gebhart/patrepeval huggingface dataset:
Overexpression, purification, sequence analysis, and characterization of the T4 bacteriophage dda DNA helicase. (1992)

The bacteriophage T4 dda protein is a 5'-3' DNA helicase that stimulates DNA replication and recombination reactions in vitro and seems to play a role in the initiation of T4 DNA replication in vivo. Oligonucleotide probes based on NH2-terminal amino acid sequence were used to precisely map the location of the dda gene on the T4 chromosome. Using polymerase chain reaction techniques, the dda gene was then cloned into an expression vector, and the overproduced protein was purified in two chromatography steps. Both the genomic and cloned dda genes were sequenced and found to be identical, encoding a protein of 439 amino acids. The dda protein contains amino acid sequences resembling those of other known helicases, and is most homologous to the Escherichia coli recD protein. Protein affinity chromatography was used to show a direct interaction between the dda protein and the T4 uvsX protein (a rec A-type DNA recombinase).
Curcumin inhibits tyrosine kinase activity of p185neu and also depletes p185neu. (1999)

Curcumin, a natural compound present in turmeric, possessing both anti-inflammatory and antioxidant effects, has been studied vigorously as a chemopreventative in several cancer models. The erbB2/neu gene-encoded p185neu tyrosine kinase is a potent oncoprotein. Overexpression of p185neu in breast cancer is known to be a poor prognostic factor. We investigated the effect of curcumin on p185neu tyrosine kinase and on the growth of breast cancer cell lines. Curcumin dose-dependently inhibited p185neu autophosphorylation and transphosphorylation in vitro and depleted p185neu protein in vivo. It dissociated the binding of p185neu with GRP94 (glucose-regulated protein), a molecular chaperone, and enhanced the depletion of p185neu. The amount of p185neu protein on the cell membrane was drastically decreased after curcumin treatment. These data demonstrated a new mechanism of the anti-tyrosine kinase activity of curcumin. The growth of several breast cancer cell lines was inhibited; the IC50 ranged from 7 to 18 microM, which, however, did not correlate with the expression level of p185neu. Colony formation in the soft agar assay, a hallmark of the transformation phenotype, was preferentially suppressed in p185neu-overexpressing cell lines by 5 microM curcumin (% of control, basal level versus overexpression: 59.3 versus 16.7%; P < 0.001 by Student's t test). Because curcumin effectively inhibited p185neu tyrosine kinase activity by depleting p185neu and potently suppressed the growth of multiple breast cancer cell lines, its therapeutic potential in advanced breast cancer is worthy of further investigation.
Development of a flexible and potent hypoxia-inducible promoter for tumor-targeted gene expression in attenuated salmonella (2006)

To increase the potential of attenuated Salmonella as gene delivery vectors for cancer treatment, we developed a hypoxia-inducible promoter system to limit gene expression specifically to the tumor. This approach is envisaged to not only increase tumor specificity, but also to target those cells that are most resistant to conventional therapies. We demonstrate that the exponential growth of the attenuated bacteria is identical under normoxia and hypoxia. A hypoxia-inducible promoter (HIP-1) was created from a portion of the endogenous Salmonella pepT promoter and was shown to drive reporter gene expression under both acute and chronic hypoxia, but not under normoxia. Genetic engineering of the TATA- and FNR-box within HIP-1 allowed fine-tuning of gene induction, resulting in hypoxic induction factors of up to 200-fold. Finally, we demonstrate that HIP-1 can drive hypoxia-mediated gene expression in bacteria which have colonized human tumor xenografts in mouse models. Expression of both GFP and RFP under control of HIP-1 demonstrated an approximately 15-fold increase relative to a constitutive promoter when tumors were made hypoxic. Moreover, the use of a constitutive promoter resulted in reporter gene expression in both tumors and normal tissues, whereas reporter gene expressing using HIP-1 was confined to the tumor.
Double-contrast CT arthrography of the cartilage of the patellofemoral joint. (1985)

