gebhart/patrepeval huggingface dataset:
Targeted mutagenesis of the human papillomavirus type 16 E2 transactivation domain reveals separable transcriptional activation and DNA replication functions (1996)

The E2 gene products of papillomavirus play key roles in viral replication, both as regulators of viral transcription and as auxiliary factors that act with E1 in viral DNA replication. We have carried out a detailed structure-function analysis of conserved amino acids within the N-terminal domain of the human papillomavirus type 16 (HPV16) E2 protein. These mutants were tested for their transcriptional activation activities as well as transient DNA replication and E1 binding activities. Analysis of the stably expressed mutants revealed that the transcriptional activation and replication activities of HPV16 E2 could be dissociated. The 173A mutant was defective for the transcriptional activation function but retained wild-type DNA replication activity, whereas the E39A mutant wild-type transcriptional activation function but was defective in transient DNA replication assays. The E39A mutant was also defective for HPV16 E1 binding in vitro, suggesting that the ability of E2 protein to form a complex with E1 appears to be essential for its function as an auxiliary replication factor.
Targeted rescue of a destabilized mutant of p53 by an in silico screened drug (2008)

The tumor suppressor p53 is mutationally inactivated in approximately 50% of human cancers. Approximately one-third of the mutations lower the melting temperature of the protein, leading to its rapid denaturation. Small molecules that bind to those mutants and stabilize them could be effective anticancer drugs. The mutation Y220C, which occurs in approximately 75,000 new cancer cases per annum, creates a surface cavity that destabilizes the protein by 4 kcal/mol, at a site that is not functional. We have designed a series of binding molecules from an in silico analysis of the crystal structure using virtual screening and rational drug design. One of them, a carbazole derivative (PhiKan083), binds to the cavity with a dissociation constant of approximately 150 muM. It raises the melting temperature of the mutant and slows down its rate of denaturation. We have solved the crystal structure of the protein-PhiKan083 complex at 1.5-A resolution. The structure implicates key interactions between the protein and ligand and conformational changes that occur on binding, which will provide a basis for lead optimization. The Y220C mutant is an excellent "druggable" target for developing and testing novel anticancer drugs based on protein stabilization. We point out some general principles in relationships between binding constants, raising of melting temperatures, and increase of protein half-lives by stabilizing ligands.
Local Intensity Order Pattern for feature description (2011)

This paper presents a novel method for feature description based on intensity order. Specifically, a Local Intensity Order Pattern(LIOP) is proposed to encode the local ordinal information of each pixel and the overall ordinal information is used to divide the local patch into subregions which are used for accumulating the LIOPs respectively. Therefore, both local and overall intensity ordinal information of the local patch are captured by the proposed LIOP descriptor so as to make it a highly discriminative descriptor. It is shown that the proposed descriptor is not only invariant to monotonic intensity changes and image rotation but also robust to many other geometric and photometric transformations such as viewpoint change, image blur and JEPG compression. The proposed descriptor has been evaluated on the standard Oxford dataset and four additional image pairs with complex illumination changes. The experimental results show that the proposed descriptor obtains a significant improvement over the existing state-of-the-art descriptors.
Partial purification, characterization and nitrogen regulation of the lysine ?-aminotransferase of Streptomyces clavuligerus (1997)

The L-lysine epsilon-aminotransferase (LAT) of Streptomyces clavuligerus was partially purified and characterized. The 51.3-kDa enzyme exhibited optimal activity at pH 7.0-7.5 and 30 degrees C. It catalyzed transfer of the terminal amino group of L-lysine or L-ornithine to alpha-ketoglutarate. Oxalacetate and pyruvate were also used as acceptors of the amino group but with very low efficiency. Increasing ammonium concentrations added to chemically-defined medium MM enhanced the formation of LAT and decreased production of cephalosporins by S. clavuligerus. In cultures grown in the absence of lysine, greater enhancement of LAT formation by ammonium and less repression of cephalosporin biosynthesis were observed. In the chemically-defined GSPG medium, ammonium ions decreased cephalosporin production without showing an effect on LAT formation.
Manufacturing processes in the textile industry. Expert Systems for fabrics production (2017)

