gebhart/patrepeval huggingface dataset:
A very short planar silica spot-size converter using a nonperiodic segmented waveguide (1998)

To reduce the coupling loss of a fiber-to-ridge waveguide connection, a planar silica spot-size converter for a wavelength of 1.55 /spl mu/m is implemented in the form of a nonperiodic segmented waveguide structure with irregular tapering. A simple single-step lithography process is sufficient for the fabrication of the planar structures. An evolutionary algorithm has been successfully applied for the optimization. The simulated results obtained with a three-dimensional (3-D) finite difference beam propagation method (FD-BPM) program are compared with measurements of implemented couplers, showing very good agreement. A waveguide-to-fiber coupling efficiency improvement exceeding 2 dB per converter is shown. Structures obtained with this approach are very short (/spl sim/140 /spl mu/m) and simple to integrate on the same wafer with other planar structures such as phased arrays or ring resonator structures.
Expression of epidermal growth factor receptor family proteins (EGFR, c-erbB-2 and c-erbB-3) in gastric cancer and chronic gastritis. (1998)

The expression and coexpression of EGFR, c-erbB-2 and c-erbB-3 in 21 gastric cancers and 20 chronic gastritis was examined using immunohistochemistry on fresh frozen tissues considering clinicopathological variables. Generally, gastric cancer patients showed a higher incidence of EGFR, c-erbB-2 and d-erbB-3 overexpression than the group with chronic gastritis (81% and 43%; 38% and 45%; 35% and 20%, respectively), however, statistically significant differences were found only for EGFR expression (p = 0.01). No association between immunoreactivity of all growth factor receptors and the histopathological structure of gastric cancer was observed. EGFR and c-erbB-3 proteins were detected more frequently in patients with III/IV than in I/II of TNM stages, while c-erbB-2 overexpression was higher in I/II vs. III/IV stages. In chronic gastritis with intestinal metaplasia and or coexisting carcinoma lesions, a higher frequency of the expression of studied proteins was observed in comparison with chronic gastritis without those alternations; however, these differences were statistically insignificant. The percentage of positive cases with coexpression of two proteins was comparable in gastric cancer and chronic gastritis (33% and 35%) but the simultaneous expression of all three receptors was evident only in gastric cancer (19%). Our results indicate that at least one or two members of EGFR related receptors could appear in the early stages of gastric tumorigenesis. The enhancement of c-erbB-2 and c-erbB-3 reactivity seems to cooperate with EGFR activation in the gastric cancer development. Our results indicate the promotional rather than direct transformational role for EGFR supergene family in gastric carcinogenesis.
Yeast mutants affected in viability upon starvation have a modified phospholipid composition (1993)

Selection of mutations, based on the suppression of rvs161 delta defects, was performed. Ten mutants were obtained, ranged amongst four complementation groups, named SUR1, SUR2, SUR3 and SUR4. All sur mutations also suppress a mutation in another gene, RVS167, indicating that all six genes are involved in the same biological pathway. The sur mutant cells have abnormal morphologies in stationary phase, i.e. dumbbell-like in sur1, sur2 or sur3 strains and multi-budded in sur4 strains. Several phenotypic characteristics of the physiological suppressors as well as the rvs161 delta strain itself led us to analyse the phospholipid composition of the mutants. The assays show an overall decrease of the phospholipid amounts and modifications in the relative contents of some phospholipid classes in sur mutant cells.
Efficient manipulation of the human adenovirus genome as an infectious yeast artificial chromosome clone. (1994)

A yeast artificial chromosome (YAC) containing a complete human adenovirus type 2 genome was constructed, and viral DNA derived from the YAC was shown to be infectious upon introduction into mammalian cells. The adenovirus YAC could be manipulated efficiently using homologous recombination-based methods in the yeast host, and mutant viruses, including a variant that expresses the human analog of the Saccharomyces cerevisiae CDC27 gene, were readily recovered from modified derivatives of the YAC. The application of powerful yeast genetic techniques to an infectious adenovirus clone promises to significantly enhance the genetic analysis of adenovirus and to simplify the construction of adenovirus-based vectors for vaccines or for gene transfer to mammalian cells or whole animals. The adenovirus YAC was produced by homologous recombination in vivo between adenovirus 2 virion DNA and YAC vector plasmids carrying segments of the viral left and right genomic termini. This recombinational cloning strategy is generally applicable to the construction of YACs containing other DNA segments, such as the genomes of other viruses. Further, it is very efficient and may permit the targeted cloning of segments of the genomes of higher organisms directly from genomic DNA.
Instance Segmentation Based on Improved YOLACT (2020)

