gebhart/patrepeval huggingface dataset:
The adenovirus E1B-55K transforming polypeptide modulates transport or cytoplasmic stabilization of viral and host cell mRNAs. (1986)

The adenovirus type 5 mutant H5dl338 lacks 524 base pairs within early region 1B. The mutation removed a portion of the region encoding the related E1B-55K and -17K polypeptides but did not disturb the E1B-21K coding region. The virus can be propagated in 293 cells which contain and express the adenovirus type 5 E1A and E1B regions, but it is defective for growth in HeLa cells, in which its final yield is reduced about 100-fold compared with the wild-type virus. The mutant also fails to transform rat cells at normal efficiency. The site of the dl338 defect was studied in HeLa cells. Early gene expression and DNA replication appeared normal. Late after infection, mRNAs coded by the major late transcription unit accumulated to reduced levels. At a time when transcription rates and steady-state nuclear RNA species were normal, the rate at which late mRNA accumulated in the cytoplasm was markedly reduced. Furthermore, in contrast to the case with the wild type, transport and accumulation of cellular mRNAs continued late after infection with dl338. Thus, the E1B product appears to facilitate transport and accumulation of viral mRNAs late after infection while blocking the same processes for cellular mRNAs.
Sudemycins, Novel Small Molecule Analogues of FR901464, Induce Alternative Gene Splicing (2011)

Two unrelated bacterial natural products, FR901464 and pladienolide B, have previously been shown to have significant antitumor activity in vivo. These compounds target the SF3b subunit of the spliceosome, with a derivative of pladienolide (E7107) entering clinical trials for cancer. However, due to the structural complexity of these molecules, their research and development has been significantly constrained. We have generated a set of novel analogues (Sudemycins) that possess the pharmacophore that is common to FR901464 and pladienolide, via a flexible enantioselective route, which allows for the production of gram quantities of drug. These compounds demonstrate cytotoxicity toward human tumor cell lines in culture and exhibit antitumor activity in a xenograft model. Here, we present evidence that Sudemycins are potent modulators of alternative splicing in human cells, both of endogenous genes and from minigene constructs. Furthermore, levels of alternative splicing are increased in tumor cells relative to normal cells, and these modifications can be observed in human tumor xenografts in vivo following exposure of animals to the drug. In addition, the change in the splicing pattern observed with the Sudemycins are similar to that observed with Spliceostatin A, a molecule known to interact with the SF3b subunit of the spliceosome. Hence, we conclude that Sudemycins can regulate the production of alternatively spliced RNA transcripts and these alterations are more prevalent in tumors, as compared to normal cells, following drug exposure. These studies suggest that modulation of alternative splicing may play a role in the antitumor activity of this class of agents.
Teflon is Hydrophilic. Comments on Definitions of Hydrophobic, Shear versus Tensile Hydrophobicity, and Wettability Characterization (2008)

Comments are made concerning the recent use of adjectives to describe solid surfaces that exhibit anomalously high water contact angle values. We suggest that the meaning of the word hydrophobic be resolved before it is modified, for example, to superhydrophobic and further modified, for example, to sticky superhydrophobic and before the definitions of these new words become issues of contention. The case is made that the first statement in the title is appropriate with experiments that demonstrate significant attractive interaction between liquid water and the surface of solid Teflon. Four types of experiments are described: the interaction of a silicon-supported covalently attached perfluoroalkyl monolayer (a model Teflon surface) with a sessile water drop (1) and with a thin film of water on a clean silicon wafer surface (2), the interaction of 1 and 12 microm diameter solid Teflon particles with a water droplet surface (3), and the interaction of a thin (<5 microm) Teflon film with a water droplet (4). The concepts of shear and tensile hydrophobicity are introduced, and the recommendation that two numbers, advancing and receding contact angle values, should be considered necessary data to characterize the wettability of a surface. That the words hydrophobic, hydrophilic, and their derivatives can and should only be considered qualitative or relative terms is emphasized.
Opaque-2 Is a Transcriptional Activator That Recognizes a Specific Target Site in 22-kD Zein Genes (1992)

Robert J. Schmidt, Mariena Ketudat, Milo J. Aukerman, Gisela Hoschek, Opaque-2 Is a Transcriptional Activator That Recognizes a Specific Target Site in 22-kD Zein Genes, The Plant Cell, Vol. 4, No. 6 (Jun., 1992), pp. 689-700
Preparation and electron transfer-induced cis-trans isomerization reactions of 1-(5-nitro-2-furyl)-, 1-(5-nitro-2-thienyl)-, and 1-(4-nitrophenyl)-2-R ethylenes (1989)

Mixtures of E - and Z -isomers of 1,2-bis(5-nitro-2-furyl)ethylene ( I ), 1-(5-nitro-2-furyl)-2-(4-nitrophenyl)ethylene ( II ), 1,2-bis(4-nitrophenyl)ethylene ( III ), 1-(5-methoxycarbonyl-2-furyl)-2-(4-nitrophenyl)ethylene ( IV ), 1-(5-methoxycarbonyl-2-furyl)-2-(5-nitro-2-furyl)ethylene ( V ) and 1-(5-methoxycarbonyl-2-furyl)-2-(5-nitro-2-thienyl)ethylene ( VI ) were prepared by the Wittig reaction. These derivatives were isomerized by electron transfer-induced reactions via the radical anion in the CT-complex using aniline as electron donor at 25 °C in the light or at 80 °C in the dark. The starting as well as the final E:Z ratio was determined by 1 H NMR spectroscopy. In all cases only the cis → trans isomerization was observed.
Improvement of Okara by fermentation with Bacillus subtilis (1998)

Okara (by-product of tofu manufacturing) was fermented by Bacillus subtilis in order to improve it as good taste and high processing characteristics as food stuff, and the morphological, physicochemical properties and composition of physical properties of okara fermented with B. subtilis (ON) were investigated. 1. After 24 hr of fermentation, the amount of free amino acids, free fatty acids, inorganic phosphorus increased and dietary fiber decreased as compared to the starting levels. In ON leucine and phenylalanine among free amino acids were the predominate, and in dietary fiber, the pectic substances increased, while hemi-cellulose decreased. 2. The temperature of ON increased rapidly with increasing CFU of B. subtilis in 5 to 10 hr of fermentation and rose up to 50°C at 15 hr. The hydrolysis ratio of proteins (formol nitrogen / total nitrogen × 100) increased with increasing protease activity. The ammonia content and pH value increased rapidly after 15 hr, and the pH value of ON at 30 hr was 8.2. 3. Scanning electron microscopic observation of ON at 24 hr revealed that the cell wall was completely disintegrated. The amount of particles less than 10 μm diameter increased with the further progress of fermentation. 4. The in vitro digestibility of protein in ON was similar to that in okara. The water absorption and oil absorption were also same in both okara. However, the emulsifying activity and emulsion stability were higher in ON than in okara.
New Methods in Automatic Extracting (1969)

This paper describes new methods of automatically extracting documents for screening purposes, i.e. the computer selection of sentences having the greatest potential for conveying to the reader the substance of the document. While previous work has focused on one component of sentence significance, namely, the presence of high-frequency content words (key words), the methods described here also treat three additional components: pragmatic words (cue words); title and heading words; and structural indicators (sentence location). The research has resulted in an operating system and a research methodology. The extracting system is parameterized to control and vary the influence of the above four components. The research methodology includes procedures for the compilation of the required dictionaries, the setting of the control parameters, and the comparative evaluation of the automatic extracts with manually produced extracts. The results indicate that the three newly proposed components dominate the frequency component in the production of better extracts.
Defects in Carbon Nanotubes (2002)

Carbon nanotubes are quasi one-dimensional nanostructures with unique eletrical prroperties that make them prime candidates for molecular electronics, which is certainly a most promising direction in nanotechnology. Early theoretical works predicted that the electronic properties of "ideal" carbon nanotubes depend on their diameter and chirality. However, carbon nanotubes are probably not as perfect as they were once thought to be. Defects such as pentagons, heptagons, vacancies, or dopant are found to modify drastically the electronic properties of these nanosystems. Irradiation processes can lead to interesting, highly defective nanostructures and also to the coalescence of nanotubes within a rope. The introduction of defects in the carbon network is thus an interesting way to tailor its intrinsic properties, to create new potential nanodevices. The aim of the present Acount is to investigate theoretically the effects of different types of defects on the electronic properties of carbon nanotubes, and to propose new potential applications in nanoelectronics.
Determination of Cellularly Processed HLA-A2402-Restricted Novel CTL Epitopes Derived from Two Cancer Germ Line Genes, MAGE-A4 and SAGE (2005)

