gebhart/patrepeval huggingface dataset:
Influence de la taille de l'amplicon sur les résultats obtenus par PCR en temps réel (2017)

Description of the subject. This paper discusses the influence of amplicon length on real-time PCR results. Objectives. The aim of the experiments was to show that amplicon size has an influence on detection. Method. Tests were performed on genomic and plasmid DNA. Double-dye probes and SYBR® Green were used for detection by real-time PCR. Primers were selected in order to produce fragments with increasing sizes. Experiments dealt with two targets: an endogenous target for soybean (part of the lectin gene) and a transgenic target (junction P35S-CTP of the MON40-3-2 soybean). Results. The results show that the kinetics of amplification curves evolve as a function of amplicon length, and smaller amplicons yield a higher level of fluorescence for the plateau phase. DNA degradation within the sample as well as the principles of fluorescence acquisition as a function of the chemistry used can also be factors. Conclusions. It was experimentally shown that the observed effect is linked to the suboptimal elongation temperature used in real-time PCR. Detection using SYBR® Green is less impacted as the loss of efficiency is partially compensated by the greater integration of SYBR® Green molecules in the larger fragments.
Small-scale polymer structures enabled by thiol-ene copolymer systems (2009)

The research described herein is aimed at exploring the thermo-mechanical properties of thiol-ene polymers in bulk form, investigating the ability of thiol-ene polymers to behave desirably as photolithographic media, and providing the first characterization of the mechanical properties of two-photon stereolithography-produced polymer structures. The thiol-ene polymerization reaction itself is well-characterized and described in the literature, but the thermomechanical properties of thiol-ene and thiol-ene/acrylate polymers still require more rigorous study. Understanding the behavior of thiol-ene networks is a crucial step towards their expanded use in bulk form, and particularly in specialized applications such as shape memory devices. Additionally, the thiol-ene polymerization reaction mechanism exhibits unique properties which make these polymers well suited to photolithography, overcoming the typical dichotomy of current materials which either exhibit excellent photolithographic behavior or have controllable properties. Finally, before two-photon stereolithography can create mechanisms and devices which can serve any mechanically functional role, the mechanical properties of the polymers they produce must be quantitatively characterized, which is complicated by the extremely small scale at which these structures are produced. As such, mechanical characterization to date has been strictly qualitative.\n\nFourier transfer infrared spectroscopy revealed functional group conversion information and sol-fraction testing revealed the presence of unconverted monomer and impurities, while dynamic mechanical analysis and tensile testing revealed the thermomechanical responses of the systems. Nanoindentation was employed to characterize the mechanical properties of polymers produced by two-photon stereolithography. Optical and electron microscopy were exploited to provide quantitative and qualitative evaluations of thiol-ene/acrylate performance in small-scale polymerization regimes.\n\nThe broad objective of the research was to explore thiol-ene polymer behavior both in bulk and at the small scale in an effort to supplement the material library currently used in these fields and to expand the design envelope available to researchers. The significance of the research is the advancement of a more complete and fundamental understanding of thiol-ene polymerization from kinetics to final properties, the quantitative establishment of the mechanical properties of materials created with two-photon stereolithography, and the comprehensive characterization of a supplementary class of photopatternable polymers with greater property tunability than is possible with currently used materials.
Computation of mode eigenfunctions in graded-index optical fibers by the propagating beam method (1980)

The propagating beam method utilizes discrete Fourier transforms for generating configuration-space solutions to optical waveguide problems without reference to modes. The propagating beam method can also give a complete description of the field in terms of modes by a Fourier analysis with respect to axial distance of the computed fields. Earlier work dealt with the accurate determination of mode propagation constants and group delays. In this paper the method is extended to the computation of mode eigenfunctions. The method is efficient, allowing generation of a large number of eigenfunctions from a single propagation run. Computations for parabolic-index profiles show excellent agreement between analytic and numerically generated eigenfunctions.
Transplantation in miniature swine. V. Characterization of Ia antigens. (1979)

