gebhart/patrepeval huggingface dataset:
Genetic evidence for an interaction between SIR3 and histone H4 in the repression of the silent mating loci in Saccharomyces cerevisiae. (1990)

Repression of transcription from the silent mating loci (HML alpha and HMRa) is essential for mating ability in Saccharomyces cerevisiae. This silencing is known to require at least five proteins (SIR1, SIR2, SIR3, SIR4, and histone H4) and is accompanied by a change in chromatin structure. We show here that four positions of histone H4 (N-terminal residues 16, 17, 18, and 19) are crucial to silencing. HML alpha and HMRa are efficiently repressed when these positions are occupied by basic amino acids but are derepressed when substituted with glycine. These results suggest that acetylation of Lys-16 would lead to derepression of the silent mating loci. Three strong extragenic suppressors of the latter H4 mutations were isolated and determined to be located in SIR3. These suppressors allow high mating efficiencies in cells expressing either wild-type H4 or H4 containing single amino acid substitutions. They did not allow efficient mating in a strain that contained an H4 N-terminal deletion. These results indicate that the SIR3 mutations do not bypass the requirement for the H4 N terminus but, rather, allow repression in the presence of a less than optimal H4 N terminus. This provides a link between one of the SIR proteins and a component of chromatin.
Laser desorption mass spectrometry for DNA analysis and sequencing (1995)

Laser desorption mass spectrometry has been considered as a potential new method for fast DNA sequencing. Our approach is to use matrix-assisted laser desorption to produce parent ions of DNA segments and a time-of-flight mass spectrometer to identify the sizes of DNA segments. Thus, the approach is similar to gel electrophoresis sequencing using Sanger's enzymatic method. However, gel, radioactive tagging, and dye labeling are not required. In addition, the sequencing process can possibly be finished within a few hundred microseconds instead of hours and days. In order to use mass spectrometry for fast DNA sequencing, the following three criteria need to be satisfied. They are (1) detection of large DNA segments, (2) sensitivity reaching the femtomole region, and (3) mass resolution good enough to separate DNA segments of a single nucleotide difference. It has been very difficult to detect large DNA segments by mass spectrometry before due to the fragile chemical properties of DNA and low detection sensitivity of DNA ions. We discovered several new matrices to increase the production of DNA ions. By innovative design of a mass spectrometer, we can increase the ion energy up to 45 KeV to enhance the detection sensitivity. Recently, we succeeded in detecting a DNA segment with 500 nucleotides. The sensitivity was 100 femtomole. Thus, we have fulfilled two key criteria for using mass spectrometry for fast DNA sequencing. The major effort in the near future is to improve the resolution. Different approaches are being pursued. When high resolution of mass spectrometry can be achieved and automation of sample preparation is developed, the sequencing speed to reach 500 megabases per year can be feasible.
<title>MPEG (moving pictures expert group) video compression algorithm: a review</title> (1991)

A video coding technique aimed at compression of video and its associated audio at about 1.5 Mbits/s has been developed by the Moving Pictures Expert Group (MPEG-Video). The Moving Pictures Expert Group is part of the ISO-IEC JTC1/SC2/WG11, an organization responsible for the standardization of coded representation of video and audio for information systems. The video compression technique developed by MPEG covers many applications from interactive systems on CD-ROM to delivery of video information over telecommunications networks. The MPEG video compression algorithm relies on two basic techniques: block based motion compensation for the reduction of the temporal redundancy and transform domain based compression for the reduction of spatial redundancy. Motion compensation techniques are applied with both predictive and interpolative techniques. The prediction error signal is further compressed with spatial redundancy reduction (DCT). The quality of the compressed video with the MPEG algorithm at about 1.5 Mbits/s has been compared to that of consumer grade VCR's. The quality, cost and features of the MPEG video algorithm make it directly applicable to personal computers and workstation thus allowing the development of many new applications integrating video, sound, images, text and graphics.
HybridPointing (2006)

We present HybridPointing, a technique that lets users easily switch between absolute and relative pointing with a direct input device such as a pen. Our design includes a new graphical element, the Trailing Widget, which remains "close at hand" but does not interfere with normal cursor operation. The use of visual feedback to aid the user's understanding of input state is discussed, and several novel visual aids are presented. An experiment conducted on a large, wall-sized display validates the benefits of HybridPointing under certain conditions. We also discuss other situations in which HybridPointing may be useful. Finally, we present an extension to our technique that allows for switching between absolute and relative input in the middle of a single drag-operation.
High pressure synchrotron x-ray powder diffraction study of Sc2Mo3O12and Al2W3O12 (2005)

Synchrotron x-ray powder diffraction was used to study Sc2Mo3O12 and Al2W3O12 at high pressure in a DAC. Both compounds adopt the orthorhombic Sc2W3O12 structure under ambient conditions and exhibit anisotropic negative thermal expansion. A phase transition from orthorhombic (Pnca) to monoclinic (P 21/a) symmetry was observed at ~0.25 GPa for Sc2Mo3O12 and at ~0.1 GPa for Al2W3O12 associated with a volume reduction of ~1.5–2%. A second crystalline to crystalline phase transition was clearly seen only for Sc2Mo3O12 (2.5–3.0 GPa). Peak broadening and almost complete amorphization were observed for Sc2Mo3O12 at ~8 GPa, and this was not fully reversible on decompression. At 7 GPa, the amorphization of Al2W3O12 was not as advanced as for the molybdate and on decompression crystalline material was recovered. The compressibility of orthorhombic Sc2Mo3O12 is highly anisotropic, but it is almost isotropic for both monoclinic Sc2Mo3O12 and Al2W3O12. Both compounds show a reduction in their bulk moduli (K0) at the orthorhombic to monoclinic transition: 32(2) GPa for orthorhombic and 16(1) GPa for monoclinic Sc2Mo3O12, and 48 GPa for orthorhombic and 28(1) GPa for monoclinic Al2W3O12. Sc2Mo3O12 displays very similar high pressure behaviour to the previously studied Sc2W3O12.
A New Approach to Cross-Bifix-Free Sets (2012)

Cross-bifix-free sets are sets of words such that no prefix of any word is a suffix of any other word. In this paper, we introduce a general constructive method for the sets of cross-bifix-free binary words of fixed length. It enables us to determine a cross-bifix-free words subset which has the property to be non-expandable.
Conservation of genome content and virulence determinants among clinical and environmental isolates of Pseudomonas aeruginosa (2003)

Pseudomonas aeruginosa is a ubiquitous environmental bacterium capable of causing a variety of life-threatening human infections. The genetic basis for preferential infection of certain immunocompromised patients or individuals with cystic fibrosis by P. aeruginosa is not understood. To establish whether variation in the genomic repertoire of P. aeruginosa strains can be associated with a particular type of infection, we used a whole-genome DNA microarray to determine the genome content of 18 strains isolated from the most common human infections and environmental sources. A remarkable conservation of genes including those encoding nearly all known virulence factors was observed. Phylogenetic analysis of strain-specific genes revealed no correlation between genome content and infection type. Clusters of strain-specific genes in the P. aeruginosa genome, termed variable segments, appear to be preferential sites for the integration of novel genetic material. A specialized cloning vector was developed for capture and analysis of these genomic segments. With this capture system a site associated with the strain-specific ExoU cytotoxin-encoding gene was interrogated and an 80-kb genomic island carrying exoU was identified. These studies demonstrate that P. aeruginosa strains possess a highly conserved genome that encodes genes important for survival in numerous environments and allows it to cause a variety of human infections. The acquisition of novel genetic material, such as the exoU genomic island, through horizontal gene transfer may enhance colonization and survival in different host environments.
Critical Role of Cyclin D1 Nuclear Import in Cardiomyocyte Proliferation (2003)