For assessment of the value of computed tomography (CT) as a method for evaluating the cartilage of the patellofemoral joint, 100 knees were examined in 91 patients. With the patient in a supine position with the knee flexed at a 30 degree angle, a sufficient quantity of air and positive contrast material was required to obtain an accurate CT picture of the cartilage. Normal cartilage images of 53 knees and abnormal images of 47 knees were obtained by use of CT. The latter group was classified into eight types. When the CT findings of 70 knees were compared with arthroscopy and/or arthrotomy, the results showed that CT diagnosis was accurate in 68 of 70 knees, with a coincidence rate of 97.1%. Cartilage thickness at an arbitrary site and the extent of the ulcer within the deep layers were observed easily by CT. Although examination exclusively with arthroscopy had distinct disadvantages (e.g., the inability to assess either the specific thickness of the cartilage or the extent of the ulcers within deep layers), the combined use of arthroscopy with CT provided a precise three-dimensional image of the cartilage. CT was found to be a valuable noninvasive imaging method for patellofemoral joint cartilage evaluation.
High density lipoprotein plasma fractions inhibit aortic fatty streaks in cholesterol-fed rabbits. (1989)

The effects of in vivo administration of high density lipoprotein-very high density lipoprotein (HDL-VHDL) on the development of aortic fatty streaks were studied in cholesterol-fed rabbits. The rabbits received a 0.5% cholesterol-rich diet for 8 weeks. During this period, the HDL-VHDL group was intravenously administered with 50 mg/week of homologous HDL-VHDL protein; the control group received normal saline (0.9% NaCl). HDL-VHDL fraction was obtained at density range 1.063 to 1.25 gm/ml by ultracentrifugation of normal rabbit plasma. Along the study, plasma lipid levels followed a similar profile in both groups. At the completion of the study, atherosclerotic-like lipid-rich lesions covered 37.9 +/- 6% (X +/- SEM) of the intimal aortic surface in the control group, and 14.9 +/- 2.1% in the treated group (p less than 0.001). The values of total and free cholesterol, esterified cholesterol, and phospholipids deposited within vessel wall were significantly lower in the aortas of the HDL-VHDL treated group than those in the control group. Cholesterol accumulation in the livers was also significantly lower (p less than 0.01) in the treated group than in the control. We concluded that administration of homologous HDL-VHDL lipoprotein fraction to cholesterol-fed rabbits, dramatically inhibited the extent of aortic fatty streaks and lowered lipid deposition in the arterial wall and liver without modification of the plasma lipid levels.
Evaluation of the Inner‐Surface Morphology of an Artificial Heart by Acoustic Microscopy (2000)

The total artificial heart (TAH) is being developed for permanent replacement of the natural heart instead of heart transplantation. The need for detecting the material fatigue in the TAH is increasing in order to guarantee long-term use. In this study, the inner surface morphology of the TAH was evaluated by a specially developed scanning acoustic microscope (SAM) system operating in the frequency range of 100-200 MHz. The inner sac of our TAH consisted of polyvinylchloride coated with polyurethane, and the SAM investigations were performed before and after the implantations in goats. The amplitude images of the SAM demonstrated protein adhesion on the inner surface of the TAH after the animal experiment, and the phase images showed distortion of the wall with spatial resolution of 0.2 microm. These results suggest the feasibility of a high-frequency ultrasound for evaluating the material fatigue of TAH.
Ultrafast Mid-IR Laser Scalpel: Protein Signals of the Fundamental Limits to Minimally Invasive Surgery (2010)

Lasers have in principle the capability to cut at the level of a single cell, the fundamental limit to minimally invasive procedures and restructuring biological tissues. To date, this limit has not been achieved due to collateral damage on the macroscale that arises from thermal and shock wave induced collateral damage of surrounding tissue. Here, we report on a novel concept using a specifically designed Picosecond IR Laser (PIRL) that selectively energizes water molecules in the tissue to drive ablation or cutting process faster than thermal exchange of energy and shock wave propagation, without plasma formation or ionizing radiation effects. The targeted laser process imparts the least amount of energy in the remaining tissue without any of the deleterious photochemical or photothermal effects that accompanies other laser wavelengths and pulse parameters. Full thickness incisional and excisional wounds were generated in CD1 mice using the Picosecond IR Laser, a conventional surgical laser (DELight Er:YAG) or mechanical surgical tools. Transmission and scanning electron microscopy showed that the PIRL laser produced minimal tissue ablation with less damage of surrounding tissues than wounds formed using the other modalities. The width of scars formed by wounds made by the PIRL laser were half that of the scars produced using either a conventional surgical laser or a scalpel. Aniline blue staining showed higher levels of collagen in the early stage of the wounds produced using the PIRL laser, suggesting that these wounds mature faster. There were more viable cells extracted from skin using the PIRL laser, suggesting less cellular damage. β-catenin and TGF-β signalling, which are activated during the proliferative phase of wound healing, and whose level of activation correlates with the size of wounds was lower in wounds generated by the PIRL system. Wounds created with the PIRL systsem also showed a lower rate of cell proliferation. Direct comparison of wound healing responses to a conventional surgical laser, and standard mechanical instruments shows far less damage and near absence of scar formation by using PIRL laser. This new laser source appears to have achieved the long held promise of lasers in minimally invasive surgery.
Endoscopic Ablation Therapy for Barrett's Esophagus With High-Grade Dysplasia: A Review (1999)

