gebhart/patrepeval huggingface dataset:
Synthetic enzyme mixtures for biomass deconstruction: Production and optimization of a core set (2010)

The high cost of enzymes is a major bottleneck preventing the development of an economically viable lignocellulosic ethanol industry. Commercial enzyme cocktails for the conversion of plant biomass to fermentable sugars are complex mixtures containing more than 80 proteins of suboptimal activities and relative proportions. As a step toward the development of a more efficient enzyme cocktail for biomass conversion, we have developed a platform, called GENPLAT, that uses robotic liquid handling and statistically valid experimental design to analyze synthetic enzyme mixtures. Commercial enzymes (Accellerase 1000 +/- Multifect Xylanase, and Spezyme CP +/- Novozyme 188) were used to test the system and serve as comparative benchmarks. Using ammonia-fiber expansion (AFEX) pretreated corn stover ground to 0.5 mm and a glucan loading of 0.2%, an enzyme loading of 15 mg protein/g glucan, and 48 h digestion at 50 degrees C, commercial enzymes released 53% and 41% of the available glucose and xylose, respectively. Mixtures of three, five, and six pure enzymes of Trichoderma species, expressed in Pichia pastoris, were systematically optimized. Statistical models were developed for the optimization of glucose alone, xylose alone, and the average of glucose + xylose for two digestion durations, 24 and 48 h. The resulting models were statistically significant (P < 0.0001) and indicated an optimum composition for glucose release (values for optimized xylose release are in parentheses) of 29% (5%) cellobiohydrolase 1, 5% (14%) cellobiohydrolase 2, 25% (25%) endo-beta1,4-glucanase 1, 14% (5%) beta-glucosidase, 22% (34%) endo-beta1,4-xylanase 3, and 5% (17%) beta-xylosidase in 48 h at a protein loading of 15 mg/g glucan. Comparison of two AFEX-treated corn stover preparations ground to different particle sizes indicated that particle size (100 vs. 500 microm) makes a large difference in total digestibility. The assay platform and the optimized "core" set together provide a starting point for the rapid testing and optimization of alternate core enzymes from other microbial and recombinant sources as well as for the testing of "accessory" proteins for development of superior enzyme mixtures for biomass conversion.
Joint optimization of scale factors and Huffman code books for MPEG-4 AAC (2005)

This paper addresses the optimization problem of minimizing the distortion subject to a rate constraint for an MPEG-4 Advanced Audio Coding (AAC) encoder. We first develop a mathematical model of the AAC encoding process. In previous work, the joint optimization problem is modeled as a Viterbi search for a cheapest path through a trellis. This method involves an iteration over a Lagrangian multiplier. We improve on this method by deriving a very accurate guess for the value of the final Lagrangian multiplier of the iteration as a function of the Perceptual Entropy of the signal and the given rate constraint. This reduces the complexity of the Trellis Search significantly. Whereas previous methods including the Trellis Search did not provide optimal solutions to the problem of minimizing the distortion subject to a rate constraint, we establish two methods that for the first time solve this problem optimally. Our first method is based on the formulation and solution of a Mixed Integer Linear Program, whereas our second method uses a Dynamic Programming solution that does not rely on the iteration over a Lagrangian multiplier. Based on our optimal methods, we evaluate the performance of the heuristic Two Loop Search (TLS), which is used in most commercial AAC implementations to solve the problem under consideration, and the performance of the Trellis Search.
Fourier array imaging (1994)

The past forty years have seen a number of imaging modalities developed for radar, sonar, diagnostic medicine, geophysical and celestial exploration, and non-destructive testing. Now, for those involved in designing and developing information processing tools for these imaging systems, author Mehrdad Soumekh offers in-depth coverage of diverse issues such as physical and mathematical modeling of the problem, signal processing, reconstruction, analysis of resolution and system parameter constraints, hardware structure used for data acquisition, and the overall imaging system block diagram (signal flow-chart) indicating how the acquired data are processed to yield the final reconstructed image. Fourier Array Imaging introduces the spatial Doppler phenomenon in conjunction with the most primitive signal processing tools and systems used in array imaging; presents terminologies and tools for two-dimensional signal processing; treats specific array imaging systems via the unifying framework of spatial Doppler processing, including phased-array imaging, synthetic aperture array (SAR and ISAR) imaging, passive array imaging, and bistatic array imaging with emphasis on transmission imaging problems of diagnostic medicine and geophysical exploration; devotes coverage to the analysis of resolution anticipated in an imaging system and to the constraints that are instrumental for selecting parameters of an imaging system; describes some of the classical methods used for image formation in array imaging systems and relates them to the spatial Doppler-based imaging via certain approximations.
Activated forms of H-RAS and K-RAS differentially regulate membrane association of PI3K, PDK-1, and AKT and the effect of therapeutic kinase inhibitors on cell survival (2005)

The abilities of mutated active RAS proteins to modulate cell survival following exposure to ionizing radiation and small molecule kinase inhibitors were examined. Homologous recombination in HCT116 cells to delete the single allele of K-RAS D13 resulted in a cell line that exhibited an approximately 75% reduction in basal extracellular signal-regulated kinase 1/2, AKT, and c-jun-NH2-kinase 1/2 activity. Transfection of cells lacking K-RAS D13 with H-RAS V12 restored extracellular signal-regulated kinase 1/2 and AKT activity to basal levels but did not restore c-jun-NH2-kinase 1/2 phosphorylation. In cells expressing H-RAS V12, radiation caused prolonged intense activation of AKT. Inhibition of H-RAS V12 function, blockade of phosphatidylinositol 3-kinase (PI3K) function using small interfering RNA/small-molecule inhibitors, or expression of dominant-negative AKT abolished radiation-induced AKT activation, and radiosensitized these cells. Inhibition of PI3K function did not significantly radiosensitize parental HCT116 cells. Inhibitors of the AKT PH domain including perifosine, SH-(5, 23-25) and ml-(14-16) reduced the plating efficiency of H-RAS V12 cells in a dose-dependent fashion. Inhibition of AKT function using perifosine enhanced radiosensitivity in H-RAS V12 cells, whereas the SH and ml series of AKT PH domain inhibitors failed to promote radiation toxicity. In HCT116 H-RAS V12 cells, PI3K, PDK-1, and AKT were membrane associated, whereas in parental cells expressing K-RAS D13, only PDK-1 was membrane bound. In H-RAS V12 cells, membrane associated PDK-1 was phosphorylated at Y373/376, which was abolished by the Src family kinase inhibitor PP2. Inhibition of PDK-1 function using the PH domain inhibitor OSU-03012 or using PP2 reduced the plating efficiency of H-RAS V12 cells and profoundly increased radiosensitivity. OSU-03012 and PP2 did not radiosensitize and had modest inhibitory effects on plating efficiency in parental cells. A small interfering RNA generated against PDK1 also radiosensitized HCT116 cells expressing H-RAS V12. Collectively, our data argue that molecular inhibition of AKT and PDK-1 signaling enhances the radiosensitivity of HCT116 cells expressing H-RAS V12 but not K-RAS D13. Small-molecule inhibitory agents that blocked stimulated and/or basal PDK-1 and AKT function profoundly reduced HCT116 cell survival but had variable effects at enhancing tumor cell radiosensitivity.
Insomnia in the elderly: a review for the primary care practitioner. (2000)

The elderly are known to have a high prevalence of insomnia. Causes of insomnia include: medical, psychiatric, and drug issues; circadian rhythm changes; sleep disorders; and psychosocial factors. The elderly frequently use sleeping aids. Risks associated with elderly patients' use of hypnotic drugs are attributable to concomitant comorbid conditions, use of multiple medications, altered pharmacokinetics, and increased central nervous system sensitivity to these drugs. Treatment options for insomnia include behavior modification and pharmacotherapy. The choice of hypnotics is based on matching the nature of the insomnia to the hypnotic agent. Benzodiazepine receptor agonists are common hypnotics prescribed for insomnia in the elderly. The ideal agent has rapid onset, duration of action that lasts through the night but no residual daytime effects, and no adverse effects. The longer-acting agents have been shown to result in a higher risk of falls and hip fractures in the elderly. This relationship is not apparent with short-acting agents. Zaleplon, the newest benzodiazepine receptor agonist, has the shortest half-life of available agents. Studies have demonstrated that zaleplon is effective in improving sleep latency, duration, and sleep quality in the elderly. Zaleplon does not appear to cause rebound insomnia, residual sedation, or adversely affect psychomotor function. The key for the healthcare professional is finding the appropriate treatment or treatment combination, including behavioral modification and pharmacotherapy. When hypnotics are indicated, the most appropriate short-acting agent should be considered.
Polymer-Supported Bases. XII. Regioselective Synthesis of Lysophospholipids Using Polymer-Supported Bicyclic Amidines or Guanidines (1994)

Abstract 1-Acylphosphatidylcholines were prepared in good yields by the regioselective monoacylation of L-α-glycerophosphorylcholine with acylimidazoles in the presence of polymer-supported bicyclic amidine of guanidine.
Plasma Thrombospondin as an Indicator of Intravascular Platelet Activation in Patients with Vasculitis (1987)

The use of plasma thrombospondin (TSP) concentration was investigated as an indicator of intravascular platelet activation. Patients (n = 20) with diseases that have known vasculitis were included in the study. The range and the mean of plasma TSP concentrations of patients with vasculitis were 117 ng/ml to 6500 ng/ml and 791 +/- 1412 ng/ml (mean +/- SD); the range and the mean of plasma TSP concentrations of control individuals (n = 33) were 13 ng/ml to 137 ng/ml and 59 +/- 29 ng/ml. When plasma TSP concentrations were correlated with plasma concentrations of another platelet activation marker, beta-thromboglobulin (beta-TG), it was found that the TSP concentration increased exponentially as the plasma beta-TG level rose. A positive correlation between plasma levels of plasma TSP and serum fibrin degradation products was also observed. The results suggest that platelets are the primary source of plasma TSP in patients with various vasculitis and that plasma TSP can be a better indicator than beta-TG to assess intravascular platelet activation due to its longer circulation half life.
Inorganic Salt Hydrates as Cryoporometric Probe Materials to Obtain Pore Size Distribution (2006)

The depression of the melting temperature of Zn(NO3)2.6H2O was used to obtain the pore size distributions in controlled pore glasses. Measured by 1H NMR, the average value of the temperature depression DeltaT and the known average pore size yield K=DeltaT.d approximately 116 K.nm as the material-dependent factor for Zn(NO3)2.6H2O in the Gibbs-Thompson equation. The melting temperature is close to room temperature. Hence, this salt hydrate and some related other ones are better materials than water (K approximately 50 K.nm) for cryoporometric studies of systems with hydrophilic pores. The data also provide 46 mN/m for the solid-liquid surface tension of this salt hydrate.
Loss-tolerance for electronic wallets (2002)

Assuming the existence of tamper-resistant devices with computational power and storage capacity similar to those of PCs and secure cryptosystems, the authors present loss tolerance schemes that leave the security, autonomy, and untraceability of the basic payment system that uses electronic wallets almost unchanged. These schemes are the distributed account list protocol and the marked standard value (MSV) protocol. The two schemes are compared. It is noted that more important than the problem of loss tolerance is that of constructing really secure temperature resistant devices.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A CDE/CHR tandem element regulates cell cycle‐dependent repression of cyclin B2 transcription (2000)

Cyclin B is an important regulator of progression through the cell division cycle. The oscillating appearance of cyclin B1 and B2 proteins during the cell cycle is in part due to fluctuating mRNA levels. We had identified earlier a tandem promoter element named cell cycle-dependent element (CDE) and cell cycle genes homology region (CHR) which regulates cell cycle-dependent transcription of cdc25C, cyclin A and cdc2. Here we describe that cyclin B2 transcription is repressed through a novel CDE/CHR element in resting and G(1) cells. By relief of this repression in S and G(2) oscillating expression of cyclin B2 mRNA is achieved during the cell cycle.
Permeabilization of Lipid Bilayers Is a Common Conformation-dependent Activity of Soluble Amyloid Oligomers in Protein Misfolding Diseases (2004)

Amyloid fibrillization is multistep process involving soluble oligomeric intermediates, including spherical oligomers and protofibrils. Amyloid oligomers have a common, generic structure, and they are intrinsically toxic to cells, even when formed from non-disease related proteins, which implies they also share a common mechanism of pathogenesis and toxicity. Here we report that soluble oligomers from several types of amyloids specifically increase lipid bilayer conductance regardless of the sequence, while fibrils and soluble low molecular weight species have no effect. The increase in membrane conductance occurs without any evidence of discrete channel or pore formation or ion selectivity. The conductance is dependent on the concentration of oligomers and can be reversed by anti-oligomer antibody. These results indicate that soluble oligomers from many types of amyloidogenic proteins and peptides increase membrane conductance in a conformation-specific fashion and suggest that this may represent the common primary mechanism of pathogenesis in amyloid-related degenerative diseases.
Overcoming the Host Immune Response to Adeno-Associated Virus Gene Delivery Vectors: The Race Between Clearance, Tolerance, Neutralization, and Escape (2017)

Immune responses in gene therapy with adeno-associated virus (AAV) vectors have been the object of almost two decades of study. Although preclinical models helped to define and predict certain aspects of interactions between the vector and the host immune system, most of our current knowledge has come from clinical trials. These studies have allowed development of effective interventions for modulating immunotoxicities associated with vector administration, resulting in therapeutic advances. However, the road to full understanding and effective modulation of immune responses in gene therapy is still long; the determinants of the balance between tolerance and immunogenicity in AAV vector-mediated gene transfer are not fully understood, and effective solutions for overcoming preexisting neutralizing antibodies are still lacking. However, despite these challenges, the goal of reliably delivering effective gene-based treatments is now in sight.
Hormonal modification of epithelial differentiation and expression of cell surface heparan sulfate proteoglycan in the mouse vaginal epithelium. An immunohistochemical and electron microscopic study. (1988)

Immunohistochemical staining of a cell surface antigen was evaluated in the adult mouse vaginal epithelium at different stages of the estrous cycle and in response to exogenous sex hormones and endocrine ablation. The antigen is recognized by a monoclonal antibody directed against the core protein of a heparan sulfate-rich proteoglycan from mouse mammary epithelial cells. Vaginal epithelium at estrus showed the most intense staining; cells of the basal and intermediate layers stained, but the more superficial parakeratotic, cornified, and sloughing layers did not. At metestrus and diestrus, immunostaining was limited to basal cells and some deeper intermediate cells. The staining was absent from the more superficial layers which were invaded by leukocytes. At late diestrus and proestrus, staining was primarily in the intermediate cells; staining was absent from parakeratotic and basal cell layers. There was no staining of submucosal cells throughout the estrous cycle. In ovariectomized mice, staining of the epithelium was reduced in intensity. Diethylstilbestrol treatment of ovariectomized mice increased the intensity and extent of epithelial staining and produced a state comparable to that seen at estrous. Administration of a combination of progesterone and estradiol to ovariectomized mice elicited vaginal stratification and mucification, a state comparable to that observed in diestrus in which basal and intermediate layers stained while the apical mucified cells did not. In animals expressing natural or diethylstilbestrol-induced estrus, electron microscopic immunoperoxidase staining revealed the presence of the antigen on the surface of cell processes in the intercellular spaces between vaginal epithelial cells. Cuprolinic blue staining for glycosaminoglycan using the critical electrolyte concentration method demonstrated filamentous structures on the epithelial surface in the same location to that of the antigen. The stained filaments were reduced by treatment with heparitinase, but not with chondroitinase ABC or heparin, suggesting that they contained heparan sulfate glycosaminoglycan. These data suggest that as vaginal epithelial differentiation fluctuates during the estrous cycle in response to changing levels of estrogens and progesterone, expression of a cell surface heparan sulfate proteoglycan undergoes dramatic changes spatially and quantitatively.
Effect of Structure on the Fe3 +  / Fe2 +  Redox Couple in Iron Phosphates (1997)

To understand the role of structure on the position of the octahedral redox couple in compounds having the same polyanions, four iron phosphates: , and were investigated. They vary in structure as well as in the manner in which the octahedral iron atoms are linked to each other. The redox couple in the above compounds lies at 2.8, 2.9, 3.1, and 3.5 eV, respectively, below the Fermi level of lithium. The reason for the difference in the position of the redox couples is related to changes in the P‒O bond lengths as well as to changes in the crystalline electric field at the iron sites.
Peripheral T-cell tolerance induced in naive and primed mice by subcutaneous injection of peptides from the major cat allergen Fel d I. (1993)

T cells control the majority of antigen-specific immune responses. Therefore, influencing the activation of the T-cell response in order to modify immune responsiveness is an obvious therapeutic goal. We have used a mouse model of response to Fel d I, the major cat protein allergen in humans, to explore the ability of peptides derived from Fel d I to inhibit T-cell-dependent immune responses to the peptides themselves and to larger polypeptides. T cells from B6CBAF1 mice respond to the Fel d I peptide IPC-2 after challenge with IPC-2. However, subcutaneous tolerization with IPC-2 prevents this response as measured by production of interleukins 2 and 4 and interferon gamma. Fel d I immunization of B6D2F1 mice results in T-cell responses primarily to one peptide derived from Fel d I. Injecting this peptide in soluble form inhibits T-cell activation (as measured by interleukin 2 production) and antibody production in Fel d I-primed animals when they are subsequently challenged with peptide in adjuvant. Most of the cat-allergic human T-cell response to Fel d I is specific for two peptides on one of its two chains. Immunization of B6CBAF1 mice with recombinant Fel d I chain 1 results in T-cell responses to the same peptides. Subcutaneous administration of these two peptides, which contain some, but not all, of the T-cell epitopes from Fel d I chain I, decreases the T-cell response to the entire recombinant Fel d I chain 1. The ability to tolerize T-cell responses with subcutaneous injections suggests a practical approach to treating human diseases with peptides containing T-cell epitopes.
A randomized, controlled trial to study the effect of exercise consultation on the promotion of physical activity in people with Type 2 diabetes: a pilot study (2001)

Exercise consultation is more effective in stimulating exercise behaviour change in the short term than a standard exercise leaflet.
Hepatocyte-directed gene transfer in vivo leads to transient improvement of hypercholesterolemia in low density lipoprotein receptor-deficient rabbits. (1992)

Familial hypercholesterolemia is an inherited disease in humans, caused by a deficiency of low density lipoprotein (LDL) receptors, that we have used as a model for developing liver-directed gene therapies. Our strategy is to reconstitute hepatic LDL receptor expression in vivo by administering a DNA-protein complex that is capable of targeting the delivery of functional LDL receptor genes to hepatocytes. Infusion of this DNA-protein complex into the peripheral circulation of a rabbit animal model for familial hypercholesterolemia resulted in hepatocyte-specific gene transfer and a temporary amelioration of hypercholesterolemia. This noninvasive approach to gene therapy should have applications in the treatment of a wide spectrum of human diseases.
Respiratory Chlamydial infections in a Hong Kong teaching hospital and association with coronary heart disease. (1997)

The microimmunofluorescence antibody technique was used to determine the seroprevalence of antibodies to Chlamydia pneumoniae and Chlamydia psittaci from hospitalized patients in Hong Kong. Antibodies to C. pneumoniae were found in 54.8% of 157 patients hospitalized with respiratory disease, in 71.1% of 83 patients with cardiac disease and in 31.2% of 93 patients without either respiratory or cardiac disease. Antibodies to C. psittaci were found in 0.9% of the combined study groups. There was serological evidence of C. pneumoniae being the responsible agent in 24.8% of the severe respiratory cases. A significant correlation between antibody prevalence and coronary heart disease was identified during the study.