gebhart/patrepeval huggingface dataset:
Subcellular Trafficking of the Cytoplasmic Expression System (1999)

Cationic liposomes have provided many advantages over viral vector formulations; however, the problem of inefficient gene expression remains. This is due in part to the nuclear membrane, which limits DNA entry into the nucleus. Cytoplasmic expression systems using T7 RNA polymerase have been developed to express genes in the cytoplasm and avoid the need for nuclear import of DNA. Although these systems show improved transgene expression, little is known about how they function in transfected cells. Direct comparisons between a cytoplasmic and nuclear expression system were carried out with a 293 cell line stably expressing T7 RNA polymerase. A formulation for optimal reporter gene expression was developed and used in conjunction with a variety of subcellular trafficking inhibitors to study the process of DNA endocytosis. Transfected cells were also studied at different stages of the cell cycle to determine the dependence of each system on mitosis. These results showed that cytoplasmic and nuclear expression systems utilize similar endocytosis pathways to the point of endosomal release. Once DNA is released into the cytoplasm, the cytoplasmic expression system shows immediate expression that is proportional to the amount of DNA released. In contrast, DNA targeted for nuclear expression requires additional time for nuclear entry. The level of nuclear expression is also restricted by the limited amount of DNA that is imported into the nucleus. Finally, mitosis is required for effective nuclear expression but not for cytoplasmic expression. Therefore, the cytoplasmic expression system has considerable advantages over traditional nuclear expression systems and may be an effective method for transfecting nondividing cells. Efficient expression of genes delivered by nonviral vectors is hindered owing to poor nuclear transport of plasmid DNA. A potential solution to this problem would be to use a cytoplasmic expression system. Previous studies have shown that this method produces enhanced gene expression when compared with traditional nuclear expression systems; however, the actual mechanisms by which the cytoplasmic expression system works remains unknown. This article focuses on a direct comparison between cytoplasmic and nuclear expression in terms of optimal DNA delivery formulations, intracellular trafficking of DNA, and cell cycle dependence. These results indicate that the cytoplasmic expression system has two primary advantages over nuclear expression in that it does not rely on nuclear DNA transport or mitosis for efficient expression.
4-Hydroxybutyryl-CoA Dehydratase from Clostridium aminobutyricum:  Characterization of FAD and Iron−Sulfur Clusters Involved in an Overall Non-Redox Reaction (1996)

4-Hydroxybutyryl-CoA dehydratase catalyzes the reversible dehydration of 4-hydroxybutyryl-CoA to crotonyl-CoA, which involves cleavage of an unactivated beta-C-H bond. The enzyme also catalyzes the apparently irreversible isomerization of vinylacetyl-CoA to crotonyl-CoA. Addition of crotonyl-CoA to the dehydratase, which contains FAD as well as non-heme iron and acid labile sulfur, led to a decrease of the flavin absorbance at 438 nm and an increase in the region from 500 to 800 nm. The protein-bound FAD was easily reduced to the semiquinone (redox equilibration within seconds) and only slowly to the hydroquinone (redox equilibration minutes to hours): the redox potentials were not unusual for flavoproteins (Eox/sq = -140 +/- 15 mV and Esq/red = -240 +/- 15 mV; pH 7.0, 25 degrees C). There was no equilibration of electrons between the flavin and the Fe-S cluster, which was difficult to reduce. After extensive photoreduction, an EPR signal indicative of a [4Fe-4S]+ cluster was detected (g-values: 2.037, 1.895, 1.844). Upon exposure to air at 0 degrees C, the enzyme lost dehydration activity completely within 40 min, but isomerase activity dropped to about 40% of the initial value and persisted for more than a day. The properties of the protein-bound FAD are consistent with a mechanism involving transient one-electron oxidation of the substrate to activate the the beta-C-H bond. The putative [4Fe-4S]2+ cluster could serve a structural role and/or as Lewis acid facilitating the leaving of the hydroxyl group.
Head-to-head comparison of the safety of tocilizumab and tumor necrosis factor inhibitors in rheumatoid arthritis patients (RA) in clinical practice: results from the registry of Japanese RA patients on biologics for long-term safety (REAL) registry (2015)

The adjusted risks for SAEs and SIs were not significantly different between TCZ and TNFIs, indicating an influence of clinical characteristics of the patients on the safety profile of the biologics in clinical practice.
The structure and function of hyaluronan: An overview (1996)

