gebhart/patrepeval huggingface dataset:
Effect of Ge profile on the frequency response of a SiGe pFET on sapphire technology (2002)

We investigate the dc and microwave properties of a SiGe pFET on sapphire technology. The results show that both cutoff frequency (f/sub T/) and low-field mobility (/spl mu//sub eff/) of SiGe pFETs improve with the integrated Ge dose in the SiGe channel, when compared to the Si pFET. Silicon CMOS on sapphire (Al/sub 2/O/sub 3/) technology is ideally suited for microwave circuits since it has a low dielectric loss substrate, low noise figure, excellent radiation hardness, and reduced punch-through effects. Recent studies of SiGe CMOS on sapphire technology have shown improvements in pFET mobility and transconductance at 300 K and 77 K, compared to Si. This work focuses on the effects of Ge profile in the SiGe channel on the low field mobility and cutoff frequency of a SiGe pFET on sapphire technology.
Regioselective Activation of Aminothiazole(iminoxyacetic acid)acetic Acid:  An Efficient Synthesis of the Monobactam Aztreonam (2002)

An efficient synthesis of the monobactam aztreonam [[2S-[2α,3β(Z)]]-3[[(2-amino-4-thiazolyl)[(1-carboxy-1-methylethoxy)imino]acetyl]amino]-2-methyl-4-oxo-1-azetidinesulfonic acid] (1) by acylation of α-aminoazetidinone 22 with the regioselectively activated aminothiazoleiminoxyacetic diacid 15 or 18 is described. Reaction of benzhydryl ester 10 with N-hydroxybenzotriazole and dicyclohexylcarbodiimide followed by ester deprotection formed the monoacid amide 15. Alternatively, chemoselective transient silylation of the diacid 9 followed by activation with N-hydroxysuccinimide formed active ester 18. Acylation of α-aminoazetidinone 22 with amide 15 or ester 18 produced aztreonam (1) in 75−85% yield.
Ultrafast photonic interface for storage networking using serial-to-parallel and parallel-to-serial conversion (2003)

Recently, there has been a rapidly growing demand for ultrafast and large-capacity storage networking technology. This is due to the explosive increase in the amount of data handled in business settings. The technology makes it possible to share and back up data synchronously at multiple remote storage sites on a real-time basis. This is also of great importance in terms of disaster recovery. Currently, fiber channels (FC) have normally been used for the connection between storage systems and network servers in a storage area network (SAN) with a maximum transmission speed of 1-2 Gbit/s and a transmission distance of below 10 km using a single-mode fiber and a 1.3-pm laser diode [1]. Despite the possibility of increasing the maximum speed to 4 Gbit/s, the FC-based SAN (FC-SAN) cannot efficiently process the 1-10 Tbyte levels of data used in a single company. Additionally the SCSI-3 protocol used in FC-SAN is a major factor increasing the system cost. IP storage technology is an attractive way to overcome the above drawbacks. For instance, 10 Gbit/s Ethernet technology can be used and is capable of cheaper and longer distance transmissions. This also means that technologies targeting future advanced IP photonic networks can be used with IP storage. In this work, we propose a novel ultrafast photonic interface for use in storage networking based on all-optical serial-to-parallel and photonic parallel-to-serial conversion. We demonstrate its operation with 40-Gbit/s 16-bit optical data using compact modules and a potential bandwidth of over 100 Gbit/s. We discuss the advantages of the interface and its possible application forms in storage networking.
Use of the counter selectable marker PheS* for genome engineering in Staphylococcus aureus (2019)

The gold standard method for the creation of gene deletions in Staphylococcus aureus is homologous recombination using allelic exchange plasmids with a temperature-sensitive origin of replication. A knockout vector that contains regions of homology is first integrated into the chromosome of S. aureus by a single crossover event selected for at high temperatures (non-permissive for plasmid replication) and antibiotic selection. Next, the second crossover event is encouraged by growth without antibiotic selection at low temperature, leading at a certain frequency to the excision of the plasmid and the deletion of the gene of interest. To detect or encourage plasmid loss, either a beta-galactosidase screening method or, more typically, a counterselection step is used. We present here the adaptation of the counter-selectable marker pheS*, coding for a mutated subunit of the phenylalanine tRNA synthetase, for use in S. aureus. The PheS* protein variant allows for the incorporation of the toxic phenylalanine amino acid analogue para-chlorophenylalanine (PCPA) into proteins and the addition of 20-40 mM PCPA to rich media leads to drastic growth reduction for S. aureus and supplementing chemically defined medium with 2.5-5 mM PCPA leads to complete growth inhibition. Using the new allelic exchange plasmid pIMAY*, we delete the magnesium transporter gene mgtE in S. aureus USA300 LAC* (SAUSA300_0910/SAUSA300_RS04895) and RN4220 (SAOUHSC_00945) and demonstrate that cobalt toxicity in S. aureus is mainly mediated by the presence of MgtE. This new plasmid will aid the efficient and easy creation of gene knockouts in S. aureus.
Determination of iodide in samples with complex matrices by hyphenation of capillary isotachophoresis and zone electrophoresis (2007)

