gebhart/patrepeval huggingface dataset:
Alterations in the Serum Glycome Due to Metastatic Prostate Cancer (2007)

Glycomic profiles derived from human blood sera of 10 healthy males were compared to those from 24 prostate cancer patients. The profiles were acquired using MALDI-MS of permethylated N-glycans released from 10-microL sample aliquots. Quantitative permethylation was attained using solid-phase permethylation. Principal component analysis of the glycomic profiles revealed significant differences among the two sets, allowing their distinct clustering. The first principal component distinguished the 24 prostate cancer patients from the healthy individuals. It was determined that fucosylation of glycan structures is generally higher in cancer samples (ANOVA test p-value of 0.0006). Although more than 50 N-glycan structures were determined, 12 glycan structures, of which six were fucosylated, were significantly different between the two sample sets. Significant differences were confirmed through two independent statistical tests (ANOVA and ROC analyses). Ten of these structures had significantly higher relative intensities in the case of the cancer samples, while the other two were less abundant in the cancer samples. All 12 structures were statistically significant, as suggested by their very low ANOVA scores (<0.001) and ROC analysis, with area under the curve values close to 1 or 0. Accordingly, these structures can be considered as cancer-specific glycans and potential prostate cancer biomarkers. Therefore, serum glycomic profiling appears worthy of further investigation to define its role in cancer early detection and prognostication.
On sampling from massive graph streams (2017)

We propose Graph Priority Sampling ( gps ), a new paradigm for order-based reservoir sampling from massive graph streams. gps provides a general way to weight edge sampling according to auxiliary and/or size variables so as to accomplish various estimation goals of graph properties. In the context of subgraph counting, we show how edge sampling weights can be chosen so as to minimize the estimation variance of counts of specified sets of subgraphs. In distinction with many prior graph sampling schemes, gps separates the functions of edge sampling and subgraph estimation. We propose two estimation frameworks: (1) Post-Stream estimation, to allow gps to construct a reference sample of edges to support retrospective graph queries, and (2) In-Stream estimation, to allow gps to obtain lower variance estimates by incrementally updating the subgraph count estimates during stream processing. Unbiasedness of subgraph estimators is established through a new Martingale formulation of graph stream order sampling, in which subgraph estimators, written as a product of constituent edge estimators, are unbiased, even when computed at different points in the stream. The separation of estimation and sampling enables significant resource savings relative to previous work. We illustrate our framework with applications to triangle and wedge counting. We perform a large-scale experimental study on real-world graphs from various domains and types. gps achieves high accuracy with &lt; 1% error for triangle and wedge counting, while storing a small fraction of the graph with average update times of a few microseconds per edge. Notably, for billion-scale graphs, gps accurately estimates triangle and wedge counts with &lt; 1% error, while storing a small fraction of &lt; 0.01% of the total edges in the graph.
Experimental parameters affecting amplitude scintillation measurements on satellite links (1985)

The letter investigates both theoretically and experimentally the influence of the duration of the basic measuring interval and the sampling rate (integration time) on the determination of the variance of amplitude deviations from their clear weather mean. Under the given experimental conditions a sampling interval of 100 ms and a basic measuring interval of about 1 min proved to be appropriate to keep errors low in determining the variance.
In vivo epidermal thickness measurement: ultrasound vs. confocal imaging (2004)

Background/purpose: In this study, in vivo skin imaging methods, ultrasound (US) and confocal microscopy (CM) were compared with regards to their accuracy in measuring the epidermal thickness. In addition an attempt was made to clarify the biological significance of the second echo‐rich line observed on US skin images, i.e. whether it represents the dermal–epidermal junction or the papillar–reticular dermis limit. Methods: US images were obtained with an in‐house device (22 MHz probe) and the CM images with the VivaScope 1000 (Lucid Inc., Rochester, NY, USA). Skin from the dorsal forearm, the back of hand and the palm skin of 11 subjects (25–40 years) were examined. Repeatability of the procedure and reproducibility of the results were evaluated on repeated measurements taken at 1‐month interval. Results: Both techniques are correlated. When a CM measurement is performed from the stratum corneum (SC) surface to the bottom of the papillae, results obtained with US and CM are very similar. Thus, the second echo‐rich line on US skin imaging is likely to reflect a virtual line joining the bottom of the papillae. CM is limited to the measurement of a relative thin epidermis, due to the signal‐to‐noise ratio, which decreases with depth. US technique offers a better repeatability and reproducibility, particularly for SC measurement. This is mainly due to the small size of the investigated field of view in CM. Conclusion: This study confirms the accuracy of US and the feasibility of CM imaging techniques for in vivo epidermal thickness measurement. Echography probably measures a maximal epidermal thickness since it encompasses the bottom of the papillae.
A yeast-based growth assay for the analysis of site-specific proteases (2003)

