gebhart/patrepeval huggingface dataset:
Distribution and Localization of Calmodulin-Binding Proteins in Bull Spermatozoa1 (2000)

Previous studies from our laboratory have shown that a decrease in the calmodulin binding properties of a few sperm proteins occurs during the capacitation process, an effect associated with a decrease in intracellular calmodulin concentrations. Using biotinylated-calmodulin nitrocellulose overlay assay on protein extracts of subcellular fractions of bull spermatozoa, one of these proteins (p32) is detected in the flagellar-enriched fractions, whereas p30 is found in the fraction enriched with sperm heads. This latter calmodulin binding protein, p30, appears to be associated with the perinuclear theca. None of these binding proteins was solubilized by nonionic detergents. Sodium dodecyl sulfate was effective solubilizing p32, whereas p30 was extracted only in conditions reported to isolate the perinuclear theca. Cellular localization of calmodulin binding proteins was also achieved by incubating spermatozoa fixed on slides with biotinylated calmodulin and revealed in a further step by fluorescein-conjugated streptavidin. Using this procedure, it was found that calmodulin binds to the sub- and postacrosomal areas of the sperm head along with the midpiece in the presence of Ca(2+). Only a sharp band of fluorescence at the subacrosomal area was observed when this procedure was performed in the absence of Ca(2+) in the presence of EGTA. The pattern of cellular calmodulin binding was highly decreased when spermatozoa were incubated under capacitating conditions, in the presence of heparin, in agreement with the published effect of capacitation on calmodulin binding proteins.
Molecular cloning and analysis of genes for production of K5, K7, K12, and K92 capsular polysaccharides in Escherichia coli (1986)

With a DNA fragment from within the region encoding the transport functions for K1 production as a hybridization probe in Southern blot experiments, homologous DNA sequences were detected in the DNA from Escherichia coli strains producing K5, K7, K92, and K100 capsular polysaccharides. No homology with the laboratory strain LE392 was detected. The same DNA probe was used to prescreen cosmid libraries in LE392 by colony hybridization, as a rapid method to isolate clones encoding the genes for K5, K7, K12, and K92 antigen production. Clones carrying sequences homologous to the probe that also produced capsular material were identified by using polyclonal and monoclonal antibodies raised against the K antigen in question and K antigen-specific phages. By restriction enzyme mapping of the appropriate cosmid clones it was possible to align the genes for the production of different K antigens in terms of common restriction endonuclease cleavage sites. A DNA fragment encoding the postulated transport functions for K7 antigen production could complement deletion mutations in the transport functions for K1 antigen production. Thus the transport to the cell surface of chemically distinct polysaccharides may be by a common process. Analysis in E. coli of the proteins produced by plasmids carrying the likely transport functions for K1, K5, and K7 antigen production revealed that each region coded for a similar polypeptide.
Fabrication of 50–100 nm Patterned InGaN Blue Light Emitting Heterostructures (2001)

We have developed fabrication approaches and studied the optical properties of arrays of submicrometer sized InGaN/GaN MQW posts, created by patterning and etching of epitaxially grown wafer material. Two approaches have been employed: a) electron beam lithography, by which posts of individual diameter of 100 nm have been realized; b) the use of nanometer-scale self-assembled templates of porous alumina as masks, to fabricate posts on a 50 nm scale. Robust violet light emission at room temperature has been observed in such nanoscale structures.
Selective ACAT Inhibitors as Promising Antihyperlipidemic, Antiatherosclerotic and Anti-Alzheimer Drugs (2003)

Inhibition of ACAT, the enzyme which catalyses the intracellular formation of cholesteryl esters, is a very attractive target for the treatment of hypercholesterolaemia and atherosclerosis. However, in the past years many ACAT inhibitors gave disappointing results in clinical trials showing very low efficacy. In addition, their development was affected by the adrenotoxicity observed in many compounds. The discovery of two isoforms of the enzyme, namely ACAT1 and ACAT2, with different substrate specificity and different potential function, offers a precious information for planning selective inhibitors with reduced secondary effects. Today some potent, bioavailable and non adrenotoxic ACAT inhibitors are under clinical evaluation. Amongst others, a very promising compound is Avasimibe, presently in phase III clinical trials as anti-hyperlipidemic and anti-atherosclerotic agent. Finally, ACAT inhibitors have recently been proposed for the treatment of Alzheimer's disease.
Hyperbranched Polylysine: A Versatile, Biodegradable Transfection Agent for the Production of Recombinant Proteins by Transient Gene Expression and the Transfection of Primary Cells (2012)

The feasibility of a new transfection agent, HBPL, for the production of recombinant IgG antibody via TGE as well as for the transfection of primary cells is studied. Under the conditions investigated, transfection of CHO-DG44 cells using HBPL results in IgG yields that are comparable to those obtained with PEI. In experiments with CHO-K1 cells and MEFs the use of HPBL allows to achieve transfection efficiencies comparable to or better than those obtained with PEI or Fugene®. HBPL-mediated transfection does not require complex pre-formation, works well in serum-containing media and is biodegradable, which may prevent cumulative cytotoxicity and facilitates downstream processing.
Output of an ultrasonic wave-driven nanogenerator in a confined tube (2009)

The output of an ultrasonic wave-driven nanogenerator (NG) has been found to depend on the excitation conditions and geometry. Incidence angle tests indicate that the effective area of an NG determines the amount of power that can be generated. The output power of an NG is also directly related to its distance from the ultrasonic source. A sinusoidal profile of the electrical output was observed when an NG was moved inside a long tube filled with water with the ultrasonic source located at one end. This is due to the oscillation of the wave intensity inside the tube as a function of the distance from the excitation source.
Delivery of CD8+T-Cell Epitopes into Major Histocompatibility Complex Class I Antigen Presentation Pathway byBordetella pertussisAdenylate Cyclase: Delineation of Cell Invasive Structures and Permissive Insertion Sites (2000)

Bordetella pertussis adenylate cyclase (AC) toxin-hemolysin (ACT-Hly) can penetrate a variety of eukaryotic cells. Recombinant AC toxoids have therefore been recently used for delivery of CD8(+) T-cell epitopes into antigen-presenting cells in vivo and for induction of protective antiviral, as well as therapeutic antitumor cytotoxic T-cell responses. We have explored the carrier potential of the ACT molecule by insertional mutagenesis scanning for new permissive sites, at which integration of two- to nine-residue-long peptides does not interfere with membrane interaction and translocation of ACT. A model CD8(+) T-cell epitope of ovalbumin was incorporated at 10 of these permissive sites along the toxin molecule, and the capacity of ACT constructs to penetrate into cell cytosol and deliver the epitope into the major histocompatibility complex (MHC) class I antigen processing and presentation pathway was examined. While all six constructs bearing the epitope within the Hly portion of ACT failed to deliver the epitope to the MHC class I molecules, all four toxoids with inserts within different permissive sites in the AC domain efficiently delivered the epitope into this cytosolic pathway, giving rise to stimulation of a specific CD8(+) T-cell hybridoma. The results suggest that, in contrast to the AC domain, the hemolysin moiety of ACT does not reach the cytosolic entry of the MHC class I pathway.
Clinical Experience in End-to-Side Venous Anastomoses With a Microvascular Anastomotic Coupling Device in Head and Neck Reconstruction (1999)

The MACD is well suited to end-to-side venous anastomosis when carefully and selectively used by experienced microvascular surgeons. The most common clinical situation requiring this configuration and technique was the lack of ipsilateral recipient veins for end-to-end anastomosis or a ligated internal jugular vein stump that required this approach for device application. Previous radiation therapy does not appear to be a contraindication to its use.
FReLU: Flexible Rectified Linear Units for Improving Convolutional Neural Networks (2018)

Rectified linear unit (ReLU) is a widely used activation function for deep convolutional neural networks. However, because of the zero-hard rectification, ReLU networks lose the benefits from negative values. In this paper, we propose a novel activation function called flexible rectified linear unit (FReLU) to further explore the effects of negative values. By redesigning the rectified point of ReLU as a learnable parameter, FReLU expands the states of the activation output. When a network is successfully trained, FReLU tends to converge to a negative value, which improves the expressiveness and thus the performance. Furthermore, FReLU is designed to be simple and effective without exponential functions to maintain low-cost computation. For being able to easily used in various network architectures, FReLU does not rely on strict assumptions by self-adaption. We evaluate FReLU on three standard image classification datasets, including CIFAR-10, CIFAR-100, and ImageNet. Experimental results show that FReLU achieves fast convergence and competitive performance on both plain and residual networks.
Reliable data structures in C (1983)

Cardiff, New Jersey: Plum Hall Inc., 1985. includes index and bibliography. Requires some knowledge of C. It introduces important topics of data structures: arrays, strings, pointers, records, stacks, queues, double-ended queues, trees, hashed files and record files. Discussion of the formal aspects of each data structure is presented with a working general purpose C function that implements the technique. It covers some advanced C features like: pointers to function, pointers to structures, dynamic allocation, enumerations and more
Fast Redox Perturbation of Aqueous Solution by Photoexcitation of Pyranine (1996)

Abstract— Intense illumination (60‐120 MW/cm 2 ) of an oxygen‐free aqueous solution of pyranine (8‐hydroxypyrene‐l,3,6‐tri‐sulfonate) by the third harmonic frequency of an Nd‐Yag laser (355 nm) drives a two successive‐photon oxidative process of the dye. The first photon excites the dye to its first electronic singlet state. The second photon interacts with the excited molecule, ejects an electron to the solution and deactivates the molecule to a ground state of the oxidized dye (φ + ). The oxidized product, φ + , is an intensely colored compound (Λ max = 445 nm, ε= 43 000 ± 1000 M −1 cm −1 ) that reacts with a variety of electron donors like quinols, ascorbate and ferrous compounds. In the absence of added reductant, φ + is stable, having a lifetime of ‐10 min. In acidic solutions the solvated electrons generated by the photochemical reaction react preferentially with H + . In alkaline solution the favored electron acceptor is the ground‐state pyranine anion and a radical, φ, of the reduced dye is formed. The reduced product is well distinguished from the oxidized one, having its maximal absorption at 510 nm with e = 25 000 ± 2000 M ‐l cm −1 . The oxidized radical can be reduced either by φ ‐ or by other electron donors. The apparent second‐order rate constants of these reactions, which vary from 10 6 up to 10 9 M −1 s −1 , are slower than the rates of diffusion‐controlled reactions. Thus the redox reactions are limited by an energy barrier for electron transfer within the encounter complex between the reactants.
Xception: Deep Learning with Depthwise Separable Convolutions (2017)

We present an interpretation of Inception modules in convolutional neural networks as being an intermediate step in-between regular convolution and the depthwise separable convolution operation (a depthwise convolution followed by a pointwise convolution). In this light, a depthwise separable convolution can be understood as an Inception module with a maximally large number of towers. This observation leads us to propose a novel deep convolutional neural network architecture inspired by Inception, where Inception modules have been replaced with depthwise separable convolutions. We show that this architecture, dubbed Xception, slightly outperforms Inception V3 on the ImageNet dataset (which Inception V3 was designed for), and significantly outperforms Inception V3 on a larger image classification dataset comprising 350 million images and 17,000 classes. Since the Xception architecture has the same number of parameters as Inception V3, the performance gains are not due to increased capacity but rather to a more efficient use of model parameters.
Gap-Junction Channels Dysfunction in Deafness and Hearing Loss (2008)

Gap-junction channels connect the cytoplasm of adjacent cells, allowing the diffusion of ions and small metabolites. They are formed at the appositional plasma membranes by a family of related proteins named connexins. Mutations in connexins 26, 31, 30, 32, and 43 have been associated with nonsyndromic or syndromic deafness. The majority of these mutations are inherited in an autosomal recessive manner, but a few of them have been associated with dominantly inherited hearing loss. Mutations in the connexin26 gene (GJB2) are the most common cause of genetic deafness. This review summarizes the most relevant and recent information about different mutations in connexin genes found in human patients, with emphasis on GJB2. The possible effects of the mutations on channel expression and function are discussed, in addition to their possible physiologic consequences for inner ear physiology. Finally, we propose that connexin channels (gap junctions and hemichannels) may be targets for age-related hearing loss induced by oxidative damage.
Class-E oscillators as wireless power transmitters for biomedical implants (2010)

This paper presents the use of Class-E oscillators as inductive power transmitters for implanted telemetry devices that transmit information sensed by biosensors. Several Class-E oscillators are compared with an equivalent Class-E amplifier, showing higher efficiency while maintaining frequency clarity, stability and accuracy. Energy has been successfully transferred to a receiving inductor 1.5 cm away, which has been rectified to produce a 1 V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">DC</sub> signal.
Structure of the Expression Site Reveals Global Diversity in MSP2 (P44) Variants in Anaplasma phagocytophilum (2006)

Anaplasma phagocytophilum, a recently reclassified bacteria in the order Rickettsiales, infects many different animal species and causes an emerging tick-borne disease of humans. The genome contains a large number of related genes and gene fragments encoding partial or apparently full-length outer membrane protein MSP2 (P44). Previous data using strains isolated from humans in the United States suggest that antigenic diversity results from RecF-mediated conversion of a single MSP2 (P44) expression site by partially homologous donor sequences. However, whether similar mechanisms operate in naturally infected animal species and the extent of global diversity in MSP2 (P44) are unknown. We analyzed the structure and diversity of the MSP2 (P44) expression site in strains derived from the United States and Europe and from infections of different animal species, including wildlife reservoirs. The results show that a syntenic expression site is present in all strains of A. phagocytophilum investigated. This genomic locus contained diverse MSP2 (P44) variants in all infected animals sampled, and variants also differed at different time points during infection. Although similar variants were found among different populations of U.S. origin, there was little sequence identity between U.S. strain variants (including genomic copies from a completely sequenced U.S. strain) and expression site variants infecting sheep and dogs in Norway and Sweden. Finally, the possibility that combinatorial mechanisms can generate additional diversity beyond the basic donor sequence repertoire is supported by the observation of shared sequence blocks throughout the MSP2 (P44) hypervariable region in reservoir hosts. These data suggest similar genetic mechanisms for A. phagocytophilum variation in all hosts but worldwide diversity of the MSP2 (P44) outer membrane protein.
Endogenous Phenazine Antibiotics Promote Anaerobic Survival of Pseudomonas aeruginosa via Extracellular Electron Transfer (2009)

Antibiotics are increasingly recognized as having other, important physiological functions for the cells that produce them. An example of this is the effect that phenazines have on signaling and community development for Pseudomonas aeruginosa (L. E. Dietrich, T. K. Teal, A. Price-Whelan, and D. K. Newman, Science 321:1203-1206, 2008). Here we show that phenazine-facilitated electron transfer to poised-potential electrodes promotes anaerobic survival but not growth of Pseudomonas aeruginosa PA14 under conditions of oxidant limitation. Other electron shuttles that are reduced but not made by PA14 do not facilitate survival, suggesting that the survival effect is specific to endogenous phenazines.
Unruptured intracranial aneurysms: a review (2002)

The current state of knowledge about unruptured aneurysms does not support the use of the largest diameter of the lesion as the sole criterion on which to base treatment decisions, although it is of undoubted importance.
Stereo vision for view synthesis (1996)

We propose a new method for view synthesis from real images using stereo vision. The method does not explicitly model scene geometry, and enables fast and exact generation of synthetic views. We also reevaluate the requirements on stereo algorithms for the application of view synthesis and discuss ways of dealing with partially occluded regions of unknown depth and with completely occluded regions of unknown texture. Our experiments demonstrate that it is possible to efficiently synthesize realistic new views even from inaccurate and incomplete depth information.
Advantages and challenges of microfluidic cell culture in polydimethylsiloxane devices (2014)

Culture of cells using various microfluidic devices is becoming more common within experimental cell biology. At the same time, a technological radiation of microfluidic cell culture device designs is currently in progress. Ultimately, the utility of microfluidic cell culture will be determined by its capacity to permit new insights into cellular function. Especially insights that would otherwise be difficult or impossible to obtain with macroscopic cell culture in traditional polystyrene dishes, flasks or well-plates. Many decades of heuristic optimization have gone into perfecting conventional cell culture devices and protocols. In comparison, even for the most commonly used microfluidic cell culture devices, such as those fabricated from polydimethylsiloxane (PDMS), collective understanding of the differences in cellular behavior between microfluidic and macroscopic culture is still developing. Moving in vitro culture from macroscopic culture to PDMS based devices can come with unforeseen challenges. Changes in device material, surface coating, cell number per unit surface area or per unit media volume may all affect the outcome of otherwise standard protocols. In this review, we outline some of the advantages and challenges that may accompany a transition from macroscopic to microfluidic cell culture. We focus on decisive factors that distinguish macroscopic from microfluidic cell culture to encourage a reconsideration of how macroscopic cell culture principles might apply to microfluidic cell culture.
SEROTONIN RECEPTOR SUBTYPES AND AFFECTIVE DISORDERS (1992)

The role of drugs that act at 5-hydroxytryptamine (5-HT or serotonin) receptor subtypes in the etiology and treatment of affective disorders is discussed. The mechanisms of action of drugs affecting 5-HT are described, with emphasis on those with anxiolytic and antidepressant activity. Evidence supporting a role for serotonin in the etiology and treatment of affective disorders in cited. Recent therapeutic advances have resulted in a new generation of serotonergic drugs.
Vasopressin and Prevention of Hypotension during Hemodialysis (2014)

Vasopressin insufficiency may have an important role in the pathogenesis of hemodynamic instability during HD and administration of exogenous vasopressin is significantly associated with a lower incidence of IDH.
ICOS Controls Effector Function but Not Trafficking Receptor Expression of Kidney-Infiltrating Effector T Cells in Murine Lupus (2009)

Renal pathology in systemic lupus erythematosus involves both autoantibody deposition and a cellular inflammatory response, both of which are mediated by effector CD4 T cells. MRL(lpr) mice spontaneously develop massive perivascular infiltrates, but the pathways that regulate the development, trafficking, and effector functions of kidney-infiltrating T cells are poorly defined. To address these questions, we first surveyed inflammatory chemokine protein levels in nephritic kidneys from lupus-prone MRL(lpr) mice. After identifying highly elevated levels of the CXCR3 ligand CXCL9, we found that kidney-infiltrating effectors are enriched for expression of CXCR3, as well as P-selectin ligand and ICOS. Using genetic ablation, we demonstrate that ICOS plays an essential role in the establishment of renal perivascular infiltrates, although a small number of infiltrating cells remain around the blood vessels. Interestingly, though IgG autoantibody production is substantially reduced in Icos(-/-) MRL(lpr) mice, the progression of immune complex glomerulonephritis is only modestly diminished and the production of inflammatory chemokines, such as CXCL9, remains high in the kidney. We find that Icos(-/-) effector cell numbers are only slightly reduced and these have normal expression of CXCR3 and P-selectin ligand with intact migration to CXCL9. However, they have impaired production of inflammatory cytokines and fail to show evidence of efficient proliferation in the kidney. Thus, while dispensable for acquisition of renal trafficking receptor expression, ICOS is strictly required for local inflammatory functions of autoreactive CD4 T cells in murine lupus.
A DWT-based image watermarking algorithm (2001)

In this paper, a new embedding strategy for DWT-based watermarking is proposed. Different from the existing watermarking schemes in which low frequency coefficients are explicitly excluded from watermark embedding, we claim that watermarks should be embedded in the low frequency subband firstly, and the remains should be embedded in high frequency subbands according to the significance of subbands. We also claim that different embedding formula should be applied on the low frequency subband and high frequency subbands respectively. Applying this strategy, an adaptive algorithm incorporating the feature of visual masking of human vision system into watermarking is proposed. In the algorithm, a novel method to classify wavelet blocks is presented. The experimental results demonstrate that the watermarks generated with the proposed algorithm are invisible and robust against noise and commonly used image processing techniques.