gebhart/patrepeval huggingface dataset:
Extensive Set of 16S rRNA-Based Probes for Detection of Bacteria in Human Feces (2002)

For the detection of six groups of anaerobic bacteria in human feces, we designed seven new 16S rRNA-based oligonucleotide probes. This set of probes extends the current set of probes and gives more data on the composition of the human gut flora. Probes were designed for Phascolarctobacterium and relatives (Phasco741), Veillonella (Veil223), Eubacterium hallii and relatives (Ehal1469), Lachnospira and relatives (Lach571), and Eubacterium cylindroides and relatives (Ecyl387), and two probes were designed for Ruminococcus and relatives (Rbro730 and Rfla729). The hybridization conditions for the new probes were optimized for fluorescent in situ hybridization, and the probes were validated against a set of reference organisms. The probes were applied to fecal samples of 11 volunteers to enumerate their target bacterial groups. The Phasco741 and Veil223 probes both detected average numbers below 1% of the total number of bacteria as determined with the bacterial kingdom-specific Bact338 probe. The Ecyl387 probe detected about 1.4%, the Lach571 and Ehal1469 probes detected 3.8 and 3.6%, respectively, and a combination of the Rbro730 and Rfla729 probes detected 10.3%. A set of 15 probes consisting of probes previously described and those presented here were evaluated in hybridization with the fecal samples of the same volunteers. Together, the group-specific probes detected 90% of the total bacterial cells.
GLUT1 and CAIX as intrinsic markers of hypoxia in bladder cancer: relationship with vascularity and proliferation as predictors of outcome of ARCON (2003)

Glucose transporter-1 protein (GLUT1) and carbonic anhydrase IX (CAIX) are regulated by hypoxia inducible factor-1 (HIF-1) and have been studied as putative intrinsic cellular markers for hypoxia. This study directly compares CAIX and GLUT1 with pimonidazole binding in a prospective series of bladder cancer patients and also studies the prognostic significance of the markers, in combination with vascularity and proliferation, in a retrospective series of bladder cancer patients treated in a phase II trial of radical radiotherapy with carbogen and nicotinamide (ARCON). A total of 21 patients with a diagnosis of transitional cell carcinoma of the bladder received 0.5 g m(-2) pimonidazole. Serial tumour sections were stained for pimonidazole, GLUT1 and CAIX and compared. Tissue sections obtained from a series of 64 patients previously treated for invasive bladder cancer using ARCON were stained for GLUT1 and CAIX together with Ki-67 and CD31/34. There was a good geographical colocalisation of both intrinsic markers with pimonidazole and a highly significant agreement in individual patients; correlation coefficients were 0.82 (P=0.0001) for GLUT1 and 0.74 (P<0.0001) for CAIX. In both series of patients, the intrinsic hypoxia markers were highly correlated with each other and a correlation with proliferation was also evident in the retrospective study. In univariate and multivariate analyses, GLUT1 and CAIX were independent predictors for overall and cause specific survival. The hypoxia markers did not predict for local control or metastases-free survival although higher Ki-67 indices showed a trend towards local failure. The data suggest that both hypoxia modification and accelerated treatment may be valid treatment options in bladder cancer.
Projected Gradient Methods for Nonnegative Matrix Factorization (2007)

Nonnegative matrix factorization (NMF) can be formulated as a minimization problem with bound constraints. Although bound-constrained optimization has been studied extensively in both theory and practice, so far no study has formally applied its techniques to NMF. In this letter, we propose two projected gradient methods for NMF, both of which exhibit strong optimization properties. We discuss efficient implementations and demonstrate that one of the proposed methods converges faster than the popular multiplicative update approach. A simple Matlab code is also provided.
Studying brain development with quail-chick neural chimeras. (1993)

Avian embryonic neural chimeras are constructed by substituting defined areas of the neural epithelium of a chick embryo by their exact counterpart obtained from a quail embryo at the same developmental stage. The experiment can also be performed using the quail as a host and the chick as a graft donor. The stages elected are either the late neurula (0 to 3 somites) or the stage after cephalic vesicles formation (10 to 14 somites) but in all cases before the onset of vascularization of the neural primordium. Quail and chick territories can be recognized in the chimeras any time after the graft owing to the particular structure of the quail nucleus or by means of species-specific antibodies. Quail-chick chimeras have been instrumental in the study of the ontogeny of the medulla oblongata and of the cerebellum. The complex morphogenetic movements and cell migrations which occur during the development of this part of the brain have been worked out by this method. The main results obtained are described in the article.
A modified Cope introducing dilator to allow straight guide wire introduction (1986)

