gebhart/patrepeval huggingface dataset:
Abstract 1287: Epigenetic deregulation of breast cancer is associated with DNA Repair Capacity. (2013)

Abstract Introduction 226,870 women are estimated to be diagnosed with breast cancer in 2012. Search for accurate methods for screening, diagnosis and treatment follow up, that will be minimally invasive are ongoing. Hypermethylation of gene promoters occurs frequently in the pathogenesis of breast cancer, and causes silencing of tumor suppressor genes. Hypermethylation of Mal, Kif1a and OGDHL in breast cancer cell lines and tissue samples was previously reported. Aberrant DNA repair capacity (DRC) has been studied and shown to elevate the risk for breast cancer. However, information on the association between the epigenetic promoter hypermethylation and DRC is lacking in the literature. Objective The aim of this study is to assess the association between breast cancer and promoter hypermethylation of Mal, Kif1a and OGDHL in serum of breast cancer patients and controls in association with the DRC. Methods 240 serum samples from breast cancer patients and controls from Puerto Rico were collected. DNA was extracted and methylation levels were measured after bisulfite treatment, by QMSP. DRC was assessed by host reactivation assay of blood samples. The overall risk for breast cancer was calculated and adjusted for patient characteristics including DRC. Results Methylation of at least one of the genes was found in 49% of breast cancer samples compared to 20% of controls. ROC curves for individual genes showed values of 0.64 for MAL, 0.51 for Kif1a and 0.53 for OGDHL. In the linear regression unadjusted analysis, mean methylation levels (what are the values?) of the three genes and odds ratio (OR) were higher in breast cancer cases compared to controls, with Kif1a and OGDHL values being statistically significant. These values became non significant after adjusting for DRC. Hypermethylation of Kif1a, but not MAL or OGDHL was found to be significantly associated with DRC. Conclusion Correlation between promoter hypermethylation of the genes Mal, Kif1a and OGDHL and breast cancer was non significant when adjusted for DRC. A significant association between hypermethylation of Kif1a and DRC was shown. The association between promoter hypermethylation and DRC needs to be further studied. Citation Format: Jaime Matta, Tal Hadar, Luisa Morales, Kim Ostrow, David Sidransky, Rafael E. Guerrero-Preston. Epigenetic deregulation of breast cancer is associated with DNA Repair Capacity. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1287. doi:10.1158/1538-7445.AM2013-1287
Duplicate Detection in the Reuters Collection (1997)

While conducting some experiments with the Reuters collection, it was discovered&#13;\nthat contained within it were a number of documents that were exact duplicates of&#13;\neach other (see Figure 1). A short study was conducted to try to discover how many&#13;\nsuch documents there were. The results of this study revealed that the notion of a&#13;\nduplicate document was not as simple as first thought.&#13;\n&#13;\nThe contents of this report are as follows. A brief review of previous duplicate detection&#13;\nresearch will be presented, followed by a description of the methods and results of&#13;\nthe duplicate detection work conducted here. In addition, there is an appendix holding&#13;\nthe document ids of the various types of duplicate found.
The safety of fine-needle aspiration guided by endoscopic ultrasound (2008)

I have read the article by Al-Haddad et al. with great interest and am impressed by their data on safety in endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA) [1]. In the discussion section they provide a table covering the results from their study as well as from eight other previously published studies on EUS-FNA safety. The number of included patients ranges from 42 to 483, with variable inclusion criteria and outcomes. In 2005 my colleagues and I published our single-center safety experience with EUS in 3324 consecutive patients of whom 670 had EUS-FNA [2]. EUS-FNA related complications were seen in 0.3 % (2/670) of the patients which compares favorably with the data reported by Al-Haddad et al. To our surprise we did not detect any significant difference between the complication rates for EUS alone and EUS-FNA, but in contrast to Al-Haddad et al. we had to classify 90 % (9/10) of the complications as severe and 20 % (2/10) as fatal. This may be explained by the reported different rates regarding the indications for EUS-FNA, and I believe that the variation in morbidity and mortality rates related to EUS-FNA (and EUS alone) mirrors the populations and indications included rather than the experience of the endosonographer(s). Thus, I fully agree with the conclusion by Al-Haddad et al. regarding the safety of EUS-FNA, but the reported differences may simply reflect different populations and indication patterns.
Thermal Conductance of Hydrophilic and Hydrophobic Interfaces (2006)

