gebhart/patrepeval huggingface dataset:
Extensive Mutagenesis of a Transcriptional Activation Domain Identifies Single Hydrophobic and Acidic Amino Acids Important for Activation In Vivo (1997)

C1 is a transcriptional activator of genes encoding biosynthetic enzymes of the maize anthocyanin pigment pathway. C1 has an amino terminus homologous to Myb DNA-binding domains and an acidic carboxyl terminus that is a transcriptional activation domain in maize and yeast cells. To identify amino acids critical for transcriptional activation, an extensive random mutagenesis of the C1 carboxyl terminus was done. The C1 activation domain is remarkably tolerant of amino acid substitutions, as changes at 34 residues had little or no effect on transcriptional activity. These changes include introduction of helix-incompatible amino acids throughout the C1 activation domain and alteration of most single acidic amino acids, suggesting that a previously postulated amphipathic alpha-helix is not required for activation. Substitutions at two positions revealed amino acids important for transcriptional activation. Replacement of leucine 253 with a proline or glutamine resulted in approximately 10% of wild-type transcriptional activation. Leucine 253 is in a region of C1 in which several hydrophobic residues align with residues important for transcriptional activation by the herpes simplex virus VP16 protein. However, changes at all other hydrophobic residues in C1 indicate that none are critical for C1 transcriptional activation. The other important amino acid in C1 is aspartate 262, as a change to valine resulted in only 24% of wild-type transcriptional activation. Comparison of our C1 results with those from VP16 reveal substantial differences in which amino acids are required for transcriptional activation in vivo by these two acidic activation domains.
Marker Rescue of Adeno-Associated Virus (AAV) Capsid Mutants: a Novel Approach for Chimeric AAV Production (2002)

Marker rescue, the restoration of gene function by replacement of a defective gene with a normal one by recombination, has been utilized to produce novel adeno-associated virus (AAV) vectors. AAV serotype 2 (AAV2) clones containing wild-type terminal repeats, an intact rep gene, and a mutated cap gene, served as the template for marker rescue. When transfected alone in 293 cells, these AAV2 mutant plasmids produced noninfectious AAV virions that could not bind heparin sulfate after infection with adenovirus dl309 helper virus. However, the mutation in the cap gene was corrected after cotransfection with AAV serotype 3 (AAV3) capsid DNA fragments, resulting in the production of AAV2/AAV3 chimeric viruses. The cap genes from several independent marker rescue experiments were PCR amplified, cloned, and then sequenced. Sequencing results confirmed not only that homologous recombination occurred but, more importantly, that a mixed population of AAV chimeras carrying 16 to 2,200 bp throughout different regions of the type 3 cap gene were generated in a single marker rescue experiment. A 100% correlation was observed between infectivity and the ability of the chimeric virus to bind heparin sulfate. In addition, many of the AAV2/AAV3 chimeras examined exhibited differences at both the nucleotide and amino acid levels, suggesting that these chimeras may also exhibit unique infectious properties. Furthermore, AAV helper plasmids containing these chimeric cap genes were able to function in the triple transfection method to generate recombinant AAV. Together, the results suggest that DNA from other AAV serotypes can rescue AAV capsid mutants and that marker rescue may be a powerful, yet simple, technique to map, as well as develop, chimeric AAV capsids that display different serotype-specific properties.
Language Modeling with Gated Convolutional Networks (2016)

The pre-dominant approach to language modeling to date is based on recurrent neural networks. Their success on this task is often linked to their ability to capture unbounded context. In this paper we develop a finite context approach through stacked convolutions, which can be more efficient since they allow parallelization over sequential tokens. We propose a novel simplified gating mechanism that outperforms Oord et al (2016) and investigate the impact of key architectural decisions. The proposed approach achieves state-of-the-art on the WikiText-103 benchmark, even though it features long-term dependencies, as well as competitive results on the Google Billion Words benchmark. Our model reduces the latency to score a sentence by an order of magnitude compared to a recurrent baseline. To our knowledge, this is the first time a non-recurrent approach is competitive with strong recurrent models on these large scale language tasks.
Bactericidal Activities of Two Daptomycin Regimens against Clinical Strains of Glycopeptide Intermediate-Resistant Staphylococcus aureus , Vancomycin-Resistant Enterococcus faecium , and Methicillin-Resistant Staphylococcus aureus Isolates in an In Vitro Pharmacodynamic Model with Simulated Endocardial Vegetations (2001)

