gebhart/patrepeval huggingface dataset:
Electrical Enhancement of Formulated Plasmid Delivery in Animals (2002)

Electroporation has been shown to significantly increase plasmid transfer to the skeletal muscle, but this procedure is also implicated in muscle damage. We are reporting a highly efficient in vivo transfer of a plasmid formulated with poly-(L-glutamate) (PLG) into murine, canine and porcine muscle fibers using electric pulses of low field intensity. In mice and pigs, the use of secreted embryonic alkaline phosphatase (SEAP) as the indicator gene caused increased PLG expression by 2-3 fold compared to naked plasmid; while delivery of a PLG-plasmid formulation to dogs showed a 10-fold increase in serum SEAP levels compared to plasmid alone. Muscle lesions were reduced by the protective PLG. Thus, PLG may constitute a useful adjuvant for increased expression and reduced muscle trauma to plasmid DNA delivered by electroporation.
Translational Regulation of Autoimmune Inflammation and Lymphoma Genesis by Programmed Cell Death 4 (2006)

Both inflammatory diseases and cancer are associated with heightened protein translation. However, the mechanisms of translational regulation and the roles of translation factors in these diseases are not clear. Programmed cell death 4 (PDCD4) is a newly described inhibitor of protein translation. To determine the roles of PDCD4 in vivo, we generated PDCD4-deficient mice by gene targeting. We report here that mice deficient in PDCD4 develop spontaneous lymphomas and have a significantly reduced life span. Most tumors are of the B lymphoid origin with frequent metastasis to liver and kidney. However, PDCD4-deficient mice are resistant to inflammatory diseases such as autoimmune encephalomyelitis and diabetes. Mechanistic studies reveal that upon activation, PDCD4-deficient lymphocytes preferentially produce cytokines that promote oncogenesis but inhibit inflammation. These results establish that PDCD4 controls lymphoma genesis and autoimmune inflammation by selectively inhibiting protein translation in the immune system.
Pseudoaccommodation and Visual Acuity With Technovision PresbyLASIK and a Theoretical Simulated Array ® Multifocal Intraocular Lens (2008)

Overall near to distance visual acuity obtained with the presbyLASIK technique is comparable to the best visual acuity that could be achieved with a simulated Array multifocal IOL. Near visual acuity with presbyLASIK falls off from the ideal.
Tuning the field in a microwave resonator faster than the photon lifetime (2008)

We have fabricated and characterized tunable superconducting transmission line resonators. To change the resonance frequency, we modify the boundary condition at one end of the resonator through the tunable Josephson inductance of a superconducting quantum interference device. We demonstrate a large tuning range (several hundred megahertz), high quality factors (104), and that we can change the frequency of a few-photon field on a time scale orders of magnitude faster than the photon lifetime of the resonator. This demonstration has implications in a variety of applications.
Structure of the raw-starch-affinity site on the Aspergillus awamori var. kawachi glucoamylase I molecule. (1989)

The raw-starch-affinity site of Aspergillus awamori var. kawachi glucoamylase I (GAI), that was proved to be essential for its adsorbability and digestibility on raw starch granules, was found to be located separately from the active site in the region corresponding to glycopeptide I (Gp-I) liberated from the glucoamylase I through the action of subtilisin. Gp-I consists of 45 amino acid residues, hydroxy amino acids being characteristically abundant, and 56 mannose residues. The sequence was determined with an automatic amino acid sequencer to be ATGGTTTTATTTGSGGVTST SKTTTTASKTSTTTSSTSCTTPTAV. A structure of parallelly arranged short mannoside chains linked o-glycosidically to the successive sequence of hydroxy amino acid residues on Gp-I was revealed. On comparison of the amino acid sequence of Gp-I with those of three glucoamylases, from Aspergillus awamori, Aspergillus niger and Rhizopus oryzae, significantly homologous regions (91%, 91% and 77% homology, respectively) were detected as the affinity site that could be functionally constrained and essential for raw-starch-digesting glucoamylase.
Plasma Circulating Tumor HPV DNA for the Surveillance of Cancer Recurrence in HPV-Associated Oropharyngeal Cancer (2020)

Detection of ctHPVDNA in two consecutive plasma samples during post-treatment surveillance has high PPV and NPV for identifying disease recurrence in patients with HPV-associated oropharyngeal cancer and may facilitate earlier initiation of salvage therapy.
Parametric Mixture Models for Multi-Labeled Text (2002)

We propose probabilistic generative models, called parametric mixture models (PMMs), for multiclass, multi-labeled text categorization problem. Conventionally, the binary classification approach has been employed, in which whether or not text belongs to a category is judged by the binary classifier for every category. In contrast, our approach can simultaneously detect multiple categories of text using PMMs. We derive efficient learning and prediction algorithms for PMMs. We also empirically show that our method could significantly outperform the conventional binary methods when applied to multi-labeled text categorization using real World Wide Web pages. 1
The Cellulase System of Trichoderma (1979)

The use of sophorose to stimulate production of the cellulase enzyme system of Trichoderma reesei QM 9414, has clarified the nature of the individual enzyme components. The multiple forms of cellobiohydrolases, endoglucanases, and β-glucosidase observed among the extracellular enzymes produced by strains of T. viride and T. reesei have complicated interpretation of the respective catalytic roles of these proteins and their biosynthetic origins. The rapid production of the system in response to 1mM sophorose has allowed isolation of the three principal components of the nascent mixture. An endoglucanase and Cellobiohydrolases I (D) and II comprise about 15%, 60% and 25%, respectively, of the cellulase proteins. Cellobiohydrolase I, form D, is distinctly different from the newly described Cellobiohydrolase II. Other proteins, such as β-glucosidase, can account for only about one percent of the total protein. This eliminates the possibility that there is induced with the cellulase system a significant complement of additional enzymes concerned with the degradation of either cellulose or other components of wood.
High-level expressing YAC vector for transgenic animal bioreactors (1999)

The position effect is one major problem in the production of transgenic animals as mammary gland bioreactors. In the present study, we introduced the human growth hormone (hGH) gene into 210-kb human alpha-lactalbumin position-independent YAC vectors using homologous recombination and produced transgenic rats via microinjection of YAC DNA into rat embryos. The efficiency of producing transgenic rats with the YAC vector DNA was the same as that using plasmid constructs. All analyzed transgenic rats had one copy of the transgene and produced milk containing a high level of hGH (0.25-8.9 mg/ml). In transgenic rats with the YAC vector in which the human alpha-lactalbumin gene was replaced with the hGH gene, tissue specificity of hGH mRNA was the same as that of the endogenous rat alpha-lactalbumin gene. Thus, the 210-kb human alpha-lactalbumin YAC is a useful vector for high-level expression of foreign genes in the milk of transgenic animals.
Methods for in vitro characterization of multichannel nerve tubes (2007)

Multichannel conduits have been developed for experimental peripheral nerve and spinal cord repair. We present a series of methods to characterize multichannel nerve tubes for properties of bending, deformation, swelling, and degradation and introduce a new method to test the permeability of multichannel nerve tubes from the rate of diffusion of different-sized fluorescent dextran molecules (10, 40, and 70 kDa). First, single-lumen nerve tubes made with different poly(lactic-co-glycolic acid) (PLGA) ratios (50:50, 75:25, and 85:15) were compared. One ratio (75:25 PLGA) was subsequently used to compare single-lumen and multichannel nerve tubes. Nerve tubes made with lower PLGA ratios were found to be more flexible than nerve tubes made with a higher PLGA ratio. For low ratios, however, swelling was also greater as a result of a faster rate of degradation. Multichannel structure did not interfere with the permeability of the tube; the rate of diffusion into multichannel 75:25 PLGA nerve tubes appeared to be even higher than that into single-lumen ones, but this was only significant for 70-kDa molecules. Also, multichannel 75:25 PLGA nerve tubes were more flexible and, at the same time, more resistant to deformation. However, swelling significantly decreased the total cross-sectional lumen area, especially in multichannel 75:25 PLGA nerve tubes. Permeability, bending, deformation, swelling, and degradation are important properties to characterize in the development of multichannel nerve tubes. The methods presented in this study can be used as a basis for optimizing these properties for future, possibly clinical, application.
Semiconductor nanoparticles for electronic device integration on foils (2011)

Semiconducting nanoparticles allow the integration of field effect transistors by spin coating of a dispersion onto a pre-integrated metal structure for the electrodes. Thin film transistors with inverted coplanar setup show mobilities of up to 0.05 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> /Vs in case of silicon nanoparticles, 0.1 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> /Vs in case of zinc oxide material. Transistors consisting of a single nanoparticle are demonstrated, but the yield is low. Due to the low temperature processing (<;200°C), nanoparticle transistor integration on plastic substrates is possible. First inverter structures consisting of two nanoparticle field effect transistors integrated on oxidized silicon wafers are demonstrated.
Remembering Key Features of Visual Images Based on Spike Timing Dependent Plasticity of Spiking Neurons (2009)

The brain has the powerful capability of remembering key features of images. Based on the principle of spike timing dependent plasticity of spiking neurons and the ON/OFF pathways in the visual system, a spiking neural network is proposed to remember key features of visual images. The simulation results show that the network is capable of remembering key features according to a learning rule based on spike timing dependent plasticity. The principle of the network can be used to explain how a spiking neuron-based system can store the key features of visual images. Furthermore, the network can be applied to spiking neuron based artificial intelligent systems to support the processing visual images.
The carrier effect in the secondary response to hapten‐protein conjugates. V. Use of antilymphocyte serum to deplete animals of helper cells (1971)

Abstract Treatment of mice primed with bovine serum albumin, chicken γ‐globulin or keyhole limpet hemocyanin with rabbit anti‐mouse lymphocyte serum (ALS) depresses the secondary response, and particularly the adoptive secondary response, to these antigens. If, however, the transferred cells are boosted with NIP (4‐hydroxy‐5‐iodo‐3‐nitro‐phenacetyl‐) or DNP (2,4‐dinitrophenyl‐) conjugates of the protein with which they had been primed, their ability to make an anti‐protein response can be partially restored by adding cells primed against the hapten. Such hapten‐primed cells can be obtained, for example, by immunization with the hapten conjugated to another carrier. These helper cells can therefore be regarded as hapten‐specific. DNP‐specific helper cells can be obtained, as expected, from lethally‐irradiated thymocyte‐repopulated, FDNB (2,4‐dinitrofluorobenzene) skin‐painted donors. Hapten‐specific helper cells can be demonstrated in guinea pigs according to the same principle. As in mice, there is no correlation between helper activity and antibody‐forming‐cell‐precursor activity in terms of anti‐hapten antibody. ALS suppression spares the secondary response to high doses of conjugate, suggesting that this type of response is helper‐independent; it also indicates that the loss of carrier‐effect obtainable with high doses of conjugate cannot be attributed to the operation of hapten‐specific helper cells. These ALS experiments strengthen the evidence for the identification of helper cells in the adoptive secondary response to conjugates as thymus‐derived lymphocytes mediating cellular immunity. The case for this identity is summarized in the discussion.
An Allosteric Ribozyme Regulated by Doxycyline (2000)

Low concentrations of the antibiotic doxycycline are sufficient to control the activity of an allosteric hammerhead ribozyme (shown schematically). This was obtained by allosteric selection of an RNA library, which was fused to helix II of the ribozyme. Such molecular switches may serve as a valuable tool for the development of tailored conditional gene expression systems that can be controlled by the presence or absence of any kind of small molecule.
Renin inhibitors (1990)

Since the early 1980s, an intensive effort has been focused on the development of orally effective and long-acting inhibitors of renin. During this time, in vitro potency has increased greatly, with several transition-state inhibitor designs yielding inhibitors with subnanomolar IC50 values. In the meantime, both the molecular weight and peptide character of the inhibitors has decreased as important binding elements have been focused into smaller and more stable structures. The resulting inhibitors have shown promising activities in several in vivo models and (in two cases) in man. Nevertheless, renin inhibitors reported to date have limited oral bioavailability and short duration of action, and improvements in both will be necessary for them to compete effectively with ACE inhibitors. Renin inhibitors which have entered clinical studies have at least one naturally occurring amino acid and three or more amide bonds. It is reasonable to expect that continued development will produce wholly nonpeptide inhibitors with still lower MW, and it may be these "second-generation" inhibitors which will succeed as therapeutic agents. Development of orally effective and long-acting inhibitors of renin will enable their long-term antihypertensive efficacy and possible advantages over ACE inhibitor to be investigated.
The Lipooligosaccharides of Pathogenic Gram-Negative Bacteria (1996)

Lipooligosaccharides (LOSs) are the major glycolipids expressed on mucosal Gram-negative bacteria, including members of the genera Neisseria, Haemophilus, Bordetella, and Branhamella. They can also be expressed on some enteric bacteria such as Campylobacter jejuni and Campylobacter coli strains. LOS is analogous to the lipopolysaccharide (LPS) found in other Gram-negative families. LOSs share similar lipid A structures with an identical array of functional activities as LPSs. LOSs lack O-antigen units with the LOS oligosaccharide structures limited to 10 saccharide units. The LOS species of pathogenic Neisseria can play a major role in pathogenesis through enhancing the resistance of the organism to killing by normal human serum. Other distinguishing characteristics of LOS are the structural and antigenic similarity of some LOS species to human glycolipids and the potential for certain LOSs to be modified in vivo by host substances or secretions. These modifications of LOS in different environments of the host result in synthesis of new LOS structures that probably benefit the survival of the pathogen. The LOS of N. gonorrhoeae can act as a ligand of human receptors, promoting invasion of host cells. It is becoming clearer that LOSs are crucial factors in the pathogenesis of bacteria that express them.
OFDM Based Air Interfaces for Future Mobile Satellite Systems (2008)

This thesis considers the performance of OFDM in a non-linear satellite channel and mechanisms for overcoming the degradations resulting from the high PAPR in the OFDM signal in the specific satellite architecture. It was motivated by new S-DMB applications but its results are applicable to any OFDM system via satellites. Despite many advantages of OFDM, higher PAPR is a major drawback. OFDM signals are therefore very sensitive to non-linear distortion introduced by the power amplifiers and thus, significantly reduce the power efficiency of the system, which is already crucial to satellite system economics. Simple power amplifier back-off to cope with high OFDM PAPR is not possible. Two transmitter based techniques have been considered: PAPR reduction and amplifier linearization.
Epstein-Barr virus-associated Hodgkin's disease: Epidemiologic characteristics in international data (1997)

Hodgkin's disease (HD) has long been suspected to have an infectious precursor, and indirect evidence has implicated Epstein-Barr virus (EBV), a ubiquitous herpesvirus, as a causal agent. Recent molecular studies using EBER in situ hybridization or latency membrane protein-I (LMP-I) immunohistochemistry have identified EBV latent infection in up to 50% of HD tumors. However, the epidemiologic features of these cases have not been examined in detail. To explore the epidemiology of EBV-positive HD so as to understand the role of EBV in HD etiology more clearly, this project accumulated patient data from 14 studies that had applied these EBV assays to HD tumors. With information on age at diagnosis, sex, ethnicity, histologic subtype, country of residence, clinical stage and EBV tumor status from 1,546 HD patients, we examined risk for EBV-positive disease using logistic regression. Forty percent of subjects had EBV-positive tumors, and EBV prevalence varied significantly across groups defined by the study variables. Odds ratios (OR) for EBV-associated HD were significantly elevated for Hispanics vs. whites (OR = 4.1), mixed cellularity vs. nodular sclerosis histologic subtypes (OR = 7.3, 13.4, 4.9 for ages 0-14, 15-49, 50+ years), children from economically less-developed vs. more-developed regions and young adult males vs. females (OR = 2.5). These findings suggest that age, sex, ethnicity and the physiologic effects of poverty may represent biologic modifiers of the EBV association and confirm that this association is strongly but variably linked to histologic subtype. The data augment biologic evidence that EBV is actively involved in HD pathogenesis in some cases but describe epidemiologic complexity in this process.
Generic properties, one-parameter deformations, and the BCU method [power system stability] (1999)

This paper discusses the theoretical justification of the BCU method for the evaluation of power system stability. Recent literature has suggested that the method can be mathematically justified in terms of a one-parameter deformation between two systems. This paper shows that the assumptions of this method do not hold generically for power system models. In particular, the one-parameter transversality conditions inherent in the deformation argument do not apply for a large region in parameter space, thus, the validity of the BCU method cannot be theoretically justified by this procedure.
Two Alternative Pathways for the Synthesis of the Rare Compatible Solute Mannosylglucosylglycerate inPetrotoga mobilis (2010)

