gebhart/patrepeval huggingface dataset:
A Cancer Detection Platform Which Measures Telomerase Activity from Live Circulating Tumor Cells Captured on a Microfilter (2010)

Circulating tumor cells (CTC) quantified in cancer patients' blood can predict disease outcome and response to therapy. However, the CTC analysis platforms commonly used cannot capture live CTCs and only apply to tumors of epithelial origin. To address these limitations, we have developed a novel cancer detection platform which measures telomerase activity from live CTCs captured on a parylene-C slot microfilter. Using a constant low-pressure delivery system, the new microfilter platform was capable of cell capture from 1 mL of whole blood in less than 5 minutes, achieving 90% capture efficiency, 90% cell viability, and 200-fold sample enrichment. Importantly, the captured cells retained normal morphology by scanning electron microscopy and could be readily manipulated, further analyzed, or expanded on- or off-filter. Telomerase activity--a well-recognized universal cancer marker--was reliably detected by quantitative PCR from as few as 25 cancer cells added into 7.5 mL of whole blood and captured on the microfilter. Moreover, significant telomerase activity elevation was also measured from patients' blood samples and from single cancer cells lifted off of the microfilter. Live CTC capture and analysis is fast and simple yet highly quantitative, versatile, and applicable to nearly all solid tumor types, making this a highly promising new strategy for cancer detection and characterization.
Mutant forms of staphylococcal nuclease with altered patterns of guanidine hydrochloride and urea denaturation (1986)

Eleven mutant forms of staphylococcal nuclease with one or more defined amino acid substitutions have been analyzed by solvent denaturation by using intrinsic fluorescence to follow the denaturation reaction. On the basis of patterns observed in the value of m--the rate of change of log Kapp (the apparent equilibrium constant between the native and denatured states) with denaturant concentration--these proteins can be grouped into two classes. For class I mutants, the value of m with guanidine hydrochloride is less than the wild-type value and is either constant or increases slightly with increasing denaturant; the value of m with urea is also less than wild type but shows a marked increase with increasing denaturant concentration, often approaching but never exceeding the wild-type value. For class II mutants, m is constant and is greater than wild type in both denaturants, with the increase being consistently larger in guanidine hydrochloride than in urea. When double or triple mutants are constructed from members of the same mutant class, the change in m is usually the sum of the changes produced by each mutation in isolation. One plausible explanation for these altered patterns of denaturation is that chain-chain or chain-solvent interactions in the denatured state have been modified--interactions which appear to involve hydrophobic groups.
High lithium ionic conductivity in the garnet‐type oxide Li 7−2 x La 3 Zr 2− x Mo x O 12 ( x =0‐0.3) ceramics by sol‐gel method (2017)

Abstract Lithium garnet‐type oxides Li 7−2 x La 3 Zr 2− x M o x O 12 ( x =0, 0.1, 0.2, 0.3) ceramics were prepared by a sol‐gel method. The influence of molybdenum on the structure, microstructure and conductivity of Li 7 La 3 Zr 2 O 12 were investigated by X‐ray diffraction, scanning electron microscopy, and impedance spectroscopy. The cubic phase Li 7 La 3 Zr 2 O 12 has been stabilized by partial substitution of Mo for Zr at low temperature. The introduction of Mo ( x ≥0.1) can accelerate densification. Li 6.6 La 3 Zr 1.8 Mo 0.2 O 12 sintered at lower temperature 1100°C for 3 hours exhibits highest total ionic conductivity of 5.09 × 10 −4 S/cm. Results indicate that the Mo doping LLZO synthesized by sol‐gel method effectively lowers its sintering temperature and improves the ionic conductivity.
Complement-regulatory proteins in ovarian malignancies (1997)

