gebhart/patrepeval huggingface dataset:
NPM-ALK transgenic mice spontaneously develop T-cell lymphomas and plasma cell tumors (2003)

Anaplastic Large Cell Lymphomas (ALCLs) carry translocations in which the anaplastic lymphoma kinase (ALK) gene is juxtaposed to various genes, the most common of which is the NPM/B23 gene. ALK fusion proteins result in the constitutive activation of ALK tyrosine kinase, thereby enhancing proliferation and increasing cell survival. A direct role for NPM-ALK in cellular transformation has been shown in vitro with immortalized cell lines and in vivo using retroviral transfer experiments. Nonetheless, there is no direct evidence of its oncogenic potential in T lymphocytes, which represent the most common target of ALK chimeras. Here, we describe a new mouse model of lymphomagenesis in which human NPM-ALK transcription was targeted to T cells. NPM-ALK transgenic (Tg) mice were born with the expected mendelian distribution, normal lymphoid organs, and a normal number and proportion of helper and suppressor T cells. However, after a short period of latency, all NPM-ALK Tg mice developed malignant lymphoproliferative disorders (mean survival, 18 weeks). NPM-ALK Tg thymic lymphomas displayed a T-cell phenotype characteristic of immature thymocytes and frequently coexpressed surface CD30. A subset of the NPM-ALK Tg mice also developed clonal B-cell plasma cell neoplasms. These tumors arose in peripheral lymphoid organs (plasmacytomas) or within the bone marrow and often led to peripheral neuropathies and limb paralysis. Our NPM-ALK Tg mice are a suitable model to dissect the molecular mechanisms of ALK-mediated transformation and to investigate the efficacy of new therapeutic approaches for the treatment of human ALCL in vivo.
Fast malware classification by automated behavioral graph matching (2010)

Malicious software (malware) is a serious problem in the Internet. Malware classification is useful for detection and analysis of new threats for which signatures are not available, or possible (due to polymorphism). This paper proposes a new malware classification method based on maximal common subgraph detection. A behavior graph is obtained by capturing system calls during the execution (in a sandboxed environment) of the suspicious software. The method has been implemented and tested on a set of 300 malware instances in 6 families. Results demonstrate the method effectively groups the malware instances, compared with previous methods of classification, is fast, and has a low false positive rate when presented with benign software.
Readthrough of nonsense mutations in Rett syndrome: evaluation of novel aminoglycosides and generation of a new mouse model (2010)

Thirty-five percent of patients with Rett syndrome carry nonsense mutations in the MECP2 gene. We have recently shown in transfected HeLa cells that readthrough of nonsense mutations in the MECP2 gene can be achieved by treatment with gentamicin and geneticin. This study was performed to test if readthrough can also be achieved in cells endogenously expressing mutant MeCP2 and to evaluate potentially more effective readthrough compounds. A mouse model was generated carrying the R168X mutation in the MECP2 gene. Transfected HeLa cells expressing mutated MeCP2 fusion proteins and mouse ear fibroblasts isolated from the new mouse model were treated with gentamicin and the novel aminoglycosides NB30, NB54, and NB84. The localization of the readthrough product was tested by immunofluorescence. Readthrough of the R168X mutation in mouse ear fibroblasts using gentamicin was detected but at lower level than in HeLa cells. As expected, the readthrough product, full-length Mecp2 protein, was located in the nucleus. NB54 and NB84 induced readthrough more effectively than gentamicin, while NB30 was less effective. Readthrough of nonsense mutations can be achieved not only in transfected HeLa cells but also in fibroblasts of the newly generated Mecp2(R168X) mouse model. NB54 and NB84 were more effective than gentamicin and are therefore promising candidates for readthrough therapy in Rett syndrome patients.
Transcription of a yeast telomere alleviates telomere position effect without affecting chromosome stability. (1994)