Using time-domain thermoreflectance, we have measured the transport of thermally excited vibrational energy across planar interfaces between water and solids that have been chemically functionalized with a self-assembled monolayer (SAM). The Kapitza length--i.e., the thermal conductivity of water divided by the thermal conductance per unit area of the interface--is analogous to the "slip length" for water flowing tangentially past a solid surface. We find that the Kapitza length at hydrophobic interfaces (10-12 nm) is a factor of 2-3 larger than the Kapitza length at hydrophilic interfaces (3-6 nm). If a vapor layer is present at the hydrophobic interface, and this vapor layer has a thermal conductivity that is comparable to bulk water vapor, then our experimental results constrain the thickness of the vapor layer to be less than 0.25 nm.
HLA A, B, C antigens are expressed on nonvillous trophoblast of the early human placenta. (1981)

Samples were taken from the human chorionic sac at 6 wk postconception and were stained with monoclonal antibodies to trophoblast and to HLA antigens by means of an indirect immunoperoxidase technique. Antibody to HLA A, B, C antigens did not stain chorionic villous trophoblast in accordance with previous studies, but did stain nonvillous trophoblast of the cytotrophoblast cell columns and cytotrophoblastic shell. Antibody to HLA DR antigens showed no staining of trophoblast. This is the first demonstration of HLA antigens on a human fetal tissue in direct maternal contact. We have discussed the immunologic implications of this finding.
Flexible infrared-transmissive metal waveguides (1976)

We report unexpectedly low-loss optical transmission at 10.6 μm through a 1-m-long hollow rectangular metallic waveguide bent through 90° in a 50-cm radius of curvature. This demonstrates that flexible infrared-transmissive (FIT) waveguides can deliver CO2 laser power to targets nearly as conveniently as optical fibers guide visible light.
Second-line hormonal therapy for advanced prostate cancer: a shifting paradigm. (1997)

Once CAB (suppression of gonadal and adrenal androgen) is undertaken, further hormonal maneuvers remain efficacious in some patients with progressive prostate cancer. Antiandrogen withdrawal is now a mandatory maneuver before proceeding to other regimens. It is clear that certain patients will continue to respond to hormonal maneuvers even after antiandrogen withdrawal. An understanding of the molecular basis of these responses may result in the development of a more targeted therapy in the future.
Kringle 5 of Human Plasminogen Induces Apoptosis of Endothelial and Tumor Cells through Surface-Expressed Glucose-Regulated Protein 78 (2005)

Kringle 5 (K5) of human plasminogen has been shown to inhibit angiogenesis by inducing the apoptosis of proliferating endothelial cells. Peptide regions around the lysine-binding pocket of K5 largely mediate these effects, particularly the peptide PRKLYDY, which we show to compete with K5 for the binding to endothelial cells. The cell surface binding site for K5 that mediates these effects has not been defined previously. Here, we report that glucose-regulated protein 78, exposed on cell surfaces of proliferating endothelial cells as well as on stressed tumor cells, plays a key role in the antiangiogenic and antitumor activity of K5. We also report that recombinant K5-induced apoptosis of stressed HT1080 fibrosarcoma cells involves enhanced activity of caspase-7, consistent with the disruption of glucose-regulated protein 78-procaspase-7 complexes. These results establish recombinant K5 as an inhibitor of a stress response pathway, which leads to both endothelial and tumor cell apoptosis.
Studies on Cereals Part V (1966)

When stored rice (40°C, two months) was cooked, the stale flavor (komai-shu) was clearly detected by sensory test. Direct gas chromatographic analysis of head space vapors over cooked rice showed three main peaks which corresponded to propionaldehyde or acetone, n-valeraldehyde and n-caproaldehyde. On the other hand, the content of linoleic and linolenic acids of the rice decreased during storage at 40°C. This means that the unsaturated fatty acids autoxidized during storage and gave rise to carbonyl compounds responsible for the stale flavor of cooked rice.
Genetic identification of the pore domain of the OmpC porin of Escherichia coli K-12 (1988)