YOLACT is the first real-time algorithm in instance segmentation. Aiming at the limitations in the algorithm such as low accuracy and poor stability for overlapping objects, an improved instance segmentation approach based on YOLACT was proposed. Specifically, the receptive field block is employed in the backbone network to extract multi-scale local region features, so that the network can learn more discriminative and robust features. To evaluate the validity of algorithm, experiments are performed on Pascal 2012 SBD. The results indicate the improved network can produce finer mask predictions in complex environment while keeping the real-time speed.
Oxygen tension regulates the nitric oxide pathway. Physiological role in penile erection. (1993)

Relaxation of the trabecular smooth muscle of the corpus cavernosum (the erectile tissue) of the penis is mediated by nitric oxide released by the nerves and endothelium. We have investigated the physiological role of oxygen tension in the regulation of trabecular smooth muscle tone. In human subjects, measurement of intracavernosal PO2 in blood drawn from corpus cavernosum in the flaccid state was comparable to that of venous blood (25-43 mmHg). Vasodilatation of the resistance arteries and trabecular smooth muscle relaxation by intracavernosal injection of papaverine and phentolamine caused oxygen tension to rise rapidly to arterial levels (PO2 approximately 100 mmHg). Isolated human and rabbit corpus cavernosum tissue strips in organ baths, exposed to arterial-like PO2 relaxed to the endothelium-dependent dilator acetylcholine and to electrical stimulation of the autonomic dilator nerves. These nitric oxide-mediated responses were progressively inhibited as a function of decreasing PO2 to levels measured in the flaccid penis. Reverting to normoxic conditions readily restored endothelium-dependent and neurogenic relaxation. Relaxation to exogenous nitric oxide was not impaired in low PO2. In rabbit corpus cavernosum, low PO2 reduced basal levels of cGMP and prevented cGMP accumulation induced by stimulation of dilator nerves. Furthermore, low PO2 inhibited nitric oxide synthase activity in corpus cavernosum cytosol. It is concluded that physiological concentrations of oxygen modulate penile erection by regulating nitric oxide synthesis in corpus cavernosum tissue.
Applying Bayesian classification to protein structure (2002)

A report is given on the advantages of Bayesian classification over traditional methods and the challenges in applying the Autoclass III program, a heuristic Bayesian classifier, in the domain of biotechnology and protein structure classification. The machine learning technique of heuristic Bayesian classification specifically addresses the question of how many classes a dataset should be divided into, as well as what the classifications should be. The method is based on a minimal message length description of the dataset. The cost (in bits) of specifying a classification is added to the cost of accounting for each exemplar in terms of its distance from the class definition and the total cost is minimized. In addition to providing a well founded estimate of the number of classes necessary to optimally characterize a dataset, this method also generates test classifications where within-class variances differ significantly.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Percutaneous Selective Radiofrequency Nerve Ablation for Glabellar Frown Lines (2011)

Although long-term studies are necessary to determine the ideal amount of energy delivery for maximum efficacy and time for treatment of glabellar frown lines, the study lends support for the safety and efficacy of percutaneous selective nerve ablation.
Synthetic tumor‐specific breakpoint peptide vaccine in patients with chronic myeloid leukemia and minimal residual disease (2009)

The current data suggested that vaccination-related transient disruption of immune tolerance may contribute to the reduction in Bcr-Abl transcripts. Clinically, this Bcr-Abl peptide vaccine may transiently improve the molecular response in a subset of patients with CML.
CD36 gene transfer confers capacity for phagocytosis of cells undergoing apoptosis. (1995)