Telomeres are required for the stable maintenance of chromosomes in the yeast Saccharomyces cerevisiae. Telomeres also repress the expression of genes in their vicinity, a phenomenon known as telomere position effect. In an attempt to construct a conditional telomere, an inducible promoter was introduced adjacent to a single telomere of a chromosome such that transcription could be induced toward the end of the chromosome. Transcription toward two other essential chromosomal elements, centromeres and origins of replication, eliminates their function. In contrast, transcription toward a telomere did not affect the stability function of the telomere as measured by the loss rate of the transcribed chromosome. Transcription proceeded through the entire length of the telomeric tract and caused a modest reduction in the average length of the transcribed telomere. Transcription of the telomere substantially reduced the frequency of cells in which an adjacent URA3 gene was subject to telomere position effect. These results indicate that telomere position effect can be alleviated without compromising chromosome stability.
Nonmeat Protein Alternatives as Meat Extenders and Meat Analogs (2010)

The direct consumption of vegetable proteins in food products has been increasing over the years because of animal diseases, global shortage of animal protein, strong demand for wholesome and religious (halal) food, and economic reasons. The increasing importance of legume and oilseed proteins in the manufacturing of various functional food products is due to their high-protein contents. However, the greatest obstacle to utilizing these legumes and oilseeds is the presence of antinutrients; but these antinutrients can be successfully removed or inactivated by employing certain processing methods. In contrast, the potential negative impact of the antinutrients is partially balanced by the fact that they may have a health-promoting role. Legumes and oilseeds provide well-balanced amino acid profiles when consumed with cereals. Soybean proteins, wheat gluten, cottonseed proteins, and other plant proteins have been used for texturization. Texturized vegetable proteins can extend meat products while providing an economical, functional, and high-protein food ingredient or can be consumed directly as a meat analog. Meat analogs are successful because of their healthy image (cholesterol free), meat-like texture, and low cost. Mycoprotein is fungal in origin and is used as a high-protein, low-fat, health-promoting food ingredient. Mycoprotein has a good taste and texture. Texturized vegetable proteins and a number of mycoprotein products are accepted as halal foods. This article summarizes information regarding the molecular, nutritional, and functional properties of alternative protein sources to meat and presents current knowledge to encourage further research to optimize the beneficial effects of alternative protein sources.
Fast and High Quality Fusion of Depth Maps (2008)

Reconstructing the 3D surface from a set of provided range images – acquired by active or passive sensors – is an important step to generate faithful virtual models of real objects or environments. Since several approaches for high quality fusion of range images are already known, the run-time efficiency of the respective methods are of increased interest. In this paper we propose a highly efficient method for range image fusion resulting in very accurate 3D mod-els. We employ a variational formulation for the surface reconstruction task. The global optimal solution can be found by gradient descent due to the convexity of the under-lying energy functional. Further, the gradient descent pro-cedure can be parallelized, and consequently accelerated by graphics processing units. The quality and runtime per-formance of the proposed method is demonstrated on well-known multi-view stereo benchmark datasets. 1.
Synthesis and Characterization of Hyperbranched Polycarbonates (1997)

Hyperbranched aromatic polycarbonates were prepared by the polymerization of an A2B monomer derived from 1,1,1-tris(4‘-hydroxyphenyl)ethane. Protection of one of the three phenols of the triphenol by a tert-butyldimethylsilyl group was followed by conversion of the remaining two phenolic groups to carbonylimidazolide functionalities to give the A2B monomer. Polymerization was accomplished via the anhydrous removal of the silicon protecting group and subsequent reaction of the phenoxide with a carbonylimidazolide moiety to yield the hyperbranched aryl polycarbonate bearing carbonylimidazolide chain ends. Subsequent cleavage of these end groups by reaction with methanol upon precipitation, yielded the phenol-terminated hyperbranched polycarbonate. Silylation of the phenol-terminated material with tert-butyldimethylsilyl chloride, followed by degradation of the carbonate linkages by reaction with lithium aluminum hydride and analysis of the products by HPLC allowed for the degree of branching to be determined as 53%. The molecular weights (Mw) of the carbonylimidazolide-, phenol-, and tert-butyldimethylsilyl ether-terminated hyperbranched polycarbonates were 16 000, 77 000, and 82 000 amu from GPC based on polystyrene standards, 23 000, 180 000, and 83 000 from GPC with LALLS, and 24 000, 160 000, and 88 000 from GPC with SEC,3 respectively.
Optimisation of Drug Delivery: 4. Transdermal Drug Delivery (1997)

