gebhart/patrepeval huggingface dataset:
Qudit quantum computation in the Jaynes-Cummings model (2013)

We have developed methods for performing qudit quantum computation in the Jaynes-Cummings model with the qudits residing in a finite subspace of individual harmonic oscillator modes, resonantly coupled to a spin-1/2 system. The first method determines analytical control sequences for the one- and two-qudit gates necessary for universal quantum computation by breaking down the desired unitary transformations into a series of state preparations implemented with the Law-Eberly scheme [Law and Eberly, Phys. Rev. Lett. 76, 1055 (1996)]. The second method replaces some of the analytical pulse sequences with more rapid numerically optimized sequences. In our third approach, we directly optimize the evolution of the system, without making use of any analytic techniques. While limited to smaller dimensional qudits, the third approach finds pulse sequences which carry out the desired gates in a time which is much shorter than either of the other two approaches.
A single domain of yeast poly(A)-binding protein is necessary and sufficient for RNA binding and cell viability. (1987)

The poly(A)-binding protein (PAB) gene of Saccharomyces cerevisiae is essential for cell growth. A 66-amino acid polypeptide containing half of a repeated N-terminal domain can replace the entire protein in vivo. Neither an octapeptide sequence conserved among eucaryotic RNA-binding proteins nor the C-terminal domain of PAB is required for function in vivo. A single N-terminal domain is nearly identical to the entire protein in the number of high-affinity sites for poly(A) binding in vitro (one site with an association constant of approximately 2 X 10(7) M-1) and in the size of the binding site (12 A residues). Multiple N-terminal domains afford a mechanism of PAB transfer between poly(A) strands.
Reflection from dual-domains in a holographically-formed polymer-dispersed liquid crystal material (1999)

A holographically-formed polymer-dispersed liquid crystal is reported with two distinctive reflective states brought about by a single laser exposure of a liquid crystal-rich emulsion. The two reflective states are the result of two structurally different domains that are formed during the holographic cure. A simple phenomenological model is presented that describes the dual-domain effect.
A theory of multirate filter banks (1987)

Multirate filter banks produce multiple output signals by filtering and subsampling a single input signal, or conversely, generate a single output by upsampling and interpolating multiple inputs. Two of their main applications are subband coders for speech processing and transmultiplexers for telecommunications. Below, we derive a theoretical framework for the analysis, synthesis, and computational complexity of multirate filter banks. The use of matrix notation leads to basic results derived from properties of linear algebra. Using rank and determinant of filter matrices, it is shown how to obtain aliasing/ crosstalk-free reconstruction, and when perfect reconstruction is possible. The synthesis of filters for filter banks is also explored, three design methods are presented, and finally, the computational complexity is considered.
Prevention of perioperative hypothermia in plastic surgery (2006)

While inadvertent perioperative hypothermia has received serious attention in many surgical specialties, few discussions of hypothermia have been published in the plastic surgery literature. This article reviews the physiology of thermoregulation, describes how both general and regional anesthesia alter the normal thermoregulatory mechanisms, indicates risk factors particularly associated with hypothermia, and discusses the most effective current methods for maintaining normothermia. Hypothermia is typically defined as a core body temperature of </=36 degrees C (</=96.8 degrees F), though patient outcomes are reportedly better when a temperature of >/=36.5 degrees C is maintained. Unless preventive measures are instituted, inadvertent hypothermia occurs in 50% to 90% of surgical patients, even those undergoing relatively short procedures lasting one to one-and-a-half hours. During either general or regional anesthesia, a patient's natural behavioral and autonomic responses to cold are unavailable or impaired, and the combination of general and neuraxial anesthesia produces the highest risk for inadvertent perioperative hypothermia. Unless hypothermia is prevented, the restoration of normothermia can take more than 4 hours once anesthesia is stopped. Consequences of hypothermia are serious and affect surgical outcomes in plastic surgery patients. Potential complications include morbid cardiac events, coagulation disorders and blood loss, increased incidence of surgical wound infection, postoperative shivering, longer hospital stays, and increased costs associated with surgery. Measures for preventing hypothermia are emphasized in this article, especially those proven most effective in prospective and controlled clinical studies. Perhaps the most important step in maintaining normothermia is to prewarm patients in the preoperative area with forced-air heating systems. Intraoperative warming with forced-air and fluid warming are also essential. Other strategies include maintaining an ambient operating room temperature of approximately 73 degrees F (22.8 degrees C), covering as much of the body surface as possible, and aggressively treating postoperative shivering. None of these measures can be adequately employed unless a patient's core body temperature is monitored throughout the perioperative period. Prevention of perioperative hypothermia is neither difficult nor expensive. Proper preventive measures can reduce the risk of complications and adverse outcomes, and eliminate hours of needless pain and misery for our patients.
Complex Roles of CpG in Liposomal Delivery of DNA and Oligonucleotides (2002)