A method has been developed for the determination of iodide in mineral water, seawater, cooking salt, serum, and urine based on hyphenation of capillary ITP and zone electrophoresis. A commercially available instrumentation for capillary ITP with column-switching system was used. ITP served for removal of chloride present in the analyzed samples in a ratio of 10(6)-10(7):1 to iodide, zone electrophoresis was used for evaluation. Isotachophoretic separation proceeded in a capillary made of fluorinated ethylene-propylene copolymer of 0.8 mm id and 90 mm total length to the bifurcation point filled with a leading electrolyte (LE) composed of 8 mM HCl + 16 mM beta-alanine (beta-Ala) + 10% PVP + 2.86 mM N(2)H(4)x2HCl, pH 3.2; and a terminating electrolyte composed of 8 mM H(3)PO(4) + 16 mM beta-Ala + 10% PVP + 5 mM N(2)H(4), pH 3.85 for all the matrices except seawater. For ITP of seawater the LE consisted of 50 mM HCl + 100 mM beta-Ala + 10% PVP + 2.86 mM N(2)H(4)x2HCl, pH 3.52. Distance of conductivity detector from the injection point and bifurcation point was 52 and 38 mm, respectively. Zone electrophoresis was performed in a capillary made of fused silica of 0.3 mm id and 160 mm total length filled with LE from isotachophoretic step. LODs reached for all matrices were 2-3x10(-8) M concentration (2.5-4 microg/L) enabled monitoring of iodide in all analyzed samples with RSD 0.4-9.3%. Estimated concentrations of iodide in individual matrices were 10(-6)-10(-8) M.
G Protein-coupled Receptors Mediate Two Functionally Distinct Pathways of Tyrosine Phosphorylation in Rat 1a Fibroblasts (1997)

The Ras-dependent activation of Erk kinases by G protein-coupled receptors (GPCRs) is thought to involve tyrosine phosphorylation of docking proteins that serve as scaffolds for the plasma membrane recruitment of Ras guanine nucleotide exchange factors, such as the Grb2-mSos complex. We have investigated the role of two GPCR-regulated tyrosine phosphoproteins, p125(FAK) (FAK) and Shc, in the Ras-dependent activation of Erk kinases by endogenously expressed GPCRs in Rat 1a fibroblasts. Several lines of evidence suggest that tyrosine phosphorylation of FAK and Shc are independently regulated. The GPCRs for lysophosphatidic acid (LPA), thrombin, and bombesin mediate equivalent increases in FAK tyrosine phosphorylation and FAK-Grb2 association. In contrast, only LPA and thrombin receptors significantly stimulate Shc tyrosine phosphorylation and Shc-Grb2 complex formation. Tyrosine phosphorylation of FAK is pertussis toxin-insensitive, can be mimicked by calcium ionophore, and is inhibited by treatment with cytochalasin D, which depolymerizes the actin cytoskeleton. In contrast, tyrosine phosphorylation of Shc is inhibited by pertussis toxin treatment, is not induced by calcium ionophore, and is insensitive to cytochalasin D. In each case, the rapid stimulation of Erk 1/2 correlates with tyrosine phosphorylation of Shc but not of FAK. The dissociation of FAK-Grb2 complex formation from receptor-mediated activation of Erk 1/2 indicates that recruitment of Grb2-mSos to the plasma membrane is not sufficient to mediate rapid Erk activation. Using four mechanistically distinct inhibitors of clathrin-mediated endocytosis, concanavalin A, hypertonic medium, depletion of intracellular potassium, and monodansylcadaverine, we find that GPCR-mediated Erk 1/2 activation is also endocytosis-dependent. Thus, we propose that an additional step involving vesicle-mediated endocytosis is required for the rapid, Ras-dependent activation of Erk kinases in fibroblasts.
Reverse Classification Accuracy: Predicting Segmentation Performance in the Absence of Ground Truth (2017)