This article reviews the current status and possible future directions for transdermal drug delivery. Skin penetration is briefly discussed and chemical and physical enhancer methods to increase skin penetration are outlined. Design considerations for transdermal drug delivery systems and products available in Australia are reviewed.
Aqueous Synthesis of Derivatized Cyclopentadienyl Complexes of Technetium and Rhenium Directed toward Radiopharmaceutical Application (2003)

Half-sandwich complexes of the type [(RCOCp)M(CO)(3)] with M = Re and (99(m))Tc were synthesized from [M(OH(2))(3)(CO)(3)](+) in water. The R group can be an organic residue or a receptor binding biomolecule with a spacer to cyclopentadienyl (Cp). This provides a general route to Cp complexes of technetium without the need for starting from [TcBr(CO)(5)]. The X-ray structure of [(C(6)H(5)CH(2)COC(5)H(4))Tc(CO)(3)] has been elucidated. The compound crystallizes in the monoclinic space group P2(1)/c with a = 16.1454(9), b = 7.6300(6), and c = 12.3922(7) A and beta = 107.792(6) degrees. We have chosen a serotonergic receptor ligand (WAY) as an example for the derivatization of Cp with a bioactive molecule. WAY is linked to Cp by an aliphatic chain of variable length. The half-sandwich complexes were prepared from water and organic solvents. The structure of [(WAY4-Cp)Re(CO)(3)] could be elucidated. The compound crystallizes in the monoclinic space group P2(1)/c with a = 15.7112(6), b = 6.8775(3), and c = 25.5217(12) A and beta = 103.778(5) degrees. Quantification of inhibition constants gave a clear structure-activity relationship. A single methylene group between the receptor binding site and the half-sandwich complex gave an IC(50) of 217 nM for HT(1A), whereas a butylene linker resulted in retention of the inhibition constant with an IC(50) of 6 nM with respect to underivatized WAY. For use as radiopharmaceuticals, the compounds have also been prepared with (99m)Tc in quantitative yield.
One‐Step Cationic Grafting of 4‐Hydroxy‐TEMPO and its Application in a Hybrid Redox Flow Battery with a Crosslinked PBI Membrane (2017)

By using a one-step epoxide ring-opening reaction between 4-hydroxy-2,2,6,6-tetramethylpiperidine 1-oxyl (4-hydroxy-TEMPO) and glycidyltrimethylammonium cation (GTMA<sup>+</sup> ), we synthesized a cation-grafted TEMPO (g<sup>+</sup> -TEMPO) and studied its electrochemical performance against a Zn<sup>2+</sup> /Zn anode in a hybrid redox flow battery. To conduct Cl<sup>-</sup> counter anions, a crosslinked methylated polybenzimidazole (PBI) membrane was prepared and placed between the catholyte and anolyte. Compared to 4-hydroxy-TEMPO, the positively charged g<sup>+</sup> - TEMPO exhibits enhanced reaction kinetics. Moreover, flow battery tests with g<sup>+</sup> -TEMPO show improved Coulombic, voltage, and energy efficiencies and cycling stability over 140 cycles. Crossover of active species through the membrane was not detected.
Drug-induced modifications of the immune response. 1. Substituted 1-phenylisoquinolines (1979)

The conversations between Chie Machida and Tim Maul cross cultural, linguistic and artistic lines. In the first conversation, Maul’s photographs speak to Machida’s un-translated Japanese text. In the second, Machida translates Maul’s English texts into Japanese and there are no images, only descriptions of images. These are followed by further conversations between strategies of representation: pages of full bleed photographs of the floor interrupted by images of the ocean floor, exposed at low tide and the phrase “Armada Graveyard.” The book concludes with two more series of photographs: actors rehearsing and small statues silently conversing.\n
Changes in nuclear size of cardiac myocytes during the development and progression of hypertrophy in rats. (1994)

