gebhart/patrepeval huggingface dataset:
Characterization of RNA in Cytologic Samples Preserved in a Methanol-Based Collection Solution. (1998)

Background: ThinPrep is a fluid-based technique for collection and processing of cytologic specimens. The present study was designed to determine whether the collection solution preserved RNA for molecular analysis. Methods and Results: Cervical cancer cell lines and cord blood lymphocytes were used to test the efficacy of various protocols for fixation, storage, and extraction of RNA. Total RNA was extracted and analyzed by denaturing gel electrophoresis. Preserved cells stored for 24 hours at room temperature or 4 degreesC had intact 28S and 18S ribosomal RNA. Both cellular and viral messenger RNAs were amplified from preserved samples by reverse transcription polymerase chain reaction (RT-PCR). Viral messenger RNA (mRNA) could be detected in a mixture of preserved cells containing 10% human papillomavirus (HPV) positive cells. RNA preservation in clinical samples was adequate for RT-PCR of cellular mRNA. Conclusions: Both experimental samples and clinical samples collected in the preservation media had intact total RNA. Amplification of both cellular and HPV ad mRNA was sucessful.
Synthesis of Optically Active Polyamides Having Axially Dissymmetric 1,1′-Binaphthalene-2,2′-dicarboxylic Acid Component and Their Optical Resolution Ability as Chiral Adsorbent for HPLC (1991)

Abstract Optically active polyamides 4a–4c were synthesized from the polycondensation of axially dissymmetric 1,1′-binaphthalene-2,2′-dicarbonyl dichloride (2) with 1,4-benzenediamine, 1,6-hexanediamine, and 1,10-decanediamine, respectively. CD spectra of the polyamides 4a–4c are essentially the same as those of the corresponding model diamides 6a–6c prepared from 2 and benzenamine, 1-hexanamine, and 1-decanamine, respectively. This similarity indicates that the conformation of the 1,1′-binaphthalene-2,2′-dicarboxamide moieties of the polyamides 4a–4c in solution state are rather similar to those of the corresponding model diamides 6a–6c. Several axially chiral biaryl compounds and 3,5-dinitrophenylcarbamates (3,5-DNPCs) derived from 1-aryl-1-alkanols were resolved by HPLC equipped with the columns packed the chiral stationary phases (CSPs) prepared from 4a–4c adsorbed on spherical silica gel. A main control factor for the chiral discrimination seems to be the hydrogen bonding between the amide groups of the CSPs and the hydrogen-bonding sites of the atropisomeric biaryls. The donor–acceptor interaction between the binaphthalene moiety of the CSPs and the 3,5-dinitrobenzene moiety of the 3,5-DNPCs may also be important for the chiral discrimination of the 3,5-DNPCs.
Synthesis of Enantiomerically Pure D- and L-Armentomycin and Its Difluoro Analogues from Aspartic Acid (1996)

The synthesis of both enantiomers of 2-amino-4,4-dichlorobutanoic acid (armentomycin) and their fluoro analogues from aspartic acid via 2-amino-4-oxobutanoic acid protected with hexafluoroacetone is described.
Oxidation energies of transition metal oxides within theGGA+Uframework (2006)

The energy of a large number of oxidation reactions of $3d$ transition metal oxides is computed using the generalized gradient approach (GGA) and $\mathrm{GGA}+\mathrm{U}$ methods. Two substantial contributions to the error in GGA oxidation energies are identified. The first contribution originates from the overbinding of GGA in the ${\mathrm{O}}_{2}$ molecule and only occurs when the oxidant is ${\mathrm{O}}_{2}$. The second error occurs in all oxidation reactions and is related to the correlation error in $3d$ orbitals in GGA. Strong self-interaction in GGA systematically penalizes a reduced state (with more $d$ electrons) over an oxidized state, resulting in an overestimation of oxidation energies. The constant error in the oxidation energy from the ${\mathrm{O}}_{2}$ binding error can be corrected by fitting the formation enthalpy of simple nontransition metal oxides. Removal of the ${\mathrm{O}}_{2}$ binding error makes it possible to address the correlation effects in $3d$ transition metal oxides with the $\mathrm{GGA}+\mathrm{U}$ method. Calculated oxidation energies agree well with experimental data for reasonable and consistent values of U.
Finite Element Modeling of Piezoelectric Ultrasonic Transducers (2011)

