gebhart/patrepeval huggingface dataset:
Spectrum of low density lipoprotein receptor mutations in Czech hypercholesterolemic patients (2001)

The aim of our study was to define mutations causing familial hypercholesterolemia (FH) phenotype in Czech hypercholesterolemic individuals. A combination of heteroduplex analysis, SSCP, DGGE, DNA sequencing and PCR/restriction analysis was used for this purpose. Molecular searching in the promoter region and coding sequence of the low density lipoprotein receptor (LDLR) gene in 130 patients from 68 unrelated families resulted in the identification of 37 sequence variations. Thirty of them are most likely disease causing mutations. Nineteen mutations were novel (two nonsense, five missense, six nucleotide(s) insertions and six nucleotide(s) deletions). Their pathological effect can be predicted on the basis of their position with respect to previously reported mutations with an estimated reduction of the receptor activity and/or premature termination of translation. These results expand our knowledge of mutations responsible for FH. Seven nucleotide variations were characterized as silent polymorphisms. © 2001 Wiley-Liss, Inc.
Hepatic encephalopathy is associated with decreased cerebral oxygen metabolism and blood flow, not increased ammonia uptake (2012)

The low values of CMRO(2) and CBF observed during HE increased after recovery from HE and were thus associated with HE rather than the liver disease as such. The changes in CMRO(2) and CBF could not be linked to blood ammonia concentration or CMRA.
Termination of Ca 2+ release by a local inactivation of ryanodine receptors in cardiac myocytes (1998)

In heart, a robust regulatory mechanism is required to counteract the regenerative Ca2+-induced Ca2+ release from the sarcoplasmic reticulum. Several mechanisms, including inactivation, adaptation, and stochastic closing of ryanodine receptors (RyRs) have been proposed, but no conclusive evidence has yet been provided. We probed the termination process of Ca2+ release by using a technique of imaging local Ca2+ release, or "Ca2+ spikes", at subcellular sites; and we tracked the kinetics of Ca2+ release triggered by L-type Ca2+ channels. At 0 mV, Ca2+ release occurred and terminated within 40 ms after the onset of clamp pulses (0 mV). Increasing the open-duration and promoting the reopenings of Ca2+ channels with the Ca2+ channel agonist, FPL64176, did not prolong or trigger secondary Ca2+ spikes, even though two-thirds of the sarcoplasmic reticulum Ca2+ remained available for release. Latency of Ca2+ spikes coincided with the first openings but not with the reopenings of L-type Ca2+ channels. After an initial maximal release, even a multi-fold increase in unitary Ca2+ current induced by a hyperpolarization to -120 mV failed to trigger additional release, indicating absolute refractoriness of RyRs. When the release was submaximal (e.g., at +30 mV), tail currents did activate additional Ca2+ spikes; confocal images revealed that they originated from RyRs unfired during depolarization. These results indicate that Ca2+ release is terminated primarily by a highly localized, use-dependent inactivation of RyRs but not by the stochastic closing or adaptation of RyRs in intact ventricular myocytes.
Inverse p16 and p63 Expression in Small Cell Carcinoma and High-Grade Urothelial Cell Carcinoma of the Urinary Bladder (2010)

Small cell carcinoma (SmCC) of the urinary bladder is a rare, highly aggressive neoplasm. The diagnosis is usually made on morphologic grounds, with the help of immunohistochemistry to document neuroendocrine differentiation. However, neuroendocrine markers generally have low sensitivity, ranging between 30-70%. Recent studies have reported p16 over-expression in SmCC of the lung, suggesting that p16 immunohistochemistry may be useful in the diagnosis of bladder SmCC. This is the first study to analyze the usefulness of p16 in the distinction of small cell and high grade urothelial cell carcinoma (HG-UCC). Fourteen cases of SmCCs and sixteen cases of HG-UCC of the bladder were stained with p16, p63, cytokeratin 20 (CK20), cytokeratin 7 (CK7), chromogranin (Chr), synaptophysin (Syn), and CD56. P16 expression was significantly higher in SmCCs (92.8%) when compared to HG-UCCs (43.7%). P63 and CK20, on the other hand, were positive in the majority of HG-UCCs (81.3% and 50%, respectively), while only 14.3% of SmCCs showed focal immunoreactivity with CK20. The sensitivity of the traditional neuroendocrine markers was low, ranging between 28.6% (Chr) and 71.4% (CD56) in SmCCs. P16 positivity in the absence of p63 and CK20 is highly characteristic of SmCC, while p63 and CK20 positivity with or without p16 expression is typical of HG-UCC.
Anisotropic Particles from LC Polymers for Optical Manipulation (2006)