Besides esophagectomy and antireflux therapy with intensive endoscopic surveillance, endoscopic ablation therapy is a new treatment modality for Barrett's esophagus (BE) with high-grade dysplasia (HGD). Endoscopic surgical ablation can be performed by either a thermal, chemical, or mechanical method. This article describes the current management of patients with BE and HGD and the various methods of endoscopic ablation, including multipolar electrocoagulation, argon plasma beam coagulation, contact laser photoablation, and photodynamic therapy. It also summarizes the results of 37 patient studies, case reports, and abstracts on experimental endoscopic therapies for BE. The advantages and disadvantages of the various treatment possibilities are considered, and the future direction of the management of BE is discussed.
Magnetic Tweezers-Based 3D Microchannel Electroporation for High-Throughput Gene Transfection in Living Cells (2014)

A novel high-throughput magnetic tweezers-based 3D microchannel electroporation system capable of transfecting 40 000 cells/cm(2) on a single chip for gene therapy, regenerative medicine, and intracellular detection of target mRNA for screening cellular heterogeneity is reported. A single cell or an ordered array of individual cells are remotely guided by programmable magnetic fields to poration sites with high (>90%) cell alignment efficiency to enable various transfection reagents to be delivered simultaneously into the cells. The present technique, in contrast to the conventional vacuum-based approach, is significantly gentler on the cellular membrane yielding >90% cell viability and, moreover, allows transfected cells to be transported for further analysis. Illustrating the versatility of the system, the GATA2 molecular beacon is delivered into leukemia cells to detect the regulation level of the GATA2 gene that is associated with the initiation of leukemia. The uniform delivery and a sharp contrast of fluorescence intensity between GATA2 positive and negative cells demonstrate key aspects of the platform for gene transfer, screening and detection of targeted intracellular markers in living cells.
Circulating Cell Adhesion Molecules and Death in Patients With Coronary Artery Disease (2001)

Soluble adhesion molecules sVCAM-1, sICAM-1, and sE-selectin were significantly related to future death from cardiovascular causes among patients with documented CAD. Especially sVCAM-1 added to the predictive value of classic risk factors and hs-CRP in determining the risk of future cardiovascular death.
Xenogeneic thyroid-stimulating hormone-like activity of the human natural anti-Gal antibody. Interaction of anti-Gal with porcine thyrocytes and with recombinant human thyroid-stimulating hormone receptors expressed on mouse cells. (1993)

Anti-Gal is a natural polyclonal antibody that constitutes 1% of circulating IgG in all humans and that interacts specifically with the mammalian carbohydrate epitope Gal alpha 1-3Gal beta 1-4GlcNAc-R (termed the alpha-galactosyl epitope). This epitope is abundant on thyrocytes, as well as, on other cells of nonprimate mammals, prosimians and New World monkeys, but its expression is diminished in Old World monkey, ape, and human tissues. We hypothesized that anti-Gal may bind in vitro to alpha-galactosyl epitopes on xenogeneic TSH receptors (TSHR) and mimic the effect of TSH on xenogeneic thyrocytes. Assays performed with porcine thyrocytes have indicated that anti-Gal can mimic in vitro TSH effects in stimulation for cAMP synthesis, 125I uptake, and cell proliferation. Furthermore, depletion of anti-Gal from serum of patients with Graves' disease resulted in elimination of a large proportion of the thyroid stimulating immunoglobulin activity and half of the thyroglobulin binding inhibiting Ig activity, when the sera were assayed with porcine thyrocytes. The effect of anti-Gal binding to alpha-galactosyl epitopes on TSHR was further demonstrated by the antibody-mediated stimulation for cAMP synthesis in mouse 3T3 cells (cells expressing alpha-galactosyl epitopes), which were transfected with recombinant human TSHR. CHO cells (cells lacking alpha-galactosyl epitopes), transfected with recombinant human TSHR were not stimulated by anti-Gal. It is, therefore, suggested that in studies on antibodies in Graves' disease sera, the effect of anti-Gal may be excluded by using target cells that are devoid of alpha-galactosyl epitopes. Alternatively, anti-Gal could be removed from the tested sera, before the assay with xenogeneic thyrocytes.
Site-specific glycosylation of human immunoglobulin G is altered in four rheumatoid arthritis patients (1996)