The optimization of piezoelectric ultrasonic transducers has tradisionally been done through trial and error, somewhat guided by one-dimentional simulations. This can often be a very time-consuming and expensive process, hence a more extensive simulation method is desired.A series of finite element models of piezoelectric ultrasonic transducer has been made in COMSOL Multiphysics. The initial models were designed to emulate the conditions assumed in a one-dimentional transducer model, and their validity could thus be confirmed by said model. Later models did not emulate these conditions, and a lossless model of a spherical disc with backing and a single matching layer was successfully implemented. Attemps had been made to include mechanical loss in the initial models, but was only partially achieved. All loss was thus excluded from later models. A final model with a piezoelectric layer poled in the radial direction was not successfully designed, as the varying poling direction proved to be difficult to implement.
Present status of the FIREX programme for the demonstration of ignition and burn (2006)

The recent fast heating of a compressed core to 0.8–1 keV temperature as well as the previous high-density compression of 600 times liquid density have provided proof-of-principle of the fast ignition (FI) concept. These results have significantly contributed to official approval of the first phase of the FI realization experiment (FIREX) project. The goal of FIREX-I is to demonstrate fast heating of a fusion fuel up to the ignition temperature of 5–10 keV. Although the fuel of FIREX-I is too small to be actually ignited, sufficient heating will provide the scientific viability of ignition and burn by increasing the laser energy, thereby increasing the fuel size. The FIREX programme is being carried out in collaboration with the Institute of Laser Engineering, Osaka University and the National Institute for Fusion Science, including the development of cryogenic targets, holistic simulation systems and diagnostic equipment.
Treatment of severe heart failure: quantity or quality of life? A trial of enoximone. Enoximone Investigators. (1994)

OBJECTIVES--To determine the effects of enoximone on mortality and quality of life in patients with severe end stage heart failure. DESIGN--A randomised, double blind, placebo controlled trial of the addition of enoximone to conventional treatment. Planned minimum follow up of one year. SETTING--District general hospitals and cardiological referral centres in the United Kingdom. PATIENTS--Planned 200 patients with severe, symptomatic heart failure despite treatment with diuretics and where appropriate and tolerated angiotensin converting enzyme inhibitors and digoxin. RESULTS--The study was ended early by the ethics committee after 151 patients had been recruited because of an excess mortality in the enoximone group: 27 deaths compared with 18 in the placebo group (P &lt; 0.05). Quality of life measured with a disease specific questionnaire showed a clinically significant improvement at week 2 with a mean increase score of 0.48 in the enoximone treated patients compared with 0.14 in those receiving placebo (P = 0.0086). With the Nottingham health profile questionnaire the physical mobility score was improved after three months in the enoximone group, median 21.3 compared with 41.8 in the placebo group (P = 0.008). CONCLUSIONS--In patients with severe heart failure who remain incapacitated despite conventional treatment enoximone reduced survival but had a beneficial effect on the quality of life. Drugs that improve symptoms in severe end stage heart failure should not be discarded lightly.
Porphyrins and phthalocyanines in solar photovoltaic cells (2010)

This review summarizes recent advances in the use of porphyrins, phthalocyanines, and related compounds as components of solar cells, including organic molecular solar cells, polymer cells, anddye-sensitized solar cells. The recent report of a porphyrin dye that achieves 11% power conversion efficiency in a dye-sensitized solar cell indicates that these classes of compounds can be as efficient as the more commonly used ruthenium bipyridyl derivatives.
Polyoxometalates: from inorganic chemistry to materials science (2004)

Polyoxometalates have been traditionally the subject of study of molecular inorganic chemistry. Yet, these polynuclear molecules, reminiscent of oxide clusters, present a wide range of structures and with them ideal frameworks for the deployment of a plethora of useful magnetic, electroionic, catalytic, bioactive and photochemical properties. With this in mind, a new trend towards the application of these remarkable species in materials science is beginning to develop. In this review we analyze this trend and discuss two main lines of thought for the application of polyoxometalates as materials. On the one hand, there is their use as clusters with inherently useful properties on themselves, a line which has produced fundamental studies of their magnetic, electronic or photoelectrochemical properties and has shown these clusters as models for quantum-sized oxides. On the other hand, the encapsulation or integration of polyoxometalates into organic, polymeric or inorganic matrices or substrates opens a whole new field within the area of hybrid materials for harnessing the multifunctional properties of these versatile species in a wide variety of applications, ranging from catalysis to energy storage to biomedicine.
Predicting the Functional Effect of Amino Acid Substitutions and Indels (2012)