We have isolated and characterized 31 mutations in the ompC gene which allow Escherichia coli to grow on maltotriose (Dex+) in the absence of the LamB and OmpF porins. These ompC(Dex) mutations include single-base-pair substitutions, small deletions, and small insertions. DNA sequence analysis shows that all of the alterations occur within the coding region for the first 110 amino acids of mature OmpC. The 26 independent point mutations repeatedly and exclusively alter residues R37, R74, and D105 of mature OmpC. In each case, a charged amino acid is changed to an uncharged residue. Biochemical and physiological tests suggest that these alterations increase the size of the pore channel. Starting with three different ompC(Dex) strains with alterations affecting R74, we isolated mutants that could grow on maltohexose (Hex+). These mutants each contained a second alteration in the ompC gene involving residues R37, D105, or R124. The combined effects on pore function of the two mutations appear to be additive. These experiments suggest that we have identified the important residues of OmpC peptide involved in pore function. On the basis of these mutations and general rules for membrane protein folding, a model for the topology of the OmpC protein is proposed.
Abnormal regulation of ion channels in cystic fibrosis epithelia (1990)

Cystic fibrosis (CF), the most common lethal genetic disease in Caucasians, is characterized by defective electrolyte transport in several epithelia. In sweat duct, pancreatic, intestinal, and airway epithelia, abnormalities in transepithelial ion transport may account for the manifestations of the disease. A Cl- impermeable apical cell membrane is a common feature in these CF epithelia. The rate of transepithelial Cl- transport is controlled in part by hormonally regulated apical membrane Cl- channels; in CF epithelia, Cl- channels are present but their regulation is defective. Most regulation studies have focused on an outwardly rectifying Cl- channel, although other channels may be involved in Cl- secretion. Phosphorylation of Cl- channels or associated regulatory proteins by cAMP-dependent protein kinase or by protein kinase C (at a low internal [Ca2+]) in excised patches of membrane activates Cl- channels in normal cells but not in CF cells. Phosphorylation with protein kinase C at a high internal [Ca2+] in excised patches of membrane inactivates the channel; such inactivation is normal in CF cells. Cl- channels can also be activated by other maneuvers including an increase in the cytosolic [Ca2+], sustained membrane depolarization, an increase in temperature, proteolysis, and changes in osmolarity; the response to such maneuvers is not defective in CF. In addition to the Cl- channel abnormalities, Na+ absorption is increased in CF epithelia. It is not certain whether the increased rate of Na+ absorption results from an increase in the number of cation channels or an alteration of their kinetics. The relation of these ion channel abnormalities to the CF gene product is unknown, but an understanding of the function of the protein product and its defective function in CF should yield important new insights into the pathogenesis and potential therapy of this disease.
Effect of an Oral Dose of 25-Hydroxyvitamin D3on Its Blood Levels in Patients with the Nephrotic Syndrome* (1980)

Patients with the nephrotic syndrome have low blood levels of 25-hydroxyvitamin D3 (25OHD3) due to urinary losses of the sterol. It is not known whether supplementation of this metabolite could raise its blood levels in these patients. The changes in the plasma levels of 25OHD3 and its kinetic behavior were studied after an oral dose of the sterol (200 microgram) in patients with the nephrotic syndrome in an effort to evaluate the usefulness of oral therapy to achieve and maintain normal blood levels of 25OHD3. Normal subjects served as controls. The results showed that intestinal absorption of 25OHD3 is significantly delayed and its elimination rate is significantly enhanced in patients with the nephrotic syndrome compared to control subjects. Despite these abnormalities, the plasma levels of 25OHD3 were within normal values even 48 h after the ingestion of the sterol. These data indicate that oral therapy with 25OHD3 given in proper doses is adequate to maintain normal blood levels of the sterol in patients with the nephrotic syndrome. Therefore, a therapeutic approach could be designed to manage the target organ disease due to 25OHD3 deficiency seen in these patients.
Scalable fabrication of micro- and nano-particles utilizing the Rayleigh instability in multi-material fibers (2011)

We describe a novel fabrication method for producing polymer, glass, and metal micro- and nano-particles whose diameters range from 200 microns to under 50 nanometers. This method relies on the Rayleigh capillary instability in a multi-material fiber. The fiber core is made of the target material and has size close to the desired particle diameter embedded in a sacrificial polymer matrix. The fiber temperature is elevated to reduce the core viscosity and the Rayleigh instability results in the breakup of the core into a periodic string of spherical particles.
Element and molecular mass spectrometry—an emerging analytical dream team in the life sciences (2004)

