gebhart/patrepeval huggingface dataset:
Polynomial interpolation schemes for internal derivative distributions on structured grids (1995)

Computational fluid dynamics problems which use a streamfunction formulation require differentiation to obtain the velocity field. If the velocity components are required at internal points on the grid (for example, for particle trajectory calculations) this necessitates some form of interpolation. Similarly, N-body computations which include self-gravity and cannot afford the luxury of an O(N2) 1r2 calculation, require interpolation to obtain the force components at locations internal to an overlaid grid. These two independent examples reduce to the same generalized problem. Given a function distribution on a structured grid, which interpolation schemes give the most suitable solutions in terms of accuracy, computational efficiency and smoothness properties? The best numerical schemes are those which use higher order finite difference approximations for the derivatives (but not vast templates), perform interpolation directly over the derivative (and not the function), and have an odd power as the leading term in the polynomial expansion for the derivative. These methods include forms of bicubic and quintic-cubic interpolation but although generating accurate and realistic internal derivative estimates, come at a higher computational price. For simulations where the interpolation routines need to be called frequently, the lower order schemes such as cubic-linear and biquadratic interpolation, although less accurate, are more computationally efficient and may be more appropriate.
Mesenchymal stem cells use extracellular vesicles to outsource mitophagy and shuttle microRNAs (2015)

Mesenchymal stem cells (MSCs) and macrophages are fundamental components of the stem cell niche and function coordinately to regulate haematopoietic stem cell self-renewal and mobilization. Recent studies indicate that mitophagy and healthy mitochondrial function are critical to the survival of stem cells, but how these processes are regulated in MSCs is unknown. Here we show that MSCs manage intracellular oxidative stress by targeting depolarized mitochondria to the plasma membrane via arrestin domain-containing protein 1-mediated microvesicles. The vesicles are then engulfed and re-utilized via a process involving fusion by macrophages, resulting in enhanced bioenergetics. Furthermore, we show that MSCs simultaneously shed micro RNA-containing exosomes that inhibit macrophage activation by suppressing Toll-like receptor signalling, thereby de-sensitizing macrophages to the ingested mitochondria. Collectively, these studies mechanistically link mitophagy and MSC survival with macrophage function, thereby providing a physiologically relevant context for the innate immunomodulatory activity of MSCs.
Epidermolysis bullosa: preliminary observations of blister formation in keratinocyte cultures (1984)

Keratinocytes from patients with different types of epidermolysis bullosa (EB) demonstrated an abnormal tendency to blister or bleb formation after 14-22 days in culture. The changes were most marked in samples from cases of junctional EB and were not observed in control cultures of normal skin. These findings suggest the possibility of a primary abnormality of keratinocyte adhesion in different varieties of EB and that keratinocyte culture should provide a useful model for further studies on disorders of adhesion in EB.
Transcriptional Profiling of Mucociliary Differentiation in Human Airway Epithelial Cells (2007)

When cultured at an air-liquid interface (ALI) in the appropriate medium, primary human airway epithelial cells form a polarized, pseudostratified epithelium composed of ciliated and mucus-secreting cells. This culture system provides a useful tool for the in vitro study of airway epithelial biology and differentiation. We have performed microarray analysis on ALI cultures of human bronchial epithelial cells (HBECs) grown over a 28-d period to identify genes involved in mucociliary differentiation. We identified over 2,000 genes that displayed statistically significant 2-fold or greater changes in expression during the time course. Of the genes showing the largest increases, many are involved in processes associated with airway epithelial biology, such as cell adhesion, immunity, transport, and cilia formation; however, many novel genes were also identified. We compared our results with data from proteomic analyses of the ciliary axoneme and identified candidate genes that may have roles in cilia formation or function. Gene networks were generated using Ingenuity Pathways Analysis (Ingenuity Systems, Redwood City, CA) to identify signaling pathways involved in mucociliary cell differentiation or function. Networks containing genes involved in TGF-beta, WNT/beta-catenin, and epidermal growth factor receptor (EGFR) pathways were identified, suggesting potential roles for these families in airway epithelia. Microarray results were validated by real-time RT-PCR for a number of representative genes. This work has provided extensive information about gene expression changes during differentiation of airway epithelial cells, and will be a useful resource for researchers interested in respiratory function, pathology, and toxicology.
Immunodeficiency Diseases Caused by Defects in Phagocytes (2000)

