling tumor growth, but were only 1/20 to 1/100 injected i.v. Tc1 injected i.v. entered the draining lymph nodes faster than Tc2 and caused a faster accumulation of host cells. Both caused an abrupt termination of host cell entry into lymph nodes and spleen after tumor elimination, but this occurred earlier for Tc1 than for Tc2. Host responses were ineffective in the absence of adoptive transfer but were essential after transfer. Perforin expression in the donor cells plays no role in adoptively transferred Tc1 or Tc2 control of the tumor, and neither IL-4 nor IL5 is needed for Tc1 or Tc2 function. Tc1 cells from mice lacking IFN-gamma, however, control tumor growth less well, whereas Tc2 effectors lacking IFN-gamma are unaffected. Tc1 from IFN-gamma-deficient mice attract fewer host cells to the draining lymph node, whereas Tc1 cells from perforin-deficient donors are unimpaired. We conclude that host cell recruitment is a crucial element in adoptive immunotherapy. The differences between the EG7 and the previous B16 melanoma model are discussed.
Cloning and expression of a human CDC42 GTPase-activating protein reveals a functional SH3-binding domain. (1993)

CDC42, a member of the Rho family of small GTP-binding proteins, regulates cytoskeletal rearrangements required for cell division. Activating mutations in CDC42 that are refractory to GTPase activation confer a phenotype of large, multinucleated cells. Like other small GTP-binding proteins, CDC42 is activated by a guanosine exchange factor and inactivated by a GTPase-activating protein (GAP). An unidentified 25-kDa platelet protein has been shown to function as a specific CDC42GAP. Here we report the cloning of a cDNA encoding this GAP from a human platelet-precursor cell line. Sequence analysis reveals the presence of three consensus box regions characteristic of rhoGAPs. A glutathione S-transferase fusion protein containing the three boxes derived from the new clone strongly stimulated the GTPase activity of CDC42 but was much less effective on other Rho proteins. This indicates that the cDNA clone encodes a specific GAP for CDC42. Sequence analysis also reveals a potential proline-rich Src homology 3 (SH3)-binding domain preceding the first consensus box. Binding experiments show that this motif can interact with the SH3 domains of p85 alpha and of c-Src. Thus, CDC42GAP may function as a link between CDC42 and other signaling pathways.
Characterization of the Insulin-regulated Endocytic Recycling Mechanism in 3T3-L1 Adipocytes Using a Novel Reporter Molecule (2000)

The endocytic trafficking of the GLUT4 glucose transporter and the insulin-regulated aminopeptidase (IRAP) are regulated by insulin. We have used a chimera between the intracellular domain of IRAP and the extracellular and transmembrane domains of the transferrin receptor (vpTR) to characterize IRAP-like trafficking in 3T3-L1 adipocytes. Our data demonstrate that the cytoplasmic domain of IRAP is sufficient to target vpTR to the insulin-regulated, slow recycling pathway in adipocytes and that the dynamic retention of vpTR is dependent on a di-leucine motif. Our kinetic analysis demonstrates that vpTR recycles as a single kinetic pool and that vpTR is very efficiently sorted from endosomes to the insulin-regulated recycling pathway. An implication of these findings is that the key step in the dynamic retention of vpTR occurs within the early endosomal system. We have previously shown that vpTR is trafficked by an insulin-regulated pathway in Chinese hamster ovary cells (Johnson, A. O., Subtil, A., Petrush, R., Kobylarz, K., Keller, S., and Mc Graw, T. E. (1998) <i>J. Biol. Chem.</i> 273, 17968–17977). The behavior of vpTR in Chinese hamster ovary cells is similar to its behavior in 3T3-L1 adipocytes. The main difference is that insulin has a larger effect on the trafficking of vpTR in the adipocytes. We concluded that the insulin-regulated slow recycling endocytic mechanism is expressed in many different cell types and therefore is not a unique characteristic of cells that express GLUT4.
Electric Control of Droplets in Microfluidic Devices (2006)

Streamlining microreactors: Electric fields enable the precise manipulation of microreactors in microfluidic channels. One of the key features of such reactors is the ability to combine different chemicals at a precise location to initiate a chemical reaction (see picture).
The Army Research Laboratory ultra wideband BoomSAR (2005)

This paper describes a mobile radar testbed that provides airborne-like collection geometries. The radar is a low frequency, ultra-wideband, synthetic aperture radar intended to provide a resource for the analysis of foliage and ground penetration phenomenology.
HSP110-HER2/ neu Chaperone Complex Vaccine Induces Protective Immunity Against Spontaneous Mammary Tumors in HER-2/ neu Transgenic Mice (2003)

