gebhart/patrepeval huggingface dataset:
Pectin Methylesterase, a Regulator of Pollen Tube Growth (2005)

The apical wall of growing pollen tubes must be strong enough to withstand the internal turgor pressure, but plastic enough to allow the incorporation of new membrane and cell wall material to support polarized tip growth. These essential rheological properties appear to be controlled by pectins, which constitute the principal component of the apical cell wall. Pectins are secreted as methylesters and subsequently deesterified by the enzyme pectin methylesterase (PME) in a process that exposes acidic residues. These carboxyls can be cross-linked by calcium, which structurally rigidifies the cell wall. Here, we examine the role of PME in cell elongation and the regulation of its secretion and enzymatic activity. Application of an exogenous PME induces thickening of the apical cell wall and inhibits pollen tube growth. Screening a Nicotiana tabacum pollen cDNA library yielded a pollen-specific PME, NtPPME1, containing a pre-region and a pro-region. Expression studies with green fluorescent protein fusion proteins show that the pro-region participates in the correct targeting of the mature PME. Results from in vitro growth analysis and immunolocalization studies using antipectin antibodies (JIM5 and JIM7) provide support for the idea that the pro-region acts as an intracellular inhibitor of PME activity, thereby preventing premature deesterification of pectins. In addition to providing experimental data that help resolve the significance and function of the pro-region, our results give insight into the mechanism by which PME and its pro-region regulate the cell wall dynamics of growing pollen tubes.
Automatic identification of cracks in road surfaces (1999)

The Highways Agency required a high speed automatic crack monitoring system capable of identifying and locating surface cracks of widths of approximately 2 mm and greater, over at least 80% of the width of a traffic lane (the width of traffic lanes on motorways and all-purpose trunk roads ranges approximately between 3 m and 3.65 m). Transport Research Laboratory Ltd., assisted by Softronic Systems Ltd, has undertaken an extensive programme of research, to develop an automatic crack monitoring system. The developed system now forms part of the Highways Agency Road Research Information System (HARRIS). In HARRIS, images of the road surface are collected by the survey vehicle and automatic processing of these images is then carried out in two stages. The first, or primary, stage of processing, to clean and reduce the images, is carried out in real time on board the vehicle during the survey. The second stage, that of processing the reduced images for the identification of cracks, is carried out off-line on Pentium II PCs, which are installed on the survey vehicle.
An algorithm for mapping the catheter tip position on a fluorograph to the three-dimensional position in magnetic resonance angiography volume data (2003)

This paper proposes an algorithm which maps the position of a catheter tip on a fluorograph to the 3D position in magnetic resonance angiography (MRA) data. This algorithm was assessed for its accuracy. We designed an algorithm consisting of a registration step and a recognition step. The registration step registers MRA and fluorography data using a digital subtraction angiography (DSA) image. The recognition step recognizes the position in the MRA data corresponding to the catheter tip position on a fluorograph. We checked the accuracy of the recognition step by employing an artificial data set consisting of 3D image data (64 x 64 x 64 matrix) and its projection image (92 x 92 matrix) and the accuracy of the registration step with the aid of three of the 3D time-of-flight MRA data sets (256 x 256 matrix and 60 slices) and their projection images in the form of DSA images. The accuracy of the recognition step depended upon that of the registration. When there was no misregistration, all of the mean errors were less than 0.2 mm. The mean errors of the registration step were 0.273 mm and 0.226 mm, respectively, for the longitudinal shift along the X and Y axes, 0.478 degrees, 1.203 degrees and 0.208 degrees, respectively, for the rotation angles around the X, Y and Z axes and 0.020 times for the magnification. The mean image error between the projection image of the registered MRA data and that of the MRA data which were employed as the DSA image was 0.034 mm.
Prospects for use of microgravity‐based bioreactors to study three‐dimensional host—tumor interactions in human neoplasia (1993)