Mammalian cardiomyocytes irreversibly lose their capacity to proliferate soon after birth, yet the underlying mechanisms have been unclear. Cyclin D1 and its partner, cyclin-dependent kinase 4 (CDK4), are important for promoting the G1-to-S phase progression via phosphorylation of the retinoblastoma (Rb) protein. Mitogenic stimulation induces hypertrophic cell growth and upregulates expression of cyclin D1 in postmitotic cardiomyocytes. In the present study, we show that, in neonatal rat cardiomyocytes, D-type cyclins and CDK4 were predominantly cytoplasmic, whereas Rb remained in an underphosphorylated state. Ectopically expressed cyclin D1 localized in the nucleus of fetal but not neonatal cardiomyocytes. To target cyclin D1 to the nucleus efficiently, we constructed a variant of cyclin D1 (D1NLS), which directly linked to nuclear localization signals (NLSs). Coinfection of recombinant adenoviruses expressing D1NLS and CDK4 induced Rb phosphorylation and CDK2 kinase activity. Furthermore, D1NLS/CDK4 was sufficient to promote the reentry into the cell cycle, leading to cell division. The number of cardiomyocytes coinfected with these viruses increased 3-fold 5 days after infection. Finally, D1NLS/CDK4 promoted cell cycle reentry of cardiomyocytes in adult hearts injected with these viruses, evaluated by the expression of Ki-67, which is expressed in proliferating cells in all phases of the cell cycle, and BrdU incorporation. Thus, postmitotic cardiomyocytes have the potential to proliferate provided that cyclin D1/CDK4 accumulate in the nucleus, and the prevention of their nuclear import plays a critical role as a physical barrier to prevent cardiomyocyte proliferation. Our results provide new insights into the development of therapeutics strategies to induce regeneration of cardiomyocytes. The full text of this article is available at http://www.circresaha.org.
Focusing and Scanning through Flexible Multimode Fibers without Access to the Distal End (2015)

Multimode fibers (MMFs) are attractive ultra-thin replacements for state-of-the-art endoscopes, but the phase randomization in propagation through MMFs poses a major hurdle for imaging and focusing of light. Recently, this challenge has been addressed by pre-measuring the compensation for the fiber's complex input-output modes relations. Unfortunately, the sensitivity of this approach to fiber bending and temperature variations renders it inappropriate for many applications. Here, we demonstrate a truly endoscopic robust method for controlled in-situ focusing and scanning through a flexible uncharacterized MMF, whereby all the instrumentation is situated at the proximal end. We show that in graded-index (GRIN) fibers, light patterns at the proximal end allow retrieving information about the distal light distribution. We utilize these properties and two-photon fluorescence for robust controlled focusing through bended GRIN fibers. Our results carry potential for lensless two-photon micro-endoscopy.
Extended Lymph Node Dissection for Gastric Cancer: Who May Benefit? Final Results of the Randomized Dutch Gastric Cancer Group Trial (2004)

Overall, extended lymph node dissection as defined in this study generated no long-term survival benefit. The associated higher postoperative mortality offsets its long-term effect in survival. For patients with N2 disease an extended lymph node dissection may offer cure, but it remains difficult to identify patients who have N2 disease. Morbidity and mortality are greatly influenced by the extent of lymph node dissection, pancreatectomy, splenectomy and age. Extended lymph node dissections may be of benefit if morbidity and mortality can be avoided.
Electrochemical and Photoelectrochemical Investigation of Single-Crystal Anatase (1996)

Single crystals of TiO2 anatase containing 0.22% of Al and traces of V, Zr, Nb, and La were grown by chemical transport reactions employing TeCl4 as the transporting agent. Electrodes having the (101) face exposed doped by reduction with hydrogen were employed. The electrochemical and photoelectrochemical behavior of a single crystal of anatase were scrutinized for the first time. Properties were compared to those of single-crystal rutile having the (001) face exposed. Impedance analysis established that the flatband potential of anatase (101) is shifted negatively by 0.2 V with regards to that of rutile (001). Interfacial capacitance measurements under forward bias indicate smaller density of surface states on anatase. Photoelectrochemical oxidation of water occurs on both rutile and anatase with incident photon-to-current conversion efficiencies close to unity at λ = 300 nm. From the comparison of Ufb and Eg, it follows that anatase (101) and rutile (001) electrodes differ mainly in the position of the conduction band edge. The complete photoelectrolysis of water to H2 and O2 is thermodynamically possible on anatase only. Photosensitized electron injection from adsorbed cis-Ru[L2(SCN)2] (L = 2,2‘-bipyridyl-4,4‘-dicarboxylic acid) proceeds with similar efficiency on both types of electrodes. However, light-induced charge separation on the single-crystal electrodes is about three times less efficient compared with nanoscopic anatase films. Anatase (101) is strikingly more active for electrochemical insertion of Li+ than rutile (001). The diffusion coefficients for Li+ insertion and extraction were estimated to be 2 × 10-13 and 6 × 10-13 cm2/s, respectively.
Hydrogen Sulfide Prolongs Postharvest Shelf Life of Strawberry and Plays an Antioxidative Role in Fruits (2012)

