gebhart/patrepeval huggingface dataset:
Breaking the Pumping Speed Barrier in Mass Spectrometry: Discontinuous Atmospheric Pressure Interface (2008)

The performance of mass spectrometers with limited pumping capacity is shown to be improved through use of a discontinuous atmospheric pressure interface (DAPI). A proof-of-concept DAPI interface was designed and characterized using a miniature rectilinear ion trap mass spectrometer. The interface consists of a simple capillary directly connecting the atmospheric pressure ion source to the vacuum mass analyzer region; it has no ion optical elements and no differential pumping stages. Gases carrying ionized analytes were pulsed into the mass analyzer for short periods at high flow rates rather than being continuously introduced at lower flow rates; this procedure maximized ion transfer. The use of DAPI provides a simple solution to the problem of coupling an atmospheric pressure ionization source to a miniature instrument with limited pumping capacity. Data were recorded using various atmospheric pressure ionization sources, including electrospray ionization (ESI), nano-ESI, atmospheric pressure chemical ionization (APCI), and desorption electrospray ionization (DESI) sources. The interface was opened briefly for ion introduction during each scan. With the use of the 18 W pumping system of the Mini 10, limits of detection in the low part-per-billion levels were achieved and unit resolution mass spectra were recorded.
A comparison of serum and breast duct fluid-immunoassayable prolactin and growth hormone with bioassayable lactogenic hormones in healthy women and patients with cystic breast disease (1987)

Serum and breast fluid obtained by nipple aspiration were collected from 46 healthy premenopausal women, and 36 patients with cystic breast disease and cyclical mastalgia of similar age. Serum prolactin and growth hormone levels determined by radioimmunoassay were similar in the two groups, but the patients showed a significant elevation in bioactive lactogenic hormones (prolactin plus growth hormone) as determined by the Nb2 rat lymphoma cell bioassay (P less than 0.001). The radioimmunoassayable prolactin levels in breast fluid were extremely variable; there was a trend towards higher concentrations in the cystic breast disease patients, but this just failed to achieve statistical significance (P = 0.06). Immunoreactive growth hormone was rarely detected in nipple aspirates obtained from either the patient or control groups. The mean breast fluid bioactive lactogenic hormone level was significantly higher in the cystic breast disease patients than in the normal controls (P less than 0.001); also ten of 46 (22%) controls, but only two of 36 (6%) patients had no detectable bioactivity. It is concluded that lactogenic hormone bioactivity, when assessed by the Nb2 cell assay, is indicative of an endocrine abnormality which is associated with benign breast disease, and is reflected in breast duct fluid, but is not identified by the conventional radioimmunoassays.
Video mail retrieval: the effect of word spotting accuracy on precision (2002)

The goal of the video mail retrieval project is to integrate state-of-the-art document retrieval methods with high accuracy word spotting to yield a robust and efficient retrieval system. This paper describes a preliminary study to determine the extent to which retrieval precision is affected by word spotting performance. It includes a description of the database design, the word spotting algorithm, and the information retrieval method used. Results are presented which show audio retrieval performance very close to that of text.
Ki67 immunoreactivity in breast carcinoma: relationships to prognostic variables and short term survival. (1992)

Immunoreactivity of the monoclonal antibody Ki67, which recognizes an antigen expressed in cells active in the cell cycle, has been investigated by immunocytochemistry in a series of 67 primary breast cancers. The percentage of tumour cell nuclei stained by Ki67 (labelling index) was related to tumour histological grade, mitotic frequency, oestrogen receptor status and tumour type. No correlation was found with patient age, tumour size or lymph node stage. A high Ki67 labelling index was significantly associated with diminished patient survival and disease-free interval, which demonstrates an important role for this monoclonal antibody as a prognostic marker in breast cancer.
Molecular cloning and characterization of N-syndecan, a novel transmembrane heparan sulfate proteoglycan (1992)