As next-generation sequencing projects generate massive genome-wide sequence variation data, bioinformatics tools are being developed to provide computational predictions on the functional effects of sequence variations and narrow down the search of casual variants for disease phenotypes. Different classes of sequence variations at the nucleotide level are involved in human diseases, including substitutions, insertions, deletions, frameshifts, and non-sense mutations. Frameshifts and non-sense mutations are likely to cause a negative effect on protein function. Existing prediction tools primarily focus on studying the deleterious effects of single amino acid substitutions through examining amino acid conservation at the position of interest among related sequences, an approach that is not directly applicable to insertions or deletions. Here, we introduce a versatile alignment-based score as a new metric to predict the damaging effects of variations not limited to single amino acid substitutions but also in-frame insertions, deletions, and multiple amino acid substitutions. This alignment-based score measures the change in sequence similarity of a query sequence to a protein sequence homolog before and after the introduction of an amino acid variation to the query sequence. Our results showed that the scoring scheme performs well in separating disease-associated variants (n = 21,662) from common polymorphisms (n = 37,022) for UniProt human protein variations, and also in separating deleterious variants (n = 15,179) from neutral variants (n = 17,891) for UniProt non-human protein variations. In our approach, the area under the receiver operating characteristic curve (AUC) for the human and non-human protein variation datasets is ∼0.85. We also observed that the alignment-based score correlates with the deleteriousness of a sequence variation. In summary, we have developed a new algorithm, PROVEAN (Protein Variation Effect Analyzer), which provides a generalized approach to predict the functional effects of protein sequence variations including single or multiple amino acid substitutions, and in-frame insertions and deletions. The PROVEAN tool is available online at http://provean.jcvi.org.
Interaction of the Corepressor Alien with DAX-1 Is Abrogated by Mutations of DAX-1 Involved in Adrenal Hypoplasia Congenita (2000)

DAX-1 is an unusual member of the nuclear hormone receptor (NHR) superfamily. Lack of DAX-1-mediated silencing leads to adrenal hypoplasia congenita and hypogonadotropic hypogonadism. Gene silencing through NHRs such as the thyroid hormone receptor (TR) is mediated by corepressors. We have previously characterized a novel corepressor, termed Alien, which interacts with TR and the ecdysone receptor but not with the retinoic acid receptors RAR or RXR. Here, we show that DAX-1 interacts with the corepressor Alien but not with the corepressor SMRT. This interaction is mediated by the DAX-1-silencing domain. Naturally occurring mutants of the DAX-1 gene fail to interact with Alien and have lost silencing function. Because the silencing domain of DAX-1 is unusual for NHRs, we mapped the interaction of Alien with DAX-1 and with TR. We show that Alien exhibits different binding characteristics to DAX-1 and TR. Furthermore, Northern experiments demonstrate that Alien is expressed in the adrenal gland and testis in tissues where DAX-1 is specifically expressed. Interestingly, a novel adrenal gland-specific mRNA of Alien was discovered. Thus, the impairment of Alien binding seems to play an important role in the pathogenesis mediated by DAX-1 mutants.
Protection against lethal polymicrobial sepsis by CNI-1493, an inhibitor of pro-inflammatory cytokine synthesis (1997)

Polymicrobial sepsis caused by cecal ligation and puncture (CLP) in mice produces the inflammatory and pathological sequelae of lung neutrophil infiltration, adult respiratory distress syndrome (ARDS) and death. These sequelae are dependent upon the synergistic interaction between several inflammatory mediators, including tumor necrosis factor (TNF), interleukin 1 (IL-1 ), and nitric oxide (NO). The overlapping spectrum of multiple mediator toxicity has hampered efforts to develop therapies for sepsis based on selective inhibition of a single mediator. Therefore, we tested the hypothesis that inhibition of multiple pro-inflammatory mediators would abrogate lethality. Our results show that administration of a tetravalent guanylhydrazone compound (CNI-1493) protected mice against 10 day mortality in CLP. Evidence of suppression of the cytokine cascade was given by decreased serum levels of TNF and IL-6 in CNI-1493 treated animals (TNF reduced 60% as compared to controls; IL-6 reduced 90% compared to controls; P &lt; 0.05), and decreased levels of the acute-phase protein serum amyloid A response measured 24 h after CLP. Serum nitrites/nitrates, which give an index of NO production, were also significantly reduced (50%). Protection against CLP induced lung damage was observed as attenuation of edema and alveolar neutrophil infiltration, suppression of pulmonary TNF levels, and reduction of TUNEL-positive staining in lung. We conclude that CNI-1493 effectively inhibits the synthesis of multiple pro-inflammatory mediators and protects against death during polymicrobial sepsis.
ChemInform Abstract: Synthesis of Protected Peptide Fragments and Release from a Solid Support Under Neutral Conditions (1993)

