gebhart/patrepeval huggingface dataset:
A Positive-Strand RNA Virus with Three Very Different Subgenomic RNA Promoters (2000)

Numerous RNA viruses generate subgenomic mRNAs (sgRNAs) for expression of their 3'-proximal genes. A major step in control of viral gene expression is the regulation of sgRNA synthesis by specific promoter elements. We used barley yellow dwarf virus (BYDV) as a model system to study transcriptional control in a virus with multiple sgRNAs. BYDV generates three sgRNAs during infection. The sgRNA1 promoter has been mapped previously to a 98-nucleotide (nt) region which forms two stem-loop structures. It was determined that sgRNA1 is not required for BYDV RNA replication in oat protoplasts. In this study, we show that neither sgRNA2 nor sgRNA3 is required for BYDV RNA replication. The promoters for sgRNA2 and sgRNA3 synthesis were mapped by using deletion mutagenesis. The minimal sgRNA2 promoter is approximately 143 nt long (nt 4810 to 4952) and is located immediately downstream of the putative sgRNA2 start site (nt 4809). The minimal sgRNA3 core promoter is 44 nt long (nt 5345 to 5388), with most of the sequence located downstream of sgRNA3 start site (nt 5348). For both promoters, additional sequences upstream of the start site enhanced sgRNA promoter activity. These promoters contrast to the sgRNA1 promoter, in which almost all of the promoter is located upstream of the transcription initiation site. Comparison of RNA sequences and computer-predicted secondary structures revealed little or no homology between the three sgRNA promoter elements. Thus, a small RNA virus with multiple sgRNAs can have very different subgenomic promoters, which implies a complex system for promoter recognition and regulation of subgenomic RNA synthesis.
Design and evaluation of genome-wide libraries for RNA interference screens (2010)

RNA interference (RNAi) screens have enabled the systematic analysis of many biological processes in cultured cells and whole organisms. The success of such screens and the interpretation of the data depend on the stringent design of RNAi libraries. We describe and validate NEXT-RNAi, a software for the automated design and evaluation of RNAi sequences on a genome-wide scale. NEXT-RNAi is implemented as open-source software and is accessible at http://www.nextrnai.org/.
Crystal Structure of Peptide-N4-(N-acetyl-.beta.-D-glucosaminyl)asparagine amidase F at 2.2-.ANG. Resolution (1994)

Peptide-N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase F (PNGase F) is an amidase that cleaves the beta-aspartylglucosylamine bond of asparagine-linked glycans. The 34.8-kDa (314 amino acids) enzyme has a very broad substrate specificity and is extensively used for studies of the structure and function of glycoproteins. Enzymatic activity of PNGase F requires recognition of both the peptide and the carbohydrate components of the substrate. Only limited information regarding the mechanism of action of the enzyme is available. The three-dimensional structure of PNGase F has been determined by X-ray crystallography at 2.2-A resolution. The protein folds into two domains comprising residues 1-137 and 143-314, respectively. Both domains have eight-stranded antiparallel beta-sandwich motifs that are very similar in geometry. Both sandwiches have parallel principal axes and lie side by side. The covalent link between the domains is located at the top end of the molecule. Extensive hydrogen-bonding contacts occur along the full length of the interface between the two domains. Three different areas, all at the interface between the two domains, have been identified as possible locations for the active site of the enzyme. These include a hydrophobic bowl of about 20 A in diameter on one surface of the molecule, a long polar cleft on the opposite side, and a cleft at the bottom, which is lined with large aromatic residues including eight tryptophans.
Anti-glycoprotein Ib/IX and IIb/IIIa antibodies in patients with antiphospholipid antibodies. (1994)

Antiphospholipid antibodies, namely lupus anticoagulant (LA), anticardiolipin (aCL) type A and type B antibodies, are frequently associated with immune-mediated thrombocytopenia. Antiphospholipid antibodies have been suggested to bind to the phospholipids of the platelet membrane, thus participating to the process of platelet destruction, which leads to thrombocytopenia. However, a clear antiphospholipid (aPL) demonstration of such a role has never been given for antibodies. Conversely, autoantibodies directed against membrane-associated glycoproteins (GP) have been shown to be pathogenetically linked to the development of thrombocytopenia in patients with idiopathic thrombocytopenic purpura. For this reason, we have measured anti-GPIb/IX and GPIIb/IIIa IgG in the plasma of 68 patients with aPL antibodies by ELISA. The monoclonal antibody-specific immobilization of platelet antigen (MAIPA) assay was used. Twenty-seven out of 68 patients with antiphospholipid antibodies (40%) had increased plasma levels of anti-GP antibodies. In particular, 7 of them had elevated anti-GPIIb/IIIa levels only, 6 had anti-GPIb/IX antibodies only, whereas in the remaining 14 cases both types of autoantibodies were found elevated. The level of anti-GP antibodies in plasma did not correlate with age, sex, clinical associated conditions, history of thrombosis, IgG aCL titer or the presence of a phospholipid-dependent inhibitor of coagulation. In contrast, a statistically significant association between thrombocytopenia and high anti-GP antibody titer was observed (p = 0.0458). To establish whether there was cross-reactivity between antiphospholipid and anti-GP antibodies, adsorption experiments were performed using cardiolipin-containing liposomes or washed, normal, resting platelets.(ABSTRACT TRUNCATED AT 250 WORDS)
<title>Robust wireless video transmission using MPML</title> (2004)

A robust wireless video transmission scheme using MPEG video Markup Language (MPML) with adaptive error correction codes (ECCs) is proposed in this work. MPML can provide selective description for various MPEG video components to meet the special application requirements. We present an efficient MPML compression algorithm to reduce the size of MPML description and apply the adaptive ECCs to protect the MPML-coded description bitstream unequally against channel noises. It is demonstrated by experimental results that the proposed MPML protection can achieve good error resilient performance comparable with the well-known error resilient techniques.
A homozygous missense mutation in human KLOTHO causes severe tumoral calcinosis (2007)

Familial tumoral calcinosis is characterized by ectopic calcifications and hyperphosphatemia due to inactivating mutations in FGF23 or UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 3 (GALNT3). Herein we report a homozygous missense mutation (H193R) in the KLOTHO (KL) gene of a 13-year-old girl who presented with severe tumoral calcinosis with dural and carotid artery calcifications. This patient exhibited defects in mineral ion homeostasis with marked hyperphosphatemia and hypercalcemia as well as elevated serum levels of parathyroid hormone and FGF23. Mapping of H193R mutation onto the crystal structure of myrosinase, a plant homolog of KL, revealed that this histidine residue was at the base of the deep catalytic cleft and mutation of this histidine to arginine should destabilize the putative glycosidase domain (KL1) of KL, thereby attenuating production of membrane-bound and secreted KL. Indeed, compared with wild-type KL, expression and secretion of H193R KL were markedly reduced in vitro, resulting in diminished ability of FGF23 to signal via its cognate FGF receptors. Taken together, our findings provide what we believe to be the first evidence that loss-of-function mutations in human KL impair FGF23 bioactivity, underscoring the essential role of KL in FGF23-mediated phosphate and vitamin D homeostasis in humans.
a-Si for AMOLED- meeting the performance and cost demands of display applications (cell phone to HDTV) (2006)

Amorphous silicon AMOLED displays are almost ready for mass production and will be found in all display applications from high resolution cell phone to HDTV. But before commercialization can occur, the problems of lifetime and image sticking need to be overcome. When it comes to pixel circuit design, there is no one-size-fits-all solution. Several drive schemes and pixel circuits are presented, each with unique advantages, and each suited for a particular application. All leverage amorphous silicon manufacturing infrastructure which leads to the lowest cost position for AMOLEDs on glass.
Association of the VEGF Gene With Proliferative Diabetic Retinopathy But Not Proteinuria in Diabetes (2004)

Diabetic retinopathy and nephropathy cause significant morbidity in patients with diabetes. Vascular endothelial growth factor (VEGF) is a potent angiogenic and vascular permeability factor and is implicated in both of these diabetes complications. We previously reported transfection studies showing the VEGF -460 and VEGF +405 polymorphisms to increase basal VEGF promoter activity by 71% compared with the wild-type sequence. Therefore, we investigated the association of these VEGF polymorphisms with proliferative diabetic retinopathy and diabetic nephropathy. DNA was isolated from 267 U.K. Caucasians with diabetes, comprising 69 patients with proliferative retinopathy and 198 patients with other grades of retinopathy. The distribution of VEGF -460 genotype was significantly different between the proliferative retinopathy and nonproliferative retinopathy groups (P = 0.027); specifically, carriage of the VEGF -460C allele was associated with proliferative diabetic retinopathy (odds ratio 2.5 [95% CI 1.20-5.23]). The VEGF -460 genotype was predictive of retinopathy, even after controlling for blood pressure, glycemic control, duration of diabetes, and obesity (P = 0.02). The VEGF +405 genotype did not associate with proliferative retinopathy, and neither polymorphism was associated with diabetic nephropathy. The VEGF -460C polymorphism is a positive independent predictive factor for the development of proliferative diabetic retinopathy. Increased VEGF production from high-expressing haplotypes, including -460C, may promote neovascularization.
Normal development of mice carrying a null mutation in the gene encoding the L14 S-type lectin (1993)

The L14 lectin is a 14 x 10(3) M(r) carbohydrate binding protein belonging to the family of S-type lectins. The pattern of expression of this protein during mouse embryogenesis suggests that it may have multiple roles during pre- and post-implantation development. Using the technique of homologous recombination in embryonic stem cells, we have introduced a null mutation in the gene encoding the L14 lectin and generated a strain of mice carrying the mutant allele. We report here that homozygous mutant animals that lack the L14 lectin develop normally and are viable and fertile. The absence of any major phenotypic abnormalities in these mutant animals suggests that other protein(s) potentially compensate for the absence of the L14 lectin. Here we show that a related protein termed L30, a lectin that has carbohydrate binding specificity similar to that of L14, is present in the same embryonic cell populations as L14 at the time of implantation, suggesting that the two S-type lectins may be capable of functional substitution at this early stage of embryogenesis.
Nucleotide analogue inhibitors of purine nucleoside phosphorylase. (1990)

The diphosphate of the antiherpetic agent acyclovir [9-[(2-hydroxyethoxy)methyl]guanine] has been shown to inhibit purine nucleoside phosphorylase with unique potency (Tuttle, J. V., and Krenitsky, T. A. (1984) J. Biol. Chem. 259, 4065-4069). A major factor contributing to the superior inhibition by this diphosphate over the corresponding mono- and triphosphates is revealed here. Homologues of acyclovir mono- and diphosphate that extend the ethoxy moiety by one to four methylene groups were synthesized. These homologues were evaluated for their ability to inhibit human purine nucleoside phosphorylase. Within the diphosphate series, the Ki values increased progressively with increasing chain length. With the monophosphates, the Ki values reached a minimum with the homologue containing a pentoxy moiety. A plot of chain length versus Ki values for both mono- and diphosphates showed that both series had similar optimal distances between the aminal carbon and the terminal oxygen anion. Monophosphates with optimal positioning were somewhat less potent than diphosphates with similar positioning. Nevertheless, it was clear that a major factor in determining potency of inhibition was the distance of the terminal phosphate from the guanine moiety.
A self-healing single core architecture using dynamically reconfigurable devices (2012)

The IT industry has been focusing for several years on providing to users and designers the possibility of creating software applications disregarding hardware resources. Multi-processor architectures seem to be more of interest in recent developments because of their capacity to exploit programmable parallelism at acceptable costs without posing severe software designing problems. But in any thinkable scenario, software will always be dependent on the hardware it is executing on. In another matter of speaking, hardware performances will always affect software's ability in providing results. There is also the question if the gathered results are correct or not, if the system that provides them is fast, safe and if it is a reliable and a maintainable one. This paper proposes a scalable architecture surrounding a single core microprocessor with the purpose of increasing computational speed and reliability. For achieving this, a flexible hardware platform would be appropriate, e.g. field programmable gate arrays (FPGAs). The single core system will revolve around a Picoblaze soft-core microprocessor. By generating a series of modules with the same functionality as the executing software, an N-module redundancy system will increase systems security and reliability.
Reagents for the preparation of two oligonucleotides per synthesis (TOPSTM) (1994)

In order to increase the efficiency of use of automated DNA synthesizers (i.e. the number of oligomers prepared per day), we have devised and prepared novel phosphoramidite reagents that contain a linking group which, while stable under the normal synthesis conditions, is cleaved under basic conditions. When one of these linkers is introduced at the desired position in the synthesis of an oligonucleotide, subsequent detritylation enables the synthesis of a second oligonucleotides sequence upon the first. During deprotection of the oligonucleotide with ammonium hydroxide, the chain is cleaved at either side of the points of introduction of the novel reagent, generating two oligonucleotides free in solution. These reagents are of particular use in applications where oligomers are used in pairs (such as PCR, chemical synthesis of genes etc.) and means that an automated synthesis facility can be used more efficiently, without the need for operator intervention, after the working day is over.
Targeting Neutrophil Apoptosis for Enhancing the Resolution of Inflammation (2013)

Resolution of acute inflammation is an active process that requires inhibition of further leukocyte recruitment and removal of leukocytes from inflamed sites. Emigrated neutrophils undergo apoptosis before being removed by scavenger macrophages. Recent studies using a variety of gene knockout, transgenic and pharmacological strategies in diverse models of inflammation established neutrophil apoptosis as a critical control point in resolving inflammation. Analysis of death mechanisms revealed distinct features in executing the death program in neutrophils, which can be exploited as targets for controlling the lifespan of neutrophils. Indeed, anti-inflammatory and pro-resolution lipid mediators derived from essential fatty acids, such as lipoxin A4 and resolvin E1, autacoids and proteins, such as annexin A1 and TRAIL, and cyclin-dependent kinase inhibitors, can enhance the resolution of inflammation through induction of neutrophil apoptosis and promoting their removal by efferocytosis. In this review, we discuss recent advances in understanding the molecular basis of these actions, highlighting the potential of therapeutic induction of neutrophil apoptosis for dampening neutrophil-mediated tissue injury and inflammation underlying a variety of diseases.
LuCaP 35: A new model of prostate cancer progression to androgen independence (2003)

The availability of hormone-dependent and -independent variants of LuCaP 35, which exhibit many properties analogous to those of CaP in man, provides an excellent model system to study the processes associated with development of androgen independence and to evaluate new treatment modalities.
Murine epidermal Langerhans cells and splenic dendritic cells present tumor‐associated antigens to primed T cells (1994)

We examined the ability of epidermal Langerhans cells and splenic dendritic cells to present tumor-associated antigens (Ag) to immune T cells. Methylcholanthrene (MCA)-induced subcutaneous fibrosarcomas derived from C57BL/6 mice were used as tumor models. Our data demonstrate that both murine Langerhans cells and splenic dendritic cells have the capacity to present tumor-associated Ag to primed T cells. We found that variously treated tumor preparations (irradiated viable tumor cells, irradiated frozen-stored tumor cells, mitomycin C-treated viable tumor cells, and snap freeze-thawed tumor cell lysates) can be utilized for tumor Ag-pulsing. Primed CD4+ T cells demonstrated in vitro specificity towards their respective tumors and did not cross-react to other syngeneic MCA-induced or non-MCA-induced tumors. The T cell proliferative response critically depended on the presence of immune CD4+ T cells. We discuss the implications of these findings for the adoptive immunotherapy of cancer using immune CD4+ T cells.
Information Complexity in Bandit Subset Selection (2013)

We consider the problem of efficiently exploring the arms of a stochastic bandit to identify the best subset of a specified size. Under the PAC and the fixed-budget formulations, we derive improved bounds by using KL-divergence-based confidence intervals. Whereas the application of a similar idea in the regret setting has yielded bounds in terms of the KL-divergence between the arms, our bounds in the pure-exploration setting involve the “Chernoff information ” between the arms. In addition to introducing this novel quantity to the bandits literature, we contribute a comparison between strategies based on uniform and adaptive sampling for pure-exploration problems, finding evidence in favor of the latter.
Computer Simulations of the Energetics and Siting of n-Alkanes in Zeolites (1994)

The adsorption of the n-alkanes, ranging from butane to dodecane, in the zeolites silicalite and (all silica) mordenite has been studied in the zero coverage limit using computer simulations.The heats of adsorption, Henry coefficients, and distribution of the n-alkanes over the different zeolite channels are calculated.The calculated heats of adsorption are in good agreement with available experimental data.The calculated heats of adsorption in silicalite show a n unexpected alkane length dependence.The incremental heat of adsorption per carbon atom is larger for the longer alkanes than for the shorter alkanes.This observation is attributed to preferential adsorption of the longer alkanes in the straight channels of silicalite.Simulations of this type were made possible through the development of a novel Monte Carlo simulation technique which is orders of magnitude more efficient than the conventional simulation techniques.
Electroluminescence from CdSe quantum-dot/polymer composites (1995)

Electroluminescence is obtained from nearly monodisperse CdSe nanocrystallites (quantum dots) incorporated into thin films (1000 Å) of polyvinylcarbazole (PVK) and an oxadiazole derivative (t-Bu-PBD) and sandwiched between ITO and Al electrodes. The electroluminescence and photoluminescence spectra (bandwidths ≤40 nm) are nearly identical at room temperature and are tunable from ∼530 to ∼650 nm by varying the size of the dots. Voltage studies at 77 K indicate that while only the dots electroluminesce at the lower voltages, both the dots and the PVK matrix electroluminesce at higher applied voltages. Variable temperature studies indicate that the electroluminescence efficiency increases substantially as the films are cooled down to cryogenic temperatures.
A Lost-Wax Approach to Monodisperse Colloids and Their Crystals (2001)

We report a nanoscale "lost-wax" method for forming colloids with size distributions around 5% and their corresponding colloidal crystals. Macroporous polymer templates are first prepared from a silica colloidal crystal. We then use the uniform and interconnected voids of the porous polymer to generate a wide variety of highly monodisperse inorganic, polymeric, and metallic solid and core-shell colloids, as well as hollow colloids with controllable shell thickness, as colloidal crystals. We can also uniformly deform the polymer template to alter colloidal shape and demonstrate the formation of elliptical particles with precisely controlled aspect ratios.
Inhibition of 90-kD heat shock protein potentiates the cytotoxicity of chemotherapeutic agents in human glioma cells (2009)

Heat shock protein 90-targeted therapy may be an effective strategy for potentiating chemotherapy using DNA-crosslinking agents for TMZ-refractory gliomas.
Plasma ACTH in rats following medical adrenalectomy. (1977)

We have previously reported that surgically adrenalectomized nonstressed rats showed delayed secretion of the expected increase in plasma ACTH concentrations following adrenalectomy.(1) However, increased plasma ACTH concentrations were always detected when these animals were subjected to severe stress, and their responsiveness increased again seven days or more following surgical adrenalectomy. We are now reporting similar results which were obtained following prolonged systemic glucocorticoid administration (medical adrenalectomy) in similar groups of rats.
NMR Water Relaxation, Water Activity and Bacterial Survival in Porous Media (1996)

Working from the simple assumption that bulk, surface and bound water in a heterogeneous system are characterised by different intrinsic nuclear magnetic resonance (NMR) relaxation rates and water activities several non-trivial relationships are derived between NMR water relaxation times and water activity. These relationships are tested for randomly packed beds of silica and Sephadex particles both in the fast and slow diffusive exchange regimes. It is shown that Archies law for electrical conductivity is obeyed by these porous beds and this observation is used to establish further relationships between NMR relaxation rates and electrical conductivity. By comparing the rates of recovery of viable cells of Salmonella typhimuriumwith the NMR, sorption isotherm and conductivity data it is shown that the bacterial cells are monitoring the local water activity in the fluid immediately surrounding them and not the experimental, global water activity coefficient. The implications of this observation for food preservation are considered.