The recent literature on the combined applications of element (ICP, inductively coupled plasma) mass spectrometry and molecular (ESI, electrospray ionisation and MALDI, matrix assisted laser desorption ionisation) mass spectrometry in the life sciences is reviewed. Emphasis is put on investigations where both techniques have been used in a synergistic way with the aim of an analytical result with molecular specificity. Multi-element specificity and quantification are the key features of element MS, whereas molecular weight determination and structural information are those contributed by ESI and MALDI MS. The analytical applications cover the study of selenoproteins, phosphoproteins, metalloproteins, unmodified proteins, metallothioneins, phytochelatins, nucleic acids, arsenosugars, thyroid hormones, cobalamines, drugs and drug metabolites. Supported by on-line or off-line coupling to chromatographic or electrophoretic separation methods, the combined application of element and molecular mass spectrometry in all these studies has created the basis for new structural and/or quantitative insights, demonstrating the analytical excellence of this approach.
Hollow fiber supported gas membrane for in situ removal of ammonium during an antibiotic fermentation (1990)

To study the influence of ammonium on an antibiotic cultivation, mass transfer measurements of ammonium through microporous hydrophobic membranes using different stripping methods were carried out and compared. The higher overall mass transfer coefficients for ammonium were obtained with an acid stripping solution compared to water, vacuum, or sweeping air. A hollow fiber module for in situ removal of ammonium during cultivation was designed and operated in an external bypass to a 10-L fermentor. Compared to a control fermentation, the cell dry mass could be increased 2.6 times and the antibiotic concentration 8 times, if the in situ ammonium removal was in operation.
Repair of Articular Cartilage Defects Using Mesenchymal Stem Cells (1995)

Degeneration of articular cartilage in osteoarthritis is a serious medical problem. We have isolated a population of cells from the connective tissue of mammals termed mesenchymal stem cells (MSCs) for their apparent unlimited growth potential and their ability to differentiate into several phenotypes of the mesodermal lineage, including cartilage and bone. These qualities make them ideal candidates for cartilage repair. We isolated MSCs from adult rabbit muscle and cultured them in vitro into porous polyglycolic acid polymer matrices. The matrices were implanted into 3-mm-diameter full thickness defects in rabbit knees with empty polymer matrices serving as the contralateral controls. The implants were harvested 6 and 12 weeks postop. At 6 weeks, the controls contained fibrocartilage while the experimentals seemed to contain undifferentiated cells. By 12 weeks postop, the controls contained limited fibrocartilage and extensive connective tissue, but no subchondral bone. In contrast, the implants containing MSCs had a surface layer of cartilage approximately the same thickness as normal articular cartilage and normal-appearing subchondral bone. There was good integration of the implant with the surrounding tissue. Implantation of MSCs into cartilage defects appears to effect repair of both the articular cartilage and subchondral bone. Studies are ongoing to further characterize the use of MSCs for cartilage repair.
Inflammatory/Antiinflammatory Properties of High-Density Lipoprotein Distinguish Patients From Control Subjects Better Than High-Density Lipoprotein Cholesterol Levels and Are Favorably Affected by Simvastatin Treatment (2003)

The inflammatory/antiinflammatory properties of HDL distinguished patients from control subjects better than HDL cholesterol and were improved with simvastatin.
Factors Associated with Early Remission of Type I Diabetes in Children Treated with Cyclosporine (1988)