The complexity of the I region analog associated with the MHC of miniature swine has been probed by sequential antibody precipitation studies of Ia antigens. Treatment of solubilized lymphocyte preparations from MSLA homozygotes of the DD haplotype with excess AA anti-DD alloantiserum led to precipitation of only a portion of the total Ia antigens, as determined by secondary precipitation of the remaining material with CC anti-DD serum. The presumed I region of miniature swine must therefore code for more than one Ia antigen-bearing polypeptide chain. In addition, certain mouse alloantisera that had previously been shown to react with rat Ia antigens were tested for reactivity with swine Ia antigens. Anti-Iak mouse alloantisera precipitated Ia molecules from every swine extract tested, regardless of MHC type, precluding genetic mapping studies. However, sequential precipitation studies demonstrated that the cross-reactive mouse alloantisera reacted only with a subclass of swine Ia antigens, again suggesting genetic complexity of the pig Ia locus.
miR-Q: a novel quantitative RT-PCR approach for the expression profiling of small RNA molecules such as miRNAs in a complex sample (2008)

miR-Q is a cost-effective and highly specific approach, which neither requires the use of fluorochromic probes, nor Locked Nucleic Acid (LNA)-modified oligonucleotides. Moreover, it provides a remarkable increase in specificity and simplified detection of small RNAs.
Diagnosing and treating Diamond Blackfan anaemia: results of an international clinical consensus conference (2008)

Diamond Blackfan anaemia (DBA) is a rare, genetically and clinically heterogeneous, inherited red cell aplasia. Classical DBA affects about seven per million live births and presents during the first year of life. However, as mutated genes have been discovered in DBA, non-classical cases with less distinct phenotypes are being described in adults as well as children. In caring for these patients it is often difficult to have a clear understanding of the treatment options and their outcomes because of the lack of complete information on the natural history of the disease. The purpose of this document is to review the criteria for diagnosis, evaluate the available treatment options, including corticosteroid and transfusion therapies and stem cell transplantation, and propose a plan for optimizing patient care. Congenital anomalies, mode of inheritance, cancer predisposition, and pregnancy in DBA are also reviewed. Evidence-based conclusions will be made when possible; however, as in many rare diseases, the data are often anecdotal and the recommendations are based upon the best judgment of experienced clinicians. The recommendations regarding the diagnosis and management described in this report are the result of deliberations and discussions at an international consensus conference.
Data acquisition system for body surface potential mapping. (1978)

Boltzmann machines offer an exciting approach to connectionist networks. Salient features of these networks are their distributed internal representations and their use of massive parallelism. This paper reviews some of the achievements in the research on Boltzmann machines and discusses in particular two different fields of application, viz. (1) solving combinatorial optimization problems and (ii) carrying out learning tasks. Some open problems are also touched upon.
Building Oracle XML Applications (2000)

XML (Extensible Markup Language)has emerged as industry standard for describing data for e-commerce, particularly for business-to-business exchange. Oracle Corporation supports XML in a wide range of products, and company describes Oracle8i, its Internet as the first XML-enabled database. XML is a key part of company's e-business strategy. Building Oracle XML Applications gives both Java and PL/SQL developers a rich and detailed look at range of available Oracle XML technologies. The book shows how to combine power of XML and XSLT with speed, functionality, and reliability of Oracle database to build flexible applications. The author delivers nearly 800 pages of entertaining text, helpful and time-saving hints, and extensive examples that developers can put to use immediately to build custom XML applications. Products covered include: XSQL pages and XSQL servletJDeveloperXSLT ProcessorXML ParserinterMediaAdvanced Queuing The accompanying CD-ROM contains JDeveloper 3.1, an integrated development environment for Java developers.
The membrane mirror as an adaptive optical element* (1977)