It is generally believed that nuclear enlargement indicates polyploidy. The purpose of this study was to establish whether nuclear enlargement is also a marker for cellular hypertrophy. Using isolated myocytes, we examined the growth of cardiac myocyte nuclei during cellular hypertrophy in rats with aortocaval fistulas or left ventricular myocardial infarction. A Coulter Channelyzer was used to measure the volume of the myocytes. Isolated myocytes were stained with the DNA-specific fluorochrome 4'-6-di-amidino-2 phenylindole-HCl for measurements of nuclear length and width, and calculation of nuclear volume. One week, 1 month and 5 months after aortocaval fistula surgery, the nuclear volume of right ventricular myocytes increased by 24, 55 and 56% respectively. Increased length, rather than width, accounted for most of the nuclear growth. Nuclear hypertrophy was associated with a progressive increase in cell volume at each time point (34, 88 and 118%). Adaptive growth of left ventricular myocytes followed the same trend, though the extent of cellular and nuclear hypertrophy was reduced. One month after producing a myocardial infarction, there was an increase in nuclear volume (18%) and nuclear length (11%) in right ventricular myocytes, but no changes in the surviving left ventricular myocytes. The cell volume increased in both right and left ventricles (72 and 18%, respectively). Thus, nuclear size increased as myocytes enlarged, though at a slower rate. Since nuclear DNA content does not increase in rats with aortocaval fistulas or myocardial infarction, the increase in nuclear volume was associated with cellular enlargement rather than increased polyploidy.
Purification and properties of D-mannitol-1-phosphate dehydrogenase and D-glucitol-6-phosphate dehydrogenase from Escherichia coli (1984)

D-Mannitol-1-phosphate dehydrogenase (EC 1.1.1.17) and D-glucitol-6-phosphate dehydrogenase (EC 1.1.1.140) were purified to apparent homogeneity in good yields from Escherichia coli. The amino acid compositions, N-terminal amino acid sequences, sensitivities to chemical reagents, and catalytic properties of the two enzymes were determined. Both enzymes showed absolute specificities for their substrates. The subunit molecular weights of mannitol-1-phosphate and glucitol-6-phosphate dehydrogenases were 40,000 and 26,000, respectively; the apparent molecular weights of the native proteins, determined by gel filtration, were 40,000 and 117,000, respectively. It is therefore concluded that whereas mannitol-1-phosphate dehydrogenase is a monomer, glucitol-6-phosphate dehydrogenase is probably a tetramer. These two proteins differed in several fundamental respects.
Transgenic mice susceptible to poliovirus. (1991)

Poliovirus-sensitive transgenic mice were produced by introducing the human gene encoding cellular receptors for poliovirus into the mouse genome. Expression of the receptor mRNAs in tissues of the transgenic mice was analyzed by using RNA blot hybridization and the polymerase chain reaction. The human gene is expressed in many tissues of the transgenic mice just as in tissues of humans. The transgenic mice are susceptible to all three poliovirus serotypes, and the mice inoculated with poliovirus show clinical symptoms similar to those observed in humans and monkeys. Rabbit antipoliovirus serum detects the antigens mainly in motor neurons in the anterior horn of the spinal cord and in nerve cells in the medulla oblongata and pons of the paralyzed transgenic mice. Therefore, cell types sensitive to poliovirus in the central nervous system of the transgenic mice appear to be identical to those of humans and monkeys. Furthermore, many more doses of oral poliovirus vaccine strains than of the virulent strains are required to cause paralysis in the transgenic mice. This may reflect the observation that the virulent strain multiplies more efficiently in the central nervous system than the attenuated strain. Thus, the transgenic mice may become an excellent new animal model to study molecular mechanisms of pathogenesis of poliovirus and to assess oral poliovirus vaccines.
Journal of Child Psychology and Psychiatry Special Section on ’Face Processing’ (2002)

The Editors of JCPP recently initiated a series of special issues on topics for which there is a particularly high level of research activity. Topics have been selected where findings are published in a wide range of journals and where there would be special benefit from publishing a collection of high-quality empirical papers in one issue of the Journal. The first topic selected was Social Cognition, edited by Jim Stevenson, and appeared in volume 43, number 7. The second topic is Genetics and Neurobiology of Internalising Disorders, edited by Frank Verhulst, and will appear in a later issue this year. The next special issue, to be edited by Francesca Happé, will be on the topic of face processing. Papers on typical and atypical development of all aspects of face processing are now invited. The papers will be subjected to the normal refereeing process and, if accepted for publication, will appear together in one special issue of the Journal. The usual guidance on manuscript preparation should be followed. Manuscripts should be submitted by August 2003 and should be clearly identified as for consideration for the Special Section on Face Processing. Please note that manuscripts can now be submitted electronically by authors themselves using Manuscript Central. Under Manuscript Type, please select ‘Special Issue’. Authors who intend submitting papers could perhaps notify the journal office in advance (e-mail: carole.s3utherland@acpp.org.uk)
Position-effect protection and enhancer blocking by the chicken β-globin insulator are separable activities (2002)