Two novel HLA-A2402-restricted CTL epitopes, MAGE-A4(143-151) and SAGE(715-723), were identified. Our approach assisted by cellular machinery of both mice and human could be widely applicable to identify naturally processed CTL epitopes.
The Genome of Drosophila Melanogaster (1992)

Genes. Chromosomes: Deficiencies. Duplications. Inversions. Rings. Translocations. Transpositions. External Anatomy (figure). Normal Chromosome Complement. Special Chromosomes: Balancers. Compound Chromosomes. X-Y Combinations. Y Derivatives. Autosynaptic Chromosomes. Transposable Elements. Departures from Diploidy. Satellite Sequences. Nonchromosomal Inheritance. Cytogenetic Map.
Hyaluronate capsule prevents attachment of group A streptococci to mouse peritoneal macrophages (1981)

The antiphagocytic properties of the streptococcal hyaluronic acid capsule were explored in a system in which binding of the organism to the phagocyte, but not ingestion, could occur. The capsule was found to be highly effective in preventing attachment of two strains of group A streptococci to mouse peritoneal macrophages. Variation in attachment with phase of growth in broth culture (low in early log phase, high in late-log phase and thereafter) could be accounted for by production and subsequent loss of capsule. Hyaluronidase treatment removed the capsule and increased adherence; treatment with proteolytic enzymes removed M protein and decreased resistance to phagocytosis in whole human blood but did not remove the capsule or increase adherence to the mouse peritoneal macrophages.
Expression of Amino-Terminal Portions or Full-Length Viral Replicase Genes in Transgenic Plants Confers Resistance to Potato Virus X Infection (1992)

Carl J. Braun, Cynthia L. Hemenway, Expression of Amino-Terminal Portions or Full-Length Viral Replicase Genes in Transgenic Plants Confers Resistance to Potato Virus X Infection, The Plant Cell, Vol. 4, No. 6 (Jun., 1992), pp. 735-744
Environmental Iodine Intake Affects the Type of Nonmalignant Thyroid Disease (2001)

The relationship between the iodine intake level of a population and the occurrence of thyroid diseases is U-shaped with an increase in risk from both low and high iodine intakes. Developmental brain disorders and endemic goiter caused by severe iodine deficiency may seriously deteriorate overall health status and economic performance of a population. Severe iodine deficiency with a median 24-hour urinary iodine excretion of the population below 25 microg needs immediate attention and correction. Less severe iodine deficiency with median urinary iodine excretion below 120 microg per 24 hours is associated with multinodular autonomous growth and function of the thyroid gland leading to goiter and hyperthyroidism in middle aged and elderly subjects. The lower the iodine intake, the earlier and more prominent are the abnormalities. At the other end of the spectrum, severely excessive iodine intake starting at median urinary iodine excretion levels around 800 microg per 24 hours is associated with a higher prevalence of thyroid hypofunction and goiter in children. A number of studies indicate that moderate and mild iodine excess (median urinary iodine >220 microg per 24 hours) are associated with a more frequent occurrence of hypothyroidism, especially in elderly subjects. The exact mechanism leading to this has not been clarified, and more studies are needed to define the limits of excessive iodine intake precisely. Due to the frequent occurrence of thyroid disorders, proper monitoring and control of the population iodine intake level is a cost-effective alternative to diagnosing, therapy and control of the many individual cases of thyroid diseases that might have been prevented.
Adhesion in Candida spp (2002)

Microbial adherence is one of the most important determinants of pathogenesis, yet very few adhesins have been identified from fungal pathogens. Four structurally related adhesins, Hwp1, Ala1p/Als5p, Als1p, from Candida albicans and Epa1p from Candida glabrata, are members of a class of proteins termed glycosylphosphatidylinositol-dependent cell wall proteins (GPI-CWP). These proteins have N-terminal signal peptides and C-terminal features that mediate glycosylphosphatidylinositol (GPI) membrane anchor addition, as well as other determinants leading to attachment to cell wall glucan. While common signalP/GPI motifs facilitate cell surface expression, unique features mediate ligand binding specificities of adhesins. The first glimpse of structural features of putative adhesins has come from biophysical characterizations of the N-terminal domain of Als5p. One protein not in the GPI-CWP class that was initially described as an adhesin, Int1p, has recently been shown to be similar to Bud4p of Saccharomyces cerevisiae in primary amino acid sequence, in co-localizing with septins and in functioning in bud site selection. Progress in understanding the role of adhesins in oroesophageal candidiasis has been made for Hwp1 in a study using beige athymic and transgenic epsilon 26 mice that have combined defects in innate and acquired immune responses. Searches of the C. albicans genome for proteins in the GPI-CWP class has led to the identification of a subset of genes that will be the focus of future efforts to identify new Candida adhesins.
5′–3′ Exonucleases in phosphorothioate-based oligonucleotide-directed mutagenesis (1988)

The application of T7 and lambda exonuclease to phosphorothioate-based oligonucleotide-directed mutagenesis was investigated. Oligonucleotide primers designed to introduce single or double base mismatches, an insertion or a deletion (each of 16 bases) were annealed to M13 phage derivatives. Double stranded closed circular DNA (RF IV) containing phosphorothioate internucleotidic linkages in the (-)strand was prepared enzymatically from these templates. A nick was introduced into the (+)strand of the hetroduplex DNA. This nicked DNA (RF II) was subjected to treatment with T7 or lambda exonuclease. Both of these enzymes were able to degrade almost all of the viral (+)strand when presented with DNA containing one or two base mismatches. Repolymerisation of the DNA after the gapping reaction, followed by transfection into E. coli cells gave mutational efficiencies of up to 95%. In the case of RF II DNA prepared with insertion or deletion primers these exonucleases could only partially degrade the viral (+)strand but were nevertheless highly efficient in such mutagenesis experiments.
EL ENCUENTRO GENERACIONAL (1988)

ENEMIGO DE CLASE ES LA REPRESENTACION DEL CHOQUE GENERACIONAL EN UNA DE SUS MULTIPLES EXPRESIONES: LA LUCHA DE UN TIEMPO ENCONTRA DE OTRO TIEMPO, LA VIOLENCIA COMO RESPUESTA A LA SENSATEZ, LA BUSCA INICUA DEL SER ENFRENTADA A LO SOCIAL ESTABLECIDO, LA PELEA POR POSEER ALGO CONTRA LA NEGACION DEL PODER DEL SER, EL YO EN CONTRA DEL YO SOCIAL, LA DISPUTA POR LA EXISTENCIA ANTE EL VACIO ESPIRITUAL. ADAPTA AL ESPANOL, ENEMIGO DE CLASE, OBRA DE NIGEL WILLIAMS HA LEVANTADO LAS CRITICAS MAS CONTROVERTIDAS Y ESCANDALOSAS EN LONDRES, NUEVA YORK Y BERLIN.
Effects of crystallization conditions on sedimentation in canola oil (1994)

Abstract The effects of various factors on sediment formation in canola oil were studied. The crystallization temperature of sediment varied with cooling rate, whereas the melting temperature depended on heating rate as well as the cooling rate during sediment formation. The final crystal size depended on cooling rate. The crystal habit of sediment was generally rod‐like but could change to a round and leaf‐like shape at low cooling rates (&lt;0.5°C/min). Crystal nucleation occurred in the initial stage of crystallization, while crystal growth was observed during the whole crystallization process, decreasing as cooling proceeded. Crystal growth rate of the sediment was proportional to the crystal surface area Lecithin did not affect the phase transition temperatures of sediment, but retarded crystal growth.
Graph matching by relaxation of fuzzy assignments (2001)

Graphs are very powerful and widely used representational tools in computer applications. We present a relaxation approach to (sub)graph matching based on a fuzzy assignment matrix. The algorithm has a computational complexity of O(n/sup 2/m/sup 2/) where n and m are the number of nodes in the two graphs being matched, and can perform both exact and inexact matching. To illustrate the performance of the algorithm, we summarize the results obtained for more than 12 000 pairs of graphs of varying types (weighted graphs, attributed graphs, and noisy graphs). We also compare our results with those obtained using the graduated assignment algorithm.
DNA Methylation of Tumor Suppressor and Metastasis Suppressor Genes in Circulating Tumor Cells (2011)

DNA methylation of tumor suppressor and metastasis suppressor genes is a hallmark of CTCs and confirms their heterogeneity. Our findings add a new dimension to the molecular characterization of CTCs and may underlie the acquisition of malignant properties, including their stem-like phenotype.
Association between HER-2/ neu and Vascular Endothelial Growth Factor Expression Predicts Clinical Outcome in Primary Breast Cancer Patients (2004)

The positive association between HER-2/neu and VEGF expression implicates VEGF in the aggressive phenotype exhibited by HER-2/neu overexpression, and supports the use of combination therapies directed against both HER-2/neu and VEGF for treatment of breast cancers that overexpress HER-2/neu.
Distributed Garbage Collection for Network Objects (1993)

In this report we present a fault-tolerant and efficient algorithm for distributed garbage collection and prove its correctness. The algorithm is a generalization of reference counting; it maintains a set of identifiers for processes with references to an object. The set is maintained with pair-wise communication between processes, so no global synchronization is required. The primary cost for maintaining the set is one remote procedure call when an object reference is transferred to a new process for the first time. The distributed collector collaborates with the local collector in detecting garbage; any local collector may be used, so long as it can be extended to provide notification when an object is collected. In fact, the distributed collector could be used without a local collector; in that case, the programmer would insert explicit dispose commands to release an object. The algorithm was designed and implemented as part of the Modula-3 network objects system, but it should be s...
HR23b expression is a potential predictive biomarker for HDAC inhibitor treatment in mesenchymal tumours and is associated with response to vorinostat (2015)

Histone deacetylases (HDAC) are key players in epigenetic regulation of gene expression and HDAC inhibitor (HDACi) treatment seems to be a promising anticancer therapy in many human tumours, including soft tissue sarcomas. HR23b has been shown to be a potential biomarker for sensitivity to HDACi therapy in cutaneous T-cell lymphoma and hepatocellular carcinoma. We aimed to evaluate HR23b as a candidate biomarker for HDACi response in sarcomas and gastrointestinal stromal tumours (GIST). Therefore, HR23b expression was analysed comprehensively by western blot in sarcoma and GIST cell lines covering all major clinically relevant subtypes. MTT assay and ApoTox-Glo(TM) Triplex assay were performed after treatment with vorinostat, belinostat, mocetinostat and entinostat. HR23b protein expression was measured under HDACi treatment. Furthermore, HR23b expression levels were immunohistochemically determined in a large set of 523 clinical samples from sarcoma and GIST patients. Western blot analyses showed that sarcomas differ significantly in their expression of HR23b protein. All HDACi were able to regulate proliferation and apoptosis in vitro. Sensitivity to vorinostat correlated significantly with HR23b protein expression. Immunohistochemical prevalence screening in clinical samples of relevant adult-type tumours revealed that 12.5% of sarcomas (among them malignant peripheral nerve sheath tumours, pleomorphic liposarcomas, leiomyosarcomas, dedifferentiated liposarcomas, synovial sarcomas and angiosarcomas) and 23.2% of GIST show high HR23b expression. Therefore, HDACi have antiproliferative and proapoptotic effects in sarcomas depending on the expression level of HR23b. These findings suggest that HR23b represents a candidate biomarker for HDACi sensitivity in certain sarcoma types and in GIST.
Low-Dose Danazol for Vascular Access and Dialyzer Thrombosis in Hemodialysis Patients (1992)

Four hemodialysis patients (1 male and 3 females, aged 29-40 years) with unusual recurrent vascular access or dialyzer thrombosis were studied to find out whether a hypercoagulable state exists. Measurements of euglobulin clot lysis time (ELT), fibrinogen, antithrombin III (AT III), protein C (PC), protein S (PS), tissue plasminogen activator (tPA), and plasminogen activator inhibitor (PAI) were done. Results indicated that all patients had prolonged ELT, low tPA, elevated PAI, normal AT III, and PS. Three patients had elevated fibrinogen level and two had low PC. Danazol 200 mg orally once a day effectively prevented any further thrombosis. In 4 weeks' time, all the abnormal coagulation studies normalized in addition to elevation of AT III, PC and PS. Only 1 female patient had a prolonged menstrual period, which was reversed by lowering the daily dose of danazol to 100 mg. No other side effects were encountered. These data indicate that hypofibrinolysis may play a major role in vascular access or dialyzer thrombosis and that low-dose danazol may provide an effective prophylaxis and treatment. Larger controlled studies are needed to confirm these findings.