The textile industry is characterized by the economic activity whose objective is the production of fibres, yarns, fabrics, clothing and textile goods for home and decoration, as well as technical and industrial purposes. Within manufacturing, the Textile is one of the oldest and most complex sectors which includes a large number of sub-sectors covering the entire production cycle, from raw materials and intermediate products, to the production of final products. Textile industry activities present different subdivisions,each with its own traits. The length of the textile process and the variety of its technicalprocesses lead to the coexistence of different sub-sectors in regards to their business structure and integration. The textile industry is developing expert systems applicationsto increase production, improve quality and reduce costs. The analysis of textile designs or structures includes the use of mathematical models to simulate the behavior of the textile structures (yarns, fabrics and knitting). The Finite Element Method (FEM) has largely facilitated the prediction of the behavior of that textile structure under mechanical loads. For classification problems Artificial Neural Networks (ANNs) have proved to be a very effective tool as a quick and accurate solution. The Case-Based Reasoning (CBR) method proposed in this study complements the results of the finite element simulation, mathematical modeling and neural networks methods.
Comparison of human blastulation rates and total cell number in sequential culture media with and without co-culture (1999)

Recent interest in delayed embryo transfers necessitated the evaluation of two improved in-vitro systems that could generate viable blastocysts. A total of 178 two-pronucleated embryos (entire cohorts) from 19 patients was cultured in IVF50 medium (100 microl) under oil for 24 h until day 2. Each patient's day 2 embryos were then equally allotted to two in-vitro systems. Embryos in system A were grown until the morning of day 3 on Vero cells covered with IVF50 medium (100 microl) under oil. The medium was then replaced on day 3 with a 1:1 mixture (100 microl) of IVF50:S2 medium and on day 4 with S2 medium only. The same culture protocol was used for system B without Vero cells. Throughout the 5 days all dishes were housed in sealed humidified modular chambers containing a triple gas atmosphere. Separately, 175 spare embryos from 80 patients were grown in system A and B up to days 6 and 7 for total cell number (TCN) analysis. Blastulation rates were not significantly different between system A and B (67.4 versus 68.5%; P > 0.01) although co-cultured embryos cleaved slightly faster by day 4. The overall pregnancy and implantation rates were 52.0% and 32.1% for the 19 patients each of whom received a mixed cohort of three day 5 embryos from both systems. TCN values for the day 6 and 7 blastocysts from both systems were high and increased steadily from days 6-7 and from expanded to hatching stages. There were no significant differences in TCN for day 6 expanded blastocysts between the two systems although day 6 hatching and hatched co-cultured blastocysts had greater values than non-co-cultured blastocysts (246.0 +/- 18.5 and 236.7 +/- 17.8 versus 173.0 +/- 13.5 and 166.5 +/- 16.0; P < 0.01). The results demonstrated that the culture protocol using the sequential IVF50-S2 media combination was a good substitute for Vero cell co-culture for the transfer of viable day 3-6 embryos.
Single dose oral oxycodone and oxycodone plus paracetamol (acetaminophen) for acute postoperative pain in adults (2009)

Single dose oxycodone is an effective analgesic in acute postoperative pain at doses over 5 mg; oxycodone is two to three times stronger than codeine. Efficacy increases when combined with paracetamol. Oxycodone 10 mg plus paracetamol 650 mg provides good analgesia to half of those treated, comparable to commonly used non-steroidal anti-inflammatory drugs, with the benefit of longer duration of action.
Comparison of the Volatile Constituents in Cold-Pressed Bergamot Oil and a Volatile Oil Isolated by Vacuum Distillation (2007)

The vacuum distillation of bergamot peels furnishes a high-quality essential oil that is totally bergapten-free. This oil was compared with that produced by distillation of cold-pressed oils and those commercially available. The oil obtained by vacuum distillation of the bergamot vegetable matrix shows a composition quite similar to that of the cold-pressed oil. It also displays qualitative characteristics that are superior with respect to those normally observed for essential oils isolated by distillation of cold-pressed oils. Oils isolated by the method presented here can constitute ideal candidates in producing foods, for example, Earl Grey tea, and cosmetic preparations.
Denosumab versus zoledronic acid to prevent aromatase inhibitors-associated fractures in postmenopausal early breast cancer; a mixed treatment meta-analysis (2016)

