gebhart/patrepeval huggingface dataset:
Upregulation of placental growth factor by vascular endothelial growth factor via a post‐transcriptional mechanism (2005)

Vascular endothelial growth factor (VEGF) and placental growth factor (PlGF) are key angiogenic stimulators during normal development and wound healing, as well as in a variety of pathological conditions. Recent studies have demonstrated a synergistic effect of VEGF and PlGF in pathological angiogenesis and suggest a role for PlGF in amplifying VEGF action in endothelial cells. We show here in the mouse model of oxygen‐induced retinopathy that VEGF is significantly increased ( P &lt; 0.01) in the retina at both the mRNA and protein levels. In this mouse model, PlGF was significantly upregulated in the retina at the protein level ( P &lt; 0.01) without a corresponding change in mRNA levels. In cultured human retinal and umbilical vein endothelial cells, VEGF induced the production of PlGF protein by over 10‐fold ( P &lt; 0.01) in a dose‐dependent manner through a post‐transcriptional mechanism. The increased PlGF expression upon VEGF treatment was significantly reduced by inhibition of the protein kinase C (PKC) and MEK signaling pathways, as well as by treatment with the calcium ionophore A23187. Taken together, our findings demonstrate that VEGF can amplify its effects on endothelial cells by inducing the production of PlGF via a post‐transcriptional mechanism in a PKC‐dependent manner, and provide a potential link between PKC inhibition and amelioration of vascular complications in the development of angiogenic diseases.
Constrained coding techniques for soft iterative decoders (2003)

Soft iterative decoding of turbo codes and low-density parity check codes has been shown to offer significant improvements in performance. To apply soft iterative decoding to digital recorders, where binary modulation constraints are often used, modifications must be made to allow reliability information to be accessible by the decoder. A solution is proposed which uses a modified concatenation scheme, in which the positions of the modulation and error-correcting codes are reversed. In addition, a soft decoder based on the BCJR algorithm is introduced for the modulation constraint, and improved performance is obtained by iterating with this soft constraint decoder.
The Assembly-Activating Protein Promotes Stability and Interactions between AAV’s Viral Proteins to Nucleate Capsid Assembly (2018)

The adeno-associated virus (AAV) vector is a preferred delivery platform for in vivo gene therapy. Natural and engineered variations of the AAV capsid affect a plurality of phenotypes relevant to gene therapy, including vector production and host tropism. Fundamental to these aspects is the mechanism of AAV capsid assembly. Here, the role of the viral co-factor assembly-activating protein (AAP) was evaluated in 12 naturally occurring AAVs and 9 putative ancestral capsid intermediates. The results demonstrate increased capsid protein stability and VP-VP interactions in the presence of AAP. The capsid's dependence on AAP can be partly overcome by strengthening interactions between monomers within the assembly, as illustrated by the transfer of a minimal motif defined by a phenotype-to-phylogeny mapping method. These findings suggest that the emergence of AAP within the Dependovirus genus relaxes structural constraints on AAV assembly in favor of increasing the degrees of freedom for the capsid to evolve.
Tetracycline, Sclerotherapy in the treatment of primary hydrocele (1997)

One hundred and eleven patients with, one hundred and twenty-one hydrocele were treated with tetracycline sclerotherapy. These were divided into four groups depending upon the volume of fluid aspirated. Ten ml of oxytetracycline was injected after complete aspiration. Repeat accumulations were retapped and sclerosed. These patients were followed up for six months. 98 percent of patients were cured on six months of follow up. Patients with large hydroceles tended to be erratic on follow up. The commonest side effects included pain in 39.8 percent and induration in 16.9 percent of patients. Tetracycline sclerotherapy is a safe and effective modality for the treatment of primary hydrocele.
Stability-increasing Mutants of Glucose Dehydrogenase from Bacillus megaterium IWG3 (1989)