A cDNA clone coding for a membrane proteoglycan core protein was isolated from a neonatal rat Schwann cell cDNA library by screening with an oligonucleotide based on a conserved sequence in cDNAs coding for previously described proteoglycan core proteins. Primer extension and polymerase chain reaction amplification were used to obtain additional 5' protein coding sequences. The deduced amino acid sequence predicted a 353 amino acid polypeptide with a single membrane spanning segment and a 34 amino acid hydrophilic COOH-terminal cytoplasmic domain. The putative extracellular domain contains three potential glycosaminoglycan attachment sites, as well as a domain rich in Thr and Pro residues. Analysis of the cDNA and deduced amino acid sequences revealed a high degree of identity with the transmembrane and cytoplasmic domains of previously described proteoglycans but a unique extracellular domain sequence. On Northern blots the cDNA hybridized to a single 5.6-kb mRNA that was present in Schwann cells, neonatal rat brain, rat heart, and rat smooth muscle cells. A 16-kD protein fragment encoded by the cDNA was expressed in bacteria and used to immunize rabbits. The resulting antibodies reacted on immunoblots with the core protein of a detergent extracted heparan sulfate proteoglycan. The core protein had an apparent mass of 120 kD. When the anti-core protein antibodies were used to stain tissue sections immunoreactivity was present in peripheral nerve, newborn rat brain, heart, aorta, and other neonatal tissues. A ribonuclease protection assay was used to quantitate levels of the core protein mRNA. High levels were found in neonatal rat brain, heart, and Schwann cells. The mRNA was barely detectable in neonatal or adult liver, or adult brain.
Elevated expression of monocyte chemoattractant protein 1 by vascular smooth muscle cells in hypercholesterolemic primates. (1992)

Atherosclerosis is marked by an overt inflammatory infiltrate, with enhanced recruitment of monocytes/macrophages observed in both human and experimental atherosclerosis. We previously determined that monocyte chemoattractant protein 1 (MCP-1) accounts for virtually all of the chemotactic activity produced by vascular (aortic) smooth muscle cells in culture. We now report that arteries from a primate model of atherosclerosis with dietary-induced hypercholesterolemia exhibit increased levels of MCP-1 mRNA expression in vivo, whereas their normal counterparts demonstrate minimal MCP-1 expression. Furthermore, immunohistochemistry and in situ hybridization clearly indicate that the expression of MCP-1 protein and mRNA is in the smooth muscle cells of the medial layer of the artery and in monocyte-like and smooth muscle-like cells found in the overlying intimal lesion. These studies indicate that one of the responses to dietary hypercholesterolemia is the expression of MCP-1 by vascular smooth muscle cells. This expression, when augmented with other cellular and molecular factors, could significantly contribute to the recruitment of monocytes/macrophages to the vessel wall.
T Cell Receptor-Like Recognition of Tumor In Vivo by Synthetic Antibody Fragment (2012)

A major difficulty in treating cancer is the inability to differentiate between normal and tumor cells. The immune system differentiates tumor from normal cells by T cell receptor (TCR) binding of tumor-associated peptides bound to Major Histocompatibility Complex (pMHC) molecules. The peptides, derived from the tumor-specific proteins, are presented by MHC proteins, which then serve as cancer markers. The TCR is a difficult protein to use as a recombinant protein because of production issues and has poor affinity for pMHC; therefore, it is not a good choice for use as a tumor identifier outside of the immune system. We constructed a synthetic antibody-fragment (Fab) library in the phage-display format and isolated antibody-fragments that bind pMHC with high affinity and specificity. One Fab, fE75, recognizes our model cancer marker, the Human Epidermal growth factor Receptor 2 (HER2/neu) peptide, E75, bound to the MHC called Human Leukocyte Antigen-A2 (HLA-A2), with nanomolar affinity. The fE75 bound selectively to E75/HLA-A2 positive cancer cell lines in vitro. The fE75 Fab conjugated with (64)Cu selectively accumulated in E75/HLA-A2 positive tumors and not in E75/HLA-A2 negative tumors in an HLA-A2 transgenic mouse as probed using positron emission tomography/computed tomography (PET/CT) imaging. Considering that hundreds to thousands of different peptides bound to HLA-A2 are present on the surface of each cell, the fact that fE75 arrives at the tumor at all shows extraordinary specificity. These antibody fragments have great potential for diagnosis and targeted drug delivery in cancer.
Selective proliferation of normal human melanocytes in vitro in the presence of phorbol ester and cholera toxin. (1982)

