gebhart/patrepeval huggingface dataset:
The apoptosis inhibitor protein survivin induces tumor-specific CD8+ and CD4+ T cells in colorectal cancer patients. (2003)

The identification of tumor-associated antigens expressed by colorectal carcinoma remains one of the major goals for designing novel immunological treatments for this tumor. By using a reverse-immunology approach, we show here that the inhibitor of apoptosis protein, survivin, is immunogenic in colorectal cancer patients. In particular, we found that survivin elicited CD8(+) T cell-mediated responses in peripheral blood or in tumor-associated lymphocytes from patients at different disease stage. Colorectal carcinoma cells were recognized by survivin-specific T lymphocytes, and the survivin-specific, class-I HLA-restricted T lymphocytes were fully activated and released interleukin-2 in response to HLA/survivin-peptide complexes expressed by tumor cells. In addition to CD8-mediated responses, survivin specifically stimulated CD4+ T-cell reactivity in peripheral blood lymphocytes from the same patients, thus suggesting that a complete activation of the immune system may occur in response to this antiapoptotic protein. These findings indicate that survivin could be considered a valuable tumor-associated antigen for immune-based clinical approaches in colorectal cancer.
Acoustic streaming induced in focused Gaussian beams (1995)

Axisymmetric flow equations for a viscous incompressible fluid are transformed into the vorticity transport and Poisson’s equations. They are numerically solved via a finite difference method imposing appropriate initial and boundary conditions. A model source of 1-cm radius and 5-cm focal length with Gaussian amplitude distribution radiates 5-MHz ultrasound beams in water. Numerical examples are shown for buildup of acoustic streaming along and across the acoustic axis. Evidently, hydrodynamic nonlinearity has an essential effect on the streaming generation in comparison with a linear flow case; the nonlinearity reduces the streaming velocity in the focal and prefocal region, whereas it tends to accelerate the flow in the postfocal region.
Soft switching boost converter for photovoltaic power generation system (2008)

In this paper, a soft switching boost converter for solar power system is proposed. It is a topology, which raises efficiency for DC-DC converter of photovoltaic PCS (power conditioning system). And it minimizes switching losses by adopting soft switching method using resonance. It analyzes the operation characteristic of topology which was suggested through simulation, and proves the validity by analyzing loss and efficiency at real operation with experiment.
Surgical Correction of “Cam‐Type” Femoroacetabular Impingement: A Cadaveric Comparison of Open Versus Arthroscopic Debridement (2008)

Purpose The goal of this study was to compare open and arthroscopic surgical techniques for “cam‐type” femoroacetabular impingement in terms of feasibility and reliability. Methods We used 5 fresh‐frozen cadaver specimens (10 hips). Anteroposterior and cross‐table radiographs were taken for each. The head‐neck union diameter was measured for each. The amount of bone resection at the anterolateral quadrant of the head‐neck union was planned for each, with specific references to width, length, depth, and position. One side was randomly assigned to the open group and the other to the arthroscopic group. Surgical time, position of the osteotomy, and variation of the length, width, and depth of the final osteotomy with respect to the proposed dimensions were compared. Results In all specimens partial resection of the anterior‐lateral femoral head‐neck junction with improvement of the femoral head‐neck offset was accomplished. A statistically significant difference ( P &lt; .05) was observed for surgical time between the open and arthroscopic groups (shorter in open group). Conclusions When comparing surgical precision, no statistically significant differences were found between the open and arthroscopic procedures in any of the measurements. The depth and width of the osteoplasty were reliably obtained by the arthroscopic technique. However, there was a tendency to underestimate the osteoplasty length with the arthroscopic procedure. Positioning the osteoplasty was also less reliable with the arthroscopic procedure than with the open procedure because of the tendency to place the osteoplasty more posterior and distally than intended. Clinical Relevance Surgical resection of the femoral neck prominence and/or part of the anterolateral neck has been reported to improve femoral head offset and alleviate impingement. This study attempts to document the accuracy of this resection when done arthroscopically compared with an open procedure.
Large‐scale propagation of a replication‐defective adenovirus vector in stirred‐tank bioreactor PER.C6™ cell culture under sparging conditions (2003)