A membrane mirror assembly is described that has a membrane deflected by a region of electrostatic actuators, consisting of conducting pads. The procedure for fabrication of typical membranes is described and involves evaporation of the material onto a substrate in a vacuum chamber. Parametric equations, developed from basic vibration theory, are given for establishing transient and steady-state performance criteria. Experimental data, using both titanium and nickel test membranes, shows that the performance satisfies the predicted requirements.
The effects of coital lubricants on sperm motility in vitro (1998)

Infertility affects approximately 15% of couples, and in about one-third the primary cause is a male factor. Patients undergoing infertility investigations frequently experience sexual dysfunction, which often is due to inadequate vaginal lubrication. This can lead to increased use of coital lubricants. The effects of such lubricants on sperm motility have not been widely studied, although sperm motility is one of the best prognostic indicators of fertilization. Using a prospective longitudinal control-based study, we analysed the effect of adding four lubricants: KY jelly, baby oil, olive oil and saliva on sperm motion in 16 samples from patients undergoing infertility investigations. Sperm samples were prepared by density gradient centrifugation prior to mixing with lubricants. Motility parameters were determined using computer-assisted semen analysis after 5, 15 and 30 min. All lubricants except baby oil significantly decreased percentage progressive motility, progressive velocity, curvilinear velocity and lateral head displacement at 12.5% concentration. At a lower concentration of 6.25%, both olive oil and saliva still significantly reduced progressive motility parameters, while KY jelly diminished head movement parameters. Hence, even at these very low concentrations, coital lubricants impair sperm motility and thus may adversely affect fertility.
Pathophysiology of urinary incontinence in murine models (2012)

Urethral closure mechanisms under stress conditions consist of passive urethral closure involving connective tissues, fascia and/or ligaments in the pelvis and active urethral closure mediated by hypogastric, pelvic and pudendal nerves. Furthermore, we have previously reported that the active urethral closure mechanism might be divided into two categories: (i) the central nervous control passing onto Onuf's nucleus under sneezing or coughing; and (ii) the bladder-to-urethral spinal reflex under Valsalva-like stress conditions, such as laughing, exercise or lifting heavy objects. There are over 200 million people worldwide with urinary incontinence, a condition that is associated with a significant social impact and reduced quality of life. Therefore, basic research for urinary continence mechanisms in response to different stress conditions can play an essential role in developing treatments for stress urinary incontinence. It has been clinically shown that the etiology of stress urinary incontinence is divided into urethral hypermobility and intrinsic sphincter deficiency, which could respectively correspond to passive and active urethral closure dysfunction. In this review, we summarize the representative stress urinary incontinence animal models and the methods to measure leak point pressures under stress conditions, and then highlight stress-induced urinary continence mechanisms mediated by active urethral closure mechanisms, as well as future pharmacological treatments of stress urinary incontinence. In addition, we introduce our previous reports including sex differences in urethral closure mechanisms under stress conditions and urethral compensatory mechanisms to maintain urinary continence after pudendal nerve injury in female rats.
Cloning, Expression, and Catabolite Repression of a Gene Encoding β-Galactosidase of <i>Bacillus megaterium</i> ATCC 14581 (1998)

A gene encoding beta-galactosidase, designated mbgA, was isolated from Bacillus megaterium ATCC 14581. Chromosomal beta-galactosidase production could be dramatically induced by lactose but not by isopropyl-beta-D-thiogalactopyranoside (IPTG) and was subject to catabolite repression by glucose. Disruption of mbgA in the B. megaterium chromosome resulted in loss of lactose-inducible beta-galactosidase production. A 27-bp inverted repeat was found to overlap the mbgA promoter sequence. Two partially overlapping catabolite-responsive elements (CREs) were identified within the inverted repeat. Base substitutions within CRE-I and/or CRE-II caused partial relief from catabolite repression. The results suggest that the 27-bp inverted repeat may serve as a target for a catabolite repressor(s).
Bortezomib plus dexamethasone as induction treatment prior to autologous stem cell transplantation in patients with newly diagnosed multiple myeloma: results of an IFM phase II study. (2006)