Alterations in the glycosylation of human IgG have been shown to occur in rheumatoid arthritis (RA). However, the precise nature and location of these changes have not been fully established. Therefore we carried out a detailed analysis of the oligosaccharides chemically released from intact human serum IgG and fragments of the molecule. Serum samples were from three healthy ('normal') individuals, and from four patients with RA. Site-specific glycolsylation of the glycoprotein was shown to occur, which extended to sites even within the Fab fragment. These were differences in galactosylation, sialylation and the presence of a bisecting N-acetylglucosomide. Disease related alterations were also shown to be site-specific. In particular, an increase in the proportion of agalactosylated oligosaccharides occurred on the Fc fragment in RA (P=0.057), but, in contrast to previous reports there was an increase on the light chain in the proportion of fully galactosylated, bisected and core fucosylated oligosaccharides (from 13% of total in normal to between 18 and 35% in RA, P=0.057)). There was also an Fab-specific increase in oligosaccharides bearing a bisecting N-acetylglucosamine and a core fucose (P=0.075) The site-specific glycosylation changes described in this paper reveal the complexity of the regulatory mechanism, perhaps reflecting the many levels at which regulation can occur.
MHC-Restricted Phosphopeptides from Insulin Receptor Substrate-2 and CDC25b Offer Broad-Based Immunotherapeutic Agents for Cancer (2014)

Cancer cells display novel phosphopeptides in association with MHC class I and II molecules. In this study, we evaluated two HLA-A2-restricted phosphopeptides derived from the insulin receptor substrate (IRS)-2 and the cell-cycle regulator CDC25b. These proteins are both broadly expressed in multiple malignancies and linked to cancer cell survival. Two phosphopeptides, termed pIRS-21097-1105 and pCDC25b38-46, served as targets of strong and specific CD8 T-cell memory responses in normal human donors. We cloned T-cell receptor (TCR) cDNAs from murine CD8 T-cell lines specific for either pIRS-21097-1105 or pCDC25b38-46. Expression of these TCRs in human CD8 T cells imparted high-avidity phosphopeptide-specific recognition and cytotoxic and cytokine-secreting effector activities. Using these cells, we found that endogenously processed pIRS-21097-1105 was presented on HLA-A2(+) melanomas and breast, ovarian, and colorectal carcinomas. Presentation was correlated with the level of the Ser(1100)-phosphorylated IRS-2 protein in metastatic melanoma tissues. The highest expression of this protein was evident on dividing malignant cells. Presentation of endogenously processed pCDC25b38-46 was narrower, but still evident on HLA-A2(+) melanoma, breast carcinoma, and lymphoblastoid cells. Notably, pIRS-21097-1105-specific and pCDC25b38-46-specific TCR-expressing human CD8 T cells markedly slowed tumor outgrowth in vivo. Our results define two new antigens that may be developed as immunotherapeutic agents for a broad range of HLA-A2(+) cancers.
Chemotherapy: friend or foe to cancer vaccines? (2001)

Cancer vaccines are on the threshold of taking their place alongside the more traditional cancer treatment modalities of surgery, radiation therapy and chemotherapy. The toxicology and immunopharmacology of therapeutic cancer vaccines, particularly those that secrete granulocyte macrophage colony stimulating factor (GM-CSF), are currently under active clinical investigation. Interestingly, drugs traditionally used for tumor cytoreduction can have both positive and negative effects on host immunity. Exploration of the potential pharmacodynamic interactions of antineoplastic drugs with GM-CSF-secreting vaccines has revealed that low doses of some chemotherapeutics can augment the antitumor immunity induced by GM-CSF-secreting vaccines. These interactions will require thorough preclinical evaluation to maximize the clinical impact of this type of therapeutic cancer vaccine.
A Novel Tetrameric PilZ Domain Structure from Xanthomonads (2011)