Unmethylated CpG in bacterial DNA has recently been recognized as a danger signal to the mammalian immune system. This CpG signal can be greatly amplified when DNA is delivered via a lipidic vector. The CpG effects are affected by the administration route, and can be either beneficial or harmful. In this review, we will summarize our current understanding about the mechanism of action of the immunostimulatory motifs. Emphasis will be placed on the discussion of the complicated roles of CpG when CpG DNA or oligonucleotides are administered in vivo using liposomes as a delivery vehicle.
Interleukin-1, tumor necrosis factor, and the production of colony- stimulating factors by cultured mesenchymal cells (1988)

Although the genes for four hematopoietic colony-stimulating factors (CSFs) have been cloned, neither the mechanism of the regulation of their production nor their cellular origins have been established with certainty. Monocytes are known to produce colony-stimulating and burst- promoting activities, as well as several monokines such as interleukin- 1 (IL-1) and tumor necrosis factor (TNF). These monokines indirectly stimulate other mesenchymal cells to produce certain colony-stimulating factors such as granulocyte-macrophage CSF (GM-CSF). To determine whether monocytes produce other CSFs and if so, to compare the mechanism of regulation of production with that of endothelial cells and fibroblasts, we investigated the synthesis of CSFs by monocytes, human umbilical vein endothelial cells, and fibroblasts. We used total cellular RNA blot analysis to determine interleukin-3 (IL-3), GM-CSF, granulocyte CSF (G-CSF), and monocyte CSF (M-CSF) messenger RNA (mRNA) content and immunoprecipitation or bioassay to confirm the presence of the specific secreted proteins. The results indicate that M-CSF mRNA and protein are produced constitutively by all three cell types and their level of expression does not increase after induction. In contrast, GM-CSF and G-CSF mRNAs are barely detectable in uninduced monocytes and show an increase in expression after lipopolysaccharide treatment. Retrovirus-immortalized endothelial cells, unlike primary endothelial cells or both primary and immortalized fibroblasts, produce IL-1 constitutively; this correlates with their constitutive production of GM-CSF and G-CSF. IL-3 mRNA was not detectable in any of these cells either before or after induction. The results indicate that these mesenchymal cells can produce three CSFs: GM-CSF, G-CSF, and M-CSF; furthermore, the data suggest that the mechanism of regulation of M-CSF production is different from that of GM-CSF and G-CSF, and that the latter two inducible CSFs are regulated by different factors in monocytes compared with the other mesenchymal cells.
Reconstructing an Indo-European Family Tree from Non-native English Texts (2013)

Mother tongue interference is the phenomenon where linguistic systems of a mother tongue are transferred to another language. Although there has been plenty of work on mother tongue interference, very little is known about how strongly it is transferred to another language and about what relation there is across mother tongues. To address these questions, this paper explores and visualizes mother tongue interference preserved in English texts written by Indo-European language speakers. This paper further explores linguistic features that explain why certain relations are preserved in English writing, and which contribute to related tasks such as native language identification. 1
Sugar additives for MALDI matrices improve signal allowing the smallest nucleotide change (A:T) in a DNA sequence to be resolved (2001)

Sample preparation for matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) of DNA is critical for obtaining high quality mass spectra. Sample impurity, solvent content, substrate surface and environmental conditions (temperature and humidity) all affect the rate of matrix-analyte cocrystallization. As a result, laser fluence threshold for desorption/ionization varies from spot to spot. When using 3-hydroxypicolinic acid (3-HPA) as the matrix, laser fluence higher than the threshold value reduces mass resolution in time-of-flight (TOF) MS as the excess energy transferred to DNA causes metastable decay. This can be overcome by either searching for 'hot' spots or adjusting the laser fluence. However, both solutions may require a significant amount of operator manipulation and are not ideal for automatic measurements. We have added various sugars for crystallization with the matrix to minimize the transfer of excess laser energy to DNA molecules. Fructose and fucose were found to be the most effective matrix additives. Using these additives, mass resolution for DNA molecules does not show noticeable deterioration as laser energy increases. Improved sample preparation is important for the detection of single nucleotide polymorphisms (SNPs) using primer extension with a single nucleotide. During automatic data acquisition it is difficult to routinely detect heterozygous A/T mutations, which requires resolving a mass difference of 9 Da, unless a sugar is added during crystallization.
Diversity of sesquiterpene synthases in the basidiomycete Coprinus cinereus (2009)