Phagocyte recognition and ingestion of intact cells undergoing apoptosis are key events in this generally important program of cell death. Insufficient phagocyte capacity for apoptotic cells can result in failure to clear dying cells before membrane integrity is lost, resulting in leakage of noxious cell contents and severe tissue damage. However, no means has been available to increase phagocytic clearance of apoptotic cells. We now report that transfection of the macrophage adhesion molecule CD36 into human Bowes melanoma cells specifically conferred greatly increased capacity to ingest apoptotic neutrophils, lymphocytes, and fibroblasts, comparable to that exhibited by macrophages. Furthermore, when CD36 was transfected into another cell type with limited capacity to take up apoptotic bodies, the monkey COS-7 cell, similar effects were observed. Therefore, CD36 gene transfer can confer "professional" capacity to ingest apoptotic cells upon "amateur" phagocytes.
Optical encryption and QR codes: Secure and noise-free information retrieval (2013)

We introduce for the first time the concept of an information "container" before a standard optical encrypting procedure. The "container" selected is a QR code which offers the main advantage of being tolerant to pollutant speckle noise. Besides, the QR code can be read by smartphones, a massively used device. Additionally, QR code includes another secure step to the encrypting benefits the optical methods provide. The QR is generated by means of worldwide free available software. The concept development probes that speckle noise polluting the outcomes of normal optical encrypting procedures can be avoided, then making more attractive the adoption of these techniques. Actual smartphone collected results are shown to validate our proposal.
CDC25B Phosphorylated by pEg3 Localizes to the Centrosome and the Spindle Poles at Mitosis (2005)

The phosphatase CDC25B is one of the key regulators that control entry into mitosis through the dephosphorylation and subsequent activation of the cyclin-dependent kinases. Here we study the phosphorylation of CDC25B at mitosis by the kinase pEg3, a member of the KIN1/PAR-1/MARK family. Using mass spectrometry analysis we demonstrate that CDC25B is phosphorylated in vitro by pEg3 on serine 169, a residue that lies within the B domain. Moreover, using phosphoepitope-specific antibodies we show that serine 169 is phosphorylated in vivo, that this phosphorylated form of CDC25B accumulates during mitosis, and is localized to the centrosomes. This labelling is abrogated when pEg3 expression is repressed by RNA interference. Taken together, these results support a model in which pEg3 contributes to the control of progression through mitosis by phosphorylation of the CDC25 phosphatases.
Formation of Gold Nanoparticles by Laser Ablation in Aqueous Solution of Surfactant (2001)

Gold nanoparticles were produced by laser ablation of a gold metal plate in an aqueous solution of sodium dodecyl sulfate. The absorption spectrum of the gold nanoparticles was essentially same as that of gold nanoparticles chemically prepared in a solution. The size distribution of the nanoparticles thus produced was measured by an electron microscope and was found to shift to a smaller size with an increase in surfactant concentration. This behavior is explained in terms of the dynamic formation model. Dependence of the nanoparticle abundance on surfactant concentration in the solution shows that stable gold nanoparticles tend to be formed as the surfactant concentration exceeds 10-5 M. The gold nanoparticles having diameters larger than 5 nm were pulverized into those having diameters of 1−5 nm by a 532-nm laser.
Protection of reoxygenated cardiomyocytes against hypercontracture by inhibition of Na+/H+ exchange (1995)

Effects of Na+/H+ exchange inhibition and cytosolic acidosis on reoxygenated adult rat ventricular cardiomyocytes were investigated. Cells were incubated in anoxic media at pH 6.4 until pCa of < or = 5, intracellular pH (pHi) of 6.5, and cytosolic [Na+] of 50 mM were reached. On reoxygenation, medium pH was changed to 7.4 to activate Na+/H+ exchange. In one group, 20 microM HOE-694, an inhibitor of Na+/H+ exchange, was added. With or without HOE-694, cytosolic Ca2+ and Na+ returned to control levels within 10 min of reoxygenation. In the absence of HOE-694, the pHi renormalized (to 7.2) within 8 min, but irreversible hypercontracture and transient Ca2+ oscillations were observed. In the presence of HOE-694, pHi stayed acidotic (at 6.5), hypercontracture was prevented, and Ca2+ oscillations were attenuated. When the Na+ pump was inhibited with 0.1 mM ouabain, even partial recovery of Ca2+ control became impossible unless HOE-694 was added. Our conclusions are 1) activation of Na+/H+ exchange does not impair recovery of cytosolic Na+ and Ca2+ control unless activity of the sarcolemmal Na+ pump is critically reduced, and 2) due to prolongation of cytosolic acidosis, inhibition of Na+/H+ exchange protects against reoxygenation-induced hypercontracture and cytosolic Ca2+ oscillations.
An InP-based HBT fab for high-speed digital, analog, mixed-signal, and optoelectronic ICs (2002)