The compatible solute mannosylglucosylglycerate (MGG), recently identified in Petrotoga miotherma, also accumulates in Petrotoga mobilis in response to hyperosmotic conditions and supraoptimal growth temperatures. Two functionally connected genes encoding a glucosyl-3-phosphoglycerate synthase (GpgS) and an unknown glycosyltransferase (gene Pmob_1143), which we functionally characterized as a mannosylglucosyl-3-phosphoglycerate synthase and designated MggA, were identified in the genome of Ptg. mobilis. This enzyme used the product of GpgS, glucosyl-3-phosphoglycerate (GPG), as well as GDP-mannose to produce mannosylglucosyl-3-phosphoglycerate (MGPG), the phosphorylated precursor of MGG. The MGPG dephosphorylation was determined in cell extracts, and the native enzyme was partially purified and characterized. Surprisingly, a gene encoding a putative glucosylglycerate synthase (Ggs) was also identified in the genome of Ptg. mobilis, and an active Ggs capable of producing glucosylglycerate (GG) from ADP-glucose and d-glycerate was detected in cell extracts and the recombinant enzyme was characterized, as well. Since GG has never been identified in this organism nor was it a substrate for the MggA, we anticipated the existence of a nonphosphorylating pathway for MGG synthesis. We putatively identified the corresponding gene, whose product had some sequence homology with MggA, but it was not possible to recombinantly express a functional enzyme from Ptg. mobilis, which we named mannosylglucosylglycerate synthase (MggS). In turn, a homologous gene from Thermotoga maritima was successfully expressed, and the synthesis of MGG was confirmed from GDP-mannose and GG. Based on the measurements of the relevant enzyme activities in cell extracts and on the functional characterization of the key enzymes, we propose two alternative pathways for the synthesis of the rare compatible solute MGG in Ptg. mobilis.
Gene therapy for haemophilia (1997)

Progress toward the development of a gene therapy protocol for the treatment of haemophilia has been substantial. Recent achievements include high level clotting factor expression in mice, dogs, and monkeys as well as phenotypic correction in both mouse and canine models of haemophilia. Studies using adenoviral vectors have contributed to much of the recent success. However, the repertoire of gene transfer vehicles being applied to the development of gene therapy strategies for haemophilia has expanded. In particular, encouraging data has been generated from studies using recombinant adeno-associated virus vectors. Progress toward human clinical trials has been inhibited by host immune responses to treatment which can limit the duration of therapy and prevent readministration. Several strategies have demonstrated the feasibility of circumventing host immune responses, but more effective, clinically applicable procedures remain to be developed. While direct in vivo gene therapy strategies have generated significant progress, the results from ex vivo strategies have not been as encouraging.
Escherichia coli ferredoxin NADP+ reductase: activation of E. coli anaerobic ribonucleotide reduction, cloning of the gene (fpr), and overexpression of the protein (1993)

A specific ribonucleoside triphosphate reductase is induced in anaerobic Escherichia coli. This enzyme, as isolated, lacks activity in the test tube and can be activated anaerobically with S-adenosylmethionine, NADPH, and two previously uncharacterized E. coli fractions. The gene for one of these, previously named dA1, was cloned and sequenced. We found an open reading frame coding for a polypeptide of 248 amino acid residues, with a molecular weight of 27,645 and with an N-terminal segment identical to that determined by direct Edman degradation. In a Kohara library, the gene hybridized between positions 3590 and 3600 on the physical map of E. coli. The deduced amino acid sequence shows a high extent of sequence identity with that of various ferredoxin (flavodoxin) NADP+ reductases. We therefore conclude that dA1 is identical with E. coli ferredoxin (flavodoxin) NADP+ reductase. Biochemical evidence from a bacterial strain, now constructed and overproducing dA1 activity up to 100-fold, strongly supports this conclusion. The sequence of the gene shows an apparent overlap with the reported sequence of mvrA, previously suggested to be involved in the protection against superoxide (M. Morimyo, J. Bacteriol. 170:2136-2142, 1988). We suggest that a frameshift introduced during isolation or sequencing of mvrA caused an error in the determination of its sequence.