Microgravity offers unique advantages for the cultivation of mammalian tissues because the lack of gravity-induced sedimentation supports three-dimensional growth in batch culture in aqueous medium. Bioreactors that simulate microgravity but operate in unit gravity provide conditions that permit human epithelial cells to grow to densities approaching 10(7) cells/ml on microcarriers in suspension, in masses up to 1 cm in diameter, and under conditions of low shear stress. While useful for many different applications in tissue culture, this culture system is especially useful for the analysis of the microenvironment in which host matrix and cells interact with infiltrating tumor cells. Growth in the microgravity-based bioreactor has supported morphological differentiation of human colon carcinoma cells when cultured with normal human stromal cells. Furthermore, these co-cultures produced factors that stimulated goblet cell production in normal colon cells in an in vivo bioassay. Early experiments also suggest that the microgravity environment will not alter the ability of epithelial cells to recognize and associate with each other and with constituents of basement membrane and extracellular matrix. These findings suggest that cells grown in bioreactors that simulate aspects of microgravity or under actual microgravity conditions will produce tissues and substances in sufficient quantity and at high enough concentration to promote characterization of molecules that control differentiation and neoplastic transformation.
Outlier-robust clustering using independent components (2008)

How can we efficiently find a clustering, i.e. a concise description of the cluster structure, of a given data set which contains an unknown number of clusters of different shape and distribution and is contaminated by noise? Most existing clustering methods are restricted to the Gaussian cluster model and are very sensitive to noise. If the cluster content follows a non-Gaussian distribution and/or the data set contains a few outliers belonging to no cluster, then the computed data distribution does not match well the true data distribution, or an unnaturally high number of clusters is required to represent the true data distribution of the data set. In this paper we propose OCI (Outlier-robust Clustering using Independent Components), a clustering method which overcomes these problems by (1) applying the exponential power distribution (EPD) as cluster model which is a generalization of Gaussian, uniform, Laplacian and many other distribution functions, (2) applying the Independent Component Analysis (ICA) for both determining the main directions inside a cluster as well as finding split planes in a top-down clustering approach, and (3) defining an efficient and effective filter for outliers, based on EPD and ICA. Our method is parameter-free and as a top-down clustering approach very efficient. An extensive experimental evaluation shows both the accuracy of the obtained clustering result as well as the efficiency of our method.
Pulse oximetry: an audit of nursing and medical staff understanding (2002)

Pulse oximetry provides continuous, non-invasive monitoring of the oxygen saturation of haemoglobin in arterial blood, which is updated with each pulse wave. The primary advantage is that it detects immediately deviations to a patient's baseline. Care givers can therefore detect changes before the patient becomes hypoxaemic. However, staff are reported to have limited education, if any, in the correct use of the pulse oximeter and what may affect the readings. In order to test this theory, an audit was conducted on 50 staff within a large general hospital, comprising trained and untrained nurses and medical staff. Participants' responses to a questionnaire and to six clinical scenarios were analysed. Overall, there was a deficit in participants' knowledge on pulse oximetry. The answers given by the medical staff to the clinical scenarios showed no greater level of knowledge than many of the trained nurses. The recommendations made following this audit were to improve the education and training of all staff in the understanding of this technique.
Effects of clozapine on rat striatal muscarinic receptors coupled to inhibition of adenylyl cyclase activity and on the human cloned m4 receptor (1997)