When integrating computational tools, such as automatic segmentation, into clinical practice, it is of utmost importance to be able to assess the level of accuracy on new data and, in particular, to detect when an automatic method fails. However, this is difficult to achieve due to the absence of ground truth. Segmentation accuracy on clinical data might be different from what is found through cross validation, because validation data are often used during incremental method development, which can lead to overfitting and unrealistic performance expectations. Before deployment, performance is quantified using different metrics, for which the predicted segmentation is compared with a reference segmentation, often obtained manually by an expert. But little is known about the real performance after deployment when a reference is unavailable. In this paper, we introduce the concept of reverse classification accuracy (RCA) as a framework for predicting the performance of a segmentation method on new data. In RCA, we take the predicted segmentation from a new image to train a reverse classifier, which is evaluated on a set of reference images with available ground truth. The hypothesis is that if the predicted segmentation is of good quality, then the reverse classifier will perform well on at least some of the reference images. We validate our approach on multi-organ segmentation with different classifiers and segmentation methods. Our results indicate that it is indeed possible to predict the quality of individual segmentations, in the absence of ground truth. Thus, RCA is ideal for integration into automatic processing pipelines in clinical routine and as a part of large-scale image analysis studies.
Optical instrumentation for respiration measurement in magnetic resonance scanners (1995)

Abstract:
Magnetic resonance imaging (MRI) is a non-invasive technique for visualising the internal structure of the body. The method involves placing the subject in a strong static magnetic field (c. 1.5 T) and using various combinations of radiofrequency energy and pulsed magnetic field gradients, known as pulse sequences, to produce images. Most MRI pulse sequences acquire data over an extended time period in order to produce an image. Any physiological motion, e.g. movement of the heart, respiration etc., during this time period will cause artefacts and blurring. Various approaches have been employed to try and reduce this sensitivity to motion, including the synchronisation of data collection with the subjects electrocardiogram (EGG) to minimise cardiac motion and the development of fast pulse sequences to acquire the data within multiple breath-hold periods, between 10 and 20s. We have been employing both techniques together to acquire dynamic images of cardiac function. The requirement for data collection over multiple breath-holds however, is that each breath-hold must be reproducible, so that the heart is in the same position within the thorax each time. Even with highly motivated subjects it is difficult for them to breath-hold in a consistent manner. This paper outlines the adaptation and development of the Fibre Optic Respiratory Plethysmograph (FORP) to produce a MRI gating system (FORP-GS). This consists of a PC based, non-invasive respiratory sensor and a joint optical feedback system to the subject, allowing accurate monitoring of the thorax position in real time without any electro-magnetic interference.
Embryonic stem cells : a practical approach (2006)

Preface 1 Introduction 2. Procedures for deriving ES cell lines from the mouse 3. Production of ES cell-derived mice 4. Generating animal models of human mitochondrial genetic disease using mouse ES cells 5. Controlling the differentiation of mouse ES cells in vitro 6. In vitro differentiation of mouse ES cells into muscle cells 7. In vitro differentiation of mouse ES cells into haematopoietic cells 8. Lineage selection and transplantation of mouse ES cell-derived neural precursors 9. In vitro differentiation of mouse ES cells into pancreatic and hepatic cells 10. Isolation and characterisation of human ES cells 11. Differentiation of human ES cells 12. ES cell lines from the cynomolgus monkey (Macaca fascicularis) Index
Antisense Oligonucleotides Containing Modified Bases Inhibit in Vitro Translation of Leishmania amazonensis mRNAs by Invading the Mini-exon Hairpin (1999)

