gebhart/patrepeval huggingface dataset:
Dual rotating-compensator multichannel ellipsometer: Instrument development for high-speed Mueller matrix spectroscopy of surfaces and thin films (2001)

A multichannel ellipsometer in the dual rotating-compensator configuration has been developed for applications in real time Mueller matrix spectroscopy of anisotropic surfaces and thin films. The sequence of optical elements for this instrument configuration can be denoted PC1r(5ω)SC2r(3ω)A, where P, S, and A represent the polarizer, sample, and analyzer. In this sequence, C1r and C2r represent the first and second compensators, rotating with angular frequencies of 5ω and 3ω, respectively, where ω=π/TC is the base angular frequency (corresponding to 2 Hz) and TC=0.25 s is the fundamental optical period. The instrument can provide 170 point spectra over the wavelength range from 235 nm (5.3 eV) to 735 nm (1.7 eV) in all 16 elements of the unnormalized Mueller matrix with minimum acquisition and repetition times of TC=0.25 s. In this study, instrumentation calibration procedures are demonstrated in the transmission geometry without a sample, including (i) alignment of the two MgF2 zero-order biplate compensators, (ii) determination of the retardance and phase spectra for the compensators, (iii) determination of the offset angles for the optical elements, and (iv) characterization of the spectral response function of the ellipsometer. Calibration procedure (iv) allows the (1,1) element of the transmission Mueller matrix to be determined; thus the unnormalized Mueller matrix can be obtained. The dual rotating-compensator multichannel ellipsometer is assessed with respect to its performance in transmission without a sample, and is then applied in the transmission geometry to study anisotropy, depolarization, and light scattering effects for a MgF2 helicoidally sculptured thin film on a glass substrate. Numerous future applications of this instrument are anticipated for real time analysis of complex surfaces and thin films in the reflection geometry as well.
Multiplexed Analysis of Human Cytokines by Use of the FlowMetrix System (1998)

reference values (FastTake ϭ 0.984YSI ϩ 13.3 mg/L, n ϭ 284, S y͉x ϭ 123 mg/L, r 2 ϭ 0.98).By linear regression analysis, results for site 1 compared well to those for site 2. For glucose concentrations measured at site 1, FastTake correlated well with plasma glucose values measured by the YSI (FastTake ϭ 0.987YSI Ϫ 8.4 mg/L, n ϭ 143, S y͉x ϭ 122 mg/L, r 2 ϭ 0.963).Site 2 demonstrated similar linear regression statistics (FastTake ϭ 0.98YSI ϩ 35.6 mg/L, n ϭ 141, S y͉x ϭ 122 mg/L, r 2 ϭ 0.975).Error grid analysis (5) (Fig. 1a) was used to show the clinical accuracy of FastTake for both sites.Over the range of glucose tested, 97.9% of the results fell within zone A (defined as "clinically accurate"), and 2.1% fell within zone B (defined as "deviating from the reference method by Ͼ20% but would lead to benign or no treatment error").Individually, the error grid results were very similar for the two sites, with site 1 and site 2 yielding 97.2% and 98.6%, respectively, in Zone A. For both locations, the remaining data points fell in zone B. During the studies, the clinical performance of the two test strip lots was observed to be identical based on error grid analysis (Fig. 1a).Across the range of observed patient hematocrits (30 -59%), the Fast-Take meter bias relative to the YSI reference was observed to be independent of hematocrit concentration (Fig. 1b).Precision and sample volume testing were conducted at LifeScan to further evaluate the FastTake prototype.Venous whole blood samples were collected from healthy donors in heparinized tubes.Because the product is not intended for use with venous blood samples, to simulate capillary blood, the Po 2 was measured (Ciba Corning Model 278 Blood Gas System, Chiron Diagnostics) and maintained between 60 and 70 mmHg.Precision was evaluated on 2 days using 10 meters and whole blood from two donors.Over the glucose concentrations tested (ϳ500, 800, 1500, 3000, and 5000 mg/ L), within-run precision (CV) ranged from 2.7% to 5.3% (n ϭ 20) for day 1 and 2.8% to 4.6% (n ϭ 20) for day 2.Sample volume testing was also conducted over 2 days by use of five meters and whole blood from two donors.Replicates (n ϭ 3) were tested on each meter at three glucose concentrations (ϳ700, 1800, and 3600 mg/L) with different sample volumes of 2.5, 3, 4, 5, 10, and 25 L. Testing at 2.5 L indicated that 95.6% of the data fell within Ϯ20% of the reference method at the three glucose concentrations tested.For blood volumes of 3.0 L and above, Ͼ97.8% of the laboratory data fell within Ϯ20% of the reference.These studies indicate that the FastTake system provides rapid, accurate, reproducible results in both the laboratory and clinical settings.Although the product is not intended for use with samples containing lower concentrations of oxygen, such as venous blood, the system performance was consistent at sea level and at the lower atmospheric oxygen testing environment encountered in the Denver clinic.System performance in a clinical setting was also found to be consistent throughout the glucose and hematocrit ranges observed.
Evidence of Structural Remodeling in the Dyssynchronous Failing Heart (2005)