Integrated circuits (ICs) utilizing indium phosphide based heterojunction bipolar transistors (HBTs) have set numerous speed and bandwidth records over the past several years. This paper describes the extension of that HBT IC technology to an IC fabrication capability which is quite versatile in being able to produce digital, analog, mixed signal, and optoelectronic ICs within the same process. This enables the fab line to quickly respond to varying demands. Three ICs are discussed which exemplify the capability of this fab: (1) a 7 GHz 12-bit accumulator; (2) a nearly ideal continuous-time-sampling second-order /spl Delta//spl Sigma/ modulator operating at a 3.2 GHz sample rate; and (3) a monolithic 4-channel optoelectronic receiver array capable of 20 Gb/s operation.
Air motion sensing hairs of arthropods detect high frequencies at near-maximal mechanical efficiency (2011)

Using measurements based on particle image velocimetry in combination with a novel compact theoretical framework to describe hair mechanics, we found that spider and cricket air motion sensing hairs work close to the physical limit of sensitivity and energy transmission in a broad range of relatively high frequencies. In this range, the hairs closely follow the motion of the incoming flow because a minimum of energy is dissipated by forces acting in their basal articulation. This frequency band is located beyond the frequency at which the angular displacement of the hair is maximum which is between about 40 and 600 Hz, depending on hair length (Barth et al. [1] Phil. Trans. R. Soc. Lond. B 340, 445-461 (doi:10.1098/rstb.1993.0084)). Given that the magnitude of natural airborne signals is known to decrease with frequency, our results point towards the possible existence of spectral signatures in the higher frequency range that may be weak but of biological significance.
Antiviral Drug Discovery Against SARS-CoV (2006)

Severe Acute Respiratory Syndrome (SARS) is a life-threatening infectious disease caused by SARS-CoV. In the 2003 outbreak, it infected more than 8,000 people worldwide and claimed the lives of more than 900 victims. The high mortality rate resulted, at least in part, from the absence of definitive treatment protocols or therapeutic agents. Although the virus spreading has been contained, due preparedness and planning, including the successful development of antiviral drugs against SARS-CoV, is necessary for possible reappearance of SARS. In this review, we have discussed currently available strategies for antiviral drug discovery and how these technologies have been utilized to identify potential antiviral agents for the inhibition of SARS-CoV replication. Moreover, progress in the drug development based on different molecular targets is also summarized, including 1) Compounds that block the S protein-ACE2-mediated viral entry; 2) Compounds targeting SARS-CoV M(pro); 3) Compounds targeting papain-like protease 2 (PLP2); 4) Compounds targeting SARS-CoV RdRp; 5) Compounds targeting SARS-CoV helicase; 6) Active compounds with unspecified targets; and 7) Research on siRNA. This review aims to provide a comprehensive account of drug discovery on SARS. The experiences with the SARS outbreak and drug discovery would certainly be an important lesson for the drug development for any new viral outbreaks that may emerge in the future.
Galectin-3 Ablation Enhances Liver Steatosis, but Attenuates Inflammation and IL-33-Dependent Fibrosis in Obesogenic Mouse Model of Nonalcoholic Steatohepatitis (2015)