Heat shock proteins (HSPs) are shown to be strong immunoadjuvants, eliciting both innate and adaptive immune responses against cancers. HSP110 is related in sequence to HSP70 and is approximately 4-fold more efficient in binding to and stabilizing denatured protein substrates compared with HSP70. In the present study we evaluated the ability of a heat shock complex of HSP110 with the intracellular domain (ICD) of human HER-2/neu to elicit effective antitumor immune responses and to inhibit spontaneous mammary tumors in FVB-neu (FVBN202) transgenic mice. The HSP110-ICD complex was capable of breaking tolerance against the rat neu protein and inhibiting spontaneous mammary tumor development. This vaccine induced ICD-specific IFN-gamma and IL-4 production. Depletion studies revealed that CD8(+) T cells were involved in protection against challenge with mouse mammary tumors, whereas CD4(+) T cells revealed partial protection. Increased IgG2a Ab titer in the sera of tumor-free animals after vaccination and elevated CD4(+) CD25(+) regulatory T cells in the PBL of tumor-bearing animals suggested that IFN-gamma-producing Th1 cells may be responsible for partial protection of CD4(+) T cells against the mammary tumor challenge, whereas CD4(+)CD25(+) regulatory T cells (Th2 cells) may suppress the antitumor immune responses. Together, these results suggest that HSP110-ICD complex can elicit effective IFN-gamma-producing T cells against spontaneous mammary tumors and that up-regulation of CD4(+) CD25(+) regulatory T cells may prevent complete eradication of the tumor following immunotherapy.
Protection of rabbit retina from ischemic injury by flupirtine. (1996)

Combined data show that flupirtine is a neuroprotective agent in retinal ischemia and that one mode of its mechanism of action is to influence ATP levels. Flupirtine may lower the activity of NMDA receptors, thus causing ATP levels to be less affected in the presence of the drug as a secondary effect.
Clinicopathological correlation in exudative age related macular degeneration: histological differentiation between classic and occult choroidal neovascularisation (2000)

Classic choroidal neovascularisation in age related macular degeneration is predominantly composed of subretinal fibrovascular tissue while occult choroidal neovascularisation is composed of fibrovascular tissue at the choroidal side of the retinal pigment epithelium.
WRS-85D: A Tryptophanyl-tRNA Synthetase Expressed to High Levels in the DevelopingDrosophilaSalivary Gland (1999)

In a screen for genes expressed in the Drosophila embryonic salivary gland, we identified a tryptophanyl-tRNA synthetase gene that maps to cytological position 85D (WRS-85D). WRS-85D expression is dependent on the homeotic gene Sex combs reduced (Scr). In the absence of Scr function, WRS-85D expression is lost in the salivary gland primordia; conversely, ectopic expression of Scr results in expression of WRS-85D in new locations. Despite the fact that WRS-85D is a housekeeping gene essential for protein synthesis, we detected both WRS-85D mRNA and protein at elevated levels in the developing salivary gland. WRS-85D is required for embryonic survival; embryos lacking the maternal contribution were unrecoverable, whereas larvae lacking the zygotic component died during the third instar larval stage. We showed that recombinant WRS-85D protein specifically charges tRNATrp, and WRS-85D is likely to be the only tryptophanyl-tRNA synthetase gene in Drosophila. We characterized the expression patterns of all 20 aminoacyl-tRNA synthetases and found that of the four aminoacyl-tRNA synthetase genes expressed at elevated levels in the salivary gland primordia, WRS-85D is expressed at the highest level throughout embryogenesis. We also discuss the potential noncanonical activities of tryptophanyl-tRNA synthetase in immune response and regulation of cell growth.
<title>Video segmentation techniques for news</title> (1996)

This paper describes our experiences in video analysis for a video library on the World Wide Web. News and documentary programs, though seemingly simple, have some characteristics which can cause problems in simple shot segmentation algorithms. We have developed a methodology, based on our experience with the analysis of several hours of news/documentary footage, which improve the results of shot segmentation on this type of material and which in turn allows for higher-quality storyboards for our video library.
The clinical implications of glutathione S-transferase-pi expression in lung cancer (1997)