Ventricular remodeling of both geometry and fiber structure is a prominent feature of several cardiac pathologies. Advances in MRI and analytical methods now make it possible to measure changes of cardiac geometry, fiber, and sheet orientation at high spatial resolution. In this report, we use diffusion tensor imaging to measure the geometry, fiber, and sheet architecture of eight normal and five dyssynchronous failing canine hearts, which were explanted and fixed in an unloaded state. We apply novel computational methods to identify statistically significant changes of cardiac anatomic structure in the failing and control heart populations. The results demonstrate significant regional differences in geometric remodeling in the dyssynchronous failing heart versus control. Ventricular chamber dilatation and reduction in wall thickness in septal and some posterior and anterior regions are observed. Primary fiber orientation showed no significant change. However, this result coupled with the local wall thinning in the septum implies an altered transmural fiber gradient. Further, we observe that orientation of laminar sheets become more vertical in the early-activated septum, with no significant change of sheet orientation in the late-activated lateral wall. Measured changes in both fiber gradient and sheet structure will affect both the heterogeneity of passive myocardial properties as well as electrical activation of the ventricles.
Highly Spin-Polarized Tunneling in Fully Epitaxial Magnetic Tunnel Junctions Using Full-Heusler Alloy Co$_2$Cr$_0.6$Fe$_0.4$Al Thin Film and MgO Tunnel Barrier (2006)

Highly spin-polarized tunneling with tunnel magnetoresistance (TMR) ratios of 90% at room temperature and 240% at 4.2 K was demonstrated for fully epitaxial magnetic tunnel junctions fabricated using a cobalt-based full-Heusler alloy Co <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> Cr <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.6</sub> Fe <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.4</sub> Al (CCFA) thin film having a composition close to the stoichiometric one and a MgO tunnel barrier. A high tunneling spin polarization of 0.79 at 4.2 K was obtained for the epitaxial CCFA films from the TMR ratios. This adds to the promise of the fully epitaxial MTJ as a key device structure for utilizing the intrinsically high spin polarizations of Co-based full-Heusler alloy thin films
Potent and Selective Inhibition of A-to-I RNA Editing with 2′-O-Methyl/Locked Nucleic Acid-Containing Antisense Oligoribonucleotides (2013)

ADARs (adenosine deaminases acting on RNA) are RNA editing enzymes that bind double helical RNAs and deaminate select adenosines (A). The product inosine (I) is read during translation as guanosine (G), so such changes can alter codon meaning. ADAR-catalyzed A to I changes occur in coding sequences for several proteins of importance to the nervous system. However, these sites constitute only a very small fraction of known A to I sites in the human transcriptome, and the significance of editing at the vast majority sites is unknown at this time. Site-selective inhibitors of RNA editing are needed to advance our understanding of the function of editing at specific sites. Here we show that 2'-O-methyl/locked nucleic acid (LNA) mixmer antisense oligonucleotides are potent and selective inhibitors of RNA editing on two different target RNAs. These reagents are capable of binding with high affinity to RNA editing substrates and remodeling the secondary structure by a strand-invasion mechanism. The potency observed here for 2'-O-methyl/LNA mixmers suggests this backbone structure is superior to the morpholino backbone structure for inhibition of RNA editing. Finally, we demonstrate antisense inhibition of editing of the mRNA for the DNA repair glycosylase NEIL1 in cultured human cells, providing a new approach to exploring the link between RNA editing and the cellular response to oxidative DNA damage.
Calming patient agitation with dexmedetomidine (2010)