The importance of Galectin-3 (Gal-3) in obesity-associated liver pathology is incompletely defined. To dissect the role of Gal-3 in fibrotic nonalcoholic steatohepatitis (NASH), Gal-3-deficient (LGALS3−/−) and wild-type (LGALS3+/+) C57Bl/6 mice were placed on an obesogenic high fat diet (HFD, 60% kcal fat) or standard chow diet for 12 and 24 wks. Compared to WT mice, HFD-fed LGALS3−/− mice developed, in addition to increased visceral adiposity and diabetes, marked liver steatosis, which was accompanied with higher expression of hepatic PPAR-γ, Cd36, Abca-1 and FAS. However, as opposed to LGALS3−/− mice, hepatocellular damage, inflammation and fibrosis were more extensive in WT mice which had an elevated number of mature myeloid dendritic cells, proinflammatory CD11b+Ly6Chi monocytes/macrophages in liver, peripheral blood and bone marrow, and increased hepatic CCL2, F4/80, CD11c, TLR4, CD14, NLRP3 inflammasome, IL-1β and NADPH-oxidase enzymes mRNA expression. Thus, obesity-driven greater steatosis was uncoupled with attenuated fibrotic NASH in Gal-3-deficient mice. HFD-fed WT mice had a higher number of hepatocytes that strongly expressed IL-33 and hepatic CD11b+IL-13+ cells, increased levels of IL-33 and IL-13 and up-regulated IL-33, ST2 and IL-13 mRNA in liver compared with LGALS3−/− mice. IL-33 failed to induce ST2 upregulation and IL-13 production by LGALS3−/− peritoneal macrophages in vitro. Administration of IL-33 in vivo enhanced liver fibrosis in HFD-fed mice in both genotypes, albeit to a significantly lower extent in LGALS3−/− mice, which was associated with less numerous hepatic IL-13-expressing CD11b+ cells. The present study provides evidence of a novel role for Gal-3 in regulating IL-33-dependent liver fibrosis.
Real-Time Detection of Abandoned and Removed Objects in Complex Environments (2008)

We present a new framework to robustly and efficiently detect abandoned and removed objects in complex environments for real-time video surveillance. In our system, the background is modeled by a mixture of Gaussians. Similar to Tian et al. [18], this mixture model is employed to detect the static foreground regions (i.e., static blobs potentially corresponding to abandoned or removed objects) without extra computation cost. Several improvements are implemented to the background subtraction method for shadow removal, quick lighting change adaptation, reduction of fragmented foreground regions, and stable background update rate for video streams with inconsistent frame rates. Then, the types of the static regions (either abandoned or removed) are determined by using a method that exploits context information about the static foreground masks, significantly outperforming previous edge-based techniques. Based on the type of the static regions and several userdefined parameters, a matching method is proposed to trigger alerts indicating abandoned and removed objects. Our method can handle occlusions in complex environments with crowds. The robustness and efficiency of the method was tested on our real time video surveillance system for public safety application in big cities and evaluated by several public databases such as i-Lids and PETS2006 datasets. 1.
Cloning of monoclonal autoantibodies to epitopes of oxidized lipoproteins from apolipoprotein E-deficient mice. Demonstration of epitopes of oxidized low density lipoprotein in human plasma. (1996)

Many reactive products may be formed when LDL undergoes lipid peroxidation, which in turn can react with lipids, apoproteins, and proteins, generating immunogenic neoepitopes. Autoantibodies recognizing model epitopes of oxidized low density lipoprotein, such as malondialdehydelysine, occur in plasma and in atherosclerotic lesions of humans and animals. Because apo E-deficient mice develop particularly high titers of such autoantibodies, we used their spleens to clone 13 monoclonal antibodies to various epitopes of oxidized LDL ("E0 antibodies"). Binding and competitive RIAs demonstrated significant differences in fine specificity even between E0 antibodies initially selected for binding to the same screening antigen. For example, some E0 antibodies selected for binding to malondialdehyde-LDL also recognized copper oxidized LDL, acrolein-LDL, or LDL modified by arachidonic or linoleic acid oxidation products. Circulating IgG and IgM autoantibodies binding to copper-oxidized LDL, 4-hydroxynonenal-LDL, acrolein-LDL, and LDL modified with arachidonic or linoleic acid oxidation products were found in apo E-deficient mice, suggesting that the respective antigens are formed in vivo. Epitopes recognized by some of the E0 monoclonal antibodies were also found on human circulating LDL. Each of the E0 monoclonal antibodies immunostained rabbit and human atherosclerotic lesions, and some of them yielded distinct staining patterns in advanced lesions. Together, this suggests that the natural monoclonal antibodies recognize different epitopes of complex structures formed during oxidation of lipoproteins, or epitopes formed independently at different lesion sites. Our data demonstrate that a profound immunological response to a large number of different epitopes of oxidized lipoproteins occurs in vivo. The availability of "natural" monoclonal autoantibodies should facilitate the identification of specific epitopes inducing this response.