Ovarian cancer has features that makes it well-suited for MAb adjuvant immunotherapy. Several of the MAbs used in clinical trials mediate cancer cell destruction by activation of complement (C). In this study, therefore, we examined the ability of ovarian-tumor cells to resist C attack. We found that the C regulators membrane cofactor protein (MCP, CD46) and protectin (CD59) were strongly expressed in the tumor cells in all 28 benign and malignant tumors examined. Decay-accelerating factor (DAF; CD55) was more heterogeneously expressed, and only 75% of the tumors exhibited a moderate amount of DAF in the tumor cells. In adenoma cells, CD59 and DAF were preferentially located apically, while in adenocarcinoma cells they were expressed also at the basolateral cell surface. The ovarian-carcinoma cell lines SK-OV-3, Caov-3, SW626 and PA-1 expressed both the 58- and the 68-kDa isoforms of MCP. DAF was present as a glycosyl-phosphatidylinositol(GPI)-anchored 70-kDa glycoprotein. The surface-expression level of DAF varied, and correlated with the vulnerability of the cells to C-mediated lysis. CD59 was expressed as a GPI-linked 19- to 25-kDa protein exhibiting multiple glycosylation variants. The surface expression of CD59 correlated with the amount of the main 1.9 + 2.1-kb CD59 mRNA transcripts. Neutralization of CD59 with an anti-CD59 MAb significantly enhanced C-mediated killing of the cell lines. Low expression of C regulators on the PA-1 teratocarcinoma cell line was associated with high sensitivity to C lysis. Thus, the expression of C regulators on malignant ovarian cells may constitute a tumor escape mechanism, and is a critical parameter to be examined when MAb therapy is being considered.
Development of strategies for conditional RNA interference (2007)

Given the potential 'off-target' effects of dsRNAs, it would be preferable in many cases to limit expression of dsRNA to the tissue of interest and moreover would significantly augment the resolution of RNAi technologies. Notably, the system under evaluation in this study could readily be adapted to achieve this objective.
Design, implementation, and evaluation of the linear road bnchmark on the stream processing core (2006)

Stream processing applications have recently gained significant attention in the networking and database community. At the core of these applications is a stream processing engine that performs resource allocation and management to support continuous tracking of queries over collections of physically-distributed and rapidly-updating data streams. While numerous stream processing systems exist, there has been little work on understanding the performance characteristics of these applications in a distributed setup. In this paper, we examine the performance bottlenecks of streaming data applications, in particular the Linear Road stream data management benchmark, in achieving good performance in large-scale distributed environments, using the Stream Processing Core (SPC), a stream processing middleware we have developed. First, we present the design and implementation of the Linear Road benchmark on the SPC middleware. SPC has been designed to scale to tens of thousands of processing nodes, while supporting concurrent applications and multiple simultaneous queries. Second, we identify the main performance bottlenecks in the Linear Road application in achieving scalability and low query response latency. Our results show that data locality, buffer capacity, physical allocation of processing elements to infrastructure nodes, and packaging for transporting streamed data are important factors in achieving good application performance. Though we evaluate our system primarily for the Linear Road application, we believe it also provides useful insights into the overall system behavior for supporting other distributed and large-scale continuous streaming data applications. Finally, we examine how SPC can be used and tuned to enable a very efficient implementation of the Linear Road application in a distributed environment.
Maternal Fat Feeding Augments Offspring Nephron Endowment in Mice (2016)

Increasing consumption of a high fat 'Western' diet has led to a growing number of pregnancies complicated by maternal obesity. Maternal overnutrition and obesity have health implications for offspring, yet little is known about their effects on offspring kidney development and renal function. Female C57Bl6 mice were fed a high fat diet (HFD, 21% fat) or matched normal fat diet (NFD, 6% fat) for 6 weeks prior to pregnancy and throughout gestation and lactation. HFD dams were overweight and glucose intolerant prior to mating but not in late gestation. Offspring of NFD and HFD dams had similar body weights at embryonic day (E)15.5, E18.5 and at postnatal day (PN)21. HFD offspring had normal ureteric tree development and nephron number at E15.5. However, using unbiased stereology, kidneys of HFD offspring were found to have 20-25% more nephrons than offspring of NFD dams at E18.5 and PN21. Offspring of HFD dams with body weight and glucose profiles similar to NFD dams prior to pregnancy also had an elevated nephron endowment. At 9 months of age, adult offspring of HFD dams displayed mild fasting hyperglycaemia but similar body weights to NFD offspring. Renal function and morphology, measured by transcutaneous clearance of FITC-sinistrin and stereology respectively, were normal. This study demonstrates that maternal fat feeding augments offspring nephron endowment with no long-term consequences for offspring renal health. Future studies assessing the effects of a chronic stressor on adult mice with augmented nephron number are warranted, as are studies investigating the molecular mechanisms that result in high nephron endowment.
Screening Tests for Intrauterine Growth Retardation: A Comparison of Umbilical Artery Doppler to Real‐Time Ultrasound (1990)

In a study designed to compare Doppler umbilical artery velocimetry to ultrasound morphometric measurements in the prediction of intrauterine growth retardation, 636 paired ultrasound and Doppler umbilical artery examinations were performed between 24 and 40 weeks gestational age. Intrauterine growth retardation was defined as birth weight less than the tenth percentile per gestational age and 25 (9.2%) of the infants born in our study met this criteria. In general, when the gestational age was limited to less than 30 weeks, none of the tests were highly predictive of intrauterine growth retardation. Doppler umbilical artery systolic-to-diastolic ratios of greater than 3 had the highest sensitivity. However, due to inclusion of a large number of false-positives, it was considered a poor test. After 30 weeks, fetal abdominal circumference less than the tenth percentile had a greater sensitivity (45%) and positive predictive value (28%) than Doppler systolic-to-diastolic ratios greater than 3 (36% and 18%, respectively). Doppler ultrasound umbilical artery systolic-to-diastolic ratios are not more predictive of intrauterine growth retardation than ultrasound morphometric measurements.
Stem Cell Transplantation in Hemoglobinopathies (2007)

beta-Thalassemia (thal) and sickle cell disease are the most common genetic diseases worldwide. Although supportive therapies such as regular transfusion and chelation for beta-thal and hydroxyurea (HU) for sickle cell disease have significantly improved clinical manifestations and the quality of life, they cannot eliminate disease and therapy-related complications. Today, hematopoietic stem cell transplantation (HSCT) is the only curative treatment for patients with hemoglobinopathies. The first successful HSCT was reported in 1981. At that time, more than 1,000 patients underwent HSCT in Pesaro, Italy. Sixty beta-thal patients underwent HSCT at the Department of Pediatric Hematology-Oncology, Akdeniz University School of Medicine, Antalya, Turkey between 1998 and 2006. We found stable mixed chimerism in 14 patients out of 45 (31%) in our transplanted thalassemia patients. The thalassemia free survival and overall survival rates were found to be 84.0 and 91.0%, respectively. The literature and our results indicate that HSCT can offer a cure for hemoglobinopathy patients.
cAMP Counter-regulates Insulin-mediated Protein Phosphatase-2A Inactivation in Rat Skeletal Muscle Cells (1996)

In this study, we examined the mechanism of recently reported inactivation of protein phosphatase-2A (PP-2A) by insulin (Srinivasan, M., and Begum, N. (1994) J. Biol. Chem. 269, 12514-12520) and its counter-regulation by cAMP agonists. Exposure of L6 myotubes to insulin resulted in a rapid inhibition of PP-2A that was accompanied by a 3-fold increase in the phosphotyrosine content of the immunoprecipitated PP-2A catalytic subunit. Pretreatment with (Sp)-cAMP, a cAMP agonist, completely blocked insulin-mediated inhibition of PP-2A activity and decreased the tyrosine phosphorylation of PP-2A catalytic subunit to control levels. To understand the mechanism of counter-regulation of PP-2A by (Sp)-cAMP, cells were pretreated with sodium orthovanadate, an inhibitor of phosphotyrosine phosphatases. Vanadate prevented the effect of (Sp)-cAMP on PP-2A activity and increased the phosphorylation status of PP-2A catalytic subunit to the level observed with insulin. Wortmannin, a phosphatidylinositol 3-kinase inhibitor, and rapamycin, an inhibitor of 70-kDa S6 kinase activation, prevented insulin-mediated inactivation of PP-2A, suggesting that these pathways may participate in insulin-mediated phosphorylation and inactivation of PP-2A. These results show that insulin signaling results in a rapid inactivation of PP-2A by increased tyrosine phosphorylation and cAMP agonists counter-regulate insulin's effect on PP-2A by decreasing phosphorylation, presumably via an activated phosphatase.
Meta-analyses of gene methylation and smoking behavior in non-small cell lung cancer patients (2015)