1. Clozapine has recently been claimed to behave as a selective and full agonist at the cloned m4 muscarinic receptor artificially expressed in Chinese hamster ovary (CHO) cells. In the present study we have investigated whether clozapine could activate the rat striatal muscarinic receptors coupled to the inhibition of adenylyl cyclase activity, considered as pharmacologically equivalent to the m4 gene product. In addition, we have examined the effect of the drug on various functional responses following the activation of the cloned m4 receptor expressed in CHO cells. 2. In rat striatum, clozapine (1 nM-10 microM) caused a slight inhibition of forskolin-stimulated adenylyl cyclase activity, which was not counteracted by 10 microM atropine. On the other hand, clozapine antagonized the inhibitory effect of acetylcholine with a pA2 value of 7.51. Moreover, clozapine (1 microM) failed to inhibit dopamine D1 receptor stimulation of adenylyl cyclase activity, but counteracted the inhibitory effect of carbachol (CCh). Clozapine displaced [3H]-N-methylscopolamine ([3H]-NMS) bound to striatal M4 receptors with a monophasic inhibitory curve and a pKi value of 7.69. The clozapine inhibition was not affected by the addition of guanosine-5'-O-(thio)triphosphate (GTPgammaS). 3. In intact CHO cells, clozapine inhibited forskolin-stimulated cyclic AMP accumulation with an EC50 of 31 nM. This effect was antagonized by atropine. CCh produced a biphasic effect on cyclic AMP levels, inhibiting at concentrations up to 1 microM (EC50=50 nM) and stimulating at higher concentrations (EC50 = 7 microM). Clozapine (0.3-5 microM) antagonized the CCh stimulation of cyclic AMP with a pKi value of 7.47. Similar results were obtained when the adenylyl cyclase activity was assayed in CHO cell membranes. 4. In CHO cells pretreated with the receptor alkylating agent 1-ethoxycarbonyl-2-ethoxy-1,2-dihydroquinoline (10 microM), the maximal inhibitory effect of clozapine on cyclic AMP formation was markedly reduced, whereas the CCh inhibitory curve was shifted to the right with no change in the maximum. 5. As in rat striatum, in CHO cell membranes the displacement of [3H]-NMS binding by clozapine yielded a monophasic curve which was not affected by GTPgammaS. 6. Clozapine (10 nM-10 microM) had a small stimulant effect (approximately 20%) on the binding of [35S]-GTPgammaS to CHO cell membranes, whereas CCh caused a 250% increase of radioligand binding. Moreover, clozapine (50 nM-5 microM) antagonized the CCh-stimulated [35S]-GTPgammaS binding with a pA2 value of 7.48. 7. These results show that at the striatal M4 receptors clozapine is a potent and competitive antagonist, whereas at the cloned m4 receptor it elicits both agonist and antagonist effects. Thus, clozapine behaves as a partial agonist, rather than as a full agonist, at the m4 receptor subtype, with intrinsic activity changing as a function of the coupling efficiency of the receptor to effector molecules.
Ultrafast clustering algorithms for metagenomic sequence analysis (2012)

The rapid advances of high-throughput sequencing technologies dramatically prompted metagenomic studies of microbial communities that exist at various environments. Fundamental questions in metagenomics include the identities, composition and dynamics of microbial populations and their functions and interactions. However, the massive quantity and the comprehensive complexity of these sequence data pose tremendous challenges in data analysis. These challenges include but are not limited to ever-increasing computational demand, biased sequence sampling, sequence errors, sequence artifacts and novel sequences. Sequence clustering methods can directly answer many of the fundamental questions by grouping similar sequences into families. In addition, clustering analysis also addresses the challenges in metagenomics. Thus, a large redundant data set can be represented with a small non-redundant set, where each cluster can be represented by a single entry or a consensus. Artifacts can be rapidly detected through clustering. Errors can be identified, filtered or corrected by using consensus from sequences within clusters.
Olfactory responses to attractants and repellents in tsetse (1999)

The aims of this study were to investigate how antennal olfactory cells of tsetse (Diptera: Glossinidae) code odour quality and how they are able to discriminate between attractive and repellent odours. For Glossina pallidipes Austen, a survey is presented of the cells' responses to attractive (1-octen-3-ol, acetone, 3-methylphenol, carbon dioxide) and repellent stimuli (2-methoxyphenol, acetophenone, lactic acid, naphthalene). In addition, the responses of these cells to binary mixtures and the dose-response curves of 1-octen-3-ol, 3-methylphenol, 2-methoxyphenol and acetophenone are presented. A minority of the cells responded to one attractant or repellent only, whereas the vast majority were excited by more than one of the attractive and/or repellent stimuli. It is proposed that the peripheral olfactory cells of tsetse discriminate between different compounds via an across-fibre pattern coding, in which the cells that specifically code for attractants or repellents may play a substantial role in composing a unique excitation pattern that informs the central nervous system about the specificity of odours.
Enhanced Protonation of Cresol Red in Acidic Aqueous Solutions Caused by Freezing (2006)