Primary phagocytic defects must be included in the differential diagnosis of recurrent infection and fever in a child and occasionally in an adult. Early diagnosis is essential, because manifestations of infection are usually blunted and rapid intervention can be lifesaving. In general, patients are identified at a young age on the basis of their susceptibility to normally nonpathogenic bacteria or fungi. In some cases, the infectious agents point to the disorder (Table 1): catalase-positive microorganisms and aspergillosis species are characteristic of chronic granulomatous disease,1 and atypical mycobacteria suggest a defect in the interferon-γ–interleukin-12 axis.2 These bacterial infections contrast with the . . .
Characterization of (CA)nmicrosatellites with degenerate sequencing primers (1992)

Construction of DNA clones which allow determination of sequences flanking (CA),, microsatellites (1, 2) is the most
Does Removal of the Primary Tumor in Metastatic Breast Cancer Improve Survival? (2013)

Although relative survival for breast cancer has improved in recent years, patients who present with metastatic disease have a less than 30% 5-year survival. Thus, improvements in treatment for these patients have the potential to have a significant impact on outcomes. Historically, removal of the primary breast tumor has been offered to these patients only for palliation. However, there have been recent reports that removal of the primary tumor may improve survival. Here, we review the theories and data at the center of the debate, the landmark studies that historically guided treatment, the retrospective data that revisited the role of removal of the primary tumor, as well as the latest advances in basic science and the accruing clinical studies to provide for future directions in this field. Although the definitive role of removal of the primary tumor in metastatic breast cancer is not settled, it is critical to understand the complexities of this debate in order to make further gains in breast cancer survivorship.
Effect of long‐term depletion of plasma methionine on the growth and survival of human brain tumor xenografts in athymic mice (1997)

Depletion of plasma methionine is expected to inhibit or reverse growth of methionine-dependent tumors; however, modulation of methionine and other sulfur amino acids is not a trivial task in experimental animals. L-Methioninase from Pseudomonas putida at 1,000 U/kg causes acute reduction of plasma methionine by 80% in mice, but recovery occurs within 14 hours. Restriction of dietary choline and replacement of dietary methionine with homocystine results in 50% chronic reduction of plasma methionine. A > 70% reduction can be accomplished with a diet deficient in methionine, homocystine, and choline, but ultimately this diet is lethal. Plasma methionine can be lowered to a steady state of < 5 microM in mice with a combination of dietary restriction of methionine, homocysteine, and choline and synchronous treatments with intraperitoneal injections of 1,000 U/kg L-methioninase and 25-50 mg/kg homocystine, each administered at 12-hour intervals. Modulation of plasma methionine by this means causes no weight loss or pathologies in liver or pancreas, and it does not markedly alter levels of cysteine, homocysteine, or glutathione in plasma or in hepatic tissue. When this procedure is applied to athymic mice bearing human medulloblastoma (Daoy) tumors subcutaneously, tumor growth is inhibited. Methionine deprivation arrests mitosis by blocking the cell cycle in G2 and induces apoptosis. Tumor stasis was achieved in 100% of treated animals within 4 days of treatment, and regression was seen in one-third of animals after a 10-day period. These data strongly support the use of methionine-depleting regimens for tumor treatments.
The incorporation of metal clusters into thin organic dye layers as a method for producing strongly absorbing composite layers: an oscillator model approach to resonant metal cluster absorption (1995)

We present data on the NIR/VIS/UV optical constants of thin composite layers, built up from a copper phthalocyanine matrix with embedded metal clusters. The metal clusters (copper, gold and silver) have diameters on a nanometre scale and act as strong absorption centres. In particular, local plasmon resonances and metal interband transitions could be observed from a fit of the experimentally determined dielectric functions by means of a Lorentzian multi-oscillator model. Average dipole transition matrix elements with respect to a single metal cluster have been estimated from the oscillator parameters.
An RNA pattern matching program with enhanced performance and portability (1994)

Journal Article An RNA pattern matching program with enhanced performance and portability Get access Alain Laferrière, Alain Laferrière Département de Biochimie, Université de MontréalCP 6128, Succ A, Montréal, Québec, Canada H3C 3J Search for other works by this author on: Oxford Academic PubMed Google Scholar Daniel Gautheret, Daniel Gautheret 1 Département de Biochimie, Université de MontréalCP 6128, Succ A, Montréal, Québec, Canada H3C 3J 1To whom correspondence should be addressed. Current address: Department of Molecular, Cellular and Developmental Biology. Campus Box 347, University of Colorado at Boulder, Boulder, Co 80309-0347, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Robert Cedergren Robert Cedergren Département de Biochimie, Université de MontréalCP 6128, Succ A, Montréal, Québec, Canada H3C 3J Search for other works by this author on: Oxford Academic PubMed Google Scholar Bioinformatics, Volume 10, Issue 2, 2 April 1994, Pages 211–212, https://doi.org/10.1093/bioinformatics/10.2.211 Published: 02 April 1994 Article history Accepted: 30 October 1993 Published: 02 April 1994
COVID-19 patients upregulate toll-like receptor 4-mediated inflammatory signaling that mimics bacterial sepsis (2020)

Abstract Observational studies of the ongoing coronavirus disease 2019 (COVID-19) outbreak suggest that a cytokine storm is involved in the pathogenesis of severe illness. However, the molecular mechanisms underlying the altered pathological inflammation in COVID-19 are largely unknown. We report here that toll-like receptor (TLR) 4-mediated inflammatory signaling molecules are upregulated in peripheral blood mononuclear cells (PBMCs) from COVID-19 patients, compared with healthy controls. Among the most highly increased inflammatory mediators in severe/critically ill patients, S100A9, an alarmin and TLR4 ligand, was found as a noteworthy biomarker, because it inversely correlated with the serum albumin levels. These data support a link between TLR4 signaling and pathological inflammation during COVID-19 and contribute to develop therapeutic approaches through targeting TLR4-mediated inflammation.
Structure-Based Inhibitors of Influenza Virus Sialidase. A Benzoic Acid Lead with Novel Interaction (1995)

Influenza virus sialidase is a surface enzyme that is essential for infection of the virus. The catalytic site is highly conserved among all known influenza variants, suggesting that this protein is a suitable target for drug intervention. The most potent known inhibitors are analogs of 2-deoxy-2,3-didehydro-N-acetylneuraminic acid (Neu5Ac2en), particularly the 4-guanidino derivative (4-guanidino-Neu5Ac2en). We utilized the benzene ring of 4-(N-acetylamino)benzoic acids as a cyclic template to substitute for the dihydropyran ring of Neu5Ac2en. In this study several 3-(N-acylamino) derivatives were prepared as potential replacements for the glycerol side chain of Neu5Ac2en, and some were found to interact with the same binding subsite of sialidase. Of greater significance was the observation that the 3-guanidinobenzoic acid derivative (equivalent to the 4-guanidino grouping of 4-guanidino-Neu5Ac2en), the most potent benzoic acid inhibitor of influenza sialidase thus far identified (IC50 = 10 microM), occupied the glycerol-binding subsite on sialidase as opposed to the guanidino-binding subsite. This benzoic acid derivative thus provides a new compound that interacts in a novel manner with the catalytic site of influenza sialidase.
Single nucleotide polymorphisms in XRCC1,XPD and platinum prognosis in non-small-cell lung cancer patients (2008)

Objective XPD and XRCC1 are emerging as essential elements in repair of pla- timun-DNA adducts.To investigate whether the single nucleotide polymorphism (SNP) in DNA re- pair gene XRCC1 (X-ray repair cross-complementing 1) and XPD are associated with the clinical prognosis of platinum-containing combination chemotherapy in the paraffin-embedded tissue of non- small-cell lung cancer.Methods XRCC1 and XPD genotypes were assessed using 5' nuclease allelic discrimination assay (TaqMan) by real-time PCR.The pathological parameters and survival data were evaluated according to the different genotypes in 53 NSCLC.Results The median survival time of patients with Arg/Arg or Arg/Gln genotypes was 24 months compared with 8.0 months of others (P=0.02).No significant association was found between XPD 751 SNP and survival (P0.05).When we compared combinations of variant alleles across both polymorphisms,we found that a greater number of variant alleles were associated with decreasingoverall survival (P=0.015, log-rank test).In Cox ratio hazard models,XRCC1 Arg399Gln could independently predict overall survival time of lung cancer(P=0.011).Conclusions It suggested that XRCC1 399 SNP might be prognostic marker of survival for lung cancer patients receiving platinum-based chemotherapy. The two polymorphism of XRCC1 and XPD might have synergic effect on the prognosis of platinum agents.
Modulation of Mediotemporal and Ventrostriatal Function in Humans by Δ9-Tetrahydrocannabinol (2009)

The modulation of mediotemporal and ventrostriatal function by Delta9-THC may underlie the effects of C. sativa on verbal learning and psychotic symptoms, respectively.
Cloning and Sequence Analysis of E Gene from Chicken Flavivirus Isolate CJD05 (2012)

[Objective] This experiment aimed to find out the origin and genetic evolution relationship of chicken flavivirus (CFV) CJD05 strain in Fujian Province. [Method] A pair of primers were designed and synthesized according to the sequences of E gene from Duck flavivirus (DFV) isolate BYD-1. E gene of CFV isolate CJD05 was specially amplified and its sequences were analyzed. [Result] The target bar which was cloned from CFV isolate CJD05 was 1 503 bp. Homology analysis was conducted to compare E gene nucleotide sequence of CFV isolate CJD05 with DFV isolate BYD-1 and goose flavivirus (GFV) isolate JS804. Results indicated that isolate nucleotide homologies were 99.2% and 99.3%, and amino acid homologies were 99.0% and 98.6% respectively. [Conclusion] CFV isolate CJD05, DFV isolate BYD-1 and GFV isolate JS804 were highly homologous. The homology of CFV isolate CJD05 with Tembusu virus (TMUV) was higher than with other arthropod-borne flaviviruses.
Powder diffraction: Least-squares and beyond (2004)

This paper addresses some of the underlying statistical assumptions and issues in the collection and refinement of powder diffraction data. While standard data collection and Rietveld analysis have been extremely successful in providing structural information on a vast range of materials, there is often uncertainty about the true accuracy of the derived structural parameters. In this paper, we discuss a number of topics concerning data collection and the statistics of data analysis. We present a simple new function, the cumulative chi-squared distribution, for assessing regions of misfit in a diffraction pattern and introduce a matrix which relates the impact of individual points in a powder diffraction pattern with improvements in the estimated standard deviation of refined parameters. From an experimental viewpoint, we emphasise the importance of not over-counting at low-angles and the routine use of a variable counting scheme for data collection. Data analysis issues are discussed within the framework of maximum likelihood, which incorporates the current least-squares strategies but also enables the impact of systematic uncertainties in both observed and calculated data to be reduced.
Halftone images: Spatial resolution and tone reproduction* (1978)

The halftone technique, which converts a continuous-tone picture into a binary image, is examined. A halftone screen function is used to specify configurations of binary image elements; their area determines the local average image irradiance and information about the spatial image irradiance variations is relfected in their boundaries. A halftone ring geometry is suggested to improve spatial image resolution. Experiments are reported to verify this prediction.
A multiprocessor for transient event detection (1997)

The multiscale transient event detector (TED) introduced by Leeb (1993) uses measurements of current and voltage made at the electric utility service entry of a building to help determine the operating schedule of all of the significant loads in the building. This paper describes a TED algorithm implemented on a custom multiprocessing machine with several inexpensive processors performing tasks in parallel. A parallel version of the serial TED algorithm is developed, and the hardware design for a multiprocessing TED is presented. The performance of the algorithm is illustrated with results from a prototype.
Isoleucyl-tRNA synthetase from the ciliated protozoan Tetrahymena thermophila. DNA sequence, gene regulation, and leucine zipper motifs. (1992)

We have determined the nucleotide sequence of a protozoan aminoacyl-tRNA synthetase. The isoleucyl-tRNA synthetase (ileRS) gene [ilsA; formerly cupC, Martindale, D. W., Martindale, H. M., and Bruns, P. J. (1986) Nucleic Acids Res. 14, 1341-1354] from the ciliate Tetrahymena thermophila was sequenced and found to have eight introns, four transcription start sites, and a putative polypeptide of 1081 amino acids. A polypeptide 20 amino acids longer could be made if a transcribed in-frame ATG close to the start sites and with suboptimal sequence context is used. This gene was identified through hybridization and amino acid sequence similarity to the previously cloned and sequenced ileRS (cytoplasmic) gene from Saccharomyces cerevisiae [Englisch, U., Englisch, S., Markmeyer, P., Schischkoff, J., Sternbach, H., Kratzin, H., and Cramer, F. (1987) Biol. Chem. Hoppe-Seyler 368, 971-979; Martindale, D. W., Gu, Z. M., and Csank, C. (1989) Curr. Genet. 15, 99-106] with which it shares 47% of its amino acids. We also compared it to ileRS genes from E. coli and an archaebacterium. Two leucine zippers motifs were identified in the carboxyl-terminal domain of the polypeptide; one of these motifs is in the same area as the zinc finger motif found in the E. coli enzyme. The transcription pattern of the ilsA gene was monitored under various culture conditions and parallels changes in protein synthesis.
Pharmacokinetic Study of Taxol-Loaded Poly(lactic-co-glycolic acid) Microspheres Containing Isopropyl Myristate after Targeted Delivery to the Lung in Mice. (1996)

This study describes the pharmacokinetic behaviours of taxol after intravenous administration of taxol-loaded poly(lactic-co-glycolic acid) microspheres containing isopropyl myristate (namely, Taxol-IPM-PLGA-MS) and taxol saline solution to mice. Taxol-IPM-PLGA-MS were prepared using a solvent evaporation technique. The drug content and trapping efficiency of taxol in the microspheres were 5.09% (w/w) and 98%, respectively; the average diameter of the microspheres was 30.1 microns. Scanning electron microscopy showed that Taxol-IPM-PLGA-MS were spherical with a smooth surface. After administration of the drug saline solution (3 mg taxol/kg), taxol disappeared rapidly from plasma within 4-6 h and distributed extensively in various tissues. The tissue levels and AUCfinite of taxol in the lung were obviously higher than those in plasma but relatively lower than those in kidneys, bile, and liver. The biodistribution of taxol after administration of Taxol-IPM-PLGA-MS (3 mg taxol/kg), on the other hand, was altered significantly from the control (taxol solution) group. No taxol was detected in plasma or bile within 3 weeks, and only very low level of taxol was detected in the kidneys or liver within 48 h. However, taxol concentrations in the lung were increased significantly with the microsphere group; the peak concentration of taxol and AUCfinite in the lung was three times and 500 times higher than those with the taxol solution group, respectively. It was also noticed that the taxol levels in the lung were maintained at relatively high levels (> 10 micrograms/ml) for 3 weeks. Thus, the present study demonstrated the effective targeted delivery of taxol to the lung of mice using Taxol-IPM-PLGA-MS.
Cryogenic processed metal-semiconductor-metal (MSM) photodetectors on MBE grown ZnSe (1999)

Molecular beam epitaxy grown 0.5-/spl mu/m and 2.0-/spl mu/m thick undoped ZnSe on semi-insulating [100] GaAs substrates were prepared for metal-semiconductor-metal (MSM) photodetector devices. The MSM photodetectors consisted of interdigitated metal fingers with 2, 3, and 4 /spl mu/m width/spacing on a wafer. A multilayer resist process was employed using polyimide and SiO/sub 2/ thin films before the pattern generation to aid in a special low temperature (LT) lift-off process. Dark current-voltage (I-V), DC photo I-V, high frequency I-V, spectral response, and frequency response techniques were employed for testing the device performance. The cryogenic processed metallization provided an improved interface between metal and semiconductor interface. The breakdown voltage in these devices is dependent on the electrode width/spacing and not on film thickness. Dark current remained at around 1 pA for a bias of /spl plusmn/10 V. The devices exhibited a high spectral responsivity of 0.6 (A/W) at a wavelength of 460 nm at 5 V applied bias. A maximum spectral responsivity of 1 (A/W) at an applied bias of 5 V was obtained in these devices indicating an internal gain mechanism. This internal gain mechanism is attributed to hole accumulation in ZnSe epilayers.