We performed immunohistochemical staining of glutathione S-transferase-pi (GST-pi) in 97 lung cancer specimens. In untreated patients, 86% (48/56) of NSCLC and none (0/8) of SCLC stained for GST-pi, and all squamous cell carcinomas were positive (28/28). The proportion of positive NSCLC with preoperative chemotherapy was similar to that of the untreated NSCLC, but the proportion of treated SCLC positive for GST-pi (14/18) was significantly higher than untreated tumors. GST-pi in NSCLC may be a tumor marker rather than being involved in drug resistance, and GST-pi-induction by chemotherapy may relate to acquired resistance in SCLC.
Os fármacos e a quiralidade: uma breve abordagem (1997)

<abstract language="eng">The concepts of stereochemistry and chirality are introduced, and the ability to distinguish among the different receptors caused by one stereoselective action against chiral drugs is presented. The importance of the behaviour of chiral drugs is emphasized.
Diagnosis of Multiple Scan Chain Faults (2005)

Abstract Precise isolation and resolution of scan chain defects are more critical than ever due to increased reliance on scan-based design to achieve desired test content. At the same time, its diagnosis is becoming more difficult as product design increases in complexity alongside shrinking fabrication processes. In this paper, we present a new scan chain diagnosis procedure that is centered on Load Pass Unload Fail/Load Fail Unload Pass (LPUF/LFUP) and Scan Shift Logic State Mapping (SSLSM) techniques to isolate both stuck-at and timing scan chain faults without the design overhead and defect assumptions of previously proposed methods. More importantly, this procedure is extended to analyze scan chain with multiple defects, which is becoming a more frequent occurrence as process scales down in size.
(1S,2R/1R,2S)-Aminocyclohexyl Glycyl Thymine PNA:  Synthesis, Monomer Crystal Structures, and DNA/RNA Hybridization Studies (2003)

[structure: see text] The synthesis of ethyl cis-(1S,2R/1R,2S)-2-aminocyclohex-1-yl-N-(thymin-1-yl-acetyl) glycinate (10a and 10b) via enzymatic resolution of the key racemic intermediate trans-2-azido cyclohexanols 3 is reported. The crystal structures of 10 show equatorial disposition of the tertiary amide group, with the torsion angle beta in the range 60-70 degrees. The PNA oligomers incorporating these show differential effects in hybridizing with complementary DNA and RNA.
Transverse flux machines with distributed windings for in-wheel applications (2009)

Transverse flux machine (TFM) useful for in-wheel motor applications is presented. This transverse flux permanent magnet motor is designed to achieve high torque-to-weight ratio and is suitable for direct-drive wheel applications. As in conventional TFM, the phases are located under each other, which will increase the axial length of the machine. The idea of this design is to reduce the axial length of TFM, by placing the windings around the stator and by shifting those from each other by electrically 120° or 90°, for three- or two-phase machine, respectively. Therefore, a remarkable reduction on the total axial length of the machine will be achieved while keeping the torque density high. This TFM is compared to another similar TFM, in which the three phases have been divided into two halves and placed opposite each other to ensure the mechanical balance and stability of the stator. The corresponding mechanical phase shifts between the phases have accordingly been taken into account. The motors are modelled in finite-element method (FEM) program, Flux3D, and designed to meet the specifications of an optimisation scheme, subject to certain constraints, such as construction dimensions, electric and magnetic loading. Based on this comparison study, many recommendations have been suggested to achieve optimum results.
[Peptide TAT modified polyethylenimine-beta-cyclodextrin for gene delivery]. (2009)

The novel vector TAT-PEI-beta-CyD has been developed successfully with low cytotoxicity and high transfection efficiency.
A plasmid vector for isolation of strong promoters in Escherichia coli (1999)

In order to isolate very strong promoters from bacteria and bacteriophage a plasmid named pProm was constructed. It possesses an origin (ORI) for replication in Gram-negative bacteria, an ORI for replication in Gram-positive bacteria, a promoterless ampicillin resistance gene with a multiple cloning site (MCS) in the position formerly occupied by the ampicillin promoter, a tetracycline resistance gene for selection in Gram-negative bacteria and a chloramphenicol resistance gene for selection in Gram-positive bacteria. Insertion in the MCS of DNA fragments of Staphylococcus aureus bacteriophages resulted in isolation of several clones very resistant to ampicillin. The DNA fragments inserted in these recombinant plasmids were sequenced and all of them contained putative promoter motifs. Direct measurement of the penicillinase activity indicated that one of the isolated promoters could be included within a group of the stronger known prokaryotic promoters. According to these results pProm is a powerful tool to perform studies on promoter strength and for industrial applications.