Many cellular and viral processes depend on site-specific proteolysis. Here, a genetic system for the identification of such proteases and inhibitors is described. The system utilizes the temperature- sensitive Saccharomyces cerevisiae CDC25-2 mutant strain and exploits the strict requirement of membrane localization of a constitutively active Ras mutant for the complementation of the yeast growth defect at the non-permissive temperature. Expression of a fusion protein in which a substrate peptide of the TEV protease separates a myristoylation signal from a constitutively active human Ras protein confers temperature insensitivity. Co-expression of the protease results in release of the Ras mutant from the membrane and growth arrest at the non-permissive temperature. This non-transcriptional assay represents a new approach to the in vivo analysis of site-specific proteases and may be a valuable alternative to existing methods. It has significant potential for the selection of inhibitors of cytoplasmic and membrane-associated proteases of biotechnical and clinical relevance.
Composite-Block Model and Joint-Prediction Algorithm for Inter-Frame Video Coding (2006)

Block-matching algorithm (BMA) is widely adopted in video coding. However, many blocks contain both background pixels and moving-object pixels, which often differ significantly in true physical motions. Using BMA for these blocks may lead to large prediction error and thus decreased coding efficiency. More accurate prediction can be achieved by object-based coding, which segments a video frame into different objects and codes these objects separately. However, additional bits are required for encoding the shape of the objects, and the computation complexity of object segmentation is often very high. In this paper, a composite-block model and a joint-prediction algorithm are proposed. This algorithm can get accurate prediction without shape coding, and its computation complexity is very close to that of the BMA. The experimental result shows that the new H.264 coder enhanced by our algorithm outperforms original H.264 coder by approximately 0.8~1.5 dB
Integration of Somatic Deletion Analysis of Prostate Cancers and Germline Linkage Analysis of Prostate Cancer Families Reveals Two Small Consensus Regions for Prostate Cancer Genes at 8p (2007)

The evidence for tumor suppressor genes at 8p is well supported by many somatic deletion studies and genetic linkage studies. However, it remains a challenge to pinpoint the tumor suppressor genes at 8p primarily because the implicated regions are broad. In this study, we attempted to narrow down the implicated regions by incorporating evidence from both somatic and germline studies. Using high-resolution Affymetrix arrays, we identified two small common deleted regions among 55 prostate tumors at 8p23.1 (9.8-11.5 Mb) and 8p21.3 (20.6-23.7 Mb). Interestingly, our fine mapping linkage analysis at 8p among 206 hereditary prostate cancer families also provided evidence for linkage at these two regions at 8p23.1 (5.8-11.2 Mb) and at 8p21.3 (19.6-23.9 Mb). More importantly, by combining the results from the somatic deletion analysis and genetic linkage analysis, we were able to further narrow the regions to approximately 1.4 Mb at 8p23.1 and approximately 3.1 Mb at 8p21.3. These smaller consensus regions may facilitate a more effective search for prostate cancer genes at 8p.
Growth, lipid content, productivity, and fatty acid composition of tropical microalgae for scale‐up production (2010)

Biomass and lipid productivity, lipid content, and quantitative and qualitative lipid composition are critical parameters in selecting microalgal species for commercial scale-up production. This study compares lipid content and composition, and lipid and biomass productivity during logarithmic, late logarithmic, and stationary phase of Nannochloropsis sp., Isochrysis sp., Tetraselmis sp., and Rhodomonas sp. grown in L1-, f/2-, and K-medium. Of the tested species, Tetraselmis sp. exhibited a lipid productivity of 3.9-4.8 g m(-2) day(-1) in any media type, with comparable lipid productivity by Nannochloropsis sp. and Isochrysis sp. when grown in L1-medium. The dry biomass productivity of Tetraselmis sp. (33.1-45.0 g m(-2) day(-1)) exceeded that of the other species by a factor 2-10. Of the organisms studied, Tetraselmis sp. had the best dry biomass and/or lipid production profile in large-scale cultures. The present study provides a practical benchmark, which allows comparison of microalgal production systems with different footprints, as well as terrestrial systems.
Ionophore antibiotic (narasin) poisoning in rabbits. (1994)