In the article by S. Agger, F. Lopez-Gallego and C. Schmidt-Dannert, there is a mistake in Fig. 6. The stereochemistries of some of the structures shown are inverted incorrectly. The correct figure is shown below. Fig. 6. Proposed reaction mechanisms for the formation of major products of C. cinereus sesquiterpene synthases Cop1–4 and Cop6. Shown cyclization pathways are based on previous investigations on cyclization reactions catalysed by various sesquiterpene synthases reported in the literature (Steele et al., 1998; Tholl et al., 2005; Vedula et al., 2008).
HLA‐DQB1 and ‐DQA1 typing by PCR amplification with sequence‐specific primers (PCR‐SSP) in 2 hours (1993)

In the present study PCR primers were designed for detecting all phenotypically expressed DQB1 and DQA1 allelic variability, 19 and 10 alleles, respectively, by PCR amplification with sequence-specific primers (PCR-SSP). For DQB1 typing, each sample was amplified by a first set of 14 PCR primer pairs, followed in some cases by two to six additional PCR reactions. The first 14 primer pairs allowed the identification/separation of all but a few of the recently described DQB1 alleles: DQB1*0504, DQB1*0605, DQB1*0606 and DQB1*0607 would not be identified; DQB1*0603 and DQB1*0608; and DQB1*0301 and DQB1*0304, respectively, would not be distinguished. Therefore an additional set of eight DQB1 primer pairs was used for a complete DQB1 typing, including all homozygous and heterozygous combinations. For DQA1 typing, 12 PCR reactions were performed per sample, 10 for detecting variability within the second exon and two for identifying first exon polymorphism. All homozygous and heterzoygous combinations of DQA1 alleles could be resolved by these primer pairs. In addition, four primer mixes were designed for determining codon 57 of the HLA-DQB1 gene. Thirty cell lines and 120 individuals were investigated by the DQB1 and DQA1 PCR-SSP technique, as well as with the HLA-DQ beta 57 primers. The concordance between PCR-SSP typing and assigning DQB1 and DQA1 alleles from TaqI DRB-DQA-DQB RFLP analysis was 100%. The reproducibility was 100% in 30 samples investigated on two separate occasions. Amplification patterns, investigated in 15 nuclear families, segregated according to dominant Mendelian inheritance. DQB1 and DQA1 PCR-SSP typing can be performed in 2 hours, including DNA extraction, PCR amplification and post-amplification processing. The method is technically simple and the typings are easy to interpret. The cost for typing one individual is low and is independent of the number of samples analyzed simultaneously, i.e. the technique is well-suited for routine clinical use.
A decrease in the expression of CD63 tetraspanin protein elevates invasive potential of human melanoma cells (2003)

CD63, which belongs to the tetraspanin membrane proteins, has been proposed to play an important role in inhibiting melanoma metastasis. To determine whether reduction of CD63 expression, which frequently occurs in the malignant progression of human melanoma, is responsible for metastasis promotion, we transfected the antisense CD63 cDNA into MelJuso melanoma cells having endogenous CD63 expression. The antisense CD63 transfectant clones showing decreased CD63 expression displayed increased cell motility, matrix- degrading activity, and invasiveness in vitro when compared with the control transfectant cells. The antisense CD63 cDNA-transfected cells also exhibited altered adhesiveness to extracellular matrix. The results suggest that reduced CD63 expression contributes to the invasive and metastatic ability of human melanoma cells.
A Strategy for Removing the Bias in the Graphical Analysis Method (2001)

The graphical analysis method, which transforms multiple time measurements of plasma and tissue uptake data into a linear plot, is a useful tool for rapidly obtaining information about the binding of radioligands used in PET studies. The strength of the method is that it does not require a particular model structure. However, a bias is introduced in the case of noisy data resulting in the underestimation of the distribution volume (DV), the slope obtained from the graphical method. To remove the bias, a modification of the method developed by Feng et al. (1993), the generalized linear least squares (GLLS) method, which provides unbiased estimates for compartment models was used. The one compartment GLLS method has a relatively simple form, which was used to estimate the DV directly and as a smoothing technique for more general classes of model structures. In the latter case, the GLLS method was applied to the data in two parts, that is, one set of parameters was determined for times 0 to T1 and a second set from T1 to the end time. The curve generated from these two sets of parameters then was used as input to the graphical method. This has been tested using simulations of data similar to that of the PET ligand [11C]-d-threo-methylphenidate (MP, DV = 35 mL/mL) and 11C raclopride (RAC, DV = 1.92 mL/mL) and compared with two examples from image data with the same tracers. The noise model was based on counting statistics through the half-life of the isotope and the scanning time. Five hundred data sets at each noise level were analyzed. Results (DV) for the graphical analysis (DV(G)), the nonlinear least squares (NLS) method (DV(NLS)), the one-tissue compartment GLLS method (DV(F)), and the two part GLLS followed by graphical analysis (DV(FG)) were compared. DV(FG) was found to increase somewhat with increasing noise and in some data sets at high noise levels no estimate could be obtained. However, at intermediate levels it provided a good estimation of the true DV. This method was extended to use a reference tissue in place of the input function to generate the distribution volume ratio (DVR) to the reference region. A linearized form of the simplified reference tissue method of Lammertsma and Hume (1996) was used. The DVR generated directly from the model (DVR(FL)) was compared with DVR(FG) (determined from a "smoothed" uptake curve as for DV(FG)) using the graphical method.
Identification of binding partners interacting with the α1-N-propeptide of type V collagen (2010)

