gebhart/patrepeval huggingface dataset:
Serum total and free prostate-specific antigen for breast cancer diagnosis in women. (2000)

Prostate-specific antigen (PSA) is a serine protease expressed at high levels in prostate epithelium, and elevated PSA in serum is a well-established marker of prostate cancer. Recently, the relative proportions of free PSA and PSA complexed to the serine protease inhibitor alpha 1-antichymotrypsin have become important variables in distinguishing between prostate cancer and benign prostatic hyperplasia. Numerous studies have demonstrated the production of PSA in female tissues such as the breast, and low levels of PSA are present in female sera. The objective of this study was to measure and compare the relative proportions of free PSA and PSA complexed to the serine protease inhibitor alpha 1-antichymotrypsin in the serum of women with breast cancer or benign breast disease or women with no known malignancies. PSA was measured with an established immunoassay for total PSA and a novel immunoassay for free PSA, both of which had a detection limit of 0.001 microgram/liter (1 ng/liter). The percentage of breast cancer patients with free PSA as the predominant molecular form (> 50% of total PSA) in serum was five times higher than that of healthy women or women with benign breast disease, and PSA decreased in the serum of breast cancer patients after surgery. The diagnostic use of free PSA for breast cancer is limited at this point, due to the low diagnostic sensitivity (approximately 20%); however, free PSA as the predominant molecular form shows a high diagnostic specificity (approximately 96%) in comparison to women free of breast cancer or with benign breast disease. These results suggest that the clinical applicability of free PSA for breast cancer diagnosis and the biological mechanism behind its increase should be further investigated.
Genome-Wide Expression Patterns in Saccharomyces cerevisiae : Comparison of Drug Treatments and Genetic Alterations Affecting Biosynthesis of Ergosterol (2000)

Enzymes in the ergosterol-biosynthetic pathway are the targets of a number of antifungal agents including azoles, allylamines, and morpholines. In order to understand the response of Saccharomyces cerevisiae to perturbations in the ergosterol pathway, genome-wide transcript profiles following exposure to a number of antifungal agents targeting ergosterol biosynthesis (clotrimazole, fluconazole, itraconazole, ketoconazole, voriconazole, terbinafine, and amorolfine) were obtained. These profiles were compared to the transcript profiles of strains containing deletions of one of the late-stage ergosterol genes: ERG2, ERG5, or ERG6. A total of 234 genes were identified as responsive, including the majority of genes from the ergosterol pathway. Expression of several responsive genes, including ERG25, YER067W, and YNL300W, was also monitored by PCR over time following exposure to ketoconazole. The kinetics of transcriptional response support the conditions selected for the microarray experiment. In addition to ergosterol-biosynthetic genes, 36 mitochondrial genes and a number of other genes with roles related to ergosterol function were responsive, as were a number of genes responsive to oxidative stress. Transcriptional changes related to heme biosynthesis were observed in cells treated with chemical agents, suggesting an additional effect of exposure to these compounds. The expression profile in response to a novel imidazole, PNU-144248E, was also determined. The concordance of responsive genes suggests that this compound has the same mode of action as other azoles. Thus, genome-wide transcript profiles can be used to predict the mode of action of a chemical agent as well as to characterize expression changes in response to perturbation of a metabolic pathway.
Deuterium NMR of a pentylcyanobiphenyl liquid crystal confined in a silica aerogel matrix (1993)

The temperature dependence of the deuterium NMR line shape was studied in a pentylcyanobiphenyl (5CB) nematic liquid crystal embedded into lecithin-treated and nontreated continuous-pore silica aerogel matrices. In the lecithin-treated matrix the temperature dependence of the NMR absorption spectra of 5CB exhibits a pronounced first-order nematic-isotropic transition, while in the nontreated matrix only a weak discontinuity was found. The observed almost continuous onset of nematic ordering in the latter case appears to be due to the spread of nematic-isotropic-transition temperatures ${\mathit{T}}_{\mathit{N}\mathit{I}}$ in different aerogel cavities. In the isotropic phase of 5CB a surface ordering effect of the silica aerogel matrix was observed and the surface order parameter was estimated to be ${\mathit{S}}_{0}$=0.02\ifmmode\pm\else\textpm\fi{}0.01. The surface anchoring of the 5CB molecules is much stronger in the case of a nontreated matrix than in the lecithin-treated one.
Ebselen in Acute Middle Cerebral Artery Occlusion: A Placebo-Controlled, Double-Blind Clinical Trial (1999)

A randomized, double-blind, placebo-controlled trial of ebselen was conducted in patients with complete occlusion of the middle cerebral artery. Ebselen or placebo granules suspended in water (150 mg b.i.d. ) were orally administered within 12 h of onset and continued for 2 weeks. The major end points were the maximum volume of cerebral infarct measured on follow-up computed tomography and the Glasgow Outcome Scale score at 1 month. One hundred and five patients were enrolled in this trial. Although the intent-to-treat analysis of 99 patients (43 given ebselen and 56 given placebo) did not reach statistical significance in reduction of the infarct volume (p = 0. 099), the protocol-compatible analysis of 83 patients with complete occlusion of the middle cerebral artery (34 given ebselen and 49 given placebo) determined a significant reduction using ebselen treatment (p = 0.034). A good outcome was seen in approximately 15% more patients from the ebselen group, but the difference between the 2 groups was not significant (p = 0.129). There was a corresponding significant reduction in the volume of cerebral infarct and an improvement in the outcome of patients who started treatment within 6 h of onset. These findings may suggest that ebselen protected the brain from ischemic damage in the acute stage.
Neutralizing Antibodies to Adenylate Cyclase Toxin Promote Phagocytosis ofBordetella pertussisby Human Neutrophils (2000)

A previous study showed that opsonization with human immune serum could either promote or antagonize phagocytosis of Bordetella pertussis by human neutrophils depending on whether the bacteria expressed adenylate cyclase toxin. Opsonization of the wild-type strain inhibited phagocytosis relative to unopsonized controls. In contrast, mutants lacking adenylate cyclase toxin were efficiently phagocytosed when opsonized with human immune serum. In this study, we examined opsonization in the presence or absence of monoclonal antibodies to adenylate cyclase toxin. Addition of neutralizing monoclonal antibodies to adenylate cyclase toxin converted a serum that previously inhibited both attachment and phagocytosis of the wild-type strain to one that increased both attachment and phagocytosis compared to the no-serum control. Monoclonal antibodies that recognize the adenylate cyclase toxin but fail to neutralize activity were without effect. These results suggest that adenylate cyclase toxin inhibits both Fc receptor-mediated attachment and phagocytosis of B. pertussis by neutrophils.
1 alpha,25-Dihydroxyvitamin D3 and 1 alpha-hydroxyvitamin D3 prolong survival time of mice inoculated with myeloid leukemia cells. (1983)

Syngeneic SL mice inoculated with murine myeloid leukemia cells (M1) all died of leukemia within 30 days. Treatment three times a week with 12.5-50 pmol per mouse of either 1 alpha,25-dihydroxyvitamin D3 [1 alpha,25(OH)2D3], the active form of vitamin D3, or its synthetic analog, 1 alpha-hydroxyvitamin D3 [1 alpha(OH)D3], considerably prolonged the survival time of mice inoculated with M1 cells. 1 alpha(OH)D3 was more effective than 1 alpha,25(OH)2D3 in increasing the survival time of the mice. 1 alpha(OH)D3 also increased the survival time of nude mice inoculated with M1 cells. The 1 alpha(OH)[3H]D3 administered intraperitoneally to tumor-bearing mice was converted very rapidly to 1 alpha,25(OH)2-[3H]D3. The chronic administration of 25 pmol of 1 alpha(OH)D3 to tumor-bearing mice for 30 days caused no appreciable hypercalcemia. These results indicate clearly that 1 alpha,25(OH)2D3 is effective not only in inducing differentiation of M1 cells in vitro, as previously reported [Abe, E., Miyaura, C., Sakagami, H., Takeda, M., Konno, K., Yamazaki, T., Yoshiki, S. & Suda, T. (1981) Proc. Natl. Acad. Sci. USA 78, 4990-4994], but also in prolonging the survival time of mice inoculated with M1 cells.
Implementation of a Real-Time Human Movement Classifier Using a Triaxial Accelerometer for Ambulatory Monitoring (2006)

The real-time monitoring of human movement can provide valuable information regarding an individual's degree of functional ability and general level of activity. This paper presents the implementation of a real-time classification system for the types of human movement associated with the data acquired from a single, waist-mounted triaxial accelerometer unit. The major advance proposed by the system is to perform the vast majority of signal processing onboard the wearable unit using embedded intelligence. In this way, the system distinguishes between periods of activity and rest, recognizes the postural orientation of the wearer, detects events such as walking and falls, and provides an estimation of metabolic energy expenditure. A laboratory-based trial involving six subjects was undertaken, with results indicating an overall accuracy of 90.8% across a series of 12 tasks (283 tests) involving a variety of movements related to normal daily activities. Distinction between activity and rest was performed without error; recognition of postural orientation was carried out with 94.1% accuracy, classification of walking was achieved with less certainty (83.3% accuracy), and detection of possible falls was made with 95.6% accuracy. Results demonstrate the feasibility of implementing an accelerometry-based, real-time movement classifier using embedded intelligence.
An introduction to ultrathin organic films: from Langmuir-Blodgett to self-assembly (1991)

The development of oriented organic monomolecular layers by the Langmuir-Blodgett (LB) and self-assembly (SA) techniques has led researchers toward their goal of assembling individual molecules into highly ordered architectures. Thus the continually growing contribution of LB and SA systems to the chemistry and physics of thin organic films is widely recognized. Equally well-known is the difficulty in keeping up to date with the burgeoning multidisciplinary research in this area. Dr. Ulman provides a massive survey of the available literature. The book begins with a section on analytical tools
Protective effect of partially purified human urinary colony-stimulating factor on granulocytopenia after antitumor chemotherapy. (1986)

We conducted a randomized crossover study comparing the hemopoietic effect of partially purified human urinary colony-stimulating factor (CSF-HU, an active drug) and human serum albumin (HSA, a control drug) in 24 patients with malignant lymphoma, solid tumors, or multiple myeloma who were receiving two consecutive courses of the same chemotherapeutic regimen. Patients received daily 2-4 X 10(6) units of CSF-HU or an equal amount of protein HSA for five days after the end of the courses of chemotherapy. Assignment to CSF-HU or HSA was determined by the envelope method. The average number of blood granulocytes of 24 cases on day 7 after chemotherapy was 2116 +/- 1649 in CSF-HU-infused courses, which was significantly higher than in HSA-infused courses (1520 +/- 1022) (p less than 0.05). The average time that patients had fewer than 2000 granulocytes/mm3 was 7.6 +/- 4.4 days in CSF-HU-infused courses and 10.3 +/- 5.0 days in HSA-infused courses (p less than 0.02). Fever greater than 38 degrees C was the most frequent side effect, occurring in 32% of the patients receiving CSF-HU infusions. A reduction in the neutropenic interval in CSF-HU-infused courses was observed in patients with fever, as well as in those without fever. Infusions of CSF-HU did not change the number of other hematological parameters, such as erythrocytes, platelets, monocytes, and lymphocytes. These results suggest that CSF-HU infusions may partially protect the patients from granulocytopenia after anticancer chemotherapy.
Nerve growth factor (NGF) sensitizes human medullary thyroid carcinoma (hMTC) cells for cytostatic therapy in vitro. (1987)

Medullary thyroid carcinoma (hMTC) cells were established from nine patients with MTC disease to initiate a new approach of adjuvant medical therapy in these patients. We measured calcitonin (CT) secretion, DNA synthesis, and cell proliferation in vitro and their response to various substances. Nerve growth factor (NGF) (0.01 to 10 micrograms/ml), glucagon (0.01 to 100 micrograms/ml), and isoproterenol (4 to 500 micrograms/ml) stimulated CT secretion and DNA synthesis in hMTC cells. Other substances, calcium (1.0 to 15 mmol), pentagastrin (1.0 to 50 mumol), dibutyryl-cyclic-adenosine-monophosphate (1.0 to 100 mumol), and phorbol ester TPA (1.0 to 100 nmol), stimulated CT secretion but not DNA synthesis. In addition, NGF enhanced cell proliferation of hMTC cells 2- to 3- fold and caused an increased sensitivity of these cells for chemotherapy in vitro. Thus 0.5 microgram/ml doxorubicin (half-maximal effective dose) induced a cell death rate of up to 32.8%, which was enhanced by preincubation with NGF to 68.1% (1.0 microgram/ml, NGF) and to 100% (10.0 micrograms/ml, NGF), respectively. Pulsative stimulation of APUD cell carcinomas with NGF may therefore improve the response rate of these tumors to chemotherapy, which would be of significant clinical importance for patients with residual postoperative MTC tissue.
Skylight for Interior Lighting Design (1994)

