gebhart/patrepeval huggingface dataset:
Automatic segmentation of the spinal cord and the dural sac in lumbar MR images using gradient vector flow field (2010)

A Computer-aided diagnosis (CAD) system aims to facilitate characterization and quantification of abnormalities as well as minimize interpretation errors caused by tedious tasks of image screening and radiologic diagnosis. The system usually consists of segmentation, feature extraction and diagnosis, and segmentation significantly affects the diagnostic performance. In this paper, we propose an automatic segmentation method that extracts the spinal cord and the dural sac from T2-weighted sagittal magnetic resonance (MR) images of lumbar spine without the need of any human intervention. Our method utilizes a gradient vector flow (GVF) field to find the candidate blobs and performs a connected component analysis for the final segmentation. MR Images from fifty two subjects were employed for our experiments and the segmentation results were quantitatively compared against reference segmentation by two medical specialists in terms of a mutual overlap metric. The experimental results showed that, on average, our method achieved a similarity index of 0.7 with a standard deviation of 0.0571 that indicated a substantial agreement. We plan to apply this segmentation method to computer-aided diagnosis of many lumbar-related pathologies.
Insertion and amplification of foreign genes in the Lactococcus lactis subsp. lactis chromosome (1989)

The plasmid pE194 is unable to replicate in Lactococcus lactis subsp. lactis (formerly Streptococcus lactis). When linked to resident bacteriophage sequences, pE194 was able to integrate into the L. lactis subsp. lactis chromosome either by Campbell-like recombination or by double crossing over with deletion. Integration occurred into the DNA of the prophage and prevented its multiplication. When a selective pressure was applied to an integrant in which pE194 was flanked by two direct repeats of prophage fragment, amplification of pE194 and the prophage fragment was observed. The pE194 copy number was assessed at six to nine, and amplification was stable upon growth under nonselective conditions.
Sustained secretion of human alpha-1-antitrypsin from murine muscle transduced with adeno-associated virus vectors (1998)

Recombinant adeno-associated virus (AAV) vectors have been used to transduce murine skeletal muscle as a platform for secretion of therapeutic proteins. The utility of this approach for treating alpha-1-antitrypsin (AAT) deficiency was tested in murine myocytes in vitro and in vivo . AAV vectors expressing the human AAT gene from either the cytomegalovirus (CMV) promoter (AAV-C-AT) or the human elongation factor 1-α promoter (AAV-E-AT) were examined. In vitro in C2C12 murine myoblasts, the expression levels in transient transfections were similar between the two vectors. One month after transduction, however, the human elongation factor 1 promoter mediated 10-fold higher stable human AAT expression than the CMV promoter. In vivo transduction was performed by injecting doses of up to 1.4 × 10 13 particles into skeletal muscles of several mouse strains (C57BL/6, BALB/c, and SCID). In vivo , the CMV vector mediated higher levels of expression, with sustained serum levels over 800 μg/ml in SCID and over 400 μg/ml in C57BL/6 mice. These serum concentrations are 100,000-fold higher than those previously observed with AAV vectors in muscle and are at levels which would be therapeutic if achieved in humans. High level expression was delayed for several weeks but was sustained for over 15 wk. Immune responses were dependent upon the mouse strain and the vector dosage. These data suggest that recombinant AAV vector transduction of skeletal muscle could provide a means for replacing AAT or other essential serum proteins but that immune responses may be elicited under certain conditions.
Gold plating of silver nanoparticles for superior stability and preserved plasmonic and sensing properties (2013)

Gold-plated silver nanoparticles (Au@AgNPs, shell@core) with high stability in various environments detrimental to AgNPs have been produced with preserved plasmonic and sensing properties.
Fusion primer and nested integrated PCR (FPNI-PCR): a new high-efficiency strategy for rapid chromosome walking or flanking sequence cloning (2011)

The successful amplification of target products through FPNI-PCR verified that this novel strategy is an effective, low cost and simple procedure. Furthermore, FPNI-PCR represents a more sensitive, rapid and accurate technique than the established TAIL-PCR and hiTAIL-PCR procedures.
An experimental model comparing the antineoplastic and the immunosuppressive effects of some cytostatics. (1989)