Accumulating evidence shows that hydrogen sulfide (H(2)S) plays various physiological roles in plants, such as seed germination, root organogenesis, abiotic stress tolerance, and senescence of cut flowers. However, whether H(2)S participates in the regulation of ripening and senescence in postharvest fruits remains unknown. In the present study, the effect of H(2)S on postharvest shelf life and antioxidant metabolism in strawberry fruits was investigated. Fumigation with H(2)S gas released from the H(2)S donor NaHS prolonged postharvest shelf life of strawberry fruits in a dose-dependent manner. Strawberry fruits fumigated with various concentrations of H(2)S sustained significantly lower rot index, higher fruit firmness, and kept lower respiration intensity and polygalacturonase activities than controls. Further investigation showed that H(2)S treatment maintained higher activities of catalase, guaiacol peroxidase, ascorbate peroxidase, and glutathione reductase and lower activities of lipoxygenase relative to untreated controls. H(2)S also reduced malondialdehyde, hydrogen peroxide, and superoxide anion to levels below control fruits during storage. Moreover, H(2)S treatment maintained higher contents of reducing sugars, soluble proteins, free amino acid, and endogenous H(2)S in fruits. We interpret these data as indicating that H(2)S plays an antioxidative role in prolonging postharvest shelf life of strawberry fruits.
Highly Efficient Arylation of Malonates with Diaryliodonium Salts (1999)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTHighly Efficient Arylation of Malonates with Diaryliodonium SaltsChang Ho Oh, Joo Sung Kim, and Hyung Hoon JungView Author Information Department of Chemistry, Hanyang University, Haengdang-17 Sungdong-Gu, Seoul 133-791, Korea Cite this: J. Org. Chem. 1999, 64, 4, 1338–1340Publication Date (Web):February 4, 1999Publication History Received3 June 1998Published online4 February 1999Published inissue 1 February 1999https://pubs.acs.org/doi/10.1021/jo981065bhttps://doi.org/10.1021/jo981065bbrief-reportACS PublicationsCopyright © 1999 American Chemical SocietyRequest reuse permissionsArticle Views3215Altmetric-Citations98LEARN 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 SUBJECTS:Arylation,Chemical reactions,Enolates,Ethyl groups,Salts Get e-Alerts
Covalent Attachment of TAT Peptides and Thiolated Alkyl Molecules on GaAs Surfaces (2005)

Four TAT peptide fragments were used to functionalize GaAs surfaces by adsorption from solution. In addition, two well-studied alkylthiols, mercaptohexadecanoic acid (MHA) and 1-octadecanethiol (ODT) were utilized as references to understand the structure of the TAT peptide monolayer on GaAs. The different sequences of TAT peptides were employed in recognition experiments where a synthetic RNA sequence was tested to verify the specific interaction with the TAT peptide. The modified GaAs surfaces were characterized by atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), and Fourier transform infrared reflection absorption spectroscopy (FT-IRRAS). AFM studies were used to compare the surface roughness before and after functionalization. XPS allowed us to characterize the chemical composition of the GaAs surface and conclude that the monolayers composed of different sequences of peptides have similar surface chemistries. Finally, FT-IRRAS experiments enabled us to deduce that the TAT peptide monolayers have a fairly ordered and densely packed alkyl chain structure. The recognition experiments showed preferred interaction of the RNA sequence toward peptides with high arginine content.
Comparison of Intramuscular Dexmedetomidine and Midazolam Premedication for Elective Abdominal Hysterectomy (1994)