Hyaluronan is a major component of synovial tissue and fluid as well as other soft connective tissues. It is a high-Mr polysaccharide which forms entangled networks already at dilute concentrations (< 1 mg/mL) and endows its solutions with unique rheological properties. Physiological functions of hyaluronan (lubrication, water homeostasis, macromolecular filtering, exclusion, etc.) have been ascribed to the properties of these networks. Recently a number of specific interactions between hyaluronan and a group of proteins named hyaladherins have also pointed towards a role of hyaluronan in recognition and the regulation of cellular activities. Many more or less well documented hypotheses have been proposed for the function of hyaluronan in joints, for example, that it should lubricate, protect cartilage surfaces, scavenge free radicals and debris, keep the joint cavities open, form flow barriers in the synovium and prevent capillary growth.
Familial Gastrointestinal Stromal Tumors and Germ-Line Mutations (2007)

Familial Gastrointestinal Stromal Tumors and Germ-Line MutationsTo the Editor: Gastrointestinal stromal tumors may be sporadic or inherited in an autosomal dominant manner, alone or as a component of a syndrome associated with other tumors, such as in the context of neurofibromatosis type 1. 1 We have described seven male and five female patients (median age, 23 years) from five unrelated families who had both gastrointestinal stromal tumors and paragangliomas.Susceptibility to the tumors was inherited in an apparently autosomal dominant manner, with incomplete penetrance. 2 This condition has been referred to as "the dyad of paraganglioma and gastrointestinal stromal tumors" or the "Carney-Stratakis syndrome" (or "Carney-Stratakis dyad"). 3Germ-line mutations of the genes encoding succinate dehydrogenase subunits B, C, and D (SDHB, SDHC, and SDHD) have been described in inherited paraganglioma and pheochromocytoma 4 but not in familial gastrointestinal tumors.The family history of a kindred with multiple paragangliomas and a germ-line SDHB mutation included a person with a gastrointestinal stromal tumor, 5 but neither blood nor tissue specimens from this patient were studied for SDHB abnormalities.We identified six germ-line SDHB, SDHC, and SDHD mutations in patients with the dyad (Fig. 1).Gastrointestinal stromal tumors from the patients showed allelic losses around the chromosomal loci of the succinate dehydrogenase subunit.The patients did not have mutations of KIT or the gene for platelet-derived growth factor receptor alpha (PDGFRA), which have been associated with gastrointestinal tumors. 1 We conclude that familial gastrointestinal stromal tumors may be caused by mutations of the succinate dehydrogenase subunit genes SDHB, SDHC, and SDHD, and abdominal paragangliomas associated with gastrointestinal tumors may be caused uniquely by SDHC mutations.
Generation and Distribution of Dislocations by Solute Diffusion (1961)

The stress introduced by solute lattice contraction of boron and phosphorus in silicon is shown to be sufficient to generate dislocations in silicon wafers. Such dislocations were observed. Expressions for the density distribution and for the total number of dislocations generated are derived and a mechanism of dislocation generation and distribution during the diffusion process is postulated. The dislocation distribution is shown to be highly dependent upon the nature of the diffusion process, expressions being derived for the conditions of (1) constant surface concentration of solute and (2) diffusion from a finite source. An expression for and means to determine the residual stresses in diffused silicon wafers are given.
Pop-up and/or Starter Fertilizers for Corn (2010)

Corn growers continue to look for ways to improve yields and production efficiency. Early planting and the use of starter fertilizers are practices that many growers utilize to maximize yield potential. “Pop-up ” fertilizer use is currently being discussed in the corn production community, and the purpose of this article is to clarify the definition of starter and pop-up fertilizers, and share thoughts about the use of these materials as part of a comprehensive soil fertility program for corn production. Early season planting means that corn is being planted in cool soils and early root growth is expected to be slow. Nutrient uptake during early growth can be low due to the small root system and cold soil temperatures which limit root exploration and nutrient movement to roots. Starter and pop-up fertilizers address this issue of early season nutrient availability to plants by placing fertilizer in the soil near or with the seed. The generally accepted definition of “pop-up ” fertilizer is that the fertilizer is placed with the seed at planting while “starter ” fertilizers are placed near but not with the seed. Standard placement of corn starter fertilizer is a band of fertilizer 2 inches to the side and 2 inches below the seed (Fig. 1). However, this distance from the seed is modified to fit various management systems. Fig.1. Illustration of pop-up and starter fertilizer placement for corn.
Morphogenesis of Ductal Networks in the Mouse Prostate1 (1986)