An experimental model evaluating comparatively the antineoplastic and the immunosuppressive effects of some cytostatics (cyclophosphamide and vinblastine) is described in the present paper. Different cytostatic doses were intraperitoneally administered in mice which were 24 hours later grafted with a suspension of human tumoral KB cells. The xenograft acceptance was macroscopically and microscopically recorded 21 days later. By the Reed and Muench method and also by graphical extrapolation the LD50 (lethal dose for 50% animals) and the TD50 (the immunosuppressive dose enabling 50% animals to accept the xenografts) could thus be determined for both cyclophosphamide and vinblastine. The number (percent) of the tumour bearing animals three weeks after grafting was considered as an indicator of the cytostatic dose at which the immunosuppressive effect exceeded the antineoplastic effect. The in vitro effect of the same drugs on the KB cells was tested by inoculating different cytostatic doses in the cell cultures and counting at different time intervals the adherent as well as the nonadherent cells. The in vitro drug toxicity on the KB cell cultures was also determined by the trypan blue exclusion test. Both cyclophosphamide and vinblastine proved to be in vitro highly potent cytostatics i.e. when directly acting on the KB cells. This effect was dose correlated for both the considered drugs. However our in vivo experiments have shown that none of the observed effects when considering the direct action of the cytostatic on the cultured cells could not safely be extrapolated in vivo. Our results have an obvious practical importance when considering the therapeutical approaches in the neoplastic diseases. They demonstrate that the increase in cytostatic dose is not directly correlated to the antineoplastic effect since it reaches a limit at which the immunosuppressive effect highly exceed the tumour growth inhibition effect. The described experimental model could also be used in comparative estimations of the biological effects of different cytostatic drugs possibly referred to a standard immunosuppressive reagent as an antilymphocyte antiserum.
High-index-contrast Optical Waveguides on Silicon (2005)

Optical waveguides with a high refractive index contrast were fabricated on silicon‐on‐insulator (SOI) and polysilicon. The attenuation of 2dB/cm was achieved for SOI, and 11 dB/cm for hydrogenated polysilicon waveguides. Unlike in SOI waveguides, where the main contribution to attenuation is due to the surface scattering, a significant part of attenuation in polysilicon originates from absorption and scattering in the material.
A suppressor gene that enables Saccharomyces cerevisiae to grow without making sphingolipids encodes a protein that resembles an Escherichia coli fatty acyltransferase. (1993)

Saccharomyces cerevisiae normally requires sphingolipid biosynthesis for growth; however, mutant strains lacking sphingolipids have been isolated by suppression of a genetic defect in sphingolipid long chain base biosynthesis. To begin to understand the nature of the suppressor(s) we isolated and characterized a suppressor gene, SLC1 (sphingolipid compensation). DNA sequence analysis showed that the wild type SLC1 allele differs from the suppressor allele by a single nucleotide which changes Gln-44 in the predicted wild type protein to Leu4-4 in the predicted SLC1-1 suppressor protein. The predicted SLC1 protein sequence is homologous to the 1-acyl-sn-glycerol-3-phosphate acyltransferase of Escherichia coli encoded by the plsC gene. The homology extends to function as well since the SLC1 gene complements the growth defect in an E. coli strain mutated in plsC. These results suggest that the SLC1 protein has a fatty acyltransferase activity. SLC1 thus may be the first eucaryotic sn2-acylglyceride fatty acyltransferase gene to be cloned. SLC strains grown in the absence of long chain base make novel phosphatidylinositol derivatives (Lester, R. L., Wells, G. B., Oxford, G., and Dickson, R. C. (1993) J. Biol. Chem. 268, 845-856) having a C26 fatty acid at the sn-2 position and the same polar head groups as normal sphingolipids. We postulate that the SLC1 suppressor allele encodes a variant enzyme with an altered substrate specificity that enables it to use a C26 in place of a C16/18 fatty acid precursor to acylate the sn-2 position of inositol-containing glycerolipids.
Potent activity of 5-fluoro-2'-deoxyuridine and related compounds against thymidine kinase-deficient (TK-) herpes simplex virus: targeted at thymidylate synthase. (1987)