Aberrant DNA methylation can be a potential genetic mechanism in non-small cell lung cancer (NSCLC). However, inconsistent findings existed among the recent association studies between cigarette smoking and gene methylation in lung cancer. The purpose of our meta-analysis was to evaluate the role of gene methylation in the smoking behavior of NSCLC patients. A total of 116 genes were obtained from 97 eligible publications in the current meta-analyses. Our results showed that 7 hypermethylated genes (including CDKN2A, RASSF1, MGMT, RARB, DAPK, WIF1 and FHIT) were significantly associated with the smoking behavior in NSCLC patients. The further population-based subgroup meta-analyses showed that the CDKN2A hypermethylation was significantly associated with cigarette smoking in Japanese, Chinese and Americans. In contrast, a significant association of RARB hypermethylation and smoking behavior was only detected in Chinese but not in Japanese. The genes with altered DNA methylation were likely to be potentially useful biomarkers in the early diagnosis of NSCLC.
Percutaneous Transhepatic Cholecystoscopic Lithotomy in the Management of Acute Cholecystitis Caused by Gallbladder Stones (1997)

Percutaneous transhepatic cholecystic drainage (PTCCD) with percutaneous transhepatic cholecystoscopic lithotomy (PTCCSL) were performed in 53 patients with acute cholecystitis caused by gallbladder stones and studied stone removal rates, complications, endoscopic findings, and stone recurrence. The stones were successfully removed in 96% of the patients, and there were no serious complications. The coexistence of cancer was confirmed in three patients, and all cases were accurately diagnosed on the basis of uitrasonographic, endoscopic, and biopsy findings. The mean duration of follow-up after stone removal was 42 months, and the stone recurrence rate was 2.5%. Among the 39 patients followed up for at least 1 year, the gallbladder could be preserved with no evidence of sludge in patients in whom drainage was performed early after the onset of symptoms, those with a normal gallbladder after PTCCSL, and those with normal gallbladder contractility after PTCCSL. Sludge was present in patients with evidence of extensive areas of yellowish white fibers on percutaneous transhepatic cholecystoscopy. If instituted early after the onset of symptoms, PTCCD combined with PTCCSL was considered useful in the treatment of patients with acute cholecystitis associated with gallbladder stones.
Intestinal response to growth factors administered alone or in combination with human [Gly2]glucagon-like peptide 2 (1997)

The control of intestinal epithelial growth is regulated by interactions of growth factors in various cellular compartments of the small and large bowel. Little information is available on the intestinal growth response to combinations of growth factors. We studied the intestinotrophic properties of a dipeptidyl peptidase IV resistant glucagon-like peptide 2 (GLP-2) analog, human [Gly2]GLP-2 (h[Gly2]GLP-2), as well as of epidermal growth factor (EGF), long [Arg3]insulin-like growth factor I (LR3IGF-I), [Gly1]IGF-II, and human growth hormone (hGH), administered by subcutaneous injection alone or in combination in mice. At the doses tested, h[Gly2]GLP-2 was the most potent agent for increasing small and large bowel mass. Mice treated with h[Gly2]GLP-2 and either GH or IGF-I exhibited greater increases in histological parameters of small intestinal growth than did mice treated with h[Gly2]GLP-2 alone. Administration of all five growth factors together induced significant increases in crypt plus villus height and in small and large bowel length and weight. The results of these experiments define regional differences in both the cellular targets and relative activities of intestinotrophic molecules and raise the possibility that selective growth factor combinations may be useful for enhancement of intestinal adaptation in vivo.
Human papillomavirus types 6 and 11 mRNAs from genital condylomata acuminata (1987)

We have identified and mapped a number of RNA species of human papillomavirus types 6 and 11 from condylomata acuminata by the electron microscopic R-loop technique. Each of the early (E)- and late (L)-region open reading frames (ORFs) deduced from the DNA sequences was represented in one or more transcripts. In addition, RNA species that could encode the modulator of DNA replication and the repressor of transcription, functions recently identified in the genetically similar bovine papillomavirus type 1, were also detected. Some ORFs were 5' proximal in one or more transcripts, whereas others were not 5' proximal in any species, suggesting that internal initiation of translation might be required to gain access to these latter ORFs. Virtually all transcripts had their 5' ends located in the E region and were polyadenylated at one of two sites, i.e., at the end of the E region or at the end of the L region. The great majority of the RNAs were derived from the E region of the genome, with one species approximately 50 to 100 times more abundant than the others. For most of the RNAs, the 5' end mapped near nucleotide 700; minor populations had 5' ends near nucleotide 100 or 1200. By correlating our mapping data with the genomic DNA sequences as well as available RNA structures and cDNA sequences of several papillomaviruses, we predict a number of mRNA splice donor and acceptor sites and suggest that the papillomaviruses have sophisticated usage of ORFs through alternative promoters, mRNA splice sites, and polyadenylation sites.
Peak Growth Hormone-Releasing Hormone-Arginine-Stimulated Growth Hormone Is Inversely Associated with Intramyocellular and Intrahepatic Lipid Content in Premenopausal Women with Obesity (2009)

In premenopausal women with obesity, peak GH is inversely associated with IMCL and intrahepatic lipids independent of age and visceral adiposity. This suggests that low GH may contribute to insulin resistance in obesity through effects on muscle and intrahepatic lipids.
BRILLIANT BLUE G SELECTIVELY STAINS THE INTERNAL LIMITING MEMBRANE/BRILLIANT BLUE G–ASSISTED MEMBRANE PEELING (2006)

BBG selectively stains the ILM. This technique can facilitate the management of MH and ERM surgery without any adverse effects, as was shown in this short-term study.
Effective immunochemotherapy of CALLA+C mu+ human pre-B acute lymphoblastic leukemia in mice with severe combined immunodeficiency using B43 (anti-CD19) pokeweed antiviral protein immunotoxin plus cyclophosphamide (1992)

A highly aggressive human CALLA+C mu+ pre-B acute lymphoblastic leukemia (ALL) cell line (NALM-6-UM1) causes disseminated and invariably fatal leukemia in CB.17 mice with severe combined immunodeficiency (SCID). We used this SCID mouse model of human pre-B ALL to evaluate and compare, in a total of 434 SCID mice, the antileukemic efficacy of B43 (anti-CD19)-pokeweed antiviral protein (PAP) immunotoxin and cyclophosphamide (CPA) as individual reagents and as combined immunochemotherapeutic regimens. B43-PAP plus CPA was superior to either the immunotoxin or drug alone, and combined immunochemotherapy markedly improved the event-free survival (EFS) of SCID mice challenged with NALM-6-UM1 pre-B ALL cells. Notably, 90% to 100% of SCID mice challenged with 1 x 10(6) leukemia cells and then treated with B43-PAP plus CPA combined immunochemotherapy regimens became long-term survivors, a result not achieved with B43-PAP alone or CPA alone. The advantage was particularly evident in mice inoculated with 5 x 10(6) leukemia cells. While neither 15 micrograms B43-PAP (median survival, 58 days) nor 1 mg CPA (median survival, 49 days) resulted in long-term EFS of SCID mice challenged with 5 x 10(6) NALM-6- UM1 pre-B ALL cells, the probability of EFS at 6 months was 50% +/- 16% for SCID mice treated with 15 micrograms B43-PAP plus 1 mg CPA (median survival, greater than 180 days) (P less than .0001). The probability of long-term EFS was only 14% +/- 7% for mice treated with 30 micrograms B43-PAP and 0% +/- 0% for mice treated with 1 mg CPA, but 40% +/- 16% for mice treated with 30 micrograms B43-PAP plus 1 mg CPA (P less than .0001). Similarly, the probability of EFS at 6 months was 40% +/- 16% for mice treated with 2 mg CPA alone, 70% +/- 15% for mice treated with 2 mg CPA plus 15 micrograms B43-PAP, and 70% +/- 15% for mice treated with 2 mg CPA plus 30 micrograms B43-PAP. Ten SCID mice in the B43-PAP plus CPA combined immunochemotherapy arms surviving long term after the inoculation of 5 x 10(6) NALM-6-UM1 pre-B ALL cells were electively killed at 174 to 181 days to assess their leukemia burden. We found no evidence of leukemia in any of the bone marrow specimens by two-color immunofluorescence and multiparameter flow cytometry.(ABSTRACT TRUNCATED AT 400 WORDS)
The interpretation of trace element analysis in body fluids. (2008)

The clinical interpretation of trace element analysis has lagged behind the technology available to measure the elements in body fluids. Reports can be difficult to interpret and requires knowledge of toxicokinetics, the dynamics of how the trace metals accumulate and pass through the body. Trace element analysis is best used for specific applications, such as establishing levels of exposure, biological exposure indices, biomonitoring of populations, and to confirm an association following a compatible diagnosis. It is not well suited for screening individual patients. Chelation treatment may follow inappropriate trace element determinations and may carry a risk of side effects, some life-threatening. Trace element analysis should be used sparingly and with full understanding of what the results are likely to mean. The physician should only order the test with a clear idea of why he or she is doing so and what he or she will do with the result.