Large-scale propagation of replication-defective adenovirus vectors has not been well studied to date. One of the challenges for efficient propagation at large scale is to overcome the sensitivity of virus infected cells to gas sparging required for oxygenation and CO(2) removal. In our initial experiments, it was observed that productivity of an adenovirus vector was significantly reduced under sparging conditions as compared to nonsparged, i.e., surface-aerated controls in serum-free cultures. Investigations led to the identification of a buffer containing surfactant (Polysorbate-80, PS-80) that was included in the virus seed stock formulation and introduced through virus infection into the culture at a very low concentration as the cause of the reduced virus productivity. This finding was not obvious and trivial, as neither uninfected sparged nor infected nonsparged PER.C6 trade mark cells in serum-free cultures were affected by the buffer at such a low PS-80 concentration of 0.00025% (v/v), which is a common component of serum-free cell culture media. These results strongly suggest that virus-infected cells behave very differently from uninfected cells under sparging conditions. To mitigate the deleterious effects of sparging, the virus seed stock was prepared in the absence of the buffer containing PS-80. At the same time, the concentration of Pluronic-F68 (PF-68) in the serum-free medium was increased to 1 g/L, at which cell growth and metabolism were unaffected, even though this measure alone did not result in virus productivity improvement. Only by implementing the two measures together was virus productivity loss completely eliminated under sparging conditions. After demonstration of the process robustness in 2-L bioreactors, this adenovirus propagation process was successfully scaled up to 250 L in a 300-L bioreactor under the worst-case sparging conditions projected for 10,000-L scale.
Designing Transmembrane α-Helices That Insert Spontaneously (2000)

Direct measurement of the free energies of transfer of hydrophobic membrane-spanning alpha-helices from water to membranes is important for the determination of an accurate experiment-based hydrophobicity scale for membrane proteins. An important objective of such a scale is to account for the presently unknown thermodynamic cost of partitioning hydrogen-bonded peptide bonds into the membrane hydrocarbon core. We describe here the physical properties of a transmembrane (TM) peptide, TMX-1, designed to test the feasibility of engineering peptides that spontaneously insert across bilayers but that have the important property of measurable monomeric water solubility. TMX-1, Ac-WNALAAVAAAL-AAVAAALAAVAAGKSKSKS-NH(2), is a 31-residue sequence with a 21-residue nonpolar core, N- and C-caps to favor helix formation, and a highly polar C-terminus to improve solubility and to control directionality of insertion into lipid vesicles. TMX-1 appeared to be soluble in water up to a concentration of at least 1 mg/mL (0.3 mM). However, fluorescence spectroscopy, fluorescence quenching, and circular dichroism (CD) spectroscopy indicated that the high solubility was due to the formation of molecular aggregates that persisted at peptide concentrations down to at least 0.1 microM peptide. Nevertheless, aqueous TMX-1 partitioned strongly into membrane vesicles with apparent mole-fraction free-energy values of -7.1 kcal mol(-1) for phosphatidylcholine (POPC) vesicles and -8.2 kcal mol(-1) for phosphatidylglycerol (POPG) vesicles. CD spectroscopy of TMX-1 in oriented multilayers formed from either lipid disclosed a very strong preference for a transmembrane alpha-helical conformation. When TMX-1 was added to preformed vesicles, it was fully helical. A novel fluorescence resonance energy transfer (FRET) method demonstrated that at least 50% of the TMX-1 insered spontaneously across the vesicle membranes. Binding and insertion were found to be fully reversible for POPC vesicles but not POPG vesicles. TMX-1 was thus found to have many of the properties required for thermodynamic measurements of TM peptide insertion. Importantly, the results obtained delineate the experimental problems that must be considered in the design of peptides that can partition spontaneously and reversibly as monomers into and across membranes. Our success with TMX-1 suggests that these problems are not insurmountable.
Coordination of nuclear and cytoplasmic oocyte maturation in eutherian mammals (1996)