Complementary oligodeoxynucleotides (ODNs) that contain 2-aminoadenine and 2-thiothymine interact weakly with each other but form stable hybrids with unmodified complements. These selectively binding complementary (SBC) agents can invade duplex DNA and hybridize to each strand (Kutyavin, I. V., Rhinehart, R. L., Lukhtanov, E. A., Gorn, V. V., Meyer, R. B., and Gamper, H. B. (1996) Biochemistry 35, 11170-11176). Antisense ODNs with similar properties should be less encumbered by RNA secondary structure. Here we show that SBC ODNs strand invade a hairpin in the mini-exon RNA of Leishmania amazonensis and that the resulting heteroduplexes are substrates for Escherichia coli RNase H. SBC ODNs either with phosphodiester or phosphorothioate backbones form more stable hybrids with RNA than normal base (NB) ODNs. Optimal binding was observed when the entire hairpin sequence was targeted. Translation of L. amazonensis mRNA in a cell-free extract was more efficiently inhibited by SBC ODNs complementary to the mini-exon hairpin than by the corresponding NB ODNs. Nonspecific protein binding in the cell-free extract by phosphorothioate SBC ODNs rendered them ineffective as antisense agents in vitro. SBC phosphorothioate ODNs displayed a modest but significant improvement of leishmanicidal properties compared with NB phosphorothioate ODNs.
Protein-bound Vaccinium fruit polyphenols decrease IgE binding to peanut allergens and RBL-2H3 mast cell degranulation in vitro (2017)

Peanut allergy is a worldwide health concern. In this study, the natural binding properties of plant-derived polyphenols to proteins was leveraged to produce stable protein-polyphenol complexes comprised of peanut proteins and cranberry (Vaccinium macrocarpon Ait.) or lowbush blueberry (Vaccinium angustifolium Ait.) pomace polyphenols. Protein-bound and free polyphenols were characterized and quantified by multistep extraction of polyphenols from protein-polyphenol complexes. Immunoblotting was performed with peanut-allergic plasma to determine peanut protein-specific IgE binding to unmodified peanut protein, or to peanut protein-polyphenol complexes. In an allergen model system, RBL-2H3 mast cells were exposed to peanut protein-polyphenol complexes and evaluated for their inhibitory activity on ionomycin-induced degranulation (β-hexosaminidase and histamine). Among the evaluated polyphenolic compounds from protein-polyphenol complex eluates, quercetin, - in aglycone or glycosidic form - was the main phytochemical identified to be covalently bound to peanut proteins. Peanut protein-bound cranberry and blueberry polyphenols significantly decreased IgE binding to peanut proteins at p < 0.05 (38% and 31% decrease, respectively). Sensitized RBL-2H3 cells challenged with antigen and ionomycin in the presence of protein-cranberry and blueberry polyphenol complexes showed a significant (p < 0.05) reduction in histamine and β-hexosaminidase release (histamine: 65.5% and 65.8% decrease; β-hexosaminidase: 60.7% and 45.4% decrease, respectively). The modification of peanut proteins with cranberry or blueberry polyphenols led to the formation of peanut protein-polyphenol complexes with significantly reduced allergenic potential. Future trials are warranted to investigate the immunomodulatory mechanisms of these protein-polyphenol complexes and the role of quercetin in their hypoallergenic potential.
Ultrasound Microbubble Contrast and Current Clinical Applications (2011)

Ultrasound imaging is widely used worldwide principally because it is cheap, easily available and contains no exposure to ionizing radiation. The advent of microbubble ultrasound contrast has further increased the diagnostic sensitivity and specificity of this technique thus widening its clinical applications. The third generation of ultrasound contrast agents consist of sulphur hexafluoride microbubbles encased in a phospholipid shell. This review will elaborate on the pharmacology, safety profile and method of action of these agents. We also aim to discuss the ever expanding uses for contrast enhanced ultrasound in a number of clinical specialities which include the liver, kidney, prostate, sentinel node detection, vascular tree and endovascular stent surveillance. We will also discuss some of the recent patents regarding the future uses of ultrasound microbubble contrast and recent technological advances in clinical applications.
You Can Figure Your Spring Freeze Hazard (1953)

If you feel like gambling on the date of the last spring freeze, here is a quick way to find out whether or not the odds are in your favor.
Biomechanical Comparison of Lasso, Pulvertaft Weave, and Side-by-Side Tendon Repairs (2009)

The strength of the lasso tendon repair compared well with the Pulvertaft weave and was more convenient to perform. Side-by-side repair was inferior because of its low maximum load. This study suggests that lasso repair may be an alternative to the Pulvertaft weave in tendon grafts and transfers.
An Optimal Algorithm for Intersecting Three-Dimensional Convex Polyhedra (1992)

This paper describes a linear-time algorithm for computing the intersection of two convex polyhedra in 3-space. Applications of this result to computing intersections, convex hulls, and Voronoi diagrams are also given.
Determination of Oxycodone Hydrochloride in Oral Solutions by High-Performance Thin-Layer Chromatography/Densitometry (2000)

Abstract A thin-layer chromatography/densitometry method was developed and validated for the determination of oxycodone hydrochloride in oral solutions by using silica gel plates. A horizontal technique was used for development of the plates. The optimum composition for the mobile phase, which provided a suitable Rf value of 0.6 for oxycodone, was propanol–acetic acid–water–25% ammonia–methanol (20 + 1 + 1 + 3 + 10). Detection was at 234 nm. Oxycodone hydrochloride was stable on the sorbent and was precisely and accurately measured in the range of 0.3–1.5 μg/band.
Microstructure and Mechanical Performance of Belite Cements from High Calcium Coal Fly Ash (2005)

The microstructure and mechanical performance of two low energy fly ash belite cements (FABC‐1‐W and FABC‐1‐N) obtained from high calcium‐coal fly ash as raw material is studied in this work. The FABC were obtained after a previous hydrothermal treatment of the fly ash in demineralized water and NaOH 1 M solution. The hydration of both FABC‐1‐W and FABC‐1‐N during 180 days was followed by thermal analysis, X‐ray diffraction, FT infrared spectroscopy, scanning electron microscopy and Brunauer‐Emmett and Teller‐N 2 surface area measurements. The mechanical properties were studied under different curing conditions: normal (21°C and <95% RH) and accelerated (40°C and <95% RH). Porosity and pore‐size distribution were also studied. The results showed a better mechanical performance for FABC‐1‐N when the curing was normal and a better mechanical performance for FABC‐1‐W when the curing was accelerated.
Exosomes and other microvesicles in infection biology: organelles with unanticipated phenotypes (2010)

The release of exosomes and other microvesicles by diverse prokaryotic and eukaryotic cells and organisms was first appreciated early in the 20th century. The functional properties of these organelles, however, have only recently been the focus of rigorous investigation. In this review, we discuss the release of microvesicles of varying complexity by diverse microbial pathogens. This includes vesicle secretion by Gram-negative bacteria, eukaryotic parasites of the kinetoplast lineage and opportunistic fungal pathogens of both the ascomycetes and basidiomycetes lineages. We also discuss vesicle release from mammalian cells brought about as a result of infection with bacteria, viruses and prions. In addition, we review the evidence showing that in their specific microenvironments, release of these organelles from diverse pathogens contributes to pathogenesis. Germane to this and based upon recent findings with Leishmania, we propose a model whereby exosome release by an intracellular pathogen serves as a general mechanism for effector molecule delivery from eukaryotic pathogen to host cell cytosol. These new findings linking exosomes and other microvesicles to infection biology have important implications for understanding the immune response to infection and for the design of research strategies aimed at the development of novel therapeutics and vaccines.
Anti-Hypertensive Medication Use and Incident Alzheimer's Disease. The Cache County Study (2006)

Background: Recent reports suggest that antihypertensive (AH) medications may reduce the risk of dementing illnesses. Objectives: To examine the relationship of AH medication use with incidence of Alzheimer disease (AD) among the elderly population (aged 65 years and older) of Cache County, Utah, and to examine whether the relationship varies with different classes of AH medications. Methods: After an initial (wave 1) multistage assessment (1995 through 1997) to identify prevalent cases of dementia, we used similar methods 3 years later (wave 2) to identify 104 incident cases of AD among the 3308 survivors. At the baseline assessment, we obtained a detailed drug inventory from the study participants. We carried out discrete time survival analyses to examine the association between the use of AH medications (including angiotensin converting enzyme inhibitors, beta-blockers, calcium channel blockers, and diuretics) at baseline with subsequent risk of AD. Results: Use of any AH medication at baseline was associated with lower incidence of AD (adjusted hazard ratio, 0.64; 95% confidence interval, 0.41-0.98). Examination of medication subclasses showed that use of diuretics (adjusted hazard ratio, 0.57; 95% confidence interval, 0.33-0.94), and specifically potassium-sparing diuretics (adjusted hazard ratio, 0.26; 95% confidence interval, 0.08-0.64), was associated with the greatest reduction in risk of AD. Corresponding analysis with a fully examined subsample controlling for blood pressure measurements did not substantially change our findings. Conclusions: These data suggest that AH medications, and specifically potassium-sparing diuretics, are associated with reduced incidence of AD. Because the latter association is a new finding, it requires confirmation in further study.