A modified Cope introducing dilator to allow straight guide wire introductionRL VogelzangAudio Available | Share
Three-Dimensional Displays: Perception, Implementation, and Applications (1989)

This report reviews the current state-of-the-art in three-dimensional display technology. The basic perceptual cues used to perceive the third(depth) dimension are first described, and empirical data bearing on the interaction between these cues are discussed. Generally, when more depth cues are present, a proportionately more salient sense of depth is conveyed. But this additive model breaks down when motion is involved. It is concluded that stereopsis motion, and occlusion are particularly salient cues. Techniques for implementing perspective and stereoptic displays are then described. This discussion is followed by a review of 3 display technology applications in the following areas: flight deck displays, air traffic control, meteorology, teleoperation, and computer graphics. Where available, studies are discussed which contrast the efficacy of 3D with 2D representations. In both laboratory and field studies, it appears that the usefulness of stereopsis is diminished and may vanish altogether when displays are dynamic.
Colon drug delivery (2005)

Oral drug delivery to the colon has attracted significant attention during the past 20 years. Colon targeting is recognised to have several therapeutic advantages, such as the oral delivery of drugs that are destroyed by the stomach acid and/or metabolised by pancreatic enzymes. Sustained colonic release of drugs can be useful in the treatment of nocturnal asthma, angina and arthritis. Local treatment of colonic pathologies, such as ulcerative colitis, colorectal cancer and Crohn's disease, is more effective with the delivery of drugs to the affected area. Likewise, colonic delivery of vermicides and colonic diagnostic agents requires smaller doses. This article aims to provide an insight into the design and manufacturing considerations, and an evaluation of colonic drug delivery systems in order to understand why there are still few delivery technologies that have reached the market, despite intensive research in this field. For this purpose, various approaches to colon-specific drug delivery are discussed.
Inhibitory effect of sildenafil on gastrointestinal smooth muscle: role of NO-cGMP transduction pathway. (2005)

Nitric oxide (NO) is an important neurotransmitter in the gut and has been demonstrated to be a key physiological mediator of non-adrenergic non-cholinergic (NANC) relaxation of gastrointestinal smooth muscle. In the present study the effect of PDE 5 inhibitor sildenafil on the gastrointestinal function (gastric emptying and intestinal transit) has been demonstrated in mice. Sildenafil (0.5-2 mg/kg, po) did not alter the percent gastric emptying however, in higher doses (5, 10 and 30 mg/kg, po) it inhibited the gastric emptying. On acute administration (0.5-5 mg/kg, po) it did not alter the intestinal transit but in higher doses (10 and 30 mg/kg, p.o.) delayed the intestinal transit. Further, the inhibitory effect of sildenafil was significantly blocked by L-NAME (10 mg/kg, ip), a non-selective NOS inhibitor and methylene blue (1 mg/kg, ip), a guanylate cyclase inhibitor. These findings suggest the participation of NO-cGMP transduction pathway in the inhibitory effect of sildenafil (higher doses) on the gastrointestinal smooth muscles and its potential application in patients with nutcracker oesophagus, hypertensive lower oesophageal sphincter (LOS), achalsia and diabetic gastroparesis or colitis where there is a loss of nNOS.
High precision touch screen interaction (2003)

Bare hand pointing on touch screens both benefits and suffers from the nature of direct input. This work explores techniques to overcome its limitations. Our goal is to design interaction tools allowing pixel level pointing in a fast and efficient manner. Based on several cycles of iterative design and testing, we propose two techniques: Cross-Keys that uses discrete taps on virtual keys integrated with a crosshair cursor, and an analog Precision-Handle that uses a leverage (gain) effect to amplify movement precision from the user's finger tip to the end cursor. We conducted a formal experiment with these two techniques, in addition to the previously known Zoom-Pointing and Take-Off as baseline anchors. Both subjective and performance measurements indicate that Precision-Handle and Cross-Keys complement existing techniques for touch screen interaction.
Succinyl-CoA:( <i>R</i> )-Benzylsuccinate CoA-Transferase: an Enzyme of the Anaerobic Toluene Catabolic Pathway in Denitrifying Bacteria (2001)