This regimen of bortezomib plus dexamethasone appears effective and well tolerated in newly diagnosed myeloma patients.
A bifunctional catalyst for carbon dioxide fixation: cooperative double activation of epoxides for the synthesis of cyclic carbonates (2012)

We have developed a very active bifunctional porphyrin catalyst showing a high turnover number (TON = 103,000) for the synthesis of cyclic carbonates from CO(2) and epoxides under solvent-free conditions.
Electro-optically tunable compact terahertz source (2006)

Aerobic exercise training (AET) improves the reverse cholesterol transport (RCT) in cholesteryl ester transfer protein-transgenic (CETP-tg) mice. We aimed at investigating the role of AET in the expression of genes and proteins involved in lipid flux in the aorta and macrophages of CETP-tg mice. Three-month-old male mice were randomly divided into trained (T; treadmill 15 m/min; 30 min/day) and sedentary (S) groups. After 6 weeks, peritoneal macrophages and the aortic arch were obtained immediately (0 h) or 48 h after the last exercise session. mRNA was determined by RT-qPCR, protein levels by immunoblot and <sup>14</sup>C-cholesterol efflux determined in macrophages. AET did not change body weight, plasma cholesterol, triglycerides, glucose and CETP activity. In macrophages, at time 0 h, a higher expression of genes that encode PPAR gamma, ABCA-1 and a lower expression of MCP-1 and IL-10, was observed in T as compared to S. After 48 h, lower expressions of MCP-1 and PPAR gamma genes were observed in T mice. Increase in ABCA-1, SR-BI and IL-6 and decrease of LOX-1, MCP-1, TNF and IL-10 gene expression was observed in the aorta of T compared to S mice (0 h) and LOX-1 and MCP-1 remained diminished after 48 h. The protein level of MCP-1 and SR-BI in the aortic arch was unchanged in T animals after 48 h as compared to S, but LOX-1 was reduced confirming data of gene expression. The apo A-I and the HDL<sub>2</sub> mediated-cholesterol efflux (8 and 24 h) were not different between T and S animals. In the presence of CETP, AET positively influences gene expression in the arterial wall and macrophages of CETP-tg mice contributing to the RCT and prevention of atherosclerosis. These changes were perceptible immediately after the exercise session and were influenced by the presence of CETP although independent of changes in its activity. Reductions in gene and protein expression of LOX-1 were parallel and reflect the ability of exercise training in reducing the uptake of modified LDL by the arterial wall macrophages.
Artifact Suppressed Dictionary Learning for Low-Dose CT Image Processing (2014)

Low-dose computed tomography (LDCT) images are often severely degraded by amplified mottle noise and streak artifacts. These artifacts are often hard to suppress without introducing tissue blurring effects. In this paper, we propose to process LDCT images using a novel image-domain algorithm called "artifact suppressed dictionary learning (ASDL)." In this ASDL method, orientation and scale information on artifacts is exploited to train artifact atoms, which are then combined with tissue feature atoms to build three discriminative dictionaries. The streak artifacts are cancelled via a discriminative sparse representation operation based on these dictionaries. Then, a general dictionary learning processing is applied to further reduce the noise and residual artifacts. Qualitative and quantitative evaluations on a large set of abdominal and mediastinum CT images are carried out and the results show that the proposed method can be efficiently applied in most current CT systems.
Transformer Quality in Linear Time (2022)

We revisit the design choices in Transformers, and propose methods to address their weaknesses in handling long sequences. First, we propose a simple layer named gated attention unit, which allows the use of a weaker single-head attention with minimal quality loss. We then propose a linear approximation method complementary to this new layer, which is accelerator-friendly and highly competitive in quality. The resulting model, named FLASH, matches the perplexity of improved Transformers over both short (512) and long (8K) context lengths, achieving training speedups of up to 4.9$\times$ on Wiki-40B and 12.1$\times$ on PG-19 for auto-regressive language modeling, and 4.8$\times$ on C4 for masked language modeling.
QAM-PON and super PON for access distribution networks (2002)