This analysis demonstrated that in postmenopausal patients receiving adjuvant aromatase inhibitors, immediate denosumab decreases the risk of fractures compared to delayed treatment at the cutoff of 36 months. Immediate zoledronic acid, however, does not provide the same level of fractures' protection in this category of patients.
Assessment of glycosaminoglycan concentration in vivo by chemical exchange-dependent saturation transfer (gagCEST) (2008)

Glycosaminogycans (GAGs) are involved in numerous vital functions in the human body. Mapping the GAG concentration in vivo is desirable for the diagnosis and monitoring of a number of diseases such as osteoarthritis, which affects millions of individuals. GAG loss in cartilage is typically an initiating event in osteoarthritis. Another widespread pathology related to GAG is intervertebral disk degeneration. Currently existing techniques for GAG monitoring, such as delayed gadolinium-enhanced MRI contrast (dGEMRIC), T(1)(rho), and (23)Na MRI, have some practical limitations. We show that by exploiting the exchangeable protons of GAG one may directly measure the localized GAG concentration in vivo with high sensitivity and therefore obtain a powerful diagnostic MRI method.
CYFIP2 is highly abundant in CD4+ cells from multiple sclerosis patients and is involved in T cell adhesion (2004)

DNA microarray profiling of CD4(+) and CD8(+) cells from non-treated relapsing and remitting multiple sclerosis (MS) patients determined that the cytoplasmic binding partner of fragile X protein (CYFIP2, also called PIR121) was increased significantly compared to healthy controls. Western analysis confirmed that CYFIP2 protein was increased approximately fourfold in CD4(+) cells from MS compared to inflammatory bowel disorder (IBD) patients or healthy controls. Because CYFIP2 acts as part of a tetrameric complex that regulates WAVE1 activation we hypothesized that high levels of CYFIP2 facilitate T cell adhesion, which is elevated in MS patients. Several findings indicated that increased levels of CYFIP2 facilitated adhesion. First, adenoviral-mediated overexpression of CYFIP2 in Jurkat cells increased fibronectin-mediated adhesion. Secondly, CYFIP2 knock-down experiments using antisense oligodeoxynucleotides reduced fibronectin-mediated binding in Jurkat and CD4(+) cells. Thirdly, inhibition of Rac-1, a physical partner with CYFIP2 and regulator of WAVE1 activity, reduced fibronectin-mediated adhesion in Jurkat and CD4(+) cells. Finally, inhibition of Rac-1 or reduction of CYFIP2 protein decreased fibronectin-mediated adhesion in CD4(+) cells from MS patients to levels similar to controls. These studies suggest that overabundance of CYFIP2 protein facilitates increased adhesion properties of T cells from MS patients.
The European Union and Serials Publishing: Impact and Influence (1996)

Serials: The Journal for the Serials Community has been digitised and can be accessed in full on this website. All content is freely available on an open-access basis. Serials was published between 1988 and 2011. In 2012, the journal was retitled and is now published as Insights: the UKSG journal.
Combining geothermal energy capture with geologic carbon dioxide sequestration (2011)

[1] Geothermal energy offers clean, renewable, reliable electric power with no need for grid-scale energy storage, yet its use has been constrained to the few locations worldwide with naturally high geothermal heat resources and groundwater availability. We present a novel approach with the potential to permit expansion of geothermal energy utilization: heat extraction from naturally porous, permeable formations with CO2 as the injected subsurface working fluid. Fluid-mechanical simulations reveal that the significantly higher mobility of CO2, compared to water, at the temperature/pressure conditions of interest makes CO2 an attractive heat exchange fluid. We show numerically that, compared to conventional water-based and engineered geothermal systems, the proposed approach provides up to factors of 2.9 and 5.0, respectively, higher geothermal heat energy extraction rates. Consequently, more regions worldwide could be economically used for geothermal electricity production. Furthermore, as the injected CO2 is eventually geologically sequestered, such power plants would have negative carbon footprints.
Internet CNN NEWSROOM: a digital video news magazine and library (2002)