Anaerobic microbial toluene catabolism is initiated by addition of fumarate to the methyl group of toluene, yielding (R)-benzylsuccinate as first intermediate, which is further metabolized via beta-oxidation to benzoyl-coenzyme A (CoA) and succinyl-CoA. A specific succinyl-CoA:(R)-benzylsuccinate CoA-transferase activating (R)-benzylsuccinate to the CoA-thioester was purified and characterized from Thauera aromatica. The enzyme is fully reversible and forms exclusively the 2-(R)-benzylsuccinyl-CoA isomer. Only some close chemical analogs of the substrates are accepted by the enzyme: succinate was partially replaced by maleate or methylsuccinate, and (R)-benzylsuccinate was replaced by methylsuccinate, benzylmalonate, or phenylsuccinate. In contrast to all other known CoA-transferases, the enzyme consists of two subunits of similar amino acid sequences and similar sizes (44 and 45 kDa) in an alpha(2)beta(2) conformation. Identity of the subunits with the products of the previously identified toluene-induced bbsEF genes was confirmed by determination of the exact masses via electrospray-mass spectrometry. The deduced amino acid sequences resemble those of only two other characterized CoA-transferases, oxalyl-CoA:formate CoA-transferase and (E)-cinnamoyl-CoA:(R)-phenyllactate CoA-transferase, which represent a new family of CoA-transferases. As suggested by kinetic analysis, the reaction mechanism of enzymes of this family apparently involves formation of a ternary complex between the enzyme and the two substrates.
Work in progress: methods of contrast enhancement for NMR imaging and potential applications. A subject review. (1983)

Contrast-enhancing pharmaceuticals and manipulation of the physical properties of tissue may extend the diagnostic usefulness of nuclear magnetic resonance (NMR) imaging. Potential applications of contrast enhancers include differentiation of isomagnetic tissues, direct evaluation of tissue function, evaluation of metabolic pathways, and measurement of tissue perfusion. Numerous means of enhancing NMR contrast are available, but many, such as manipulation of tissue viscosity or temperature, are not clinically feasible. Changing the chemical composition of tissue, and particularly the use of paramagnetic pharmaceuticals, appears to be more advantageous. Nitroxide stable free radicals are a group of synthetic, strongly paramagnetic compounds that have several characteristics that make them promising contrast enhancers.
Femtosecond temporal encoding in barium titanate (1991)

We describe two-beam coupling and temporal encoding experiments in barium titanate. Volume gratings are created in the photorefractive material by 50-fs optical pulses. Information in the writing pulses may be encoded as spatially distributed volume gratings in the crystal. Femtosecond temporal waveform reconstruction is demonstrated.
Dried blood spot measurement: application in tacrolimus monitoring using limited sampling strategy and abbreviated AUC estimation (2007)

Dried blood spot (DBS) sampling and high-performance liquid chromatography tandem-mass spectrometry have been developed in monitoring tacrolimus levels. Our center favors the use of limited sampling strategy and abbreviated formula to estimate the area under concentration-time curve (AUC(0-12)). However, it is inconvenient for patients because they have to wait in the center for blood sampling. We investigated the application of DBS method in tacrolimus level monitoring using limited sampling strategy and abbreviated AUC estimation approach. Duplicate venous samples were obtained at each time point (C(0), C(2), and C(4)). To determine the stability of blood samples, one venous sample was sent to our laboratory immediately. The other duplicate venous samples, together with simultaneous fingerprick blood samples, were sent to the University of Maastricht in the Netherlands. Thirty six patients were recruited and 108 sets of blood samples were collected. There was a highly significant relationship between AUC(0-12), estimated from venous blood samples, and fingerprick blood samples (r(2) = 0.96, P < 0.0001). Moreover, there was an excellent correlation between whole blood venous tacrolimus levels in the two centers (r(2) = 0.97; P < 0.0001). The blood samples were stable after long-distance transport. DBS sampling can be used in centers using limited sampling and abbreviated AUC(0-12) strategy as drug monitoring.
Structural remodeling of cardiac myocytes in rats with arteriovenous fistulas. (1988)