A glucose dehydrogenase gene was isolated from Bacillus megaterium IWG3, and its nucleotide sequence was identified. The amino acid sequence of the enzyme deduced from the nucleotide sequence is very similar to the protein sequence of the enzyme from B. megaterium M1286 reported by Jany et al. (Jany, K.-D., Ulmer, W., Froschle, M., and Pfleiderer, G. (1984) FEBS Lett. 165, 6-10). The isolated gene was mutagenized with hydrazine, formic acid, or sodium nitrite, and 12 clones (H35, H39, F18, F20, F191, F192, N1, N13, N14, N28, N71, and N72) containing mutant genes for thermostable glucose dehydrogenase were obtained. The nucleotide sequences of the 12 genes show that they include 8 kinds of mutants having the following amino acid substitutions: H35 and H39, Glu-96 to Gly; F18 and F191, Glu-96 to Ala; F20, Gln-252 to Leu; F192, Gln-252 to Leu and Ala-258 to Gly; N1, Glu-96 to Lys and Val-183 to Ile; N13 and N14, Glu-96 to Lys, Val-112 to Ala, Glu-133 to Lys, and Tyr-217 to His; N28, Glu-96 to Lys, Asp-108 to Asn, Pro-194 to Gln, and Glu-210 to Lys; and N71 and N72, Tyr-253 to Cys. These mutant enzymes have higher stability at 60 degrees C than the wild-type enzyme. The results of this study indicate that the tetrameric structure of glucose dehydrogenase is stabilized by several kinds of mutation, and at least one of the following amino acid substitutions stabilizes the enzyme: Glu-96 to Gly, Glu-96 to Ala, Gln-252 to Leu, and Tyr-253 to Cys.
The effects of rapid thermal annealing on the performance of ZnO thin-film transistors (2009)

We fabricated and characterized zinc oxide (ZnO)-based thin-film transistors (TFTs) oil a glass substrate, which can also be applied to plastic substrates such as polyimide or polynorbornene, at a maximum process temperature of 300 degrees C. Most of the component layers in ZnO-TFTs with a bottom-gate configuration were deposited by using rf magnetron sputtering techniques, except for the SiO(2) gate insulating layer, which was deposited by using inductively coupled plasma chemical vapor deposition (ICP-CVD). Silicon-dioxide (SiO(2)) and ZnO layers were separately heat-treated at 300 degrees C by rapid thermal annealing (RTA) to study its effect oil the device performance. The RTA-treated film had a surface morphology similar to that of the as-deposited film, but demonstrated higher crystallinity and transmittance, in addition to enhanced electrical properties, such as carrier concentration and mobility. When the SiO(2) layer was RTA-treated before the ZnO deposition, the ZnO TFTs showed high field effect mobility and high on/off current ratio. As a result of the low-temperature RTA treatment, we successfully fabricated high-performance and highly-transparent ZnO-TFTs. This process should be promising for various displays, such as organic light emitting diode (OLED) and liquid crystal display (LCD) that require low-temperature processes.
<title>Imaging of tumors by time-delayed laser-induced fluorescence</title> (1991)

A technique to improve signal-to-background ratio in fluorescence images of superficially growing tumors marked with photosensitizers is described. Time-delayed detection of fluorescence following pulsed-laser excitation allows suppression of the autofluorescence background falling into the fluorescence band of the photosensitizer. This technique exploits the longer fluorescence-decay times of porphyrin-based photosensitizers compared to average decay times of tissue autofluorescence. The feasibility of time-delayed fluorescence imaging of tumors has been demonstrated in vitro. From time-delayed fluorescence spectra the authors infer that the ratio between photosensitizer signal and autofluorescence background can be improved by about one order of magnitude.
Tailoring the Acoustic Properties of Truss-Core Sandwich Structure (2012)

Undesirable cabin noise has an adverse physiological effect on passengers and crews in an aircraft. In order to reduce the noise level, a passive approach using a truss-core sandwich (TCS) panel as a sound insulator is proposed. Design guidelines and analysis methodologies were developed in order to explore the vibro-acoustic characteristics of TCS structure. Its sound isolation properties can be thereby assessed. Theoretical analyses show that the transmission-loss and sound radiation properties of a TCS structure can be represented by the root-mean-square velocity of its surface, and a beam structure analysis is sufficient to reveal many of the important aspects of TCS panel design. Using finite element analysis, a sensitivity study was performed to create design guidelines for TCS structures. Transmission-loss experiments show that the analytical and numerical analyses correctly predict the trend of TCS structure’s vibro-acoustic performance.
Scheduling Tree-Shaped Task Graphs to Minimize Memory and Makespan (2013)