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.
Ultra-high-speed PLL-type clock recovery circuit based on all-optical gain modulation in traveling-wave laser diode amplifier (1993)

A new phase lock loop (PLL) is developed for very-high-speed optical timing extraction using traveling-wave laser-diode amplifier (TW-LDA) as a phase detector. The all-optical gain modulation of the TW-LDA is utilized to detect the relative phase difference between an optical signal and an optical clock The frequency response of the optical gain modulation measured with the optical heterodyne technique agrees with the theoretical results based on a rate equation model. With the developed PLL, 10-GHz optical timing clock is successfully extracted from randomly modulated optical signal pulses and the measured bit-error-rate performance shows no power penalty. Influence of the received optical noise on the phase variance of the PLL is also evaluated and it is concluded that 100 GHz operation is possible by increasing the input optical power to 10 mW.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Structure of the penicillin acylase gene from Escherichia coli: a periplasmic enzyme that undergoes multiple proteolytic processing. (1985)

Penicillin acylase is processed from a 90-kD precursor through the cleavage of a leader peptide and two further endopeptidase cleavages to yield an enzyme that contains a 22-kD (or 23-kD) and a 65-kD subunit. The endopeptidase cleavages require an intact carboxy terminus. This type of processing appears to be unique for a prokaryotic enzyme, having its most closely related analog in the synthesis and processing of preproinsulin and other eukaryotic hormones.
A Scalable Approach to Prevent Teratoma Formation of Human Embryonic Stem Cells (2012)

As the renewable source of all cell types in the body, human embryonic stem cells (hESCs) hold great promise for human cell therapy. However, one major bottleneck that hinders the clinic application of hESCs is that hESCs remaining with their differentiated derivatives pose cancer risk by forming teratomas after transplantation. NANOG is a critical pluripotency factor specifically expressed in hESCs but rarely in their differentiated derivatives. By introducing a hyperactive variant of herpes simplex virus thymidine kinase gene into the 3'-untranslated region of the endogenous NANOG gene of hESCs through homologous recombination, we developed a safe and highly scalable approach to efficiently eliminate the teratoma risk associated with hESCs without apparent negative impact on their differentiated cell types. As thymidine kinase is widely used in human gene therapy trials and is the therapeutic target of U. S. Food and Drug Administration-approved drugs, our strategy could be effectively applied to the clinic development of hESC-based human cell therapy.
The Inheritance of Chemical Phenotype in Cannabis sativa L. (2003)

Four crosses were made between inbred Cannabis sativa plants with pure cannabidiol (CBD) and pure Delta-9-tetrahydrocannabinol (THC) chemotypes. All the plants belonging to the F(1)'s were analyzed by gas chromatography for cannabinoid composition and constantly found to have a mixed CBD-THC chemotype. Ten individual F(1) plants were self-fertilized, and 10 inbred F(2) offspring were collected and analyzed. In all cases, a segregation of the three chemotypes (pure CBD, mixed CBD-THC, and pure THC) fitting a 1:2:1 proportion was observed. The CBD/THC ratio was found to be significantly progeny specific and transmitted from each F(1) to the F(2)'s derived from it. A model involving one locus, B, with two alleles, B(D) and B(T), is proposed, with the two alleles being codominant. The mixed chemotypes are interpreted as due to the genotype B(D)/B(T) at the B locus, while the pure-chemotype plants are due to homozygosity at the B locus (either B(D)/B(D) or B(T)/B(T)). It is suggested that such codominance is due to the codification by the two alleles for different isoforms of the same synthase, having different specificity for the conversion of the common precursor cannabigerol into CBD or THC, respectively. The F(2) segregating groups were used in a bulk segregant analysis of the pooled DNAs for screening RAPD primers; three chemotype-associated markers are described, one of which has been transformed in a sequence-characterized amplified region (SCAR) marker and shows tight linkage to the chemotype and codominance.
The Structurally Flexible Bicyclic Bis(2-hydroxyethanethiolato)bismuth(III) Complex:  A Model for Asymmetric Monoanionic Chelation of Bismuth(III) (1997)