5-Fluorouracil, 5-fluorouridine (FUrd), 5-fluoro-2'-deoxyuridine (FdUrd), 5-fluorocytidine (FCyd), 5-fluoro-2'-deoxycytidine (FdCyd), 5-trifluoro-2'-deoxythymidine (F3dThd), and the 5'-monophosphates and 3',5'-cyclic monophosphates thereof were found to inhibit thymidine kinase-deficient (TK-) mutant strains of herpes simplex virus (HSV) at a much lower concentration than the wild-type (TK+) HSV strains. Other 5-substituted 2'-deoxyuridines that have previously been recognized as potent thymidylate synthase inhibitors behaved in a similar fashion. The activity of FdUrd, FdCyd, F3dThd, and their 3',5'-cyclic monophosphates against TK-HSV was readily reversed by 2'-deoxythymidine (dThd) but not by 2'-deoxyuridine (dUrd). These compounds also inhibited the incorporation of [6-3H]dUrd into DNA at a concentration which was up to 5 orders of magnitude lower than the concentration at which the incorporation of [methyl-3H] dThd was inhibited. Thus, while not being a target for the well established anti-HSV compounds in TK+HSV-infected cells, thymidylate synthase appears to be an important target in TK-HSV-infected cells. In addition to dTMP synthase, TK-HSV-infected cells appear to reveal other therapeutically exploitable targets such as OMP decarboxylase (towards pyrazofurin), CTP synthase (towards carbodine and its cyclopentenyl analogue), dihydrofolate reductase (towards methotrexate), and S-adenosylhomocysteine hydrolase (towards neplanocins).
Prevention of hepatic metastasis of human colon cancer by angiogenesis inhibitor TNP-470. (1995)

The antimetastatic effect of a potent angiogenesis inhibitor, O-(chloroacetyl-carbamoyl)fumagillol (TNP-470), was investigated in nude mice implanted with human colon cancer. Small pieces of tumors from three established human colon cancer cell lines (TK-3, TK-4, and TK-9), which were maintained in nude mice, were implanted into the cecal wall of nude mice via a small incision in the serosa. TNP-470 (20 or 30 mg/kg) was given s.c. every other day from day 10 after implantation, and the mice were sacrificed after 6 weeks. There was no difference in the weight of the implanted tumors (control group: 0.45 +/- 0.29 g versus treated group: 0.49 +/- 0.27 g). An antimetastatic effect of TNP-470 was clearly demonstrated in a dose-dependent manner. In the mice given 20 mg/kg TNP-470, liver metastasis developed in 3 of 10 cases. In the 30-mg/kg group, metastasis developed in only 1 of 17 mice, while it developed in 22 of 32 mice of the control group. The number of metastatic foci was significantly less in the treated groups. TNP-470 effectively prevented liver metastasis, however, but had no effect on the growth of the primary tumor. These results indicate that the angiogenesis inhibitor TNP-470 has a strong inhibitory activity against in vivo hepatic metastasis of human colon cancer.
Surface modification and characterization of microfabricated poly(carbonate) devices: manipulation of electroosmotic flow (2002)

Poly(carbonate), PC, surfaces are chemically modified by treatment with sulfur trioxide gas. Sulfur trioxide gas sulfonates the aromatic rings of the poly(carbonate) surfaces, making the surfaces more hydrophilic. Sulfonation of the poly(carbonate) surface is confirmed by infrared spectroscopy. The modified polymer surfaces are found to be smoother in comparison to their unmodified counterparts, as noted by scanning force microscopy. The effects of the surface modification on electroosmotic flow are studied at a pH range of 4-10. The electroosmotic flow in sulfonated poly(carbonate) microchannels was found to be significantly higher than that in unmodified poly(carbonate) microchannels at pH values below 8.
The Effect of Various Polymers and Salts on Borehole and Cutting Stability in Water-Base Shale Drilling Fluids (1986)

ABSTRACT Shale hydration tests have been carried out at confining pressures, ranging from 0 to 350 bar. The results show a high swelling pressure, without significant expansion, at high confining pressure and a large expansion without swelling pressure in the unconfined situation. It is also shown that different salts have different effects on swelling and that the effect of mud additives other than salts is negligible. The test results indicate that, for the shales tested, water structure modification and not ion exchange is principally responsible for the inhibitive effect of salts. In addition, borehole erosion and cutting disintegration tests have been carried out. The results of these tests show a significant effect of various polymeric mud additives in terms of cohesion.
Clinical outcome of preimplantation genetic diagnosis and screening using next generation sequencing (2014)