Structural changes in the heart associated with chronic volume overloading have not been adequately documented. In anesthetized adult rats, microsurgical techniques were used to produce two types of arteriovenous shunts. The end of a femoral artery was connected to the side of a femoral vein to produce a femoral shunt. Aortocaval fistulas were produced by placing a venous graft (femoral vein) between the abdominal aorta and inferior vena cava. A polyethylene ring was placed around the venous graft to control the size of the shunt. After 10 weeks, rats were anesthetized and hearts were excised, weighed, and perfused with collagenase to obtain isolated myocytes. Heart weight/body weight of rats increased 15% (p less than 0.005) with unilateral femoral fistulas and 41% (p less than 0.001) with aortocaval fistulas. Length of isolated cardiac myocytes was measured directly with a microscope. Cell volume was measured with a Coulter Channelyzer. Myocyte cross-sectional area was calculated from cell volume/cell length. Cell volume increased in proportion to heart weight in each experimental model. With both types of shunts, the majority of myocyte hypertrophy was due to an increase in cell length. There was a trend toward an increase in cross-sectional area in each region of both fistula groups, although this change was not statistically significant. These results indicate that eccentric cardiac hypertrophy was associated with enlargement of individual myocytes primarily as a result of increased length.
The Impact of Fracturing Fluids on Conductivity and Performance in Low-Temperature Wells (1989)

ABSTRACT A study investigating the performance of low temperature wells following hydraulic fracturing is presented. Emphasis is placed on proper fracturing fluid and breaker selection to minimize proppant damage and maximize fracture conductivity. The study indicates borate crosslinked fluids yield minimal damage whereas organometallic crosslinked fluids consistantly yield severe damage. A detailed discussion of the impact of fluid-induced proppant damage on well performance is given. Although previously reported laboratory work has addressed the topic of in-situ fracture conductivity, the results of conductivity damage in wells with low bottomhole static temperatures have not been reported. A detailed discussion of extensive laboratory conductivity testing at 100 ° F is presented to address the issue of conductivity impairment (damage) in low temperature wells. The conductivity and permeability of Jordan sand placed with several fluids incorporating various crosslinkers and breaker systems is reported. The data indicate crosslinked fracturing fluids can be used in low temperature wells to yield high fracture conductivity. However, the amount of damage observed is a function of both the crosslinker and breaker system. Subsequent to laboratory testing, the impact of the fluid/breaker system on the performance of oil and gas wells was evaluated. Numerous fracture design and production simulations were performed to evaluate the effect of fluid systems on well performance. These data indicate production can increase 50% or more simply by incorporating a "cleaner" fracturing fluid system. In conclusion, fracturing fluid and breaker selection are variables that must be considered when designing a fracture treatment in a low temperature well. This study indicates proppant placed with a borate crosslinked fracturing fluid containing a persulfate/amine breaker exhibits minimal conductivity impairment resulting in improved well performance.
Antigenic analysis of the second extra-cellular loop of the human beta-adrenergic receptors. (1989)

Polyclonal antibodies were raised in rabbits by immunization with free peptides corresponding to positions 197-222 of the human beta 1-adrenergic receptor (beta 1 peptide) and the corresponding sequence (172-197) of the human beta 2-adrenergic receptor (beta 2 peptide). While the beta 2 peptide yielded antibodies that cross-reacted with the beta 1 peptide, the antibodies against the beta 1 peptide did not cross-react with the beta 2 sequence. Cross-reactivity of the anti-beta 2 peptide antibodies and the selectivity of the anti-beta 1 peptide antibodies were also revealed in the recognition by immunoblots of the beta 1- and beta 2-adrenergic receptors of different species or of the receptor gene products expressed in a bacterial vector. These antibodies could be used immunohistochemically to visualize the beta-adrenergic receptors on rabbit heart. The anti-beta 2 peptide antibodies did not show any functional effect on the beta-adrenergic receptors; the anti-beta 1 peptide antibodies were able to displace agonist affinity to higher values. Recognition of truncated peptides by the anti-beta 1 and anti-beta 2 peptide antibodies suggested that the cross-reaction of the anti-beta 2 peptide antibodies was due to the recognition of a common epitope on the C-terminal part of the peptides. The anti-beta 1 peptide antibodies recognized the N-terminal part of the peptide better than the C-terminal part. These results suggest that the second extracellular loop postulated in the structure of the human beta-adrenergic receptor contains the T and B cell epitopes necessary for induction of an immune response. The selectivity and the functional properties of the antibodies raised against that loop in the beta 1 adrenergic receptor could have relevance in induction of auto antibodies in certain cardiomyopathic conditions.
Determination of the LO phonon energy by using electronic and optical methods in AlGaN/GaN (2011)