We have developed a method to convert 10 different LC acrylate monomers into colloids by dispersion polymerization. This yields nine different types of anisotropic colloids with nematic and different smectic phases. The diameter of these colloids mostly varied between 0.5 and 3.5 μm; it can be adjusted by variation of the solvent mixture and it can be systematically increased by seed polymerization. The polydispersity of the anisotropic colloids is thereby often below 10%. Polarizing microscopy shows that colloids of a size between about 2 to 4 μm appear to have a bipolar director configuration. Smaller colloids appear uniaxially oriented, the resolution does, however, not allow a more refined investigation of the director pattern. These anisotropic spheres (diameter between 0.7 and 3.7 μm) can be trapped with an optical tweezers. Circularly polarized light transfers a torque to the particles, enabling one to rotate them clockwise and anticlockwise, which makes these spheres attractive as actuators. The size dependence of their rotational frequency makes it additionally possible to determine changes of the director configuration with size. For a nematic colloid (P 6), it could be shown that the anisotropy stays constant from 1.6 to 3.4 μm.
Experiments in the biosynthesis of curcumin (1973)

The biogenesis of natural diarylheptanoids is discussed, with particular reference to curcumin [1,7-bis-(4-hydroxy-3-methoxyphenyl)hepta-1,6-diene-3,5-dione], the pigment of Curcuma Ionga rhizome. Methods for the isolation, characterisation, and degradation of curcumin, suitable for biosynthetic work, are reported. In administration of labelled precursors to C. Ionga,[1- and 3-14C]phenylalanine were incorporated into curcumin without scrambling of the label. [1- and 2-14C]-Acetate and -malonate were also incorporated, and the fractional distribution of label along the heptane chain was determined; the results do not provide satisfactory support for the expected biosynthetic scheme, in which two cinnamate units condense with one malonate unit. Other interpretations are discussed. [3H]-4-Hydroxy-3-methoxy-, -4-hydroxy-, and -3,4-dihydroxy-cinnamic acids were prepared, and supplied to C. Ionga with [14C]phenylalanine. The first two cinnamic acids are incorporated into curcumin significantly better than the last, although none was utilised quite as efficiently as phenylalanine.
Bordetella pertussis Commits Human Dendritic Cells to Promote a Th1/Th17 Response through the Activity of Adenylate Cyclase Toxin and MAPK-Pathways (2010)

The complex pathology of B. pertussis infection is due to multiple virulence factors having disparate effects on different cell types. We focused our investigation on the ability of B. pertussis to modulate host immunity, in particular on the role played by adenylate cyclase toxin (CyaA), an important virulence factor of B. pertussis. As a tool, we used human monocyte derived dendritic cells (MDDC), an ex vivo model useful for the evaluation of the regulatory potential of DC on T cell immune responses. The work compared MDDC functions after encounter with wild-type B. pertussis (BpWT) or a mutant lacking CyaA (BpCyaA-), or the BpCyaA- strain supplemented with either the fully functional CyaA or a derivative, CyaA*, lacking adenylate cyclase activity. As a first step, MDDC maturation, cytokine production, and modulation of T helper cell polarization were evaluated. As a second step, engagement of Toll-like receptors (TLR) 2 and TLR4 by B. pertussis and the signaling events connected to this were analyzed. These approaches allowed us to demonstrate that CyaA expressed by B. pertussis strongly interferes with DC functions, by reducing the expression of phenotypic markers and immunomodulatory cytokines, and blocking IL-12p70 production. B. pertussis-treated MDDC promoted a mixed Th1/Th17 polarization, and the activity of CyaA altered the Th1/Th17 balance, enhancing Th17 and limiting Th1 expansion. We also demonstrated that Th1 effectors are induced by B. pertussis-MDDC in the absence of IL-12p70 through an ERK1/2 dependent mechanism, and that p38 MAPK is essential for MDDC-driven Th17 expansion. The data suggest that CyaA mediates an escape strategy for the bacterium, since it reduces Th1 immunity and increases Th17 responses thought to be responsible, when the response is exacerbated, for enhanced lung inflammation and injury.
Single-pulse phase-control interferometric coherent anti-Stokes Raman scattering spectroscopy (2005)