Daptomycin is an investigational lipopeptide antibiotic active against gram-positive organisms. The mechanism of action is unique, resulting in interference with cell membrane transport. The bactericidal activity of daptomycin was evaluated against glycopeptide-intermediate susceptible Staphylococcus aureus (GISA), vancomycin-resistant Enterococcus faecium (VREF), and methicillin-resistant S. aureus (MRSA) in an in vitro infection model with simulated endocardial vegetations. Simulated regimens of daptomycin at 6 mg/kg/day (D6) and 10 mg/kg/day (D10) were utilized. MICs and MBCs for daptomycin were determined in the absence and in the presence of albumin with the following results (MIC/MBC): for GISA-992, 0.5/1.0 and 16/16; for VREF-590, 2.0/2.0 and 32/32; and for MRSA-494, 0.25/0.25 and 1.0/4.0 microg/ml, respectively. During the first 8 h daptomycin significantly reduced the inoculum for all organisms. Daptomycin at 6 mg/kg/day and 10 mg/kg/day had log(10) CFU/g reductions of 5 and 6, 3.4 and 5, and 6.4 and 6.5 by 8 h for GISA-992, VREF-590, and MRSA-494, respectively. Against both GISA-992 and VREF-590, the D10 regimen achieved the limit of detection at 72 h, with D6 regimens showing slight regrowth. A concentration-dependent killing effect was noted to occur, with daptomycin demonstrating a more rapid and greater kill from the D10 versus the D6 regimen. The results of this study suggest that daptomycin demonstrates significant (P < 0.05) activity against gram-positive organisms in a simulated sequestered infection site.
Kinetics and Strain Specificity of Rhizosphere and Endophytic Colonization by Enteric Bacteria on Seedlings of Medicago sativa and Medicago truncatula (2003)

The presence of human-pathogenic, enteric bacteria on the surface and in the interior of raw produce is a significant health concern. Several aspects of the biology of the interaction between these bacteria and alfalfa (Medicago sativa) seedlings are addressed here. A collection of enteric bacteria associated with alfalfa sprout contaminations, along with Escherichia coli K-12, Salmonella enterica serotype Typhimurium strain ATCC 14028, and an endophyte of maize, Klebsiella pneumoniae 342, were labeled with green fluorescent protein, and their abilities to colonize the rhizosphere and the interior of the plant were compared. These strains differed widely in their endophytic colonization abilities, with K. pneumoniae 342 and E. coli K-12 being the best and worst colonizers, respectively. The abilities of the pathogens were between those of K. pneumoniae 342 and E. coli K-12. All Salmonella bacteria colonized the interiors of the seedlings in high numbers with an inoculum of 10(2) CFU, although infection characteristics were different for each strain. For most strains, a strong correlation between endophytic colonization and rhizosphere colonization was observed. These results show significant strain specificity for plant entry by these strains. Significant colonization of lateral root cracks was observed, suggesting that this may be the site of entry into the plant for these bacteria. At low inoculum levels, a symbiosis mutant of Medicago truncatula, dmi1, was colonized in higher numbers on the rhizosphere and in the interior by a Salmonella endophyte than was the wild-type host. Endophytic entry of M. truncatula appears to occur by a mechanism independent of the symbiotic infections by Sinorhizobium meliloti or mycorrhizal fungi.
GIT Physicochemical Modeling - A Critical Review (2006)