Postnatal growth and development of the glandular architecture of the ventral and dorsolateral lobes of the mouse prostate (VP and DLP) were investigated by microdissection techniques that permitted precise quantification of the numbers of primary ducts emerging from the urethra, the terminal ductal tips, and ductal branch-points. At birth both the right and left lobe of the VP consisted of 1-3 main ducts that had already undergone secondary and tertiary branching. In contrast, at birth the more complex DLP had 9-12 unbranched main ducts per lobe on both the right and left sides. During the first 15 days after birth, 80.7% of tips and 76.4% of branch-points of the adult gland formed in the VP, and 70.4% of tips and 53.6% of the branch-points formed in the DLP. Ductal branching was completed by 60 to 90 days. The DLP developed in three stages: first, formation of unbranched main ducts (first 10 days); second, distal branching of each main duct resulting in 3-5 terminal branches per main duct (10-15 days after birth); third, elaboration of intraductal mucosal infolding in distal ducts after 30 days of age. Ducts of the lateral prostate (LP), a ventrolateral subdivision of the DLP, initiated branching morphogenesis between 1 to 5 days after birth. The LP grew into and became embedded within the capsule of the VP, which may explain why the ductal architecture of these two lobes are similar. These heretofore unrecognized differences in the organogenesis and morphology of the mouse VP and DLP and the striking morphological heterogeneity both between and within the lobes of the mouse prostate may be morphological manifestations of functional heterogeneities within the prostate.
A short review on SSF – an interesting process option for ethanol production from lignocellulosic feedstocks (2008)

Simultaneous saccharification and fermentation (SSF) is one process option for production of ethanol from lignocellulose. The principal benefits of performing the enzymatic hydrolysis together with the fermentation, instead of in a separate step after the hydrolysis, are the reduced end-product inhibition of the enzymatic hydrolysis, and the reduced investment costs. The principal drawbacks, on the other hand, are the need to find favorable conditions (e.g. temperature and pH) for both the enzymatic hydrolysis and the fermentation and the difficulty to recycle the fermenting organism and the enzymes. To satisfy the first requirement, the temperature is normally kept below 37 degrees C, whereas the difficulty to recycle the yeast makes it beneficial to operate with a low yeast concentration and at a high solid loading. In this review, we make a brief overview of recent experimental work and development of SSF using lignocellulosic feedstocks. Significant progress has been made with respect to increasing the substrate loading, decreasing the yeast concentration and co-fermentation of both hexoses and pentoses during SSF. Presently, an SSF process for e.g. wheat straw hydrolyzate can be expected to give final ethanol concentrations close to 40 g L-1 with a yield based on total hexoses and pentoses higher than 70%.
Abductive explanation of dialogue misunderstandings (1993)

To respond to an utterance, a listener must interpret what others have said and why they have said it.Misunderstandings occur when agents differ in their beliefs about what has been said or why.Our work combines intentional and social accounts of discourse, unifying theories of speech act production, interpretation, and the repair of misunderstandings.A unified theory has been developed by characterizing the generation of utterances as default reasoning and using abduction to characterize interpretation and repair.
Loss of E-Cadherin Promotes Metastasis via Multiple Downstream Transcriptional Pathways (2008)

Loss of the epithelial adhesion molecule E-cadherin is thought to enable metastasis by disrupting intercellular contacts-an early step in metastatic dissemination. To further investigate the molecular basis of this notion, we use two methods to inhibit E-cadherin function that distinguish between E-cadherin's cell-cell adhesion and intracellular signaling functions. Whereas the disruption of cell-cell contacts alone does not enable metastasis, the loss of E-cadherin protein does, through induction of an epithelial-to-mesenchymal transition, invasiveness, and anoikis resistance. We find the E-cadherin binding partner beta-catenin to be necessary, but not sufficient, for induction of these phenotypes. In addition, gene expression analysis shows that E-cadherin loss results in the induction of multiple transcription factors, at least one of which, Twist, is necessary for E-cadherin loss-induced metastasis. These findings indicate that E-cadherin loss in tumors contributes to metastatic dissemination by inducing wide-ranging transcriptional and functional changes.
Physical mapping of virulence-associated genes in Pseudomonas aeruginosa by transverse alternating-field electrophoresis (1991)

The relative chromosomal locations of 20 virulence-associated genes in four clinical isolates of Pseudomonas aeruginosa were investigated by using transverse alternating-field electrophoresis. Each strain had a characteristic restriction pattern when digested with either SpeI or DraI and electrophoresed with 15-s pulses. All four strains had restriction fragments that hybridized with each of the gene probes used, although there were variations in fragment size. An SpeI physical map constructed by Ratnaningsih et al. (E. Ratnaningsih, S. Dharmsthiti, V. Krishnapillai, A. Morgan, M. Sinclair, and B. W. Holloway, J. Gen. Microbiol. 136:2351-2357, 1990) for one of these strains, PAO1, was used to identify the location of 11 previously unmapped genes. The physical locations of the remaining genes were found to be consistent with their genetically mapped loci. Whereas phospholipase C and alginate structural and regulatory genes were associated in three separate clusters in the early, middle, and late regions of the chromosome, no virulence cluster was identified. Our data suggest that the pathogenicity of P. aeruginosa results from the gradual acquisition of genes encoding various virulence determinants.
Phosphorescence Lifetime of Benzene. An Intermolecular Heavy-Atom Effect, a Deuterium Effect, and a Temperature Effect (1960)