As oocytes near the end of their growth phase, they become competent to undergo two aspects of maturation, cytoplasmic and nuclear. Both are essential for the formation of an egg having the capacity for fertilization and development to live offspring. Nuclear maturation encompasses the processes reversing meiotic arrest at prophase I and driving the progression of meiosis to metaphase II. Cytoplasmic maturation refers to the processes that prepare the egg for activation and preimplantation development. This review focuses on the developmental programmes whereby oocytes at the germinal vesicle (GV) stage acquire competence to undergo nuclear and cytoplasmic maturation, the coordination of programmes regulating the acquisition of these competencies in GV-stage oocytes, and the coordination of the maturational processes themselves. Although the developmental programme of the GV-stage oocyte for acquiring competence to complete preimplantation development does not appear to be tightly linked to the acquisition of competence to complete nuclear maturation, GV breakdown (GVB) is probably essential for activating some critical aspects of cytoplasmic maturation, particularly those related to fertilization and activation. Nuclear and cytoplasmic maturation are normally coordinated by this mechanism requiring the mixing of the GV contents with the cytoplasm at the time of GVB, but some processes of cytoplasmic maturation related to successful preimplantation development probably still occur without coordination with nuclear maturation. Thus, continued differentiation of GV-stage oocytes is necessary after the acquisition of competence to undergo nuclear maturation, to allow for the deposition of the maternal factors required for the development of preimplantation embryos beyond the 2-cell stage.
Structural Basis of BFL-1 for Its Interaction with BAX and Its Anti-apoptotic Action in Mammalian and Yeast Cells (2000)

BFL-1 is the smallest member of the BCL-2 family and has been shown to retard apoptosis in various cell lines. However, the structural basis for its function remains unclear. Molecular modeling showed that BFL-1 could have a similar core structure as BCL-xL, consisting of seven alpha helices, although both proteins share only the conserved BCL-2 homology domains (BH1 and BH2 domains), but otherwise have very limited sequence homology, particularly in the N-terminal region. We demonstrated in the yeast two-hybrid system that BFL-1 interacts strongly with human BAX but is not able to form homodimers nor to interact with human BCL-2 or BCL-xL. Overexpression experiments in REF52 rat fibroblasts showed that BFL-1 conferred increased resistance to apoptosis induced by serum deprivation. BFL-1 had also the ability to neutralize BAX lethality in yeast. BAX requires the BH3 domain for interaction with BFL-1. However, the minimal region of BFL-1 for the interaction with BAX in coimmunoprecipitation experiments was not sufficient to protect cells from apoptosis. Further examination of BFL-1 and several other anti-apoptotic proteins suggests a more general type of structure based on structural motifs, i.e. a hydrophobic pocket for the binding of proapoptotic proteins, rather than extended sequence homologies.
Ultrathin Direct Atomic Layer Deposition on Composite Electrodes for Highly Durable and Safe Li‐Ion Batteries (2010)

Direct atomic layer deposition (ALD) on composite electrodes leads to ultrathin conformal protective coatings without disrupting inter-particle electronic pathways. Al2O3-coated natural graphite (NG) electrodes obtained by direct ALD on the as-formed electrode show exceptionally durable capacity retention even at an elevated temperature of 50 °C. In sharp contrast, ALD on powder results in poorer cycle retention than bare NG. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Clinical study on electro-acupuncture treatment for 30 cases of mental depression. (2004)

Electro-acupuncture, therapy can produce the same clinical therapeutic effect as that produced by the tetracyclic drug maprotiline, giving less side effect and better symptomatic improvement.
HER-2/neu Evaluation in Breast Cancer (2004)

The HER-2/neu oncogene is located on chromosome 17q and encodes a transmembrane glycoprotein with intracellular tyrosine kinase activity. Several studies have shown an association of HER-2 gene amplification or protein overexpression with prognosis and predictor of therapeutic response. Most important, the presence of amplification or overexpression is the basis of eligibility for trastuzumab therapy. However, there are several methods of determining HER-2 status, each measuring a different aspect such as DNA content, gene copy number, protein expression, expression of RNA, and circulating HER-2 extracellular domain protein. There is no consensus with regard to the optimal test for HER-2 assessment. This review examines the various methods used in an attempt to define the most accurate and reliable test. The most widely used assays are immunohistochemical analysis and fluorescence in situ hybridization (FISH), which measure protein expression and gene amplification, respectively. Based on current data, FISH is the most accurate and reproducible test with a better correlation with prognosis and response to therapy.
Activity of TER286 against human tumor colonyforming units (1997)

Glutathione S-transferase (GST) isozymes have been shown to be elevated in many human cancer types as compared to normal tissues. TER286, one in a class of glutathione-based GST-activated cytotoxins, was tested in a soft agar cloning assay to determine its in vitro activity against primary human tumor colony-forming units. Breast and lung specimens from patients who had received prior therapy and those who were previously untreated were exposed to TER286 at concentrations of 1, 10 and 50 microM using both 1 h and continuous exposures. Overall in vitro responses (50% or less survival compared to untreated controls) were observed in 0% (0/14), 14% (2/14) and 29% (4/14), respectively, in specimens exposed to TER286 for 1 h, and in 5% (2/41), 10% (4/41) and 61% (25/41), respectively, in specimens exposed to TER286 continuously. TER286 has cytotoxic activity against both breast and lung cancer colony-forming units, and demonstrates a concentration-response effect. At 50 microM, there is a significant difference between 1 h and continuous exposures in head-to-head comparisons. These data suggest that TER286 can be activated in human tumor colony-forming units and should be pursued as a treatment candidate for patients whose tumors are resistant to drug treatment based on up-regulation of GST.
Pharyngeal suspension suture with Repose bone screw for obstructive sleep apnea (2000)

OBJECTIVE Multilevel surgery for obstructive sleep apnea syndrome (OSA) may improve success. This study's goal is to prospectively evaluate the feasibility and short‐term subjective effectiveness of a new tongue‐suspension technique. METHODS A multicenter nonrandomized open enrollment trial used the Repose device to treat tongue obstruction in 39 snoring and OSA patients. Outcomes include 1‐ and 2‐month subjective reports of general health, snoring, and sleep. RESULTS Twenty‐three patients completed 1 month and 19 completed 2 months of follow‐up. In OSA patients, activity level, energy/fatigue, and sleepiness improved. Two‐month outcomes were less (activity level, energy/fatigue, and sleepiness). Fewer changes were observed in snorers than in OSA patients. There were 6 complications (18%), including sialadenitis (4), gastrointestinal bleeding (1), and dehydration (1) after the procedure. CONCLUSION A pharyngeal suspension suture changes subjective outcomes. Improvement is incomplete. The procedure is nonexcisional, but significant complications may occur. Further evaluation is required to demonstrate effectiveness.
Expandable cylindrical cages in the cervical spine: a review of 22 cases (2006)

The preliminary results support the use of ECCs in the cervical spine in the treatment of patients with various disease processes. No significant subsidence was noted, and pain and functional scores improved in all cases. Expandable cylindrical cages appear to be well suited for cervical reconstruction and for correcting sagittal malalignment.
Growth hormone insensitivity syndromes: a preliminary report on changes in insulin‐like growth factors and their binding proteins during treatment with recombinant insulin‐like growth factor I (1993)

Serum levels of insulin-like growth factor (IGF) binding proteins (IGFBPs) 1, 2 and 3 were studied by radioimmunoassay in 29 patients with growth hormone (GH) insensitivity syndromes (GHIS) before and during treatment with IGF-I. As in normal subjects, there was a highly significant correlation between IGFs and IGFBP-3 but not between IGFs and the other binding proteins, though IGFBP-3 represented only about one-third of the total IGFBP concentration. In 6 patients with GH deficiency and in 5 patients with GHIS, the pharmacokinetic profile of IGF-I after a single injection was strongly dependent on the IGFBP-3 concentration. A slight but significant increase in IGFBP-3 was observed coincident with the IGF-I peak, whereas IGFBP-2 increased after a delay of about 10 hours. In the patients with GHIS, chronic IGF-I treatment, with twice-daily injections for 6 months, caused a significant steady decline of IGF-II and an increase in IGFBP-2, but had no effect on IGFBP-1 and IGFBP-3 levels. During IGF-I treatment, an inverse relationship between baseline IGF-I and GH levels was observed. The data suggest that total IGF-I and IGF-II serum levels are determined mainly by IGFBP-3, even in extreme situations such as GHIS, while other IGFBPs are less important. The IGFBP-3 concentration seems to be a major regulator of the pharmacokinetics of exogenous IGF-I, which, in turn, influences IGFBP-3 levels. This effect of IGF-I on IGFBP-3 is not through induction of IGFBP-3 synthesis, but possibly by reduction of IGFBP-3 clearance.(ABSTRACT TRUNCATED AT 250 WORDS)
Dietary nitrate supplementation reduces the O2cost of low-intensity exercise and enhances tolerance to high-intensity exercise in humans (2009)