Many attempts to model the human gastrointestinal tract (GIT) were made since the beginning of the last decade. The main purpose was either to simulate an in vivo testing of drugs on animals or to investigate the viability of the probiotic intake. Two well-known physio-chemical models regarding the viability of the probiotics have been produced. In 1993, Molly et al. developed a simulator of the human intestinal microbial ecosystem (SHIME). Six reactors simulating the conditions of human stomach, duodenum/jejunum, ileum, caecum/ascending colon, transverse colon and descending colon were artificially developed. In 1995, Minekus et al. created a TNO gastro-intestinal model (TIM) with four computer-controlled chambers simulating the conditions of stomach, duodenum, jejunum and ileum. The simulated parameters included the body temperature, pH, salivary, gastric and intestinal mixing with peristaltic movements, secretions and absorption of water and small molecules. Despite the use of pharmacological, physiological and biochemical knowledge of the human and animal GIT and associated secretions, conflicting results such as the extremely low viability of probiotics were obtained. The failure of the above two models indicates the necessity of devising a suitable in vitro model that would be capable of simulating the digestion process as an exact replica of the actual in vivo model. In this paper, the key aspects of the above have been summarized and discussed.
Elevated membrane-type matrix metalloproteinases in gliomas revealed by profiling proteases and inhibitors in human cancer cells. (2003)

Matrix metalloproteinases (MMPs) and tissue inhibitors of metalloproteinases (TIMPs) regulate proteolysis of the extracellular matrix and other extracellular proteins, including growth factors and their receptors. The aberrant expression of these genes is common in most cancers. We profiled the RNA levels of every human MMP and TIMP in a variety of cell types (fibroblast, endothelial, hematopoietic, carcinoma, melanoma, and glioma) using quantitative PCR, with the aim of identifying novel expression patterns. Almost all members of the membrane-type (MT-) MMP and TIMP families were elevated in glioma lines compared to carcinomas. In clinical glioma specimens, there were positive correlations between glioma grade and RNA levels of MT-1, MT-2, and MT-6 MMP, TIMP-1 and TIMP-2, and for several growth factors and receptors. These findings suggest that advanced malignant gliomas have elevated levels of membrane-associated MMPs and TIMPs, which may potentially regulate vascularization and invasion. Concurrent elevation of signaling molecules suggests potential bidirectional relationships that enhance tumor aggressiveness.
Germinação de sementes e desenvolvimento inicial de plântulas de achachairu (2008)

O achachairu (Garcinia sp), fruta largamente produzida na Bolívia, vem sendo comercializado no Brasil há vários anos. O fruto é globoso-oblongo, de polpa branca, suculenta e textura mucilaginosa e de sabor doce-acidulado equilibrado (ºBrix 15 e pH 4,1). Devido ao crescente interesse em seu cultivo no Brasil, pesquisaram-se a germinação das sementes e o desenvolvimento das plântulas durante os primeiros 12 meses após sua emergência. As sementes, extraídas de frutos bem maduros, foram postas a germinar em duas situações: 1) ambiente controlado em estufa tipo B.O.D., sob as temperaturas de 25 e 30 ºC, fotoperíodo de 16 horas e irradiância de 32 µmol.m-1.s-1, e 2) ambiente de temperatura não-controlada: 3) B.O.D, cuja temperatura oscilava entre 20 e 30 ºC, e 4) sob temperatura ambiente de laboratório (25± 2 ºC). O melhor resultado foi obtido na temperatura constante de 30 ºC, com germinação de 92% e índice de velocidade de germinação (IVG) de 0,255. Quando germinada em ambiente de laboratório, a germinação das sementes mostrou-se baixa (30%), com IVG de 0,015. O desenvolvimento das plântulas em casa de vegetação ocorreu de forma bastante lenta, principalmente nas primeiras semanas após a emergência. O primeiro par de folhas surgiu após três semanas da emergência das plântulas, quando essas mediam 8 cm em média. A partir do oitavo mês de desenvolvimento, as plântulas emitiram várias ramificações laterais a partir da porção mediana para a região apical.
Inhibition of High Affinity Basic Fibroblast Growth Factor Binding by Oligonucleotides (1995)

Oligonucleotides can be used to inhibit the binding of basic fibroblast growth factor to cells. Though standard phosphodiester oligonucleotides show a slight inhibition of binding, the oligonucleotides with phosphorothioate internucleoside linkages have inhibition levels equivalent to that of the polyanion heparin. Variations in sequence of the oligonucleotides does lead to differences in the inhibitory action of the oligonucleotides. This inhibition of basic fibroblast growth factor by phosphorothioate oligonucleotides may account for much of the published data on inhibition of various genes by proposed antisense oligonucleotides and needs to be taken into account when considering the mechanism of action of oligonucleotides in biological systems.
Positron emission tomography for predicting recurrence in stage I lung adenocarcinoma: standardized uptake value corrected by mean liver standardized uptake value (2011)

The SUV index is a significantly predictive and reproducible factor for recurrence in pathological stage I lung cancers. Patients with an SUV index <1.0 were more likely to have a good prognosis. Additional multi-institutional studies are needed to confirm these study results.
Electronic Commerce: Technical, Business, and Legal Issues (1998)

1. Introduction. Overview. EC Statistics. Objectives of EC. Requirements and Services. 2. EC Components. Electronic Data Interchange. Digital Currency. Electronic Catalogs. Intranets and Extranets. 3. EC in Business. The Business Case. Business Uses of Electronic Commerce. Business Models and Business Functions. Industrial Applications. EC Use within Government. 4. Technical Issues for Electronic Commerce. Telecommunication Infrastructure. Decision Support Systems for EC. Interoperability. Storage and Retrieval of Multimedia Information. Workflow Management. Markup Languages. 5. Security for Electronic Commerce. Functions and Requirements. Security Management and Business Controls. User Perceptions and Trust. Security Technologies. The Cryptography Debate. Legal Validity of Digital Signatures. 6. Legal Frameworks: Policy & Regulatory Issues for Electronic Commerce. Intellectual Property. Legal Issues for Electronic Payment Systems. Contractual and Legal Settlements. Regulatory Framework for Electronic Commerce. 7. Conclusions and Future Directions. Interoperability. Automated Interactions. Information Overload. Mobile Computing. Multimedia Information. Matchmaking Services. Economic, Social, and Cultural Issues. References. Index.
<title>Fabrication and testing of microchannel heat exchangers</title> (1995)

Micro-channel heat-exchanger test articles were fabricated and performance tested. The heat exchangers are being developed for innovative applications, and have been shown to be capable of handling heat loads of up to 100 W/cm<SUP>2</SUP>. The test articles were fabricated to represent two different designs for the micro-channel portion of the heat exchanger. One design consists of 166 micro-channels etched in silicon substrate, and a second design consists of 54 micro-channels machined in copper substrate. The devices were tested in an experimental loop designed for performance testing in single- and two-phase flow with water and R124. Pressure and liquid subcooling can be regulated over the range of interest, and a secondary heat removal loop provides stable loop performance for steady-state tests. The selected operating pressures are approximately 0.344 MPa for distilled water and 0.689 MPa for R124. The temperature ranges are 15.5 to 138 C for distilled water and 15.5 to 46 C for R-124. The mass flow range 7.6 X 10<SUP>-8</SUP> to 7.6 X 10<SUP>MIN5</SUP> kg/min for both distilled water and R124.
Morphology of Saccharum-Sorghum Hybrid Derivatives (1978)

The intergeneric hybrid between sugarcane (Saccharum sp.) and sorghum (Sorghum bicolor (L.) Moench.) was produced by pollinating sugarcane inflorescences of clone F 36-819 (2n = ca. 112) with diploid (2n = 20) ‘Rex’ sorghum pollen. The backcross four (BC4) population, produced by back-crossing twice with diploid and then twice more with tetraploid (2n = 40) ‘Rio’ sorghum, combined 40 Sorghum and 4-10 Saccharum chromosomes. Different BC4 individuals were morphologically distinct within and between chromosome complexes, indicating that their genomes must comprise different combinations of Sorghum and Saccharum chromosomes. Selfing for one or more generations results in almost complete elimination of Saccharum chromosomes and morphologically modified sorghums are recovered. Modified sorghums have various combinations of Saccharum characteristics superimposed on a basic Sorghum morphology. The presence of Saccharum characters in some of the recovered sorghums with 2n = 40 chromosomes indicates the potential for a gene transfer from sugarcane to sorghum.
ChemInform Abstract: Self‐Assembly of Single Electron Transistors and Related Devices (1998)

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.
Construction of a Cytomegalovirus-Based Amplicon: A Vector with a Unique Transfer Capacity (2003)