This paper investigates the execution of tree-shaped task graphs using multiple processors. Each edge of such a tree represents a large IO file. A task can only be executed if all input and output files fit into memory, and a file can only be removed from memory after it has been consumed. Such trees arise, for instance, in the multifrontal method of sparse matrix factorization. The maximum amount of memory needed depends on the execution order of the tasks. With one processor the objective of the tree traversal is to minimize the required memory. This problem was well studied and optimal polynomial algorithms were proposed. Here, we extend the problem by considering multiple processors, which is of obvious interest in the application area of matrix factorization. With the multiple processors comes the additional objective to minimize the time needed to traverse the tree, i.e., to minimize the makespan. Not surprisingly, this problem proves to be much harder than the sequential one. We study the computational complexity of this problem and provide an inapproximability result even for unit weight trees. Several heuristics are proposed, each with a different optimization focus, and they are analyzed in an extensive experimental evaluation using realistic trees.
Magnetic Barcode Nanowires for Osteosarcoma Cell Control, Detection and Separation (2012)

Multilayered gold/nickel “barcode” nanowires were grown using electrodeposition for multiplexed detection in biomolecular assays. Non-specific uptake of barcoded nanowires by osteosarcoma cells (OSCA-8) was observed by scanning and transmission electron microscopy images. Barcode-tagged cells were manipulated with an external magnetic field and were readily separated from untagged cells. Separation efficiency increased from a maximum of 30.14% to a maximum of 47.9% as clustering was reduced. Cells exposed to nanowires (both those that incorporated wires and those that did not) appeared to be viable suggesting that the nanowires are not toxic.
Handbook of Process Chromatography: A Guide to Optimization, Scale Up, and Validation (1997)

Foreword. Introduction. Development of a Process. Product Source and Its Impact. Setting Downstream Project Goals. Purification Design, Optimization, and Scale Up. Production Scenarios. Validation. Cleaning, Sanitization, and Storage. Analysis. Economy. Properties of Biological Molecules. Basic Chromatography Theory and Practice. Modeling of Chromatographic Processes. Equipment. Column Packing. Appendices: Equations and Definitions Used in Chromatography. Regulatory Documents Listing. Subject Index.
Photoinduced Chirality in Thin Films of Achiral Polymer Liquid Crystals Containing Azobenzene Chromophores (2004)

Circular dichroism and circular birefringence were induced in thin films of achiral polymer liquid crystals containing 7 or 15 mol % azobenzene chromophores by irradiation with circularly polarized light (CPL). Circular dichroism was observed not only for the azobenzene moieties but also for the nonphotoactive mesogens, cyanobiphenyl groups, due to a cooperative motion. CPL with opposite handedness produces enantiomeric structures, and a chiroptical switch can be achieved by alternating irradiation with left and right CPL. The level of photoinduced chirality depends on the incorporation methods (doped or chemically bound) of the azobenzene chromophores, the amount of azobenzene units, and the sample temperature. The photoinduced circular dichroism can be erased by heating the films above the clearing temperatures or by annealing the films in the liquid-crystalline phase.
A uniplanar compact photonic-bandgap (UC-PBG) structure and its applications for microwave circuit (1999)

This paper presents a novel photonic bandgap (PBG) structure for microwave integrated circuits. This new PBG structure is a two-dimensional square lattice with each element consisting of a metal pad and four connecting branches. Experimental results of a microstrip on a substrate with the PEG ground plane displays a broad stopband, as predicted by finite-difference time-domain simulations. Due to the slow-wave effect generated by this unique structure, the period of the PBG lattice is only 0.1/spl lambda//sub 0/ at the cutoff frequency, resulting in the most compact PEG lattice ever achieved. In the passband, the measured slow-wave factor (/spl beta//k/sub 0/) is 1.2-2.4 times higher and insertion loss is at the same level compared to a conventional 50-/spl Omega/ line. This uniplanar compact PBG (UC-PBG) structure can be built using standard planar fabrication techniques without any modification. Several application examples have also been demonstrated, including a nonleaky conductor-backed coplanar waveguide and a compact spurious-free bandpass filter. This UC-PBG structure should find wide applications for high-performance and compact circuit components in microwave and millimeter-wave integrated circuits.
Generation of diversity of the beta chain of the human T-lymphocyte receptor for antigen. (1986)

Human T-cell receptor beta-chain (Ti beta) genes are formed by the rearrangement of variable (V), diversity (D), and joining (J) gene segments. A comparison of the nucleotide and deduced amino acid sequences of the variable regions of six human Ti beta cDNAs reveals that they display a level of homology similar to that shared by human immunoglobulin heavy chain V genes. In contrast to immunoglobulin V regions, which contain three discrete regions of hypervariability, the Ti beta V regions display a more widely distributed pattern of variability. Southern blot analyses show that most human Ti V beta gene families contain one to three members. However, a single family containing at least eight members is identified. This analysis allows the identification of at least 15 human Ti V beta germ-line genes. The sequence data show that at least one germ-line Ti beta J gene is used preferentially in Ti beta cDNAs. Moreover, they suggest the presence of at least four human germ-line Ti beta D genes. At least three mechanisms are involved in generating the diversity of human Ti beta genes: (i) the combinatorial rearrangement of different V, D, and J genes; (ii) imprecise V-D-J joining, including V-D joining in any of three translational reading frames; and (iii) the addition of extra nucleotides at the V-D-J joints (N-region diversity).
Immune Response to the West Nile Virus in Aged Non-Human Primates (2010)

Results are consistent with strong and age-independent innate resistance of macaques against WNV challenge. This animal model is therefore not suitable for vaccine and therapeutic testing against WNV. However, understanding the basis of their innate resistance against WNV in macaques could provide helpful clues to improve anti-WNV protection of older adults.
Improved method for electroporation of Staphylococcus aureus (1992)

We have developed a significantly improved method for the electroporation of plasmid DNA into Staphylococcus aureus. The highest transformation efficiency achieved with this procedure was 4.0 x 10(8) transformants per microgram of plasmid pSK265 DNA. This represents a 530-fold improvement over the previously reported optimum efficiency of 7.5 x 10(5) transformants per microgram of plasmid DNA after electroporation of S. aureus cells [9]. Identical results were obtained when electrocompetent cells, which had been stored frozen at -80 degrees C, were used. The improved efficiency is due primarily to the use of a modified medium (designated as B2 medium) and secondarily to the use of 0.1-cm cuvettes. Several other plasmids (pI258, pMH109, and pSK270) were also electrotransformed into competent cells using our procedure, and for each plasmid, the transformation efficiency was significantly reduced compared to that observed when pSK265 DNA was used. With respect to plasmid pI258, the transformation efficiency was 3500-fold higher than that reported previously for transformation of this plasmid into S. aureus RN4220 [9]. The optimized electroporation procedure was less successful in transforming other staphylococci. Electrocompetent cells of S. aureus ATCC 29213 and S. epidermidis ATCC 12228 produced 5.5 x 10(5) and 5 x 10(3) transformants per microgram of pSK265 DNA, respectively.
Another Advanced Test of Theory of Mind: Evidence from Very High Functioning Adults with Autism or Asperger Syndrome (1997)

Previous studies have found a subgroup of people with autism or Asperger Syndrome who pass second-order tests of theory of mind. However, such tests have a ceiling in developmental terms corresponding to a mental age of about 6 years. It is therefore impossible to say if such individuals are intact or impaired in their theory of mind skills. We report the performance of very high functioning adults with autism or Asperger Syndrome on an adult test of theory of mind ability. The task involved inferring the mental state of a person just from the information in photographs of a person's eyes. Relative to age-matched normal controls and a clinical control group (adults with Tourette Syndrome), the group with autism and Asperger Syndrome were significantly impaired on this task. The autism and Asperger Syndrome sample was also impaired on Happé's strange stories tasks. In contrast, they were unimpaired on two control tasks: recognising gender from the eye region of the face, and recognising basic emotions from the whole face. This provides evidence for subtle mindreading deficits in very high functioning individuals on the autistic continuum.
Application of generalized parallel delta networks to a hybrid broadband switch (2003)

The authors describe a broadband switch architecture that is able to offer both the asynchronous and the circuit emulation transfer modes (ATM and CEM) for nonisochronous and isochronous services, respectively. The switch is based on the generalized parallel delta network (GPDN) and operates according to the cut-through technique. The rearrangeability and the self-routing properties of GPDNs ensure that CEM information units cross the interconnection network without conflicts, with a constant delay time, and with a fully distributed transfer control. A general description of the switch operation and the results of a preliminary performance evaluation are provided.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Suppressor T cells – they’re back and critical for regulation of autoimmunity! (2001)

Regulation of the immune response to self-antigens is a complex process that depends on maintaining self-tolerance while retaining the capacity to mount a robust immune response to foreign antigens. Autoreactive T cells specific for these autoantigens are present in most normal individuals but are kept under control by multiple diverse peripheral tolerance mechanisms. In the last few years, there has been a re-emergence of suppressor cells as among the most central of these regulatory mechanisms. These cells, which express CD4, CD25, and CD62L, develop in the thymus and survive in a CD28-dependent manner in the periphery to maintain the homeostatic equilibrium of immunity and tolerance. In this review, we will summarize studies of these regulatory cells as they relate to autoimmune diseases and more specifically to type 1 diabetes and attempt to address some of the many outstanding questions. Finally, evidence is provided to support the ability of anti-CD3 mAbs to stimulate the regulatory T cells and reset the rheostat of immune tolerance in an animal model of autoimmune diabetes, the NOD mouse.
Direct measurement of the poliovirus RNA polymerase error frequency in vitro (1988)

The fidelity of RNA replication by the poliovirus-RNA-dependent RNA polymerase was examined by copying homopolymeric RNA templates in vitro. The poliovirus RNA polymerase was extensively purified and used to copy poly(A), poly(C), or poly(I) templates with equimolar concentrations of noncomplementary and complementary ribonucleotides. The error frequency was expressed as the amount of a noncomplementary nucleotide incorporated divided by the total amount of complementary and noncomplementary nucleotide incorporated. The polymerase error frequencies were very high and ranged from 7 x 10(-4) to 5.4 x 10(-3), depending on the specific reaction conditions. There were no significant differences among the error frequencies obtained with different noncomplementary nucleotide substrates on a given template or between the values determined on two different templates for a specific noncomplementary substrate. The activity of the polymerase on poly(U) and poly(G) was too low to measure error frequencies on these templates. A fivefold increase in the error frequency was observed when the reaction conditions were changed from 3.0 mM Mg2+ (pH 7.0) to 7.0 mM Mg2+ (pH 8.0). This increase in the error frequency correlates with an eightfold increase in the elongation rate that was observed under the same conditions in a previous study.
Cholera toxin B subunit: an efficient transmucosal carrier-delivery system for induction of peripheral immunological tolerance. (1994)

Oral administration of antigens, including allergens and autoantigens, may be an efficient way to prevent diseases associated with untoward immune responses to self- and non-self-antigens. However, this approach has met with limitations because it usually requires repeated administrations of large doses of antigen and is less efficient in an already immune host, and the effect is of short duration. We report that a single oral administration of minute amounts of particulate or soluble antigen coupled to the B subunit of cholera toxin (CTB) can markedly suppress systemic immune responses in naive and in systemically immune animals. Both early (2-4 hr) and late (24-48 hr) delayed type-hypersensitivity reactivities were strongly suppressed after feeding a single dose of CTB-conjugated antigen. Serum antibody responses were also decreased, although moderately, after oral administration of CTB-conjugated antigen. This strategy of tolerance induction, based on oral administration of small amounts of antigens conjugated to a mucosa-binding molecule, may find broad applications for preventing or abrogating untoward immune responses.