Pharmacological sodium nitrate supplementation has been reported to reduce the O2 cost of submaximal exercise in humans. In this study, we hypothesized that dietary supplementation with inorganic nitrate in the form of beetroot juice (BR) would reduce the O2 cost of submaximal exercise and enhance the tolerance to high-intensity exercise. In a double-blind, placebo (PL)-controlled, crossover study, eight men (aged 19-38 yr) consumed 500 ml/day of either BR (containing 11.2 +/- 0.6 mM of nitrate) or blackcurrant cordial (as a PL, with negligible nitrate content) for 6 consecutive days and completed a series of "step" moderate-intensity and severe-intensity exercise tests on the last 3 days. On days 4-6, plasma nitrite concentration was significantly greater following dietary nitrate supplementation compared with PL (BR: 273 +/- 44 vs. PL: 140 +/- 50 nM; P < 0.05), and systolic blood pressure was significantly reduced (BR: 124 +/- 2 vs. PL: 132 +/- 5 mmHg; P < 0.01). During moderate exercise, nitrate supplementation reduced muscle fractional O2 extraction (as estimated using near-infrared spectroscopy). The gain of the increase in pulmonary O2 uptake following the onset of moderate exercise was reduced by 19% in the BR condition (BR: 8.6 +/- 0.7 vs. PL: 10.8 +/- 1.6 ml.min(-1).W(-1); P < 0.05). During severe exercise, the O2 uptake slow component was reduced (BR: 0.57 +/- 0.20 vs. PL: 0.74 +/- 0.24 l/min; P < 0.05), and the time-to-exhaustion was extended (BR: 675 +/- 203 vs. PL: 583 +/- 145 s; P < 0.05). The reduced O2 cost of exercise following increased dietary nitrate intake has important implications for our understanding of the factors that regulate mitochondrial respiration and muscle contractile energetics in humans.
A Rhamnogalacturonan Lyase in the Clostridium cellulolyticum Cellulosome (2003)

Clostridium cellulolyticum secretes large multienzymatic complexes with plant cell wall-degrading activities named cellulosomes. Most of the genes encoding cellulosomal components are located in a large gene cluster: cipC-cel48F-cel8C-cel9G-cel9E-orfX-cel9H-cel9J-man5K-cel9M. Downstream of the cel9M gene, a new open reading frame was discovered and named rgl11Y. Amino acid sequence analysis indicates that this gene encodes a multidomain pectinase, Rgl11Y, containing an N-terminal signal sequence, a catalytic domain belonging to family 11 of the polysaccharide lyases, and a C-terminal dockerin domain. The present report describes the biochemical characterization of a recombinant form of Rgl11Y. Rgl11Y cleaves the alpha-L-Rhap-(1-->4)-alpha-D-GalpA glycosidic bond in the backbone of rhamnogalacturonan I (RGI) via a beta-elimination mechanism. Its specific activity on potato pectic galactan and rhamnogalacturonan was found to be 28 and 3.6 IU/mg, respectively, indicating that Rgl11Y requires galactan decoration of the RGI backbone. The optimal pH of Rgl11Y is 8.5 and calcium is required for its activity. Rgl11Y was shown to be incorporated in the C. cellulolyticum cellulosome through a typical cohesin-dockerin interaction. Rgl11Y from C. cellulolyticum is the first cellulosomal rhamnogalacturonase characterized.