The paper discusses the development of CNN NEWSROOM on the Internet, a new multimedia news magazine based on CNN NEWSROOM, an educational news program produced by Turner Broadcasting and distributed by cable television operators nationwide. The multimedia program is assembled automatically on a daily basis as a digital video news magazine distributed via the Internet. High quality 1.5 Mbit/second MPEG-I video is used in the program, giving the video clips VHS level quality. Potential advantages of Internet NEWSROOM are outlined, and innovative plans for its network deployment are discussed.
Diversity of Vertebrate Splicing Factor U2AF35 (2004)

U2 small nuclear ribonucleoprotein auxiliary factor small subunit (U2AF(35)) is encoded by a conserved gene designated U2AF1. Here we provide evidence for the existence of alternative vertebrate transcripts encoding different U2AF(35) isoforms. Three mRNA isoforms (termed U2AF(35)a-c) were produced by alternative splicing of the human U2AF1 gene. U2AF(35)c contains a premature stop codon that targets the resulting mRNA to nonsense-mediated mRNA decay. U2AF(35)b differs from the previously described U2AF(35)a isoform in 7 amino acids located at the atypical RNA Recognition Motif involved in dimerization with U2AF(65). Biochemical experiments indicate that isoform U2AF(35)b, which has been highly conserved from fish to man, maintains the ability to interact with U2AF(65), stimulates U2AF(65) binding to a pre-mRNA, and promotes U2AF splicing activity in vitro. Real time, quantitative PCR analysis indicates that U2AF(35)a is the most abundant isoform expressed in murine tissues, although the ratio between U2AF(35)a and U2AF(35)b varies from 10-fold in the brain to 20-fold in skeletal muscle. We propose that post-transcriptional regulation of U2AF1 gene expression may provide a mechanism by which the relative cellular concentration and availability of U2AF(35) protein isoforms are modulated, thus contributing to the finely tuned control of splicing events in different tissues.
A Genome-Wide Analysis of FRT-Like Sequences in the Human Genome (2011)

Efficient and precise genome manipulations can be achieved by the Flp/FRT system of site-specific DNA recombination. Applications of this system are limited, however, to cases when target sites for Flp recombinase, FRT sites, are pre-introduced into a genome locale of interest. To expand use of the Flp/FRT system in genome engineering, variants of Flp recombinase can be evolved to recognize pre-existing genomic sequences that resemble FRT and thus can serve as recombination sites. To understand the distribution and sequence properties of genomic FRT-like sites, we performed a genome-wide analysis of FRT-like sites in the human genome using the experimentally-derived parameters. Out of 642,151 identified FRT-like sequences, 581,157 sequences were unique and 12,452 sequences had at least one exact duplicate. Duplicated FRT-like sequences are located mostly within LINE1, but also within LTRs of endogenous retroviruses, Alu repeats and other repetitive DNA sequences. The unique FRT-like sequences were classified based on the number of matches to FRT within the first four proximal bases pairs of the Flp binding elements of FRT and the nature of mismatched base pairs in the same region. The data obtained will be useful for the emerging field of genome engineering.
Expression profiling of metalloproteinases and their inhibitors in cartilage (2004)

This is the first comprehensive expression profile of all known MMP, ADAMTS, and TIMP genes in cartilage. Elucidation of patterns of expression provides a foundation with which to understand mechanisms of gene regulation in OA and potentially to refine the specificity of antiproteolytic therapies.
Why drugs fail: of mice and men revisited. (2001)

Of the large number of promising anticancer agents entering into clinical testing, only a disappointingly small number ultimately assume a place in the armamentarium of the practicing oncologist as clinically useful therapies. Thus, despite the obligatory requirement for showing promising activity
Seamless integration of image and molecular analysis for spatial transcriptomics workflows (2020)

STUtility lets the user process, analyze and visualize multiple samples of spatially resolved RNA sequencing and image data from the 10x Genomics Visium platform. The package builds on the Seurat framework and uses familiar APIs and well-proven analysis methods. An introduction to the software package is available at https://ludvigla.github.io/STUtility_web_site/ .
Fibrinopeptide A and platelet factor levels in unstable angina pectoris. (1987)