Cultures consisting almost entirely of human melanocytes were obtained from epidermal single-cell suspensions by using phorbol 12-myristate 13-acetate (10 ng/ml) in the culture medium. At this concentration, phorbol ester is toxic to human keratinocytes but not to melanocytes. When the seeding density was optimal (0.8-2 x 10(4)/cm2) and the medium contained both phorbol ester and cholera toxin, melanocytes proliferated extensively. Under these conditions, human melanocytes could be passaged serially in vitro and grown in quantity. This cell culture system can thus be used to answer basic questions related to pigment cell biology and may serve as a control for studies of malignant melanocytes.
T-cell therapy of cytomegalovirus and human immunodeficiency virus infection (2000)

Acute and persistent virus infections are limited by the development and maintenance of host T-cell responses to viral antigens. Individuals with congenital or acquired immunodeficiencies are at risk of progressive and often life-threatening infection. Recent studies have provided insight into the nature of protective T-cell responses to viruses and advances in T-cell culture technology have made it possible to evaluate the adoptive transfer of T-cell clones of defined antigen specificity and function to restore deficient responses in immunocompromised hosts. The progress of these studies in cytomegalovirus and human immunodeficiency virus infection is the subject of this review.
Bordetella bronchiseptica dermonecrotizing toxin suppresses in vivo antibody responses in mice (1992)

The effects of Bordetella bronchiseptica dermonecrotic toxin (DNT) on the in vivo antibody response of mice were investigated. Intravenous injection of DNT at doses of 0.5 and 2.0 ng resulted in a significant suppression of the antibody response both to sheep red blood cells and to Escherichia coli lipopolysaccharide as measured by plaque-forming cell and hemagglutination assays. Spleen weights of mice given the same doses of DNT were significantly reduced, while the weights of thymuses and mesenteric lymph nodes were not. Numbers of Thy-1,2+ T lymphocytes, L3T4+ T lymphocytes, Lyt-2+ T lymphocytes and surface-immunoglobulin-positive lymphocytes decreased in spleens of the DNT-treated mice. Since the ratio of each lymphocyte population to the total number of splenic lymphocytes was not significantly different between the DNT-treated and non-treated mice, it is unlikely that DNT has a cytotoxic activity or a mitogen activity to some specific population of lymphocytes. Thus, we considered that the immunosuppression was attributable to a dysfunction of the spleen atrophied by the DNT.
Constant radial shearing interferometry with circular gratings (1989)

A radial shearing interferometer with two equispaced circular gratings is described for obtaining a constant radial displacement of the test wavefront. The procedure for the fringe analysis is shown by applying the Fourier transform method to the circular fringe pattern for precisely obtaining the differentiation of the test wavefront. A novel method is also shown for holographically making the equispaced circular gratings by using a cylindrical mirror and a collimating lens. It is shown that the deflection and misalignment of the gratings will not appear in the interferogram by using the holographic production method.
Structural features in eukaryotic mRNAs that modulate the initiation of translation. (1991)

In higher eukaryotes, translation is modulated at the level of initiation by five aspects of mRNA structure: (i) the m7G cap; (ii) the primary sequence or context surrounding the AUG codon; (iii) the position of the AUG codon, i.e. whether or not it s “first”; (iv) secondary structure both upstream and downstream from the AUG codon; and (v) leader length. Here I briefly discuss how experimental manipulation of these features affects the fidelity and/or efficiency of initiation. Elsewhere (1) I discuss the extent to which natural mRNA leader sequences conform to these experimentally determined requirements for initiation. Although my primary concern is to document the occurrence and consequences of the five structural elements in mRNAs, I will allude now and then to why each feature has the effect it does. The explanations will invariably hark back to the scanning process by which ribosomes are thought to initiate translation. In its simplest form, the scanning model (2) postulates that a 40 S ribosomal subunit, carrying MettRNA? and an imperfectly defined set of initiation factors (3), enters at the 5‘-end of the mRNA and migrates linearly until it reaches the first AUG codon, whereupon a 60 S ribosomal subunit joins and the first peptide bond is formed (Fig. 1). Evidence in support of the scanning model has been adduced previously (2, 4, 5). The most recent evidence includes the apparent queuing of 40 S ribosomal subunits on a long, unstructured leader sequence (6) and the demonstration that 40 S subunits stall on the 5’-side of a stable hairpin structure introduced between the cap and the AUG codon (7).
Spectral measurements of fluorescence emission in Caribbean cnidarians (1995)

Fluorescence effects in cnidarian host tissues have been investigated only sporadically and have largely been described qualitatively. In past studies specimens were selected for investigation based on their apparent fluorescence under either daylight or ultraviolet (UV-A or UV-B) illumination, thereby missing relationships between the 2 effects. In this study samples of a variety of Caribbean cnidarian species were selected based on their in situ responses to daylight and/or UV-A illumination. Fluorescence emission spectra (excitation wavelength 365 or 405 nm) were measured for sources in the host tissues. A sorting of specimens by similarity in spectral shape resulted in groupings containing members of different species. Emission spectra measured from separate specimens of a single species exhibited clear differences in some cases. There was no correlation between the spectral shape and the relative fluorescence intensity observed under illumination by ultraviolet light (UV-A, emission maximum = 360 nm). Emission maxima fell in the range of 480 to 590 nm. The only source of fluorescence at wavelengths greater than 650 nm was chlorophyll in zooxanthellae. Some specimens contained material with an emission spectrum identical to that of phycoerythrin (peak wavelength = 575 nm). The results are of interest for studies of photoecology and for applications of coral reef optical remote sensing
Identification and chromosomal mapping of new human tyrosine kinase genes. (1990)

To identify novel protein tyrosine kinase (PTK) genes expressed in human lymphoid cells, we have screened B- and T-cell cDNA libraries at low stringency using a c-fms tyrosine kinase domain probe. Three new PTK genes were identified, based on the presence of conserved amino acid sequence motifs characteristic of the catalytic domain of tyrosine kinases. Of these three genes, one (tyk1) appears to be the human homologue of a previously cloned murine gene (ltk), which has been reported to encode a tyrosine kinase with a unique structure; while the second gene, tyk2 cannot be clearly assigned to any of the known PTK subfamilies, and therefore may be the prototype of a new PTK gene subfamily. The third gene (tyk3/fer) has been very recently cloned by others; we present additional characterization in this report. We have performed Northern blots to establish the size of the mRNA encoded for by these genes, and to confirm their expression in lymphoid cells. Finally, we have determined the chromosomal location of all three genes by analyzing human-mouse somatic cell hybrids.
An antiresonant ring interferometer for coupled laser cavities, laser output coupling, mode locking, and cavity dumping (1973)

An antiresonant ring-mirror configuration, the optical analog of a microwave reentrant hybrid tee, is suggested for several potential laser applications including coupled laser cavities, variable laser output coupling, intracavity harmonic output coupling, mode locking, cavity dumping, and pulse code modulation.
Contraception in men: efficacy and immediate toxicity. A study of 18 cases. (1989)

Ten years ago research into a reversible method of male contraception proved unsuccessful, not for any objective reasons but because volunteers failed to comply with treatment. A change in social attitudes towards contraception, a constant demand for a reversible method of male contraception and the current interest in protecting germinal cell lines by blockage of spermatogenesis during chemotherapy led the authors to reactivate the study. Eighteen volunteers received a synthetic progestogen (Norluten) and a percutaneous testosterone gel. Clinical, biological, hormonal and seminal tests were performed each month. One patient, however, had to withdraw from the trial on medical grounds (hyperlipidaemia). Ten patients achieved azoospermia which is the only guarantee of efficacy. Immediate tolerance was good but protocol compliance was poor since 8 of the 17 volunteers abandoned the trial within a year. Treatment reversibility was evaluated in 15 patients whose F.S.H. level and spermatogenesis returned to normal when contraception was ended. This additional study demonstrates that hormone contraception in males is effective and well-tolerated, but the protocol placed too great a demand on the patients and 50% withdrew from the trial within a year.
Regrowth behavior of ion-implanted amorphous layers on 〈111〉 silicon (1976)

The regrowth of Si crystal from amorphous layers created by Si implantation into 〈111〉, 〈100〉, and 〈110〉 Si was studied. Channeling effect measurements show that the growths on the 〈110〉 and 〈100〉 substrates are epitaxial and linear with time. For the 〈111〉 samples the growth at 550 °C was significantly slower and nonlinear in time and the regrown layer contained a high concentration of defects. TEM micrographs indicate the presence of stacking faults and/or microtwins in the 〈111〉 samples.
Local overexpression of TIMP-1 prevents aortic aneurysm degeneration and rupture in a rat model. (1998)

Although matrix metalloproteinases (MMPs) are expressed in abundance in arterial aneurysms, their contribution to arterial wall degeneration, dilation, and rupture has not been determined. We investigated MMP function in a rat model of aneurysm associated with arterial dilation, elastin loss, medial invasion by mononuclear inflammatory cells, and MMP upregulation. Rupture was correlated with increased gelatinase B (MMP-9) and activated gelatinase A (MMP-2). Syngeneic rat smooth muscle cells retrovirally transfected with tissue inhibitor of matrix metalloproteinases (TIMP)-1 cDNA (LTSN) or with the vector alone as a control (LXSN) were seeded onto the luminal surface of the vessels. The seeding of LTSN cells resulted in TIMP-1 local overexpression. The seeding with LTSN cells, but not LXSN cells, decreased MMP-9, activated MMP-2 and 28-kD caseinase and elastase activity, preserved elastin in the media, and prevented aneurysmal degeneration and rupture. We conclude that MMP overexpression is responsible for aneurysmal degeneration and rupture in this rat model and that local pharmacological blockade might be a reasonable strategy for controlling the formation of aneurysms in humans.
Novel Approach for Improving the Productivity of Antibiotic-Producing Strains by Inducing Combined Resistant Mutations (2001)

We developed a novel approach for improving the production of antibiotic from Streptomyces coelicolor A3(2) by inducing combined drug-resistant mutations. Mutants with enhanced (1.6- to 3-fold-higher) actinorhodin production were detected at a high frequency (5 to 10%) among isolates resistant to streptomycin (Str(r)), gentamicin (Gen(r)), or rifampin (Rif(r)), which developed spontaneously on agar plates which contained one of the three drugs. Construction of double mutants (str gen and str rif) by introducing gentamicin or rifampin resistance into an str mutant resulted in further increased (1.7- to 2.5-fold-higher) actinorhodin productivity. Likewise, triple mutants (str gen rif) thus constructed were found to have an even greater ability for producing the antibiotic, eventually generating a mutant able to produce 48 times more actinorhodin than the wild-type strain. Analysis of str mutants revealed that a point mutation occurred within the rpsL gene, which encodes the ribosomal protein S12. rif mutants were found to have a point mutation in the rpoB gene, which encodes the beta-subunit of RNA polymerase. Mutation points in gen mutants still remain unknown. These single, double, and triple mutants displayed in hierarchical order a remarkable increase in the production of ActII-ORF4, a pathway-specific regulatory protein, as determined by Western blotting analysis. This reflects the same hierarchical order observed for the increase in actinorhodin production. The superior ability of the triple mutants was demonstrated by physiological analyses under various cultural conditions. We conclude that by inducing combined drug-resistant mutations we can continuously increase the production of antibiotic in a stepwise manner. This new breeding approach could be especially effective for initially improving the production of antibiotics from wild-type strains.
Mediation of Cardioprotection by Transforming Growth Factor-β (1990)

Myocardial ischemia causes heart injury that is characterized by an increase in circulating tumor necrosis factor (TNF), the local production of superoxide anions, the loss of coronary vasodilation (relaxation) in response to agents that release endothelial cell relaxation factor, and cardiac tissue damage. Ischemic injury can be mimicked by TNF. When given before or immediately after ischemic injury, transforming growth factor-beta (TGF-beta) reduced the amount of superoxide anions in the coronary circulation, maintained endothelial-dependent coronary relaxation, and reduced injury mediated by exogenous TNF. Thus, TGF-beta prevented severe cardiac injury, perhaps by alleviating damage mediated by increases in circulating TNF.