The purpose of this study was to compare the perioperative effects of the intramuscular (i.m.) alpha 2 agonist, dexmedetomidine (DEX), and midazolam (MID) premedication. The study comprised 192 women (64 per group) scheduled for abdominal hysterectomy. The doses of the study drugs were chosen to obtain equal sedative effects. The three groups were: 1) i.m. DEX (2.5 micrograms/kg) and intravenous (i.v.) placebo (DexPla group), 2) i.m. DEX and i.v. fentanyl (FENT) (1.5 micrograms/kg) (DexFent group), and 3) i.m. MID (0.08 mg/kg) and i.v. FENT (MidFent group). I.m. drugs were administered 45-90 min before induction of anesthesia. Preoperative sedation and anxiolysis after DEX was comparable to that after MID. The maximum arterial blood pressure response to endotracheal intubation was blunted in the DexFent group, while in the two other groups blood pressure increased 30-34 mm Hg after endotracheal intubation. The mean isoflurane concentration during surgery was 0.14% in the DexFent group, 0.24% in the DexPla group, and 0.34% in the MidFent group (P < 0.001). During surgery, bradycardia (heart rate < 40 bpm) was observed in 6.2% of DEX patients, and no MID patients, whereas postoperatively 14.1% of DEX patients and 1.6% of MID patients had bradycardia. Fewer patients suffered from postoperative shivering after DEX (10%) than after MID (52%). We conclude that DEX has many desirable effects, but side effects such as bradycardia may limit its routine use in ASA physical status I-II patients.
How Bacteria Assemble Flagella (2003)

The bacterial flagellum is both a motor organelle and a protein export/assembly apparatus. It extends from the cytoplasm to the cell exterior. All the protein subunits of the external elements have to be exported. Export employs a type III pathway, also utilized for secretion of virulence factors. Six of the components of the export apparatus are integral membrane proteins and are believed to be located within the flagellar basal body. Three others are soluble: the ATPase that drives export, a regulator of the ATPase, and a general chaperone. Exported substrates diffuse down a narrow channel in the growing structure and assemble at the distal end, often with the help of a capping structure.
Amyloid β Protein (Aβ) in Alzheimeri's Disease Brain (1995)

Biochemical and immunocytochemical analyses were performed to evaluate the composition of the amyloid beta protein (A beta) deposited in the brains of patients with Alzheimer's disease (AD). To quantitate all A beta s present, cerebral cortex was homogenized in 70% formic acid, and the supernatant was analyzed by sandwich enzyme-linked immunoabsorbent assays specific for various forms of A beta. In 9 of 27 AD brains examined, there was minimal congophilic angiopathy and virtually all A beta (96%) ended at A beta 42(43). The other 18 AD brains contained increasing amounts of A beta ending at A beta 40. From this set, 6 brains with substantial congophilic angiopathy were separately analyzed. In these brains, the amount of A beta ending at A beta 42(43) was much the same as in brains with minimal congophilic angiopathy, but a large amount of A beta ending at A beta 40 (76% of total A beta) was also present. Immunocytochemical analysis with monoclonal antibodies selective for A beta s ending at A beta 42(43) or A beta 40 confirmed that, in brains with minimal congophilic angiopathy, virtually all A beta is A beta ending at A beta 42(43) and showed that this A beta is deposited in senile plaques of all types. In the remaining AD brains, A beta 42(43) was deposited in a similar fashion in plaques, but, in addition, widely varying amounts of A beta ending at A beta 40 were deposited, primarily in blood vessel walls, where some A beta ending at A beta 42(43) was also present. These observations indicate that A beta s ending at A beta 42(43), which are a minor component of the A beta in human cerebrospinal fluid and plasma, are critically important in AD where they deposit selectively in plaques of all kinds.
Efficient synthesis of double dye-labeled oligodeoxyribonucleotide probes and their application in a real time PCR assay (1998)

A fast cleaving non-nucleosidic tetramethylrhodamine dye-labeled support has been developed for automated synthesis of double dye-labeled oligodeoxyribonucleotides in high yield. A mixture (1:1:2) of t-butylamine:methanol:water is used for cleavage and deprotection of dye-labeled oligodeoxyribonucleotides without any degradation or modification of dyes and nucleobases. The cleavage rate of oligodeoxyribonucleotides is significantly increased by using a diglycolate ester linkage instead of the commonly used succinate linkage. These double dye-labeled probes are used in PCR for real time detection of a specific PCR product. Using a 5'-exonuclease assay, detected on the ABI PRISM 7700 Sequence Detection System, there was no distinguishable difference in performance of probes synthesized using the dye-labeled support compared with traditional post-synthetic attachment of rhodamine.