The protonation degree of cresol red (CR) in frozen aqueous solutions at 253 or 77 K, containing various acids (HF, HCl, HNO3, H2SO4, and p-toluenesulfonic acid), sodium hydroxide, NaCl, or NH4Cl, was examined using UV/Vis absorption spectroscopy. CR, a weak organic diacid, has been selected as a model system to study the acid-base interactions at the grain boundaries of ice. The multivariate curve resolution alternating least-squares method was used to determine the number and abundances of chemical species responsible for the overlaying absorption visible spectra measured. The results showed that the extent of CR protonation, enhanced in the solid state by 2-4 orders of magnitude in contrast to the liquid solution, is principally connected to an increase in the local concentration of acids. It was found that this enhancement was not very sensitive to either the freezing rate or the type of acid used and that CR apparently established an acid-base equilibrium prior to solidification. In addition, the presence of inorganic salts, such as NaCl or NH4Cl, is reported to cause a more efficient deprotonation of CR in the former case and an enhanced protonation in the latter case, being well explained by the theory of Bronshteyn and Chernov. CR thus served as an acid-base indicator at the grain boundaries of ice samples. Structural changes in the CR molecule induced by lowering the temperature and a presence of the constraining ice environment were studied by the absorption and 1H NMR spectroscopies. Cryospheric and atmospheric implications concerning the influence of acids and bases on composition and reactivity of ice or snow contaminants were examined.
Safety and Immunogenicity of a Replication‐Incompetent Adenovirus Type 5 HIV‐1 Clade Bgag/pol/nefVaccine in Healthy Adults (2008)

The vaccine was generally well tolerated and induced cell-mediated immune responses against human immunodeficiency virus type 1 peptides in most healthy adults. Despite these findings, vaccination in a proof-of-concept trial with use of this vaccine was discontinued because of lack of efficacy.
Reactive astrocytes express the embryonic intermediate neurofilament nestin (1994)

Nestin is a neurofilament protein expressed by the immediate precursors to neurons and glia in rats and humans. Nestin immunoreactivity in the rat CNS was studied following kainic acid (KA) hippocampal lesions. Numerous nestin positive cells within the KA lesion were confirmed to be reactive astrocytes by their immunoreactivity for glial fibrillary acidic protein (GFAP). The number of these cells decreased with time after the KA lesion and no astrocyte immunostaining for nestin was observed in control animals. A subset of nestin-positive cells in the ventricular subependymal region appeared to be radial glial cells, extending to cell body layers. Nestin is one of several embryonic markers expressed by reactive astrocytes, suggesting an embryonic reversion induced by the KA lesion, possibly to enhance functional recovery.
Determination of the wavelength dependence of the differential pathlength factor from near-infrared pulse signals (1998)

For the calculation of changes in oxyhaemoglobin, deoxyhaemoglobin and the redox state of cytochrome-c-oxidase from attenuation data via a modified Beer-Lambert equation the wavelength dependence of the differential pathlength factor (DPF(lambda)) has to be taken into account. The DPF, i.e. the ratio of the mean optical pathlength and the physical light source-detector separation at each wavelength, determines the crosstalk between the different concentrations and is therefore essential for a sensitive detection of chromophore changes. Here a simple method is suggested to estimate the wavelength dependence of the DPF(lambda) from pulse-induced attenuation changes measured on the head of adult humans. The essence is that the DPF is the ratio of the attenuation changes over absorption coefficient changes, and that the spectral form of the pulse correlated absorption coefficient change can be assumed to be proportional to the extinction coefficient of blood. Indicators for the validity of the DPF(lambda) derived for wavelengths between 700 and 970 nm are the stability of the calculated haemoglobin and cytochrome signals with variations of the wavelength range included for their calculation and its overall agreement with the data available from the literature.
Method to budget and optimize total device overlay (1999)

We combine lithographic simulation, experimental data and statistical modeling to build a predictive estimator of total device overlay. To generate accurate predictions of total overlay, we include error estimates on lens image placement, CD control, reticle and exposure tool alignment. Instead of combining these errors in ad hoc root sum square fashion to make overlay estimates, we construct a physical model of the device and metrology marker edge placement processes. The model comprehends the differential placement of metrology structures and device features due to lens and illumination system asymmetries and is therefore applicable to the evaluation of arbitrary illumination and pattern geometry conditions. Since we attempt to model the relative placement distribution of specific device features, the model produces overlay estimates that are directly relevant for device performance. The comparison of our total overlay estimate to device overlay sensitivity data allows a projection of the overlay related yield loss for a given device, process and tools et. Finally, our model allows the process engineer to made informative choices on the optimum error sources to pursue for improving overlay.
Thermal Treatment of Beads with Wax for Controlled Release (1989)