This study provides the first evaluation of the clinical outcomes of NGS-based pre-implantation genetic diagnosis/screening, and shows the reliability of this method in a clinical and array-based laboratory setting. NGS provides an accurate approach to detect embryonic imbalanced segmental rearrangements, to avoid the potential risks of false signals from SNP array in this study.
Release of both preformed and newly synthesized tumor necrosis factor alpha (TNF-alpha)/cachectin by mouse mast cells stimulated via the Fc epsilon RI. A mechanism for the sustained action of mast cell-derived TNF-alpha during IgE-dependent biological responses. (1991)

Mast cell-associated mediators are generally classified into two groups: the preformed mediators, which are stored in the cells' cytoplasmic granules and are released upon exocytosis, and the newly synthesized mediators, which are not stored but are produced and secreted only after appropriate stimulation of the cell. We now report that tumor necrosis factor alpha (TNF-alpha)/cachectin represents a new type of mast cell-associated mediator, in that IgE-dependent mast cell activation results in the rapid release of preformed stores of the cytokine followed by the synthesis and sustained release of large quantities of newly formed TNF-alpha. We also demonstrate that challenge with specific antigen induces higher levels of TNF-alpha mRNA at skin sites sensitized with IgE in normal mice or mast cell-reconstituted genetically mast cell-deficient WBB6F1-W/W1' mice than at identically treated sites in WBB6F1-W/W1' mice that are devoid of mast cells. These findings identify mast cells as a biologically significant source of TNF-alpha/cachectin during IgE-dependent responses and define a mechanism whereby stimulation of mast cells via the FC epsilon RI can account for both the rapid and sustained release of this cytokine.
GENETIC BEHAVIOR OF EUCHROMATIC SEGMENTS INSERTED INTO HETEROCHROMATIN (1940)

NE type of viable chromosomal rearrangement frequently induced 0 by X-ray treatment
Determination of cellular shape by the extracellular matrix and its correlation with the control of cellular growth. (1978)

Although the problem of cellular proliferation may seem at first glance to be tremendously complex, the mechanisms which control it may be extremely simple. One of the primary factors which regulates the mitogenic response of a given cell type to a given class of mitogenic agents seems to be the cellular shape. We have found that corneal epithelial cells, for example, adopt a flattened configuration when maintained in vitro on plastic and are very sensitive to fibroblast growth factor, but not to epidermal growth factor. When maintained on collagen, on the other hand, they become tall and columnar and respond primarily to epidermal growth factor. The cellular shape is dictated in vivo by the extracellular material upon which the cells rest and in vitro by the substrate upon which the cells are maintained. The substrate itself may, in turn, induce the cells to manufacture their extracellular material and specific cell surface proteins which control the cellular shape.
Defective retroviruses can disperse in the human genome by intracellular transposition (1991)

Using an assay for retrotransposition detection (T. Heidmann, O. Heidmann, and J. F. Nicolas, Proc. Natl. Acad. Sci. USA 85:2219-2223, 1988), we demonstrated that a defective retrovirus deleted for the gag, pol, and env open reading frames can disperse in the genome of human HeLa cells by intracellular transposition, at a frequency close to 10(-6) events per cell per generation. Transposition requires cooperation in trans for the gag and pol gene products and may be associated with the release of low amounts of noninfectious retroviruslike particles which are the hallmarks but not the intermediates of this transposition process. Similar events could account for the dispersion at high copy number of some of the human endogenous sequences related to retroviruses and for the occurrence of noninfectious retroviruslike particles in human placenta and several tumor cell lines (reviewed by E. Larsson, N. Kato, and M. Cohen, Curr. Top. Microbiol, Immunol, 148:115-132, 1989).
Correlations of lysyl oxidase with MMP2/MMP9 expression and its prognostic value in non-small cell lung cancer. (2014)