PilZ domain is one of the key receptors for the newly discovered secondary messenger molecule cyclic di-GMP (c-di-GMP). To date, several monomeric PilZ domain proteins have been identified. Some exhibit strong c-di-GMP binding activity, while others have barely detectable c-di-GMP binding activity and require an accessory protein such as FimX to indirectly respond to the c-di-GMP signal. We now report a novel tetrameric PilZ domain structure of XCC6012 from the plant pathogen Xanthomonas campestris pv. campestris (Xcc). It is one of the four PilZ domain proteins essential for Xcc pathogenicity. Although the monomer adopts a structure similar to those of the PilZ domains with very weak c-di-GMP binding activity, it is nevertheless interrupted in the middle by two extra long helices. Four XCC6012 proteins are thus self-assembled into a tetramer via the extra heptad repeat α3 helices to form a parallel four-stranded coiled-coil, which is further enclosed by two sets of inclined α2 and α4 helices. We further generated a series of XCC6012 variants and measured the unfolding temperatures and oligomeric states in order to investigate the nature of this novel tetramer. Discovery of this new PilZ domain architecture increases the complexity of c-di-GMP-mediated regulation.
Epithelial-to-Mesenchymal Transition and Integrin-Linked Kinase Mediate Sensitivity to Epidermal Growth Factor Receptor Inhibition in Human Hepatoma Cells (2008)

Hepatocellular carcinoma (HCC) is associated with a poor prognosis due to late diagnoses and a lack of effective treatment options. Epidermal growth factor receptor (EGFR)-targeted therapies have been effective in other cancers. However, erlotinib and cetuximab have shown only modest efficacy in clinical trials of HCC. We examined epithelial-to-mesenchymal transition (EMT) as a determinant of sensitivity of HCC to EGFR inhibitors. A panel of 12 human hepatoma cell lines were classified as epithelial or mesenchymal based on their expression of E-cadherin and vimentin. The resulting classification correlated with a previous microarray analysis of human hepatoma cell lines whereby the mesenchymal cell lines were shown to have increased expression of genes involved in metastasis and invasion. Sensitivity to erlotinib, gefitinib, and cetuximab was assessed and the epithelial cell lines were found to be significantly more susceptible to all three agents. Analysis of the EGFR pathway showed that EMT status was independent of EGFR expression or downstream extracellular signal-regulated kinase activation and only the epithelial cell lines expressed ErbB3. Interestingly, mesenchymal cells resistant to EGFR inhibitors had increased AKT and signal transducer and activator of transcription-3 activation through elevated expression of integrin-linked kinase (ILK). Mesenchymal cell lines were therefore experimentally transformed with kinase-inactive ILK (KI-ILK) with a resulting decrease in ILK activity and activation of AKT. KI-ILK transformants showed increased sensitivity to EGFR inhibitors both in vitro and in an in vivo xenograft model. These data suggest that EMT predicts HCC sensitivity to EGFR-targeted therapies and that ILK is a novel target to overcome HCC resistance to EGFR inhibition.
Packet-Dispersion Techniques and a Capacity-Estimation Methodology (2004)

The packet-pair technique aims to estimate the capacity of a path (bottleneck bandwidth) from the dispersion of two equal-sized probing packets sent back to back. It has been also argued that the dispersion of longer packet bursts (packet trains) can estimate the available bandwidth of a path. This paper examines such packet-pair and packet-train dispersion techniques in depth. We first demonstrate that, in general, packet-pair bandwidth measurements follow a multimodal distribution and explain the causes of multiple local modes. The path capacity is a local mode, often different than the global mode of this distribution. We illustrate the effects of network load, cross-traffic packet-size variability, and probing packet size on the bandwidth distribution of packet pairs. We then switch to the dispersion of long packet trains. The mean of the packet-train dispersion distribution corresponds to a bandwidth metric that we refer to as average dispersion rate (ADR). We show that the ADR is a lower bound of the capacity and an upper bound of the available bandwidth of a path. Putting all of the pieces together, we present a capacity-estimation methodology that has been implemented in a tool called pathrate. We report on our experiences with pathrate after having measured hundreds of Internet paths over the last three years.
Assessing the impact of a 2-day laparoscopic intestinal workshop (2011)

A comprehensive laparoscopic intestinal workshop contributed to the perceived acquisition of advanced laparoscopic surgical skills. Local laparoscopic preceptorship was an important adjunct to the workshop for the incorporation of laparoscopic colorectal surgery into practice.