In coherent anti-Stokes Raman scattering (CARS) spectroscopy experiments, usually the amplitude of the signal is measured and the phase information is lost. With a polarization- and phase-controlled pulse shaping technique, the relative phase between the resonant and nonresonant CARS signals is controlled, and spectral interferometry is performed without an interferometer. Both the real and imaginary parts of the background-free resonant CARS spectrum are measured via spectral interferometry between the resonant and nonresonant signals from the same sample. The resonant signal is amplified significantly by homodyne mixing with the nonresonant signal as a local oscillator, greatly improving the detection limit.
Fe L- and K-edge XAS of Low-Spin Ferric Corrole: Bonding and Reactivity Relative to Low-Spin Ferric Porphyrin (2009)

Corrole is a tetrapyrrolic macrocycle that has one carbon atom less than a porphyrin. The ring contraction reduces the symmetry from D(4h) to C(2v), changes the electronic structure of the heterocycle, and leads to a smaller central cavity with three protons rather than the two of a porphyrin. The differences between ferric corroles and porphyrins lead to a number of differences in reactivity including increased axial ligand lability and a tendency to form 5-coordinate complexes. The electronic structure origin of these differences has been difficult to study experimentally as the dominant porphyrin/corrole pi --> pi* transitions obscure the electronic transitions of the metal. Recently, we have developed a methodology that allows for the interpretation of the multiplet structure of Fe L-edges in terms of differential orbital covalency (i.e., the differences in mixing of the metal d orbitals with the ligand valence orbitals) using a valence bond configuration interaction model. Herein, we apply this methodology, combined with a ligand field analysis of the Fe K pre-edge to a low-spin ferric corrole, and compare it to a low-spin ferric porphyrin. The experimental results combined with DFT calculations show that the contracted corrole is both a stronger sigma donor and a very anisotropic pi donor. These differences decrease the bonding interactions with axial ligands and contribute to the increased axial ligand lability and reactivity of ferric corroles relative to ferric porphyrins.
New Class of Quantum Error-Correcting Codes for a Bosonic Mode (2016)

Optimal quantum error-correction codes are necessary to extend the lifetime of quantum memories. A new error-correction code to rectify photon loss, gain, and dephasing errors in electromagnetic cavities is presented.
An improved procedure for derivatization of controlled-pore glass beads for solid-phase oligonucleotide synthesis (1990)

A simplified and economical method for the attachment of 2'-deoxyribo, ribo and arabinonucleosides onto long-chain alkylamidopropanoic acid controlled-pore glass (LCAAP-CPG, P-3) is described. In this procedure, 5'-O-tritylated nucleosides are coupled directly to LCAAP-CPG in excellent yields using 1-(3-dimethylaminopropyl)-3-ethylcarbodiimide (DEC) as coupling reagent. The conventional and time-consuming preparation of nucleoside-3'-O-succinates is no longer required.
Clinical responses to selumetinib (AZD6244; ARRY‐142886)‐based combination therapy stratified by gene mutations in patients with metastatic melanoma (2012)

Higher response rates and longer TTP were observed with selumetinib-containing regimens in patients who had tumors that harbored a BRAF mutation compared with patients who had wild-type BRAF.
Prefractionation of protein samples for proteome analysis using reversed-phase high-performance liquid chromatography (2001)

We describe an approach for fractionating complex protein samples prior to two-dimensional gel electrophoresis using reversed-phase high-performance liquid chromatography. Whole lysates of cells and tissue were prefractionated by reversed-phase chromatography and elution with a five-step gradient of increasing acetonitrile concentrations. The proteins obtained at each step were subsequently separated by high-resolution two-dimensional gel electrophoresis (2-DE). The reproducibility of this prefractionation technique proved to be optimal for comparing 2-DE gels from two different cell states. In addition, this method is suitable for enriching low-abundance proteins barely detectable by silver staining to amounts that can be detected by Coomassie blue and further analyzed by mass spectrometry.
Task-oriented access model for secure data sharing over cloud (2015)