Outbreaks of narasin poisoning in rabbits from several commercial rabbit-raising farms in the state of Parana, Brazil, are reported. Approximately 5,000/35,000 rabbits died after having consumed a pelleted ration to which poultry ration premix had been added. Clinical signs included apathy, anorexia, muscle weakness, impaired walking, diarrhea, respiratory distress, and opistothonus. Gross findings were not remarkable, but varying degrees of degeneration, necrosis and regeneration of skeletal muscles were consistent histopathological features in affected rabbits. Myocardial changes were mild or absent. Thirty ppm of narasin were detected in the ration fed the rabbits. The disease was experimentally reproduced by feeding the suspected ration and by administering narasin po to rabbits.
Putting the architecting back into software architecture with systems thinking agent-based modelling (2010)

This paper details exploratory research which treats architecting as a system. This human architecting system has a structure composed of decisions, interdependencies amongst decisions, decision making, decision makers and the decision-making environment. Agent-based modelling is used to model the architecting system, and simulation is used to visualise system behaviour over time. The goal is to map legitimate / optimal speed of architectural decision-making to an architecting system behaviour pattern. Knowing the appropriate behaviour pattern of early architecture evolution will provide a mechanism for fine-grained progress tracking of architectural design. Divergence from this behaviour pattern should provide early warning signs of an incomplete or overdone architecture.
High-speed optical coherence domain reflectometry (1992)

We describe a high-speed optical coherence domain reflectometer. Scan speeds of 40 mm/s are achieved with a dynamic range of &gt;90 dB and a spatial resolution of 17 μm. Two applications are presented: the noninvasive measurement of anterior eye structure in a rabbit inυiυo and the characterization of reflections and interelement spacing in a multielement lens.
A Computerized Microstereotactic Method to Approach, 3-DimensionaIIy Reconstruct, Remove and Adjuvantly Treat Small CNS Lesions (1980)

The authors update a novel method recently utilized in humans with various CNS pathology for stereotactic localization, removal, and adjuvant therapy of small CNS lesions using additional computer processing of the date from a GE 8800 CT Scanner. Multiple computer algorithms developed at Cal Tech enhance regions of interest by filtering, magnifying, color-coding and 3-dimensional reconstruction based on routine CT scans. This stereotactic approach is calculated by the computer and coordinates are mated to a modified head fixation system; small lesions can be removed with the apparatus described herein under direct binocular vision with minimal tissue damage. This technique may offer the possibility of successful secondary application of adjuvant therapy to, particularly, a CNS glioma site.
Platelet-derived growth factor-mediated Ca2+ entry is blocked by antibodies to phosphatidylinositol 4,5-bisphosphate but does not involve heparin-sensitive inositol 1,4,5-trisphosphate receptors (1991)

Elevation of intracellular Ca2+ by platelet-derived growth factor (PDGF) and other growth factors involves both release of Ca2+ from intracellular Ca2+ stores and Ca2+ entry from the extracellular medium. Release from intracellular stores is believed to be mediated by inositol 1,4,5-trisphosphate (IP3) and the heparin-sensitive IP3 receptor. We studied the mechanism by which entry of extracellular Ca2+ is induced by PDGF. Intracellular free Ca2+ (Ca2+i) was measured in single cultured rat vascular smooth muscle cells using fura 2 microspectrofluorometry. In nominally Ca2(+)-free medium, PDGF (recombinant BB, 10 ng/ml) raised intracellular Ca2+ transiently (less than 5 min); addition of 2 mM Ca2+ to the bathing medium after 5 min caused a second, prolonged increase in intracellular Ca2+. Repeated changes in extracellular Ca2+ from 0 to 2 mM over 90 min caused rapid, parallel changes in Ca2+i of approximately 200 nM. This change in Ca2+i in response to changes in extracellular Ca2+ was virtually undetectable in control or thrombin-treated cells. The intracellular response to changes in medium Ca2+ after PDGF was completely blocked by 10 mM CoCl2, but not by 10(-7) M nicardipine. Microinjection of monoclonal antibodies to phosphatidylinositol 4,5-bisphosphate (PIP2) (kt 10, 2 mg/ml) totally abolished both mobilization of intracellular Ca2+ stores and entry of extracellular Ca2+. Consistent with this finding, maintenance of Ca2+ entry required ongoing receptor occupancy, since displacement of PDGF from its receptor with suramin (1 mM) eradicated extracellular Ca2+ entry in less than 5 min. To determine whether extracellular Ca2+ entry involves the heparin-sensitive IP3 receptor, cells were microinjected with heparin (4 mg/ml) prior to addition of PDGF. Heparin, but not chondroitin sulfate, prevented mobilization of intracellular Ca2+ stores but did not affect extracellular Ca2+ entry. We PDGF requires ongoing receptor occupancy and involves PIP2 or PIP2 metabolism. However, the signal which mediates PDGF-induced Ca2+ entry does not require the heparin-sensitive IP3 receptor.
Space-time-frequency block coding over Rayleigh fading channels for OFDM systems (2004)

In this paper, a novel space-time-frequency code scheme - bit-interleaved space-time-frequency block coding (BI-STFBC) - being fit for OFDM system is considered for frequency-selective Rayleigh fading channels. Incorporating subcarrier grouping and choosing appropriate system parameters, we convert out system into a set of group STF (GSTF) system, within which STF coding is considered. Code bits are bit-wise interleaved across every grouping subcarrier before being grouped and mapped to space-time-frequency code, followed the unitary constellation-rotating precodes. The spectral efficiency and pairwise error probability (PEP) are also considered. Comparing with the existing alternatives, the proposed scheme can attain maximum diversity with low decoding flexibility. Simulation results confirmed the effectiveness of the proposed scheme.
Correlative study on expression of CA 19-9 and DU-PAN-2 in tumor tissue and in serum of pancreatic cancer patients. (1988)

The serum levels of CA 19-9 and DU-PAN-2 antigens and their expression in tumor tissue were examined in 22 pancreatic cancer patients and the results were correlated with the Lewis (Le) blood group phenotypes of the individuals. In tumor tissue, CA 19-9 was expressed in 17 of 22 (77%) specimens. The negative cases included three patients with Lea-b-, one with Lea+b- and the other with Lea-b+ phenotypes. DU-PAN-2 antigen was expressed in 20 of 22 (91%) cancer tissues. The two DU-PAN-2-negative cases were CA 19-9-positive. The combination of two markers increased the sensitivity to 100%. In the serum, CA 19-9 level was elevated (greater than 37 U/ml) in 16 of 21 (73%) cases. All Lea-b- patients had values less than 37 U/ml. An elevated level of DU-PAN-2 (greater than 300 U/ml) was detected in 14 of 21 (67%) patients including three cases with Lea-b- type. In only one patient were both antigens below the cutoff levels so that the combination of two biomarkers elevated the sensitivity to 95%. The study indicated that the cocktail of 19-9 and DU-PAN-2 antibodies might increase the sensitivity and specificity for clinical diagnosis of pancreatic cancer. In 19 of 21 (90%) cases, the serum CA 19-9 level correlated with the expression of the antigen in the cancer tissue. Discrepancy was seen in two cases; one patient had an elevated level of CA 19-9 in the serum, but lacked this antigen in the cancer cells. In the second case, the situation was reversed. For DU-PAN-2, positive correlation was seen in 14 of 21 (67%) cases. Six of seven patients with low DU-PAN-2 levels expressed the antigen in their tumor cells, and one patient with DU-PAN-2-negative cancer tissue had an elevated level of this marker in the serum. Thus, CA 19-9 expression in serum corresponded more closely to expression in tissue than did that of DU-PAN-2 antigen. The serum levels of these antigens, however, is likely due to multiple factors, only one of which is the qualitative and quantitative expression of the antigens in tumors.
Inhibition of KIT Tyrosine Kinase Activity: A Novel Molecular Approach to the Treatment of KIT-Positive Malignancies (2002)

PURPOSE: Activation of the KIT tyrosine kinase by somatic mutation has been documented in a number of human malignancies, including gastrointestinal stromal tumor (GIST), seminoma, acute myelogenous leukemia (AML), and mastocytosis. In addition, paracrine or autocrine activation of this kinase has been postulated in numerous other malignancies, including small-cell lung cancer and ovarian cancer. In this review, we discuss the rationale for and development of KIT tyrosine kinase inhibitors for the treatment of human malignancies. MATERIALS AND METHODS: Studies were identified through a MEDLINE search, review of bibliographies of relevant articles, and review of abstracts from national meetings. RESULTS: Four tyrosine kinase inhibitors that have activity against KIT are currently being used in clinical trials, and one, STI571, has recently been approved by the United States Food and Drug Administration for treating patients with chronic myelogenous leukemia. The role of KIT inhibitors in treating KIT-positive malignancies is reviewed. CONCLUSION: Targeted therapy to inhibit the kinase activity of KIT is a rational approach to the treatment of KIT-positive malignancies. Two key factors are the potency of a given inhibitor and the relative contribution of KIT activation to the growth of the tumor. Given our current understanding of KIT activity in human malignancy, the best candidate diseases for treatment with KIT inhibitors are GIST, mastocytosis, seminoma and possibly some cases of AML. Additionally, KIT inhibitors may play an adjunctive role in diseases such as small-cell lung cancer, in which KIT activation is secondary to ligand binding rather than an acquired mutation.
I-MOS: a novel semiconductor device with a subthreshold slope lower than kT/q (2003)

One of the "fundamental" problems in the continued scaling of MOSFETs is the 60 mV/decade room temperature limit in subthreshold slope. In this paper, we report initial studies on a new kind of transistor, the I-MOS. The I-MOS uses modulation of the breakdown voltage of a gated p-i-n structure in order to switch from the OFF to the ON state and vice versa. Since impact-ionization is an abrupt function of the electric field (or the carrier energy), simulations show that the device has a subthreshold slope much lower than kT/q. Simulations also show that it is indeed possible to make complementary circuits with switching speeds comparable to or exceeding CMOS. Experimental results on a silicon based prototype verify the basic concept and show very steep subthreshold slopes with high speed turn-on and turn-off. Lower bandgap materials are also being investigated to reduce the value of the breakdown voltage and permit lower voltage operation.
An Efficient and Regioselective Monobromination of Electron-Rich Aromatic Compounds Using Catalytic Hypervalent Iodine(III) Reagent (2010)

An efficient and regioselective monobromination of electron-rich aromatic compounds is reported in which iodobenzene is used as the recyclable catalyst in combination with m-chloroperbenzoic acid as the terminal oxidant. The bromination of electron-rich aromatic compounds with lithium bromide was fast in tetrahydrofuran at room temperature, providing regioselective monobrominated products in good yields.
Adeno-Associated Virus (AAV) Serotype 9 Provides Global Cardiac Gene Transfer Superior to AAV1, AAV6, AAV7, and AAV8 in the Mouse and Rat (2008)

Heart disease is the leading cause of morbidity and mortality. Cardiac gene transfer may serve as a novel therapeutic approach. This investigation was undertaken to compare cardiac tropisms of adeno-associated virus (AAV) serotypes 1, 6, 7, 8, and 9. Neonatal mice were injected with 2.5 x 10(11) genome copies (GC) of AAV serotype 1, 6, 7, 8, or 9 expressing LacZ under the control of the constitutive chicken beta-actin promoter with cytomegalovirus enhancer promoter via intrapericardial injection and monitored for up to 1 year. Adult rats were injected with 5 x 10(11) GC of the AAV vectors via direct cardiac injection and monitored for 1 month. Cardiac distribution of LacZ expression was assessed by X-Gal histochemistry, and beta-galactosidase activity was quantified in a chemiluminescence assay. Cardiac functional data and biodistribution data were also collected in the rat. AAV9 provided global cardiac gene transfer stable for up to 1 year that was superior to other serotypes. LacZ expression was relatively cardiac specific, and cardiac function was unaffected by gene transfer. AAV9 provides high-level, stable expression in the mouse and rat heart and may provide a simple alternative to the creation of cardiac-specific transgenic mice. AAV9 should be used in rodent cardiac studies and may be the vector of choice for clinical trials of cardiac gene transfer.