The 1.2-kb DNA sequence element (5'HS4) at the 5' end of the chicken beta-globin locus has the two defining properties of an insulator: it prevents an "external" enhancer from acting on a promoter when placed between them ("enhancer blocking") and acts as a barrier to chromosomal position effect (CPE) when it surrounds a stably integrated reporter. We previously reported that a single CTCF-binding site in 5'HS4 is necessary and sufficient for enhancer blocking. We show here that a 250-bp "core" element from within 5'HS4 is sufficient to confer protection against silencing of transgenes caused by CPE. Further dissection of the core reveals that 5'HS4 is a compound element in which it is possible to separate enhancer blocking and barrier activities. We demonstrate that full protection against CPE is conferred by mutant 5'HS4 sequences from which the CTCF-binding site has been deleted. In contrast, mutations of four other protein binding sites within 5'HS4 result in varying reductions in the ability to protect against CPE. We find that binding sites for CTCF are neither necessary nor sufficient for protection against CPE. Comparison of the properties of 5'HS4 with those of other CTCF-binding enhancer-blocking elements suggests that CPE protection is associated with maintenance of a high level of histone acetylation near the insulator, conferred by insulator binding-proteins other than CTCF.
Mesoporous silica nanoparticles enhance the cytotoxicity of curcumin (2013)

Curcumin encapsulated in mesoporous silica nanoparticles showed improved solubility, in vitro release profile and significantly enhanced cell cytotoxicity compared to the pure drug.
A stationary-phase stress-response sigma factor from Mycobacterium tuberculosis. (1996)

Alternative RNA polymerase sigma factors are a common means of coordinating gene regulation in bacteria. Using PCR amplification with degenerate primers, we identified and cloned a sigma factor gene, sigF, from Mycobacterium tuberculosis. The deduced protein encoded by sigF shows significant similarity to SigF sporulation sigma factors from Streptomyces coelicolor and Bacillus subtilis and to SigB, a stress-response sigma factor, from B. subtilis. Southern blot surveys with a sigF-specific probe identified cross-hybridizing bands in other slow-growing mycobacteria, Mycobacterium bovis bacille Calmette-Guérin (BCG) and Mycobacterium avium, but not in the rapid-growers Mycobacterium smegmatis or Mycobacterium abscessus. RNase protection assays revealed that M. tuberculosis sigF mRNA is not present during exponential-phase growth in M. bovis BCG cultures but is strongly induced during stationary phase, nitrogen depletion, and cold shock. Weak expression of M. tuberculosis sigF was also detected during late-exponential phase, oxidative stress, anaerobiasis, and alcohol shock. The specific expression of M. tuberculosis sigF during stress or stationary phase suggests that it may play a role in the ability of tubercle bacilli to adapt to host defenses and persist during human infection.
Narrow Molecular Weight Distribution Precursors for Polymer-Drug Conjugates (2001)

Atom transfer polymerization has been used to prepare a narrow molecular weight distribution (MWD), active ester homopolymer that acted as a precursor to prepare families of narrow MWD polymer-drug conjugates during preclinical studies.
Subunit Protein Vaccines: Theoretical and Practical Considerations for HIV-1 (2003)

With the spread of AIDS still rampant in many parts of the world, there is a global urgency to develop a vaccine against HIV-1. Without a doubt, developing an effective vaccine against the virus has been a monumental scientific challenge. Although advances in molecular biology and biotechnology over the years have enabled us to generate "designer antigens," our ability to transform them into successful vaccine candidates has been limiting. This review will be divided into three sections: First, the theoretical benefits and limitations of subunit protein vaccine strategy will be presented. Secondly, recent progress in our understanding of immune responses against AIDS vaccine candidates that incorporate recombinant proteins or peptides will be reviewed, mainly those that are designed to elicit humoral immune responses. Finally, some of the factors that must be considered in designing and evaluating future vaccine candidates will be discussed.