Cloud computing has become a prevalent technology and with its increased maturity more and more data including sensitive and non sensitive, is being centralized into it. While outsourcing the sensitive data into public cloud, its prior encryption is strongly recommended. Provisioning of encryption and existing work that guarantee security and privacy concerns on sensitive data, have removed the holdouts against cloud adoption at a large. One of the main issue with this data in cloud environment is to manage user access and its auto revocation in a controlled and flexible way. The issue becomes more complex when privacy on user access has to be ensured as well to hide additional leakage of information. For automatic revocation over cloud data, access can be bounded within certain anticipated time limit so that the access expires beyond effective time period as proposed by one of the existing system as time based proxy re-encryption. This time-oriented approach is more rigid and not a one-size-fits-all solution. In certain circumstances exact time anticipation is not an easy choice. Instead, the alternate solution could be task-oriented to restrict user beyond certain number of permissible attempts to access the data. In this paper we have proposed a system that allows authorized users to access encrypted data for predefined attempts rather pre-defined time. Our approach allows user to avail permissible attempts without time restriction and at the same time also preserves the privacy aspect of user access by concealing access limit until availed. Performance analysis revealed that the cost of operations performed are within the range of .097 to .278 $ per 1000 requests.
Phosphorylated tau can promote tubulin assembly (1999)

Phosphorylation can affect the function of microtubule-associated protein tau. Here, the human brain tau with 441 amino acids was phosphorylated by cyclic-AMP-dependent protein kinase (PKA) or glycogen synthase kinase-3beta. PKA-phosphorylated tau (2.7 mol phosphates/mol) does not promote tubulin assembly as judged by spectrophotometric and atomic force microscopy measurements, unless trimethylamine N-oxide (TMAO), a natural occurring osmolyte, is included in these assays. TMAO is also found to promote tubulin assembly of glycogen synthase kinase-3beta-phosphorylated tau (1.6 mol phosphates/mol). TMAO does not act by causing a chemical dephosphorylation of phosphorylated tau, but it acts to overcome the functional deficit caused by phosphorylation. PKA-phosphorylated tau binds to tubulin in the presence of TMAO and lowers the critical concentration of tubulin needed for assembly. From these data, we conclude that PKA-phosphorylated tau retains the ability to bind tubulin and promote tubulin assembly. TMAO is required, however, to sensitize the reaction. Possible uses of TMAO in relation to studies of tubulin assembly in vitro, in intact cells, and in relation to Alzheimer's disease are presented in this report.
Reversible in vitro growth of Alzheimer disease beta-amyloid plaques by deposition of labeled amyloid peptide. (1992)

The salient pathological feature of Alzheimer disease (AD) is the presence of a high density of amyloid plaques in the brain tissue of victims. The plaques are predominantly composed of human beta-amyloid peptide (beta A4), a 40-mer whose neurotoxicity is related to its aggregation. Radioiodinated human beta A4 is rapidly deposited in vitro from a dilute (less than 10 pM) solution onto neuritic and diffuse plaques and cerebrovascular amyloid in AD brain tissue, whereas no deposition is detectable in tissue without performed plaques. This growth of plaques by deposition of radiolabeled beta A4 to plaques is reversible, with a dissociation half-time of approximately 1 h. The fraction of grey matter occupied by plaques that bind radiolabeled beta A4 in vitro is dramatically larger in AD cortex (23 +/- 11%) than in age-matched normal controls (less than 2%). In contrast to the human peptide, rat/mouse beta A4 (differing at three positions from human beta A4) does not affect the deposition of radiolabeled human beta A4. beta A4 has no detectable interaction with tachykinin receptors in rat or human brain. The use of radioiodinated beta A4 provides an in vitro system for the quantitative evaluation of agents or conditions that may inhibit or enhance the growth or dissolution of AD plaques. This reagent also provides an extremely sensitive method for visualizing various types of amyloid deposits and a means for characterizing and locating sites of amyloid peptide binding to cells and tissues.
Time-Stretched Short-Time Fourier Transform (2006)