Lysyl oxidase (LOX) has been reported to regulate tumor metastasis and has been found to involve in modification of extracellular matrix (ECM) in the context of tumorigenesis. The aim of this study is to determine the prognostic significance of LOX in non-small cell lung cancer (NSCLC) patients and to examine the correlation between LOX expression and ECM remodeling-associated MMP2/MMP9 in NSCLC tissues. The mRNA expression of LOX, MMP2 and MMP9 was investigated by quantitative real-time reverse transcriptase-polymerase chain reaction (qRT-PCR) in 30 NSCLC patients. The protein expression of LOX was measured by immunohistochemistry (IHC) in 110 paraffin-embedded tissues with NSCLC and the protein expression of MMP2/MMP9 was measured by in 30 NSCLC patients. The correlation between LOX expression and clinical parameters and MMP2/MMP9 was analyzed by appropriate statistics. The Kaplan-Meier method, univariate and multivariate regression analysis was used to analyze the correlation between LOX expression and overall survival (OS). The relative mRNA expression or protein expression of LOX were significantly higher in NSCLC tumor tissues than in the corresponding noncancerous tissues (P < 0.05). High LOX expression was significantly associated with MMP2, MMP9, tumor size, lymph node metastasis, pathological stage and OS (P < 0.05). Univariate and multivariate analysis showed that LOX was an independent prognostic factor for OS. Our results indicate that LOX may play a role in the metastasis of NSCLC by promoting MMP2/MMP9 expression. LOX expression is an independent prognostic factor in OS in NSCLC.
The emerging roles of DNA methylation in the clinical management of prostate cancer (2006)

Aberrant DNA methylation is one of the hallmarks of carcinogenesis and has been recognized in cancer cells for more than 20 years. The role of DNA methylation in malignant transformation of the prostate has been intensely studied, from its contribution to the early stages of tumour development to the advanced stages of androgen independence. The most significant advances have involved the discovery of numerous targets such as GSTP1, Ras-association domain family 1A (RASSF1A) and retinoic acid receptor β2 (RARβ2) that become inactivated through promoter hypermethylation during the course of disease initiation and progression. This has provided the basis for translational research into methylation biomarkers for early detection and prognosis of prostate cancer. Investigations into the causes of these methylation events have yielded little definitive data. Aberrant hypomethylation and how it impacts upon prostate cancer has been less well studied. Herein we discuss the major developments in the fields of prostate cancer and DNA methylation, and how this epigenetic modification can be harnessed to address some of the key issues impeding the successful clinical management of prostate cancer.
Protection against Tetanus by Needle-Free Inoculation of Adenovirus-Vectored Nasal and Epicutaneous Vaccines (2001)

The effectiveness of vaccination programs would be enhanced greatly through the availability of vaccines that can be administered simply and, preferably, painlessly without the need for timed booster injections. Tetanus is a prime example of a disease that is readily preventable by vaccination but remains a major threat to public health due to the problems associated with administration of the present vaccine. Here we show that a protective immune response against live Clostridium tetani infection in mice can be elicited by an adenovirus vector encoding the tetanus toxin C fragment when administered as a nasal or epicutaneous vaccine. The results suggest that these vaccination modalities would be effective needle-free alternatives. This is the first demonstration that absorption of a small number of vectored vaccines into the skin following topical application of a patch can provide protection against live bacteria in a disease setting.
Diversity in the signals required for nuclear accumulation of U snRNPs and variety in the pathways of nuclear transport. (1991)

The requirements for nuclear targeting of a number of U snRNAs have been studied by analyzing the behavior of in vitro-generated transcripts after microinjection into the cytoplasm of Xenopus oocytes. Like the previously studied U1 snRNA, U2 snRNA is excluded from the nucleus when it does not have the 2,2,7mGpppN cap structure typical of the RNA polymerase II (pol II)-transcribed U snRNAs. Surprisingly, two other pol II-transcribed U snRNAs, U4 and U5, have a much less stringent requirement for the trimethyl cap structure. The gamma-monomethyl triphosphate cap structure of the RNA polymerase III-transcribed U6 snRNA, on the other hand, is shown not to play a role in nuclear targeting. Wheat germ agglutinin, which is known to prevent the import of many proteins into the nucleus, inhibits nuclear uptake of U6, but not of U1 or U5 snRNAs. Conversely, a 2,2,7mGpppG dinucleotide analogue of the trimethyl cap structure inhibits transport of the pol II U snRNAs, but does not detectably affect the transport of either U6 snRNA or a karyophilic protein. From these results it can be deduced that U6 enters the nucleus by a pathway similar or identical to that used by karyophilic proteins. The composite nuclear localization signals of the trimethyl cap-containing U snRNPs, however, do not function in the same way as previously defined nuclear targeting signals.
Stromal Cell-Derived Factor-1 Retention and Cardioprotection for Ischemic Myocardium (2011)

These results show that a single dose of protease-resistant SSDF-1(S4V) after myocardial infarction leads to dramatic improvement in angiogenesis and ventricular function even 3 hours after the onset of ischemia, revealing a simple, clinically feasible approach to prevention of heart failure.