In Brief An ICU stay can make patients agitated, delirious, and anxious. This drug may help calm patients without causing respiratory depression, and has a fast onset and analgesic action.
Synthesis of a novel C2-aryl substituted 1,2-unsaturated pyrrolobenzodiazepine (2003)

A novel C2-aryl 1,2-unsaturated PBD (14) has been prepared via an enol triflate intermediate (8). The regiochemistry of triflation is dependent upon the point at which the reaction is performed during the synthetic route.
Asthma Control during the Year after Bronchial Thermoplasty (2007)

Bronchial thermoplasty in subjects with moderate or severe asthma results in an improvement in asthma control. (ClinicalTrials.gov number, NCT00214526 [ClinicalTrials.gov].).
Structure of the HIV-1 integrase catalytic domain complexed with an inhibitor: A platform for antiviral drug design (1999)

HIV integrase, the enzyme that inserts the viral DNA into the host chromosome, has no mammalian counterpart, making it an attractive target for antiviral drug design. As one of the three enzymes produced by HIV, it can be expected that inhibitors of this enzyme will complement the therapeutic use of HIV protease and reverse transcriptase inhibitors. We have determined the structure of a complex of the HIV-1 integrase core domain with a novel inhibitor, 5ClTEP, 1-(5-chloroindol-3-yl)-3-hydroxy-3-(2H-tetrazol-5-yl)-pro penone, to 2.1-A resolution. The inhibitor binds centrally in the active site of the integrase and makes a number of close contacts with the protein. Only minor changes in the protein accompany inhibitor binding. This inhibitor complex will provide a platform for structure-based design of an additional class of inhibitors for antiviral therapy.
Clinical advances in inflammatory bowel disease (1992)

New clinical advances in inflammatory bowel disease are highlighted. Conditions that mimic the presentation of either ulcerative colitis or Crohn's disease are discussed along with the role that endoscopy, radiography, and histology play in establishing the correct diagnosis of each respective disorder. Assessment of Crohn's disease activity has progressed, with evaluation of soluble interleukin-2 receptor, serum tumor necrosis factor-α, fecal αarantitrypsin clearance, erythrocyte sedimentation rate, IgG content of gut lavage fluid, and IIIIn scintigraphy. Systemic complications associated with inflammatory bowel disease are reviewed, with particular attention to oral complication of Crohn's disease, complications resulting from a hypercoagulable state, bronchopulmonary manifestations, hematologic malignancies, and factors associated with intestinal perforation. Although the etiologic agents responsible for Crohn's disease and ulcerative colitis remain elusive we still continue to advance our knowledge base, making significant strides toward better understanding the pathophysiology of these two disorders, thus enabling us to better treat afflicted patients. These advances are established with hopes that we will soon unearth the cause and cure of both Crohn's disease and ulcerative colitis.
Fumagillin class inhibitors of methionine aminopeptidase-2 (2005)

The growth of solid tumors and the formation of metastases are critically dependent on neovascularization. This dependence on neovascularization, however, is not limited to cancer but is also a major contributing factor in the pathology of autoimmune diseases such as rheumatoid arthritis. Hence, antiangiogenic therapy was recognized as a potentially powerful therapeutic approach in the treatment of these devastating diseases. The discovery of fumagillin and its potent antiangiogenic and antiproliferative activities provided the rationale for the development of fumagillin analogues as a novel class of antiproliferative agents. Molecules of the fumagillin class inhibit the enzymatic activity of methionine aminopeptidase-2 (MetAP-2), and this inhibition is the first step required for the selective growth inhibition of cell types that are dependent on MetAP-2 function for growth. Mechanistically, this growth inhibition is characterized by cytostasis and arrest in the late G1 phase of the cell cycle. TNP-470 was the first MetAP-2 inhibitor of the fumagillin class to enter phase I clinical trials in cancer. Despite some encouraging results in several solid tumors in early phase I/II studies, further clinical development of this molecule was halted, primarily due to dose-limiting neurotoxicities and a poor clinical pharmacokinetic profile. More recently, fumagillin analogues specifically designed to improve upon the clinical deficiencies of TNP-470, such as PPI-2458, have advanced into phase I trials in cancer.
Regulation and Function of T1/ST2 Expression on CD4+ T Cells: Induction of Type 2 Cytokine Production by T1/ST2 Cross-Linking (2001)

The orphan receptor T1/ST2, a member of the IL-1R family, is preferentially expressed on the surface of murine Th2 cells. In this study, we analyzed the kinetics and function of T1/ST2 expression on Th2 cells in vitro. Whereas naive CD4(+) cells did not express T1/ST2, most CD4(+) cells became T1/ST2(+) upon repeated antigenic stimulation under Th2-polarizing conditions. Flow cytometric analyses revealed that the kinetics of T1/ST2 expression on Th2 cells was delayed compared with the kinetics of type 2 cytokine production. Exogenous IL-6, IL-5, IL-1, and TNF-alpha enhanced the expression of T1/ST2 on Th2 cells, and IL-6 was by far most effective in this regard. However, the expression of T1/ST2 did not depend on the presence of IL-6 and was also detected in IL-6-deficient mice. Most important, cross-linking of T1/ST2 provided a costimulatory signal for Th2 but not Th1 cells and directly induced proliferation and type 2 cytokine production. Thus, T1/ST2 is not only a Th2 cell marker but also plays an important role in the activation of Th2 cells.
Synthesis of conformationally locked carbocyclic 1,3-diazepinone nucleosides as inhibitors of cytidine deaminase (2008)

We synthesized a series of carbocyclic nucleoside inhibitors of cytidine deaminase (CDA) based on a seven-membered 1,3-diazepin-2-one moiety. In the key step, the seven-membered ring was formed by a ring-closing-metathesis reaction. Therefore, the bis-allyl-urea moiety had to be protected by benzoylation in order to obtain an orientation suitable for ring closure. To our surprise, the analogue built on a flexible sugar template (4) showed a 100-fold stronger inhibition of CDA than the derivative with the preferred south-conformation.
Multiple Determinants Direct the Orientation of Signal–Anchor Proteins: The Topogenic Role of the Hydrophobic Signal Domain (1997)

The orientation of signal-anchor proteins in the endoplasmic reticulum membrane is largely determined by the charged residues flanking the apolar, membrane-spanning domain and is influenced by the folding properties of the NH2-terminal sequence. However, these features are not generally sufficient to ensure a unique topology. The topogenic role of the hydrophobic signal domain was studied in vivo by expressing mutants of the asialoglycoprotein receptor subunit H1 in COS-7 cells. By replacing the 19-residue transmembrane segment of wild-type and mutant H1 by stretches of 7-25 leucine residues, we found that the length and hydrophobicity of the apolar sequence significantly affected protein orientation. Translocation of the NH2 terminus was favored by long, hydrophobic sequences and translocation of the COOH terminus by short ones. The topogenic contributions of the transmembrane domain, the flanking charges, and a hydrophilic NH2-terminal portion were additive. In combination these determinants were sufficient to achieve unique membrane insertion in either orientation.
Similar patterns of cortical expansion during human development and evolution (2010)

The cerebral cortex of the human infant at term is complexly folded in a similar fashion to adult cortex but has only one third the total surface area. By comparing 12 healthy infants born at term with 12 healthy young adults, we demonstrate that postnatal cortical expansion is strikingly nonuniform: regions of lateral temporal, parietal, and frontal cortex expand nearly twice as much as other regions in the insular and medial occipital cortex. This differential postnatal expansion may reflect regional differences in the maturity of dendritic and synaptic architecture at birth and/or in the complexity of dendritic and synaptic architecture in adults. This expression may also be associated with differential sensitivity of cortical circuits to childhood experience and insults. By comparing human and macaque monkey cerebral cortex, we infer that the pattern of human evolutionary expansion is remarkably similar to the pattern of human postnatal expansion. To account for this correspondence, we hypothesize that it is beneficial for regions of recent evolutionary expansion to remain less mature at birth, perhaps to increase the influence of postnatal experience on the development of these regions or to focus prenatal resources on regions most important for early survival.
CD133-negative glioblastoma cancer stem cells represent the ‘mesenchymal’ subclass of glioblastoma (2008)

3786 Whether CD133-positive (CD133(+)) cells are the only cancer stem cells of glioblastoma (GBM) is a hot issue these days. We isolated CD133(+) and CD133-negative (CD133(-)) cells from one GBM patient (total 6 GBM patients) and found that both can produce tumor mass in the mouse brain. However, tumor masses produced by CD133(-) cells had more vessels and PCNA-positive proliferating cells. Akt was activated more in the tumor masses produced by CD133(+) cells. These results suggested that there are cancer stem cells in CD133(-) cell population, however, they have different characteristics compared with CD133(+) cells. To analyze different characteristics of CD133(-) cells further, we gathered 20 GBM patients, analyzed their CD133(+) cell ratios using FACS analysis method and divided them into two groups according to CD133(+) cell ratio (CD133(+) cell ratio high (≥3%, n=10) and low (
Tissue Distribution of Beta-Lactam Antibiotics: Experimental Studies in Rabbits (1981)

Tissue distribution of ampicillin, dicloxacillin and cefuroxime was studied in rabbits. Different methods allowing frequent samples to be obtained from the same animal were used. Tissue fluid was obtained from subcutaneously implanted steel net cages and by implantation of thin cotton threads under the muscle fascia. A microtechnique was developed for determination of antibiotic concentrations in small muscle samples. The concentration time course in serum and tissue was followed after a single intravenous or intramuscular injection of the antibiotic. In tissue cage fluid, levels of ampicillin and dicloxacillin were low as compared to the serum concentrations. Also, maximum levels occurred later than in serum and elimination was slower. In contrast, rapid peak levels were achieved in muscle tissue with all three investigated antibiotics and the muscle concentrations declined parallel to the serum levels. The results also indicated that beta-lactam antibiotics are not homogeneously distributed in muscle tissue but mainly confined to the extracellular fluid volume. Whole tissue levels could therefore underestimate the actual antibiotic concentrations in the tissue fluid where the bacteria causing soft tissue infections are most likely to be found. Serum levels, however, seemed to be a good indicator for the concentration time course in tissue fluid.
Efficient Multi-Channel Acoustic Echo Cancellation Using Constrained Sparse Filter Updates in the Subband Domain (2014)

In this paper we present constrained sparse tap-selection schemes for updating Multi-Channel Acoustic Echo Cancellation (MAEC) filters in the subband domain. At first, M-Max tap-selection on the complete multi-channel reference spectra is performed and the effect of the subsequent sparse filter update on the speed of convergence of the MAECfilters is investigated. We consider a measure to quantify signal sparsity, and use it to investigate the spectral and inter-channel sparsity present in real-world surround sound signals. A heuristic tap-selection scheme is proposed which exploits the signal sparsity properties, and performs tap-selection with much lower computational effort as compared to the M-Max and the full-update tapselection schemes, while giving similar echo cancellation performance.
Renal denervation at weaning retards development of hypertension in New Zealand genetically hypertensive rats. (1982)

The development of hypertension was studied in 3 to 13-week old New Zealand genetically hypertensive (NZGH) rats subjected to bilateral renal denervation (D) or sham operations (S) at 4 weeks of age. Denervation retarded the development of hypertension and delayed the establishment of stable hypertension; blood pressure of D-NZGH rats was 15-40 mm Hg lower than that of S-NZGH rats from 3 to 7 weeks after surgery, but was similar in the two groups thereafter. D-rat renal catecholamine content was reduced to 17% of control at 1 week after surgery; by the fourth week post surgery, renal catecholamine content had risen to 40% of control, and blood pressure of the D-group had begun to rise, suggesting that spontaneous renal reinnervation prevented the antihypertensive effect of renal denervation from being a permanent one. During the period when blood pressure of the S-rats was greater than that of the D-rats, urinary sodium excretion of the two groups was not significantly different, suggesting that over this interval the relationship between blood pressure and urinary sodium excretion shifted to the right along the pressure axis in the S-rats but not in the renal denervated rats. Throughout the 60-day period of observation, urinary excretion of prostaglandin E2 and kallikrein did not differ between the renal-denervated and sham-operated rats.