Abstract It is inevitable for indoor lighting design to render a room lit by natural light, especially for an atelier or an indoor pool where there are many windows. This paper proposes a method for calculating the illuminance due to natural light, i.e. direct sunlight and skylight, passing through transparent planes such as window glass. The proposed method makes it possible to efficiently calculate such illuminance accurately, because it takes into account both non‐uniform luminous intensity distribution of skylight and the distribution of transparency of glass according to incident angles of light. Several examples including the lighting design in an indoor pool, are shown to demonstrate the usefulness of the proposed method.
A real-time digital speech processing system for an auditory prosthesis (2003)

A fully programmable digital speech-processing system for multichannel electrical stimulation of the cochlea is described. The system consists of laboratory testing station as well as a battery-powered portable processing unit, both of which use the Texas Instrument 320C25 signal processing chip. The laboratory station uses a Microvax II equipped with the TI signal-processing chip on a custom-built coprocessing board to combine the capability of real-time speech analysis and coding with the ability for real-time adaptation of processing algorithms to individual cochlear implant patients. The portable speech processor is a low-power (0.8-W) unit designed to run algorithms that were tested and customized with the laboratory station. An example application of the system is discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The physiological regulation of glucose flux into musclein vivo (2010)

Skeletal muscle glucose uptake increases dramatically in response to physical exercise. Moreover, skeletal muscle comprises the vast majority of insulin-sensitive tissue and is a site of dysregulation in the insulin-resistant state. The biochemical and histological composition of the muscle is well defined in a variety of species. However, the functional consequences of muscle biochemical and histological adaptations to physiological and pathophysiological conditions are not well understood. The physiological regulation of muscle glucose uptake is complex. Sites involved in the regulation of muscle glucose uptake are defined by a three-step process consisting of: (1) delivery of glucose to muscle, (2) transport of glucose into the muscle by GLUT4 and (3) phosphorylation of glucose within the muscle by a hexokinase (HK). Muscle blood flow, capillary recruitment and extracellular matrix characteristics determine glucose movement from the blood to the interstitium. Plasma membrane GLUT4 content determines glucose transport into the cell. Muscle HK activity, cellular HK compartmentalization and the concentration of the HK inhibitor glucose 6-phosphate determine the capacity to phosphorylate glucose. Phosphorylation of glucose is irreversible in muscle; therefore, with this reaction, glucose is trapped and the uptake process is complete. Emphasis has been placed on the role of the glucose transport step for glucose influx into muscle with the past assertion that membrane transport is rate limiting. More recent research definitively shows that the distributed control paradigm more accurately defines the regulation of muscle glucose uptake as each of the three steps that define this process are important sites of flux control.
Complex cellular and subcellular regulation of notch expression during embryonic and imaginal development of Drosophila: implications for notch function. (1991)

The Notch gene in Drosophila encodes a transmembrane protein with homology to EGF that appears to mediate cell-cell interactions necessary for proper epidermal vs. neural fate decisions. In this study, we examine Notch expression in detail throughout embryonic and imaginal development using confocal laser-scanning microscopy and specific mAb probes. We find that Notch is expressed in a tissue-specific manner as early as the cellular blastoderm stage, when cells of the presumptive mesoderm clearly express less Notch than adjacent ectodermal precursors. Notch is abundantly expressed during the initial determination of neuronal lineages, such as the embryonic neuroblasts and the precursors of sensory neurons in the imaginal disc epithelia, but expression quickly decreases during subsequent differentiation. These changing patterns of Notch expression do not correlate well with cell movements, and thus do not appear to support the notion that the major function of Notch is to maintain epithelial integrity via adhesive mechanisms. Our data suggest instead that Notch may act as a cell-surface receptor, perhaps functioning in the lateral inhibition mechanism that is necessary for proper spacing of neuronal precursors.
Serum vascular endothelial growth factor is often elevated in disseminated cancer. (1997)

In adults, marked angiogenesis takes place only during the female reproductive cycles, during wound healing, and accompanying some disease processes, such as tumor development. Vascular endothelial growth factor (VEGF) is a secreted, endothelial cell-specific growth factor, which is induced by tissue hypoxia and is angiogenic in vivo. We measured serum VEGF (S-VEGF) concentrations by ELISA in patients with a variety of types of cancer, as well as in healthy volunteers, and in patients with diabetes or rheumatoid arthritis. Elevated S-VEGF concentrations were found in patients with locoregional (n = 39; median, 158 pg/ml; range, 8-664 pg/ml) or disseminated (n = 58; median, 214 pg/ml; range, 17-1711 pg/ml) cancer in comparison to individuals without cancer (n = 113; median, 17 pg/ml; range, 1-177 pg/ml; P < 0.0001 for both comparisons). Values higher than 200 pg/ml were observed in 74% of patients with untreated metastatic cancer, and high serum levels were measured regardless of the histological type of cancer. S-VEGF levels were found to be higher in untreated patients with disseminated cancer than in those with local cancer (P = 0.006), and patients undergoing cancer therapy had lower values than those without cancer therapy (P = 0.03). The results indicate that both patients with locoregional cancer and patients with disseminated cancer may have elevated S-VEGF levels, regardless of the histological type of cancer, and that S-VEGF is often elevated in cancer with distant metastases.
Study of DNA Amplification Efficiency Based on Temperature Analyses of the Moving Fluid in a Liquid-Plug Flow PCR System (2011)

Abstract Flow-through PCR devices for performing rapid and small-volume DNA amplification on a single chip have attracted great interest. Flow-through DNA amplification was performed by moving PCR solution as a liquid plug through three individual temperature zones. Since precise control of the temperature setting is the most important technique for successful DNA amplification, real-time temperature analyses of the moving fluid were investigated using a polyolefin pressure-sensitive adhesive (PPSA) film to cover the microchannel. The temperature profile at 20 °C during annealing phase was the closest to the recommended conditions for PCR compared to the profile from 55 to 20 °C, and it showed the highest amplification of the tested regimes. The microchannel design was optimized using an infrared (IR) thermal imager to significantly increase the fluorescence intensity of the amplified products. A flow time of five to six seconds per cycle resulted in a temperature profile close to the recommended thermal gradient. These studies resulted in effective findings for simple and rapid amplification by moving a PCR solution as liquid-plug on a single chip.
Double-strand signal sequence breaks in V(D)J recombination are blunt, 5'-phosphorylated, RAG-dependent, and cell cycle regulated. (1993)

Immunoglobulin and T-cell receptor genes are assembled during lymphocyte development by a novel, highly regulated series of gene rearrangement reactions known as V(D)J recombination. All rearranging loci are flanked by conserved heptamer-nonamer recombination signal sequences. Gene rearrangement results in the imprecise fusion of coding sequences and the precise fusion of signal sequences. DNA molecules with double-stranded breaks near signal sequences have been detected in cells undergoing V(D)J recombination of the TCR delta locus. We have devised a ligation-mediated PCR assay that detects broken-ended molecules in purified genomic DNA. Using this assay we found that DNA breaks occurring precisely at the signal sequence-coding sequence junction are a general feature of V(D)J recombination, appearing in association with each type of rearranging immunoglobulin gene segment. We show that a significant fraction of these broken ends are blunt and 5'-phosphorylated. In addition, detection of these broken-ended signal sequences is dependent on the activity of RAG-1 and RAG-2, and is restricted to the G0/G1 phase of the cell cycle. The pattern of broken-ended molecules detected in cells at various stages of development reflects the activity of the V(D)J recombinase at different loci during B- and T-cell development.