AbstractBeads prepared by extruder/marumerizer technology were formulated with water soluble drugs, microcrystalline cellulose and several waxy materials. The waxes (10 to 50% by weight) were included in an effort to slow drug release. Subsequent thermal treatment of these beads was applied. Beads were processed to determine the effect of varying wax level, excipient, active drug, and effect of heat treatment. In-vitro drug release profiles were evaluated for the untreated and thermal treated beads. In general, the simple incorporation of wax into the granulation did not provide the desired controlled release dissolution profile. Thermal treatment of the finished beads, however, resulted in products which behaved in a different manner during dissolution testing and in general provided slower release. Drug release was found to vary with the type and level of wax, drug, excipient, and the thermal treatment.
Exposure of Human, Boar, or Bull Sperm to a Synthetic Peptide Increases Binding to an Egg‐Membrane Substrate (1999)

We evaluated the effects of in vitro exposure of sperm to synthetic FertPlus peptide, which represents a 60-amino acid sequence within rat prosaposin, using a microwell sperm-binding assay (SBA), in which an extract of hen's egg served as the binding substrate. Sperm suspensions were incubated with FertPlus peptide (six to eight concentrations; 0 and 20-1,280 pM) at 37 degrees C for 10 minutes, diluted > or = 20 times, and placed onto SBA plates. After 60 minutes at 37 degrees C, unbound sperm were washed away and the DNA of bound sperm was quantified. Percentage of sperm bound was independent of the percentage of motile sperm, but immotile sperm did not bind. For fresh human sperm (25 ejaculates), the percentage of sperm bound was increased by exposure to 640 pM peptide (P < 0.01). For 11 of 25 samples, the percentage of sperm bound for the aliquot exposed to 640 pM peptide was > or = 1.4 times the value for a 0 pM control aliquot. With frozen-thawed human sperm, for six of seven samples, binding was > or = 1.4 times greater after exposure to 640 pM peptide. For boar sperm held for approximately 24 hours at approximately 18 degrees C before use (28 ejaculates), there was a higher percentage of sperm bound for aliquots previously exposed to 1,280 pM peptide than there was for control aliquots (P < 0.01). For 16 of 28 samples, exposure to peptide increased the percentage of sperm bound by > or = 1.4 times. For frozen-thawed bull sperm, percentage of sperm bound was > or = 1.4 times greater for 4 of 10 samples that were briefly exposed to 160 pM peptide. Clearly, human, boar, and bull sperm were beneficially modified by brief in vitro exposure to FertPlus peptide, so that for many samples a greater percentage of sperm was bound in vitro. As presented in an accompanying paper, fertility of bull sperm was increased by brief exposure to FertPlus peptide.
Small Molecule Ligands Define a Binding Site on the Immune Regulatory Protein B7.1 (2002)

The interaction of co-stimulatory molecules on T cells with B7 molecules on antigen presenting cells plays an important role in the activation of naive T cells. Consequently, agents that disrupt these interactions should have applications in treatment of transplant rejection as well as autoimmune diseases. To this end, specific small molecule inhibitors of human B7.1 were identified and characterized. These compounds inhibit the binding of B7.1 to both CD28 and CTLA4. Both classes of compounds appear to bind the same site, a relatively small portion of the GFCC'C" face of the N-terminal V-set domain of human B7.1, not present in the homologous B7.2 or even mouse B7.1. This site may represent a rare hot spot for small molecule antagonist design of inhibitors of cell-cell interactions, whose ligands may yield leads for the development of novel immunomodulatory medicines.
Size at birth and adrenocortical function in childhood (1996)

These findings suggests that the intra-uterine environment, as measured by fetal size at birth, has long-lasting effects on the function of the hypothalamo-pituitary-adrenal axis.