Reaction of Bi(NO(3))(3) with 2-mercaptoethanol gives [Bi(SCH(2)CH(2)OH)(2)][NO(3)], 5(NO(3)), independent of stoichiometry. Other salts or derivatives of 5, 5(Cl) and 5(Br), are readily prepared by anion exchange reactions and can also be obtained by reaction of BiX(3) (X = Cl, Br) with 2-mercaptoethanol. Reaction of Bi(CH(3)COO)(3) with 2-mercaptoethanol gives the conjugate base of 5 which is readily protonated with glacial acetic acid to give the acetate salt 5(CH(3)COO). The compounds have been characterized by IR, Raman, and NMR spectroscopies and APCI mass spectrometry. X-ray crystallographic studies of 5(NO(3)) [crystal data: C(4)H(10)O(5)BiS(2)N.H(2)O, I4(1)/a, a = 20.337(6) Å, b = 20.337(6) Å, c = 11.303(7) Å, Z = 16], 5(Cl) [crystal data: C(4)H(10)O(2)BiS(2)Cl, P2(1)/n, a = 8.653(2) Å, b = 10.618(3) Å, c = 10.564(2) Å, beta = 100.51(2) degrees, Z = 4], and 5(CH(3)COO) [crystal data: C(6)H(13)O(4)BiS(2), P2(1)/c, a = 8.089(2) Å, b = 16.313(3) Å, c = 8.708(2) Å, beta = 98.37(3) degrees, Z = 4] show them to each contain the bicyclic bis(2-hydroxyethanethiolato)bismuth framework 5. The conformational features of 5 are dramatically different in each of the structures, perhaps reflecting the relative donor capabilities of the anions. The observations reveal a substantial thermodynamic preference for the thiolate-alcohol chelate in a 2:1 stoichiometry over other possible structural arrangements, which is interpreted in terms of hard and soft acid-base theory and mediation of the acidity of the bismuth site by the double hydroxyl coordination.
Chronic norepinephrine infusion stimulates glucose uptake in white and brown adipose tissues (1994)

Cold exposure activates the sympathetic nervous system and markedly stimulates glucose uptake in rat peripheral tissues [A. L. Vallerand, F. Pérusse, and L. J. Bukowiecki. Am. J. Physiol 259 (Regulatory Integrative Comp. Physiol. 28): R1043-R1049, 1990]. To test whether norepinephrine (NE) mimics the effects of cold exposure, we estimated the effects of chronic NE treatment on tissue glucose uptake by determining the glucose metabolic index using the 2-[1,2-3H(N)]deoxy-D-glucose method. NE was administered in conscious rats at various doses (ranging from 1.9 to 25.1 nmol.kg-1.min-1) during 4 days via minipumps implanted subcutaneously. At doses > 10 nmol.kg-1.min-1, NE maximally stimulated glucose uptake in interscapular brown adipose tissue (approximately 50 times above controls) and epididymal white adipose tissue (approximately 3 times above controls). NE infusion (18.8 nmol.kg-1.min-1) increased the circulating levels of NE from 1.1 +/- 0.1 to 19.2 +/- 0.4 nM (P < 0.001), which is in the range of concentrations for the stimulatory effects of NE on glucose uptake in isolated brown adipocytes. At all concentrations tested, NE infusion did not stimulate glucose uptake in the heart and skeletal muscles. NE treatment did not significantly alter plasma insulin or glucose levels but increased the concentration of circulating free fatty acids. The capacity of brown adipose tissue for NE stimulation of glucose uptake (expressed per g of tissue) was much higher than that of white adipose tissue (100 times), various types of white or red skeletal muscles (10-80 times), or the heart (3-4 times).(ABSTRACT TRUNCATED AT 250 WORDS)
YFilter: efficient and scalable filtering of XML documents (2003)

Much of the data exchanged over the Internet will soon be encoded in XML, allowing for sophisticated filtering and content-based routing. We have built a filtering engine called YFilter, which filters streaming XML documents according to XQuery or XPath queries that involve both path expressions and predicates. Unlike previous work, YFilter uses a novel NFA-based execution model. We present the structures and algorithms underlying YFilter, and show its efficiency and scalability under various workloads.