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Bridges and routers (1988)

An examination is made of data link bridges and internetwork routers, two technologies that provide for the extension and interconnection of local networks, which may occur using high-speed wide-area digital data communications services. The discussion of bridges covers simple bridges, learning bridges, source routing, and quality of service offered by bridges. The discussion of routers considers the Transmission Control Protocol and Internet Protocol (known as TCP/IP) used by ARPAnet, DECnet, and quality of service offered by routers.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Genetically determined differences in newborn rat islet sensitivity to interleukin-1 in vitro: no association with the diabetes prone phenotype in the BB-rat (1989)

This study was designed to investigate whether the genetic predisposition to insulin-dependent diabetes mellitus (IDDM) might be caused by an inherited increased sensitivity of the pancreatic B-cells to immune effector molecules e.g. the monokine interleukin 1 (IL-1), which is selectively cytotoxic to B-cells in vitro. Islets of Langerhans isolated from newborn diabetes prone and diabetes resistant Bio-Breeding rats, as well as from the inbred non-diabetic rat strains Wistar Furth, Brown-Norway and Lewis-Scripps were exposed to 0-1000 ng/l [corrected] of recombinant human IL-1 beta for 7 days. Strain-related differences in the sensitivity to IL-1 were studied by comparing the dose-responses of insulin release at 11 mmol/l glucose and islet light microscopic morphology to varying concentrations of IL-1. Statistical analyses showed a significant impact of strain on B-cell sensitivity to IL-1, Brown-Norway islets being relatively resistant to the action of IL-1. However, the the diabetes prone islets were not more sensitive to the cytotoxic effect of IL-1 than the non-diabetic control strain islets. We conclude that genetic differences in the response to IL-1 exist in vitro, but that this phenomenon is unrelated to the propensity to develop IDDM.
Elevated creatine kinase activity in primary hepatocellular carcinoma (2005)

The findings do not support significant expression of CK in normal liver and most liver pathologies. Instead, many of the previous misconceptions in this field can be explained by interference from AdK isoenzymes. Moreover, the data suggest a possible interplay between p53 mutations, HCC, CK expression, and the growth-inhibitory effects of cyclocreatine in HCC. These results, if confirmed, could provide important hints at improved therapies and cures for HCC.
Thevenin's Theorem : An Easy Proof Suitable for Undergraduate Teaching (2014)

espanolSe presenta una sencilla demostracion del teorema de Thevenin, adecuada para la ensenanza de pregrado. Se ha desarrollado para este proposito Una tecnica de ecuacion modificada de nodo. EnglishA simple proof of Thevenin’s theorem suitable for undergraduate teaching is presented. A modified node equation technique is developed for this purpose.
A New Method to Assess Metastatic Potential of Human Prostate Cancer: Relative Nuclear Roundness (1982)

A new technique has been developed that helped in an accurate prediction of the prognosis of 27 patients with stages B1 and B2 prostatic cancer following radical prostatectomy. This method involves computer-assisted image analysis of histological specimens of the primary lesion removed at the time of radical perineal prostatectomy. On the basis of a nuclear shape factor, known as nuclear roundness, we have been able to distinguish those tumors with a high metastatic potential from tumors that are less aggressive. This technique provides pathologists with quantitative information about the metastatic potential of a tumor, which may aid in the management of the individual patient.
Modelling plasma discharges at high electronegativity (1997)

Macroscopic models for the equilibrium of a three-component electronegative gas discharge are developed. Assuming the electrons and the negative ions to be in Boltzmann equilibrium, a positive ion ambipolar diffusion equation is derived. Such a discharge can consist of an electronegative core and may have electropositive edge regions, but the electropositive regions become small for the highly electronegative plasma considered here. In the parameter range for which the negative ions are Boltzmann, the electron density in the core is nearly uniform, allowing the nonlinear diffusion equation to be solved in terms of elliptic integrals. If the loss of positive ions to the walls dominates the recombination loss, a simpler parabolic solution can be obtained. If recombination loss dominates the loss to the walls, the assumption that the negative ions are in Boltzmann equilibrium is not justified, requiring coupled differential equations for positive and negative ions. Three parameter ranges are distinguished corresponding to a range in which a parabolic approximation is appropriate, a range for which the recombination significantly modifies the ion profiles, but the electron profile is essentially flat, and a range where the electron density variation influences the solution. The more complete solution of the coupled ion equations with the electrons in Boltzmann equilibrium, but not at constant density, is numerically obtained and compared with the more approximate solutions. The theoretical considerations are illustrated using a plane parallel discharge with chlorine feedstock gas of p = 30, 300 and 2000 mTorr and , corresponding to the three parameter regimes. A heuristic model is constructed which gives reasonably accurate values of the plasma parameters in regimes for which the parabolic profile is not adequate.