Fibrinopeptide A, platelet factor 4, beta-thromboglobulin, thromboxane B2, and 6-keto-prostaglandin F1 alpha were estimated by radioimmunoassay on venous plasma samples taken within 48 hr of admission from 16 consecutive patients with unstable angina and 15 patients with stable angina matched for clinical variables. The ratio of circulating platelet aggregates, platelet aggregation to increasing concentrations of ADP (0.455 to 1.82 micrograms/ml), and platelet thromboxane B2 production in vitro were also tested. The two groups of patients were statistically similar in terms of sex distribution, age, presence of risk factors, use of medication, extent of coronary artery disease and history of previous myocardial infarction. Mean plasma levels of fibrinopeptide A were 2.7 +/- 0.4 ng/ml (geometric means +/- SEM, range 1.5 to 5.5) in patients with stable angina vs 5.5 +/- 1.8 ng/ml (range 2.4 to 32; p less than .001) in those with unstable angina. In the latter group, after 6 to 8 days, fibrinopeptide A levels decreased to 3.6 +/- 0.5 ng/ml (range 1.5 to 9.3; p less than .04 vs admission). All other variables measured were statistically identical in the two groups. We conclude that plasma fibrinopeptide A levels, as opposed to platelet factors, discriminate between patients with unstable and stable angina, indicating an activation of the coagulation system in unstable angina.
Temporary closure of open abdominal wounds: the vacuum pack. (1995)

Temporary closure of abdominal surgical wounds is occasionally required when conditions of the abdominal wall or peritoneal cavity prevent closure or when early re-exploration is planned. The optimal temporary closure should contain and protect the contents of the peritoneal cavity from external contamination and injury; preserve the integrity of the abdominal wall; be simple to perform and maintain; provide ease of reentry; and have minimal adverse physiologic effects. Based on these criteria, a method of temporary abdominal wound closure (termed the vacuum pack) has been designed and evaluated. The operative technique includes 1) placement of a fenestrated polyethylene sheet between the abdominal viscera and anterior parietal peritoneum; 2) placement of a moist, sterile laparotomy towel over the polyethylene sheet; 3) placement of two closed suction drains over the towel; 4) placement of an adhesive backed drape over the entire wound, including a wide margin of surrounding skin; and 5) suction applied to the drains, creating a vacuum and rigid compression of the layers of closure material. This creates a tight, external seal of the adhesive backed drape and facilitates drainage of the peritoneal cavity. From April 1992-December 1993, this temporary abdominal wound closure was performed 56 times in 28 patients, ages 6-78 years, for periods of 1-11 days. The procedure was used in 17 trauma patients and 11 non-trauma patients. Indications for use included increased intra-abdominal pressure in nine, mandatory re-exploration in 10, and a combination of these indications in nine patients. Pre- and postprocedural airway and systemic blood pressures were unaffected by this closure.(ABSTRACT TRUNCATED AT 250 WORDS)
A complementary palette of fluorescent silver nanoclusters (2010)

We report the synthesis and photophysical properties of silver-nanoclusters templated on DNA, with fluorescence excitation and emission at distinct wavelengths that are tuned to common laser excitation wavelengths.
Class II Aminoacyl Transfer Rna Synthetases: Crystal Structure of Yeast Aspartyl-trna Synthetase Complexed with tRNA Asp (1991)

The crystal structure of the binary complex tRNA(Asp)-aspartyl tRNA synthetase from yeast was solved with the use of multiple isomorphous replacement to 3 angstrom resolution. The dimeric synthetase, a member of class II aminoacyl tRNA synthetases (aaRS's) exhibits the characteristic signature motifs conserved in eight aaRS's. These three sequence motifs are contained in the catalytic site domain, built around an antiparallel beta sheet, and flanked by three alpha helices that form the pocket in which adenosine triphosphate (ATP) and the CCA end of tRNA bind. The tRNA(Asp) molecule approaches the synthetase from the variable loop side. The two major contact areas are with the acceptor end and the anticodon stem and loop. In both sites the protein interacts with the tRNA from the major groove side. The correlation between aaRS class II and the initial site of aminoacylation at 3'-OH can be explained by the structure. The molecular association leads to the following features: (i) the backbone of the GCCA single-stranded portion of the acceptor end exhibits a regular helical conformation; (ii) the loop between residues 320 and 342 in motif 2 interacts with the acceptor stem in the major groove and is in contact with the discriminator base G and the first base pair UA; and (iii) the anticodon loop undergoes a large conformational change in order to bind the protein. The conformation of the tRNA molecule in the complex is dictated more by the interaction with the protein than by its own sequence.