We propose a passive optical network (PON) system based on quadrature amplitude modulated (QAM) sub-carrier multiplexing (SCM) of 53 6 MHz 64/256-QAM channels. Sensitivities of -22 dBm and -17.5 dBm are achieved over 51 km of fiber under full duplex and broadcast delivery to 128 nodes for 64 and 256 QAM, respectively.
On the origin of some QSO absorption lines (1986)

Some QSO absorption-line systems (QSOALSs) may arise when a QSO sight line intersects a Magellanic-type irregular galaxy (i.e., a gas-rich dwarf). Much of the complexity in the line profiles of metals can be naturally explained in this manner. The frequency of occurrence of QSOALSs then requires that much of the mass of modern galaxies once resided in a halo of gas-rich dwarfs (at the epoch of QSOALS formation).
Demonstration and Mitigation of Aerosol and Particle Dispersion During Mastoidectomy Relevant to the COVID-19 Era (2020)

Mastoidectomy with a high-speed drill is an aerosol-generating procedure, a designation that connotes the potential high risk of viral transmission and need for higher levels of personal protective equipment. A simple barrier drape significantly reduced particulate dispersion in this study and could be an effective mitigation strategy in addition to appropriate personal protective equipment.
Selective contribution of IFN-α/β signaling to the maturation of dendritic cells induced by double-stranded RNA or viral infection (2003)

A complex mechanism may be operational for dendritic cell (DC) maturation, wherein Toll-like receptor and other signaling pathways may be coordinated differently depending on the nature of the pathogens, in order for DC maturation to be most effective to a given threat. Here, we show that IFN-alpha/beta signaling is selectively required for the maturation of DCs induced by double-stranded RNA or viral infection in vitro. Interestingly, the maturation is still observed in the absence of either of the two target genes of IFN-alpha/beta, TLR3 and PKR (double-stranded-RNA-dependent protein kinase R), indicating the complexity of the IFN-alpha/beta-induced transcriptional program in DCs. We also show that the DCs stimulated in vivo by these agents can migrate into the T cell zone of the spleen but fail to mature without the IFN signal. The immune system may have acquired the selective utilization of this cytokine system, which is essential for innate antiviral immunity, to effectively couple with the induction of adaptive immunity.
O-GlcNAc Modification of NFκB p65 Inhibits TNF-α-Induced Inflammatory Mediator Expression in Rat Aortic Smooth Muscle Cells (2011)

There is a reciprocal relationship between O-GlcNAcylation and phosphorylation of NFκB p65, such that increased NFκB p65 O-GlcNAc modification inhibits TNF-α-Induced expression of inflammatory mediators through inhibition of NFκB p65 signaling. These findings provide a mechanistic basis for our previous observations that GlcN and PUGNAc treatments inhibit inflammation and remodeling induced by acute endoluminal arterial injury.
Dorsal-ventral patterning and differentiation of noggin-induced neural tissue in the absence of mesoderm (1995)

In Xenopus development, dorsal mesoderm is thought to play a key role in both induction and patterning of the nervous system. Previously, we identified a secreted factor, noggin, which is expressed in dorsal mesoderm and which can mimic that tissue's neural-inducing activity, without inducing mesoderm. Here the neural tissue induced in ectodermal explants by noggin is further characterized using four neural-specific genes: two putative RNA-binding proteins, nrp-1 and etr-1; the synaptobrevin sybII; and the lipocalin cpl-1. First we determine the expression domain of each gene during embryogenesis. Then we analyze expression of these genes in noggin-treated explants. All markers, including the differentiated marker sybII, are expressed in noggin-induced neural tissue. Furthermore, cpl-1, a marker of dorsal brain, and etr-1, a marker absent in much of the dorsal forebrain, are expressed in non-overlapping territories within these explants. We conclude that the despite the absence of mesoderm, noggin-induced neural tissue shows considerable differentiation and organization, which may represent dorsal-ventral patterning of the forebrain.