To improve criteria for entry into future trials of immunosuppression, we enrolled 40 children with recent-onset Type I insulin-dependent diabetes in a pilot trial of cyclosporine. Twenty-seven patients were able to discontinue insulin therapy 48 +/- 5 days after the start of immunosuppression. At four months, their fasting and postprandial blood glucose concentrations averaged 110 and 160 mg per deciliter (6.1 and 8.9 mmol per liter) with a mean hemoglobin A1c level of 6.15 percent. Seventy-five percent of these patients with early remission still did not need insulin at 12 months, and their glycemic control was similar to that at 4 months. The major differences between the 27 patients with remission and the 13 without remission were the duration of symptoms before diagnosis (26.8 vs. 48.0 days, P less than 0.01), the degree of weight loss (3.2 vs. 10 percent of body weight, P less than 0.001), the initial hemoglobin A1c level (10.7 vs. 13.2 percent, P less than 0.001), and the frequency of ketoacidosis (11 vs. 61.5 percent, P less than 0.001). The lesser degree of weight loss was the strongest independent predictor of remission. The response of C-peptide to intravenous glucagon (0.50 vs. 0.17 pmol per milliliter, P less than 0.05) was also an independent predictor. No differences were observed between the two groups of patients in age, sex, HLA phenotype, autoantibodies to insulin or islet-cell antigens, or doses or trough levels of cyclosporine. Only minimal manifestations of toxicity were detected over the period of observation. We conclude that early treatment with cyclosporine in children with recent-onset Type I diabetes can induce remission from insulin dependence, with half the patients not requiring insulin after a full year.
Molecular allelokaryotyping of early‐stage, untreated chronic lymphocytic leukemia (2008)

Genetic abnormalities, including whole chromosome 13 UPD, are very common events in early-stage CLL. SNP-chip analysis can detect small genetic abnormalities in CLL and may be able to support or even supplant FISH and cytogenetics.
Catheter Ablation for Paroxysmal Atrial Fibrillation (2003)

In patients undergoing catheter ablation for PAF, LACA to encircle the PVs is more effective than SOCA.
Atrial Pacing: Efficacy and Safety (1989)

Atrial pacing has the advantages of simplicity, maintenance of AV synchrony, and economy. The major detraction has been the potential for deterioration of atrioventricular conduction. In this study, we followed 43 patients with sick sinus syndrome treated with atrial (AAI) pacing. Excellent initial implant parameters were obtained in all. Three early lead repositionings were required. Minor sensing and pacing problems could all otherwise be handled by reprogramming. Follow-up for a mean of 25 +/- 20 months demonstrated excellent performance of the pacing systems. Pacing and sensing thresholds and lead impedance indicated excellent lead performance. There were no late lead failures. Nine patients have had mild deterioration in atrioventricular conduction and one of these had a change to DDD pacing at the time of elective battery change. All patients are asymptomatic. Thus, chronic atrial pacing in selected patients is safe and reliable with good chronic lead performance and low risk of subsequent conduction system disease.
Selective launching of higher-order modes into an optical fiber with an optical phase shifter (1994)

We demonstrate a simple, effective technique for launching higher-order modes into a double-mode optical fiber by using an optical phase shifter at the input end. The suppression of the lowest-order mode was measured (but not limited) to be 27 dB.
Effects of Compression on Speech Acoustics, Intelligibility, and Sound Quality (2002)

The topic of compression has been discussed quite extensively in the last 20 years (eg, Braida et al., 1982; Dillon, 1996, 2000; Dreschler, 1992; Hickson, 1994; Kuk, 2000 and 2002; Kuk and Ludvigsen, 1999; Moore, 1990; Van Tasell, 1993; Venema, 2000; Verschuure et al., 1996; Walker and Dillon, 1982). However, the latest comprehensive update by this journal was published in 1996 (Kuk, 1996). Since that time, use of compression hearing aids has increased dramatically, from half of hearing aids dispensed only 5 years ago to four out of five hearing aids dispensed today (Strom, 2002b). Most of today's digital and digitally programmable hearing aids are compression devices (Strom, 2002a). It is probable that within a few years, very few patients will be fit with linear hearing aids. Furthermore, compression has increased in complexity, with greater numbers of parameters under the clinician's control. Ideally, these changes will translate to greater flexibility and precision in fitting and selection. However, they also increase the need for information about the effects of compression amplification on speech perception and speech quality. As evidenced by the large number of sessions at professional conferences on fitting compression hearing aids, clinicians continue to have questions about compression technology and when and how it should be used. How does compression work? Who are the best candidates for this technology? How should adjustable parameters be set to provide optimal speech recognition? What effect will compression have on speech quality? These and other questions continue to drive our interest in this technology. This article reviews the effects of compression on the speech signal and the implications for speech intelligibility, quality, and design of clinical procedures.