The predominant form of type V collagen is the [α1(V)]₂α2(V) heterotrimer. Mutations in COL5A1 or COL5A2, encoding respectively the α1(V)- and α2(V)-collagen chain, cause classic EDS (Ehlers-Danlos syndrome), a heritable connective tissue disorder, characterized by fragile hyperextensible skin and joint hypermobility. Approximately half of the classic EDS cases remain unexplained. Type V collagen controls collagen fibrillogenesis through its conserved α1(V)-N-propeptide domain. To gain an insight into the role of this domain, a yeast two-hybrid screen among proteins expressed in human dermal fibroblasts was performed utilizing the N-propeptide as a bait. We identified 12 interacting proteins, including extracellular matrix proteins and proteins involved in collagen biosynthesis. Eleven interactions were confirmed by surface plasmon resonance and/or co-immunoprecipitation: α1(I)- and α2(I)-collagen chains, α1(VI)-, α2(VI)- and α3(VI)-collagen chains, tenascin-C, fibronectin, PCPE-1 (procollagen C-proteinase enhancer-1), TIMP-1 (tissue inhibitor of metalloproteinases-1), MMP-2 (matrix metalloproteinase 2) and TGF-β1 (transforming growth factor β1). Solid-phase binding assays confirmed the involvement of the α1(V)-N-propeptide in the interaction between native type V collagen and type VI collagen, suggesting a bridging function of this protein complex in the cell-matrix environment. Enzymatic studies showed that processing of the α1(V)-N-propeptide by BMP-1 (bone morphogenetic protein 1)/procollagen C-proteinase is enhanced by PCPE-1. These interactions are likely to be involved in extracellular matrix homoeostasis and their disruption could explain the pathogenetic mechanism in unresolved classic EDS cases.
Treatment of metastatic renal cell carcinoma (mRCC) with CAIX CAR-engineered T-cells–a completed study overview (2016)

We studied safety and proof of concept of a phase I/II trial with chimeric antigen receptor (CAR) T-cells in patients with metastatic renal cell carcinoma (mRCC). The CAR was based on the G250 mAb that recognized an epitope of carboxy-anhydrase-IX (CAIX). Twelve patients with CAIX+ mRCC were treated in three cohorts with a maximum of 10 daily infusions of 2×10(7) to 2×10(9) CAR T-cells. Circulating CAR T-cells were transiently detectable in all patients and maintained antigen-specific immune functions following their isolation post-treatment. Blood cytokine profiles mirrored CAR T-cell presence and in vivo activity. Unfortunately, patients developed anti-CAR T-cell antibodies and cellular immune responses. Moreover, CAR T-cell infusions induced liver enzyme disturbances reaching CTC grades 2-4, which necessitated cessation of treatment in four out of eight patients (cohort 1+2). Examination of liver biopsies revealed T-cell infiltration around bile ducts and CAIX expression on bile duct epithelium, adding to the notion of on-target toxicity. No such toxicities were observed in four patients that were pretreated with G250 mAb (cohort 3). The study was stopped due to the advent of competing treatments before reaching therapeutic or maximum tolerated dose in cohort 3. No clinical responses have been recorded. Despite that, from this trial numerous recommendations for future trials and their immune monitoring could be formulated, such as choice of the target antigen, format and immunogenicity of receptor and how the latter relates to peripheral T-cell persistence.
Properties of 1,3-dialkylimidazolium chloride-aluminum chloride ionic liquids. 2. Phase transitions, densities, electrical conductivities, and viscosities (1984)

ADVERTISEMENT RETURN TO ISSUEPREVarticleNEXTProperties of 1,3-dialkylimidazolium chloride-aluminum chloride ionic liquids. 2. Phase transitions, densities, electrical conductivities, and viscositiesArmand A. Fannin Jr., Danilo A. Floreani, Lowell A. King, John S. Landers, Bernard J. Piersma, Daniel J. Stech, Robert L. Vaughn, John S. Wilkes, and John L. WilliamsCite this: J. Phys. Chem. 1984, 88, 12, 2614–2621Publication Date (Print):June 1, 1984Publication History Published online1 June 1984Published inissue 1 June 1984https://pubs.acs.org/doi/10.1021/j150656a038https://doi.org/10.1021/j150656a038research-articleACS PublicationsCopyright © 1984 American Chemical SocietyRequest reuse permissionsArticle Views3189Altmetric-Citations423LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts