gebhart/patrepeval huggingface dataset:
Liver-directed gene therapy: quantitative evaluationof promoter elements by using in vivo retroviral transduction. (1994)

Liver-directed gene therapy will be applicable to many inherited diseases. Although various protocols have been devised for in vivo delivery of retrovirus, comparison of hepatocyte transduction frequencies has been difficult due to variations in retroviral titer and a paucity of DNA data. We have previously reported an in vivo rat hepatocyte transduction technique which involves 70% hepatectomy followed 24 hr later by portal vein injection of retrovirus during hepatic in-flow occlusion. In this study, we employed this method and concentrated retroviral preparations to achieve transduction of up to 15% of hepatocytes as determined by a quantitative PCR assay. As an initial step toward identifying promoters which lead to high-level long-term expression of retroviral transduced genes, we used our in vivo delivery system to compare the Moloney murine leukemia virus long terminal repeat (LTR) promoter with the promoter for the large subunit of murine RNA polymerase II (Pol-II). Human alpha 1-antitrypsin (hAAT) was used as the reporter gene to facilitate long-term analysis of expression. Serum hAAT levels were higher for the Pol-II promoter (143 ng/ml) than for the LTR promoter (50 ng/ml). This difference was consistent with the higher transduction frequency observed for the Pol-II-hAAT vector. Although serum hAAT expression was sustained for up to 1 year in six of eight Pol-II-hAAT-transduced rats and three of five LTR-hAAT-transduced rats and was proportional to hAAT mRNA level and proviral DNA frequency, in vivo expression was significantly lower than in transduced tissue culture cells. We conclude that a high frequency of in vivo transduction can be achieved by using retroviral vectors and our rapid transduction protocol, but transduced gene expression remains a serious problem. The quantitative assays described herein will facilitate in vivo comparisons of gene regulatory elements.
Therapeutic Value of Adeno Associated Virus as a Gene Therapy Vector for Parkinson's Disease – A Focused Review (2016)

Although adeno-associated viral vectors have been studied for a long time, its importance as a viable gene therapy strategy has been thrusted into the limelight only in the recent years. Due to the admirable characteristics of these vectors, their potential has been thoughtfully utilized in the treatment of several neurodegenerative diseases. This mini-review focuses at recapitulating the therapeutic advances of adeno-associated viral vectors in the treatment of Parkinson's disease by studying the various animal model experiments and clinical trials conducted since the advent of adeno-associated viral vector - based gene therapy. Additionally, the chronological analysis of the studies in the review makes it easier to understand the challenges and foretell the future prospects in this field of therapeutics.
The Effects of Refeeding on Peripheral and Respiratory Muscle Function in Malnourished Chronic Obstructive Pulmonary Disease Patients (1990)

We carried out a prospective randomized controlled trial to investigate the effects of short-term refeeding (16 days) in 10 malnourished inpatients with chronic obstructive pulmonary disease (COPD). Six patients were randomized to receive sufficient nasoenterically administered calories to provide a total caloric intake equal to 1,000 kcal above their usual intake. The other four patients were sham fed, receiving only 100 kcal more. Measurements of nutritional status, respiratory muscle strength and endurance, adductor pollicis function, and pulmonary function were performed initially and at study end. The refed group gained significantly more weight and showed significant increases in maximal expiratory pressure and mean sustained inspiratory pressure. There were no significant changes in the maximal inspiratory pressure or in adductor pollicis function. In malnourished inpatients with COPD, short-term refeeding leads to improvement in respiratory muscle endurance and in some parameters of respiratory muscle strength in the absence of demonstrable changes in peripheral muscle function.
A laboratory experiment to teach some concepts on sensor-based robot assembly systems (1988)

A laboratory experiment is described that can be performed by electrical engineering graduate students and senior undergraduates. The experiment involves the assembly of a diesel-engine oil pump with an IBM RS-1 robot. The robot is instrumented with a force-sensing gripper and an optical binary sensor to detect parts in the gripper. A GE Optomation binary vision system is also used to monitor the manipulator workspace through a charge-coupled device (CCD) camera mounted on the robot arm. The students are required to program the manipulator and to process the information from the various sensors, which are used to recognize assembly components and to verify assembly operations in real-time. This assembly experiment is designed to familiarize electrical engineering students with the problems which dominate robot-based assembly systems and to demonstrate a number of practical sensor-based motion strategies which can overcome part and robot positional uncertainty found in typical manufacturing environments. These sensor-based motion strategies improve the reliability of a robot assembly system. The sensor-based assembly experiment, the laboratory setup, and the sensor-based motion strategies are discussed in detail.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Heterogeneous nuclear ribonucleoprotein A2/B1 up-regulation in bronchial lavage specimens: a clinical marker of early lung cancer detection. (1999)

This study examines the use of a new epithelial marker in the detection of early lung cancer in bronchial lavage samples. The monoclonal antibody 703D4 recognizes the heterogeneous nuclear ribonucleoprotein (hnRNP) A2/B1, and its overexpression/up-regulation was assessed and compared with routine diagnostic cytology. One hundred and three individuals were recruited into a prospective study. These individuals were referred to a chest physician with a request to examine for possible lung cancer, and a full clinical work-up was undertaken, including bronchoscopy and radiological investigations. In this study, we analyzed hnRNP expression in individuals with metaplastic bronchial epithelial cells or tumor cells in the bronchial lavage specimens, in a blinded study. The results from 103 bronchial lavage specimens indicate that hnRNP overexpression was more accurate in detecting evidence of a neoplasia than routine cytological examination. Twenty-two of 23 specimens in which malignant cells were identified cytologically demonstrated overexpression of hnRNP A2/B1. However, in the 80 specimens that were reported as cytologically negative, 41 of 80 demonstrated hnRNP overexpression, and 29 of these individuals were shown to have a lung neoplasm based on radiological findings and/or the biopsy taken at the bronchoscopy. An additional 4 of these 41 patients were shown to have a lung neoplasm within 8 months of the initial bronchoscopy. In conclusion, detection of hnRNPA2/B1 in bronchial lavage specimens that contain metaplastic bronchial epithelial cells or cancer cells predicts the presence of a neoplasm with a sensitivity of 96%, 82%, specificity.
Synthesis and high stability of complementary complexes of N-(2-hydroxyethyl)phenazinium derivatives of oligonucleotides (1992)

Two simple methods for the synthesis of oligonucleotides bearing a N-(2-hydroxyethyl)phenazinium (Phn) residue at the 5'- and/or 3'-terminal phosphate groups are proposed. By forming complexes between a dodecanucleotide d(pApApCpCpTpGpTpTpTpGpGpC), a heptanucleotide d(pCpCpApApApCpA), and Phn derivatives of the latter, it is shown that the introduction of a dye at the end of an oligonucleotide chain strongly stabilizes its complementary complexes. The Tmax and the thermodynamic parameters (delta H, delta S, delta G) of complex formation were determined. According to these data, coupling of a dye with the 5'-terminal phosphate group is the most advantageous: delta G(37 degrees C) is increased by 3.59 +/- 0.04 kcal/mol compared to 2.06 +/- 0.04 kcal/mol for 3'-Phn derivatives. The elongation of the linker, which connects the dye to the oligonucleotide, from a dimethylene up to a heptamethylene usually leads to destabilization of the oligonucleotide complex. The complementary complex formed by the 3',5'-di-Phn derivative of the heptanucleotide was found to be the most stable among all duplexes investigated. Relative to the unmodified complex the increase in free energy was 4.96 +/- 0.04 kcal/mol. The association constant of this modified complex at 37 degrees C is 9.5 x 10(6) M-1, whereas the analogous value for the unmodified complex is only 3 x 10(3) M-1.
Reducing Immunogenicity of Pegloticase With Concomitant Use of Mycophenolate Mofetil in Patients With Refractory Gout: A Phase II, Randomized, Double‐Blind, Placebo‐Controlled Trial (2021)

Our findings indicate that MMF therapy with pegloticase is well tolerated and shows a clinically meaningful improvement in targeted serum urate level of ≤6 mg/dl at 12 and 24 weeks. This study suggests an innovative approach to pegloticase therapy in gout.
Cross-Domain Action-Model Acquisition for Planning via Web Search (2011)

Applying learning techniques to acquire action models is an area of intense research interest. Most previous works in this area have assumed that there is a significant amount of training data available in a planning domain of interest, which we call target domain, where action models are to be learned. However, it is often difficult to acquire sufficient training data to ensure that the learned action models are of high quality. In this paper, we develop a novel approach to learning action models with limited training data in the target domain by transferring knowledge from related auxiliary or source domains. We assume that the action models in the source domains have already been created before, and seek to transfer as much of the the available information from the source domains as possible to help our learning task. We first exploit a Web searching method to bridge the target and source domains, such that transferrable knowledge from source domains is identified. We then encode the transferred knowledge together with the available data from the target domain as constraints in a maximum satisfiability problem, and solve these constraints using a weighted MAX-SAT solver. We finally transform the solutions thus obtained into high-quality target-domain action models. We empirically show that our transfer-learning based framework is effective in several domains, including the International Planning Competition (IPC) domains and some synthetic domains.
Polymer Latex Technology: An Overview (2010)

Polymer nanoparticles find use in a number of applications like coatings, adhesives, paints, etc. The applications of these nanoparticles are significantly affected by their physical properties as well as surface morphology, which can be controlled by the synthesis process used to generate such particles. Emulsion poly mer i za tion and its modified methodologies are the most commonly used techniques to achieve poly mer nanoparticles. These techniques also allow the generation or surface functionalization of the particles either in situ or by following separate specific steps. Polymerization of monomer by emulsion poly mer i za tion offers significant advantages in the whole poly meri za tion process as compared to bulk and solution poly mer i za tion methods. It allows better control of the heat and viscosity of the system, and emulsion poly mer i za tion allows the achievement of an increase in molecular weight of the poly mer chains without negatively impacting the rate of poly mer i za tion [1]. In emulsion poly mer i za tion, most of the monomer is present as monomer droplets in the aqueous phase, which diffuses to the polymerizing particles during the course of poly mer i za tion. The diffusion of the monomer isCONTENTS1.1 Introduction ....................................................................................................1 1.2 Emulsion Polymerization .............................................................................2 1.3 Controlled Polymerization and its Use in EmulsionPolymerization Processes .............................................................................9 1.4 Conventional and Controlled Miniemulsion Polymerization ............... 16 1.5 Generation of Copolymer or Core-Shell Particles ................................... 20 References ...............................................................................................................25
Bacterial Regulation: Global Regulatory Networks (1984)

We have made rapid progress in recent years in identifying the genetic causes of many human diseases. However, despite this recent progress, our mechanistic understanding of these diseases is often incomplete. This is a problem because it limits our ...Read More
Use of global amino acid replacements to define the requirements for MHC binding and T cell recognition of moth cytochrome c (93-103). (1994)

Substitution with all naturally occurring L-amino acids at each of 11 residues of the IEk-restricted month cytochrome c (93-103) epitope has allowed us to analyze the requirements for MHC binding and T cell recognition to a level of definition not previously possible. Substitutions at only three positions systematically affect MHC binding and three others appear to be the major TCR contacts. Interestingly, changing residues involved in MHC binding can ablate T cell recognition without altering MHC association. Additionally, residue identity at two positions that do not appear critical for MHC binding, nor to be involved in specific T cell contact, nonetheless dramatically affect T cell responses. This suggests that peptides differing only slightly in sequence can have significantly altered conformations within the class II MHC binding groove. We have also developed a simple scoring program that uses the binding data to quantitate how well a given peptide fits the MCC motif. All strongly immunogenic IEk-restricted epitopes score highly (> or = 0.70, where 1.0 is perfect concordance), and only 3% of all potential nonameric peptides in the two main protein sequence databases have scores greater than 0.70. This indicates that the global amino acid replacement approach using a single peptide is an efficient means of deriving binding motifs for a given class II MHC molecule, and should aid in the identification of novel T cell epitopes.
Optimal Storage Conditions for Highly Dilute DNA Samples: A Role for Trehalose as a Preserving Agent (2005)

DNA extraction from trace samples or noninvasively collected samples often results in the recovery of low concentration solutions of DNA that are prone to DNA degradation or other loss. Because of the difficulty in obtaining such samples, and their potentially high value in wildlife and forensic studies, it is critical that optimal methods are employed for their long-term storage. We assessed the amplification yield of samples kept under different storage conditions with the addition of potential preserving agents. We stored dilutions of known concentration human placental DNA, and gorilla fecal DNA, under four conditions (+4 degrees C, -20 degrees C, -80 degrees C, dry at room temperature), and with three additives (Tris EDTA (TE) buffer, Hind III digested Lambda DNA, trehalose). The effectiveness of the treatment methods was tested at regular intervals using qPCR to assess the quantity of amplifiable DNA, and a PCR assay of a larger 757 bp fragment to evaluate the quality of that remaining DNA. The highest quantity of DNA remained in samples stored at -80 degrees C, regardless of storage additives, and those dried at room temperature in the presence of trehalose. Surprisingly, DNA quality was best preserved in the presence of trehalose, either dried or at -80 degrees C; significant quality loss occurred with -20 degrees C and +4 degrees C storage.
The Computerized Carroll Rating Scale (1985)

A group of 64 female psychiatric patients were given the computerized, self administered version of the Carroll Rating Scale for depression. The test identified depression earlier than the clinical methods being used.
Synthesis and Characterization of Copper(I) Amidinates as Precursors for Atomic Layer Deposition (ALD) of Copper Metal (2005)

A series of copper(I) amidinates of the general type [(R‘NC(R)NR‘ ‘)Cu]2 (R‘ and R‘ ‘ = n-propyl, isopropyl, n-butyl, isobutyl, sec-butyl, tert-butyl; R = methyl, n-butyl) have been synthesized and characterized. These compounds are planar dimers, bridged by nearly linear N−Cu−N bonds. Their properties (volatility, low melting point, high thermal stability, and self-limited surface reactivity) are well-suited for atomic layer deposition (ALD) of copper metal films that are pure, highly conductive, conformal, and strongly adherent to substrates.
ChemInform Abstract: Immunophilins: Beyond Immunosuppression (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Novel Alleles for Black and Gray Seed Color Genes in Common Bean (2017)

Seed coat color is one of the most important characteristics of common bean ( Phaseolus vulgaris L.). To understand the genetic basis of this trait a cross was made of two small seeded Mesoamerican bean plants from China, the varieties Longyundou 4 (Long 4) with black seed and Longyundou 5 (Long 5) with white seed. Using phenotypic classification, the genetic analysis showed that the inheritance of black, gray, and white seed color could be explained primarily by two independent genes in an additive‐dominant, two gene epistasis model with a significant (χ 2 = 1.65, p = 0.44) fit to the 12:3:1 segregation ratio. We also analyzed seed color as a quantitative trait to see whether significant loci aligned with any known seed color genes. To that end we developed 2357 new physically confirmed simple sequence repeat (SSR) markers (BMp series) based on the whole‐genome sequences of common bean and genetically mapped 105 into the F 2 bean map. Combining the results of the phenotypic analysis and the new genetic map, two major additive quantitative trait loci (QTL) were found on chromosome Pv07; near the markers BMg87 , BMp7s201 , and BMp7s206 that explained more than 38% of the phenotypic variation. This region may contain the Asp gene but was distal to the P gene. Several other epistatic QTL for seed color were detected on chromosome Pv08 possibly related to the V locus and on chromosome Pv11. The new linked markers would accelerate the cloning of seed coat color genes of common bean and their selection.
Breakup of a laminar capillary jet of a viscoelastic fluid (1969)