Abstract The longitudinal optical (LO) phonon energy in AlGaN/GaN heterostructures is determined from temperature-dependent Hall effect measurements and also from Infrared (IR) spectroscopy and Raman spectroscopy. The Hall effect measurements on AlGaN/GaN heterostructures grown by MOCVD have been carried out as a function of temperature in the range 1.8-275 K at a fixed magnetic field. The IR and Raman spectroscopy measurements have been carried out at room temperature. The experimental data for the temperature dependence of the Hall mobility were compared with the calculated electron mobility. In the calculations of electron mobility, polar optical phonon scattering, ionized impurity scattering, background impurity scattering, interface roughness, piezoelectric scattering, acoustic phonon scattering and dislocation scattering were taken into account at all temperatures. The result is that at low temperatures interface roughness scattering is the dominant scattering mechanism and at high temperatures polar optical phonon scattering is dominant.
Developmental regulation of transcription of a novel prespore-specific gene (Dp87) in <i>Dictyostelium discoideum</i> (1993)

The Dp87 is a novel prespore specific gene of Dictyostelium discoideum which has a long open reading frame of 555 amino acids. The entire amino acid sequence had low but significant homology to the spore coat proteins, SP96 and SP70, of this organism. When a chimeric gene, containing a 1380 bp of the 5' upstream region of this gene fused with CAT gene, as reporter, was introduced into cells of this organism, it was expressed only in prespore cells of the slug. Transformation experiments, using chimeric genes, containing a series of 5' deletions of the upstream region, showed that -447 bp to -357 bp is an important cis-acting regulatory region for transcription. A nuclear factor(s) that specifically bind to this cis-acting region were detected from slug cell nuclei. Transformation experiments using a chimeric gene consisting of the 5' region between -666 bp and +149 bp of this gene, a beta-galactosidase reporter and an actin 8 terminator, showed that the reporter gene was expressed as early as in aggregation streams, indicating that Dp87 become transcribed a few hours earlier than the other prespore-specific genes so far reported. This was confirmed by northern hybridization detected using an image plate analyzer. The fact that cells expressing Dp87 appeared at random in aggregation streams gives solid support to the idea that position-independent differentiation of prespore and prestalk cells, followed by their sorting, brings about pattern formation in this organism.
Preparation of the major plasma fractions by solid-phase polyelectrolytes. (1978)

The solid-phase ethylene/maleic anhydride PE's E-5 and E-100 were used to developed a flexible integrated system of batch methods for the fractionation of albumin and gamma globulin as well as the clinically important coagulation factors. Each method for the isolation and purification of the fractions or a modification of it could also be used independently or could be added onto another method or methods. Each fraction was prepared in three steps: adsorption on solid-phase PE's elution from the PE's, and concentration by ultrafiltration or by use of PEG or both. Since the methods required no organic solvent but relied primarily on electrostatic bonding, they were essentially nondenaturing. Solid-liquid phase separation was easily accomplished by centrifugation or filtration. The yield and purity of each fraction was as follows: (1) coagulation factors II, VII, IX, and X concentrates 63% and 200-fold purified; (2) AHF 43% and 52-fold; (3) vWF 43% and 71-fold; (4) PPF, as albumin, 93% yield and 92% pure; (5) albumin 92% yield and 98.5% pure; and (6) gamma globulin 92% yield and 97.5 pure. During the preparation of gamma globulin the E-100 also tended to adsorb and remove the HBSAg and infectivity, when present.