The authors propose and demonstrate the time-stretched short-time Fourier transform (TS-STFT) technique to overcome the limitation of an analog-digital converter (ADC) in the time-frequency analysis of ultrafast signals. Experimentally, the time-frequency analysis of highly chirped RF signals, with a chirp rate as high as 350 GHz/ns, is demonstrated. An effective real-time sampling rate of 320 GSa/s is achieved. Time stretching enhances the analog bandwidth and the effective sampling rate of the ADC and enables measurement of the instantaneous behavior of highly nonstationary ultrawideband signals.
Sequence polymorphisms of the Der p 3 house dust mite allergen (1996)

These data along with our previous genomic sequence shows that for the most part, the Der p 3 allergen has only minor sequence variations (variants) although the isoallergen indicated by clone 4 needs further investigation. It is now evident that Der p 3 is encoded by a single gene and that most cDNA clones constructed from commercial mites show only minor sequence variation similar to that observed for the group 1 and group 2 house dust mite allergens.
Effects of brain polarization on reaction times and pinch force in chronic stroke (2006)

tDCS of M1affected hemisphere can modulate performance of motor tasks simpler than those previously studied, a finding that could potentially benefit patients with relatively higher impairment levels.
Patients with relapsing-remitting multiple sclerosis have normal Treg function when cells expressing IL-7 receptor α-chain are excluded from the analysis (2008)

Multiple sclerosis (MS) is a chronic inflammatory disease that results in demyelination in the central nervous system, and a defect in the regulatory function of CD4+CD25high T cells has been implicated in the pathogenesis of the disease. Here, we reanalyzed the function of this T cell subset in patients with MS, but we depleted cells expressing IL-7 receptor alpha-chain (CD127), a marker recently described as present on activated T cells but not Tregs. Similar to other studies, we observed a marked defect in the suppressive function of unseparated CD4+CD25high T cells isolated from MS patients. However, when CD127(high) cells were removed from the CD4+CD25high population, patient and control cells inhibited T cell proliferation and cytokine production equally. Likewise, when the CD25 gate used to sort the cells was stringent enough to eliminate CD127high cells, CD4+CD25high T cells from patients with MS and healthy individuals had similar regulatory function. Additional analysis indicated that the CD127high cells within the CD4+CD25high T cell population from patients with MS appeared more proliferative and secreted more IFN-gamma and IL-2 than the same cells from healthy individuals. Taken together, we conclude that CD4+CD25highCD127low Tregs from MS patients and healthy individuals exhibit similar suppressive functions. The decreased inhibitory function of unfractioned CD4+CD25high cells previously observed might be due to abnormal activation of CD127high T cells in patients with MS.
Inter- -Trypsin Inhibitor and Its Related Proteins in Syrian Hamster Urine and Plasma (1996)

Urinary excretion of trypsin inhibitor increased after injection of a carcinogen, N-nitrosobis(2-oxopropyl)amine, into Syrian hamsters. Two inhibitors were purified to apparent homogeneity from urine collected during the course of the carcinogenesis experiment. Their complete amino acid sequences were determined by Edman degradation of the intact proteins and partially degraded fragments. One corresponded to a hamster liver cDNA clone that hybridized with human bikunin probe [Ide et al, (1994) Biochim, Biophys. Acta 1209, 286-292], except that the protein sequence lacked C-terminal serine and the other was trypstatin, the C-terminal half of the bikunin molecule. Three proteins containing covalently linked bikunin were also identified in pooled blood plasma. They were all dissociated into heavy and light chains by treatment with chondroitinase ABC or 50 mM NaOH, but not by heating at 100 degrees C in the presence of sodium dodecyl sulfate and dithiothreitol, N-terminal amino acid sequence analyses of the native chains and partially degraded fragments thereof revealed that these proteins are (i) human-type inter-alpha-trypsin inhibitor, consisting of heavy chains 1 and 2 and bikunin, (ii) bovine-type inter-alpha-trypsin inhibitor, consisting of heavy chains 2 and 3 and bikunin, and (iii) pre-alpha-trypsin inhibitor, consisting of heavy chain 3 and bikunin. Heterodimer of bikunin/heavy chain 1 or bikunin/heavy chain 2 was not detected. These results suggest that the composition, and hence function, of the inter-alpha-trypsin inhibitor family differs considerably from species to species.