The stability of non-Newtonian jets was investigated. A linearized stability analysis shows that a liquid column of a viscoelastic fluid exhibits more rapid growth of axisymmetric wave disturbances than a Newtonian fluid of the same zero shear viscosity. This result is independent of the form of constitutive equation chosen. Experiments in weakly elastic fluids confirm this expectation, whereas data on fluids with more pronounced elastic properties indicate that non-linear phenomena are dominating. The disturbances appear as a series of droplets connected by random lengths of threads, which thin with distance and eventually lead to jet breakup. Even in dilute viscoelastic solutions, jet breakup does not occur by the growth of clearly defined waves.
Competitive neural network for affine invariant pattern recognition (2005)

This paper presents a layered neural network which consists of clusters of competitive cells for affine invariant pattern recognition. The first layer outputs affine invariant patterns via winner-take-all competition between input cells whose weight vectors are equivalent to each other in a cluster. Responding to affine-different patterns, the first layer outputs different patterns when the weight vectors of the input cells in all clusters involve a sufficient number of linearly independent affine-different vectors. Thus, responding to the output patterns of the first layer, the second-layer is capable of affine invariant pattern recognition via winner-take-all competition between the input cells whose weight vectors are generated by the output patterns of the first layer responding to input patterns to be recognized. Similarly, the network with appropriate weight vectors has the ability of pattern recognition invariant to transformations in a subclass of affine transformations. The shift invariance via both the Fourier transform and neocognitron relates to the present network. The performance is examined by computer simulation.
A 15.8 pJ/bit/iter quasi-cyclic LDPC decoder for IEEE 802.11n in 90 nm CMOS (2010)

We present a low-power quasi-cyclic (QC) low density parity check (LDPC) decoder that meets the throughput requirements of the highest-rate (600 Mbps) modes of the IEEE 802.11n WLAN standard. The design is based on the layered offset-min-sum algorithm and is runtime-programmable to process different code matrices (including all rates and block lengths specified by IEEE 802.11n). The register-transfer-level implementation has been optimized for best energy efficiency. The corresponding 90 nm CMOS ASIC has a core area of 1.77 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and achieves a maximum throughput of 680 Mbps at 346 MHz clock frequency and 10 decoding iterations. The measured energy efficiency is 15.8pJ/bit/iteration at a nominal operating voltage of 1.0 V.
Pegylated interferon plus ribavirin for the treatment of chronic hepatitis C. (2003)

Peginterferon alfa-2a and peginterferon alfa-2b have been approved for the treatment of chronic hepatitis C virus (HCV) infection in adults who have compensated liver disease and have not been previously treated with interferon alfa. Peginterferon alfa-2a and peginterferon alfa-2b have also been approved for use in combination with ribavirin as therapy for these adults. Combining peginterferon alfa-2a or alfa-2b with ribavirin produces better activity against HCV than either drug alone. Interferon works by binding to specific receptors on the cell surface that initiate a complex cascade of protein-protein interactions leading to rapid activation of gene transcription. The effects of this interferon-stimulated gene modulation depend on the biologic system and may result in the inhibition of viral replication in infected cells, inhibition of cell proliferation, and immunomodulation. Pegylation of the interferon molecule increases its size; the absorption of the larger pegylated molecule is slower, its half-life is longer, and its rate of clearance from the plasma is lower than that of the native interferon. Thus, the pegylated molecule increases the duration of biologic activity. Factors that appear to influence the success of pegylated interferon therapy are HCV genotype, baseline viral load, presence of fibrosis or inflammation shown on the liver biopsy at baseline, and the patient's body weight or body surface area. Patients infected with HCV genotype 1 tend to have a lower response rate, require longer courses of therapy, and respond better when treated with a pegylated interferon plus ribavirin. Patients infected with HCV genotypes 2 or 3 have comparable responses when treated with interferon plus ribavirin or pegylated interferon plus ribavirin and can be treated with a lower dose of ribavirin and a shorter course of therapy (24 weeks vs 48 weeks for patients with genotype 1). Studies directly comparing peginterferon alfa-2a and peginterferon alfa-2b have not been performed.