Cytomegalovirus (CMV) has a number of interesting properties that qualifies it as a vector for gene transfer. Especially appealing is the ability of the CMV genome to persist in hematopoietic progenitor cells and the packaging capacity of the viral capsid that accommodates a DNA genome of 230 kbp. In order to exploit the packaging capacity of the CMV capsid we investigated whether the principles of an amplicon vector can be applied to CMV. Amplicons are herpesviral vectors, which contain only the cis-active sequences required for replication and packaging of the vector genome. For construction of a CMV amplicon the sequences comprising the lytic origin of replication (orilyt) and the cleavage packaging recognition sites (pac) of human CMV were cloned onto a plasmid. A gene encoding the green fluorescent protein was used as a model transgene. The amplicon plasmid replicated in the presence of a CMV helper virus and was packaged into CMV particles, with replication and packaging being dependent on the presence of the orilyt and pac sequences. The packaged amplicon could be transferred to recipient cells and reisolated from the transduced cells. Analysis of the DNA isolated from CMV capsids revealed that the CMV amplicon was packaged as a concatemer with a size of approximately 210 kbp. The CMV amplicon vector has the potential to transfer therapeutic genes with a size of more than 200 kbp and thus provides a unique transfer capacity among viral vectors.
Evaluation of 4-(2-Hydroxyethyl)-1-piperazineethanesulfonic Acid (HEPES) as a Tissue Culture Buffer (1969)

The amino acid 4-(2-hydroxyethyl)-1-piperazineëthanesulfonic acid (HEPES) has been evaluated as a tissue culture buffer. HEPES has a molecular weight of 238.3, a pKa2 of 7.31 at 37°, a δpK/° of —0.014, exhibits no metal binding and is soluble to the extent of 2.25 M at 0°. HEPES (0.01 M) produced adequate buffering in all cell systems tested. HEPES was not toxic to primary monkey kidney, chick embryo fibro-blasts or puppy salivary gland cells, human embryonic lung, BHK-21/4, BS-C-1, Detroit 6-YT, GPS. HEp-2 KB, LM, MA-134, or RK-13 cells. The GPS cells were grown in suspension in HEPES and NaHCO3 buffered media. Although the population doubling times were not significantly different, a higher maximum cell density and viability were seen in the HEPES buffered system. HEPES had a minimal effect on the oxidation-reduction potential of well-poised media. HEPES had no effect on rubella virus titrations or on hemagglutination assays of polyoma or Sendai virus. The formulation of a HEPES buffered salt solution is presented.
Reduction of Soluble Aβ and Tau, but Not Soluble Aβ Alone, Ameliorates Cognitive Decline in Transgenic Mice with Plaques and Tangles (2006)

Increasing evidence points to soluble assemblies of aggregating proteins as a major mediator of neuronal and synaptic dysfunction. In Alzheimer disease (AD), soluble amyloid-beta (Abeta) appears to be a key factor in inducing synaptic and cognitive abnormalities. Here we report the novel finding that soluble tau also plays a role in the cognitive decline in the presence of concomitant Abeta pathology. We describe improved cognitive function following a reduction in both soluble Abeta and tau levels after active or passive immunization in advanced aged 3xTg-AD mice that contain both amyloid plaques and neurofibrillary tangles (NFTs). Notably, reducing soluble Abeta alone did not improve the cognitive phenotype in mice with plaques and NFTs. Our results show that Abeta immunotherapy reduces soluble tau and ameliorates behavioral deficit in old transgenic mice.
Transfer-Printing of Highly Aligned DNA Nanowires (2003)

We developed a simple method of reproducibly creating highly aligned DNA nanowires without any surface modifications or special equipment. Stretched DNA molecules initially present on the PDMS sheet were transferred onto another surface using transfer-printing (TP). Fluorescent microscopic and atomic force microscopic images revealed that many DNA molecules were highly aligned on surfaces after TP. Furthermore, it was also possible to realize the two-dimensional assembly of DNA nanowires by repeating TP.
Oligomerization of .alpha.-olefins to higher oligomers (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleOligomerization of .alpha.-olefins to higher oligomersJadwiga. SkupinskaCite this: Chem. Rev. 1991, 91, 4, 613–648Publication Date (Print):June 1, 1991Publication History Published online1 May 2002Published inissue 1 June 1991https://pubs.acs.org/doi/10.1021/cr00004a007https://doi.org/10.1021/cr00004a007research-articleACS PublicationsRequest reuse permissionsArticle Views3985Altmetric-Citations517LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts