gebhart/patrepeval huggingface dataset:
Phylogeny of the family Pasteurellaceae based on rpoB sequences (2004)

Sequences of the gene encoding the beta-subunit of the RNA polymerase (rpoB) were used to delineate the phylogeny of the family Pasteurellaceae. A total of 72 strains, including the type strains of the major described species as well as selected field isolates, were included in the study. Selection of universal rpoB-derived primers for the family allowed straightforward amplification and sequencing of a 560 bp fragment of the rpoB gene. In parallel, 16S rDNA was sequenced from all strains. The phylogenetic tree obtained with the rpoB sequences reflected the major branches of the tree obtained with the 16S rDNA, especially at the genus level. Only a few discrepancies between the trees were observed. In certain cases the rpoB phylogeny was in better agreement with DNA-DNA hybridization studies than the phylogeny derived from 16S rDNA. The rpoB gene is strongly conserved within the various species of the family of Pasteurellaceae. Hence, rpoB gene sequence analysis in conjunction with 16S rDNA sequencing is a valuable tool for phylogenetic studies of the Pasteurellaceae and may also prove useful for reorganizing the current taxonomy of this bacterial family.
Knowledge Provenance Infrastructure. (2003)

The web lacks support for explaining information provenance. When web applications return answers, many users do not know what information sources were used, when they were updated, how reliable the source was, or what information was looked up versus derived. Support for information provenance is expected to be a harder problem in the Semantic Web where more answers result from some manipulation of information (instead of simple retrieval of information). Manipulation includes, among other things, retrieving, matching, aggregating, filtering, and deriving information possibly from multiple sources. This article defines a broad notion of information provenance called knowledge provenance that includes proof-like information on how a question answering system arrived at its answer(s). The article also describes an approach for a knowledge provenance infrastructure supporting the extraction, maintenance and usage of knowledge provenance related to answers of web applications and services.
Pseudocapacitive Lithium Storage in TiO2(B) (2005)

Phase-pure TiO2(B) with microfibrous morphology was prepared via a newly developed method from amorphous TiO2. Cyclic voltammetry evidences that Li-insertion into TiO2(B) is governed by a pseudocapacitive faradaic process, whose rate is not limited by solid-state diffusion of Li+ in a broad interval of scan rates. This unusual behavior was discussed in terms of the crystal structure of the TiO2(B) host, having freely accessible parallel channels for Li+-transport perpendicular to the (010) face. The characteristic Li-insertion electrochemistry of TiO2(B) allows re-interpretation of several previous reports, which did not consider explicitly this relation or the presence of TiO2(B) in various TiO2 materials of different origin.
Treatment of Duck Hepatitis B Virus by Antisense Poly-2′-O-(2,4-Dinitrophenyl)-Oligoribonucleotides (1998)

The poly-2'-O-(2,4-dinitrophenyl)-oligoribonucleotide (poly-DNP-RNA) with antisense sequence 5'ggguguauggaaaagccguc-3' was designed to target the sequence 2468-2487 in the polymerase gene of duck hepatitis B virus (DHBV). The stereochemically pure RNA was synthesized by using T7 RNA polymerase with synthetic DNA template and subsequently derivatized with 2,4-dinitrofluorobenzene in mild basic conditions to make the poly-DNP-RNA with an average DNP/base ratio of 0.7. In vitro studies showed that this antisense poly-DNP-RNA can hybridize with sense DNA and has high resistance to RNase A digestion. These poly-DNP-RNA were also found to be potent sequence-independent inhibitors of the reverse transcriptase activity of DHBV DNA-polymerase. For in vivo studies, DHBV-infected ducks were treated with antisense, sense, and random noncomplementary sequence poly-DNP-RNA, respectively. The data showed that the antisense poly-DNP-RNA completely inhibited the duck viremia in all nine ducks that had been treated with a dose of 1 mg/kg (i.v.) per day for 25 days. The viremia did not come back after 10 months recession. In the sense group, three of the four ducks showed no inhibition, and in the random group, both ducks maintained their viremia. After 45 days of treatment with the antisense poly-DNP-RNA, followed by 2 weeks of recession, PCR as well as QC-PCR assay and microscopic examination showed that viral DNA had disappeared in liver and that the histology of the damaged liver (filled with fat granules) had returned to normal.
Adaptive TCX Windowing Technology for Unified Structure MPEG-D USAC (2012)

The MPEG-D unified speech and audio coding (USAC) standardization process was initiated by MPEG to develop an audio codec that is able to provide consistent quality for mixed speech and music contents. The current USAC reference model structure consists of frequency domain (FD) and linear prediction domain (LPD) core modules and is controlled using a signal classifier tool. In this letter, we propose an LPD single-mode USAC structure using an adaptive widowing-based transform-coded excitation module. We tested our system using official test items for all mono-evaluation modes. The results of the experiment show that the objective and subjective performances of the proposed single-mode USAC system are better than those of the FD/LPD dual-mode USAC system.
Precipitation in solutions containing mixtures of synthetic anionic surfactant and soap. I. Effect of sodium octanoate on hardness tolerance of sodium dodecyl sulfate (1998)

Abstract The effect of sodium octanoate (SO) and pH on the precipitation of sodium dodecyl sulfate (SDS) with calcium (hardness tolerance) in water was investigated. SO can exist as octanoate anion (O − ) or as the protonated nonionic fatty acid (HO) with the HO/O − ratio increasing with decreasing pH. At intermediate pH levels, SO or SO/SDS systems are composed of mixtures of anionic and nonionic surfactants, resulting in enhancement of micelle formation due to nonideal mixed micelle formation. Above the critical micelle concentration (CMC), the highest hardness tolerance at each pH level occurs at a mole ratio of 80∶20 SDS/SO due to synergism in the SDS/SO mixtures. This synergism also results in an increase in hardness tolerance of SDS with decreasing pH above the CMC.
Role of renalase in the regulation of blood pressure and the renal dopamine system (2010)

Urinary renalase metabolizes urinary catecholamines, and perhaps regulates dopamine concentration in luminal fluid, and modulate proximal tubular sodium transport. Renalase deficiency is associated with increased sympathetic tone and resistant hypertension. Recombinant renalase is a potent antihypertensive agent in Dahl salt-sensitive rats and in rats with chronic kidney disease.
Complementary Adoption and Optimization of Enterprise Resource Planning Systems. (2003)

The incidence of major childhood adversity is high among Chinese college students. Childhood adversity increases the risk of depression and suicide attempts. As the number of types of childhood adversity experienced by an individual increases, their risk ratio for suicide attempts and depression increases. To promote mental health, special attention should be given to those who have suffered childhood adversities.
Enhancement of somatic intrachromosomal homologous recombination in Arabidopsis by the HO endonuclease. (1996)

The HO endonuclease promotes gene conversion between mating-type alleles in yeast by a DNA double-strand break at the site of conversion (the MAT-Y/Z site). As a first step toward understanding the molecular basis of homologous recombination in higher plants, we demonstrate that expression of HO in Arabidopsis enhances intrachromosomal recombination between inverted repeats of two defective beta-glucuronidase (gus) genes (GUS- test construct). One of these genes has the Y/Z site. The two genes share 2.5 kb of DNA sequence homology around the HO cut site. Somatic recombination between the two repeats was determined by using a histochemical assay of GUS activity. The frequency of Gus+ sectors in leaves of F1 plants from a cross between parents homozygous for the GUS- test construct and HO, respectively, was 10-fold higher than in F1 plants from a cross between the same plant containing the GUS- test construct and a wild-type parent. Polymerase chain reaction analysis showed restoration of the 5' end of the GUS gene in recombinant sectors. The induction of intrachromosomal gene conversion in Arabidopsis by HO reveals the general utility of site-specific DNA endonucleases in producing targeted homologous recombination in plant genomes.
New Therapy for Endometriosis (1988)

Endometriosis is the presence of tissue resembling endometrial glands and stroma outside the uterus. The anatomical sites most often affected by endometriosis are the ovaries, uterosacral ligaments, pelvic peritoneum, rectovaginal septum, cervix, vagina, vulva, and large bowel. Most authorities believe that endometriotic tissue arises as the result of retrograde transport of small fragments of viable endometrium from the uterine cavity through the Fallopian tubes and into the peritoneal cavity. Disease processes such as congenital cervical stenosis, which increase the severity of retrograde menstruation, appear to increase the risk of endometriosis.Endometriotic tissue is completely dependent on estrogen for continued growth. . . .
Radiation-induced crystallinity changes in linear polyethylene: Long-term aging effects in pressure-crystallized ultra-high molecular weight polymer (1990)

Abstract It has been shown previously that linear polyethylenes undergo increases in crystallinity and peak melting temperature after irradiation, the magnitude of the effects being dependent upon the dose and the molecular weight of the polymer. The crystallinity was also found to increase with time after irradiation (aging) up to 112 months, although peak melting temperature declined slowly with aging time. The results were explained in terms of the scission of tie molecules followed by the slow growth of new crystal lamellae. This paper presents similar studies on a single ultra-high molecular weight polyethylene resin which has been crystallized under 5.1 kbar pressure. As before, irradiation causes an immediate rise in crystallinity followed, over a period of 93 months, by further increases. The highest crystallinity achieved by this combination of pressure crystallization, irradiation, and aging is some 82%. This demonstrates that UHMWPE is intrinsically capable of the same degree of crystallinity as normal molecular weight resins.
A 20 mV Input Boost Converter With Efficient Digital Control for Thermoelectric Energy Harvesting (2010)

This paper presents a low power boost converter for thermoelectric energy harvesting that demonstrates an efficiency that is 15% higher than the state-of-the-art for voltage conversion ratios above 20. This is achieved by utilizing a technique allowing synchronous rectification in the discontinuous conduction mode. A low-power method for input voltage monitoring is presented. The low input voltage requirements allow operation from a thermoelectric generator powered by body heat. The converter, fabricated in a 0.13 ¿m CMOS process, operates from input voltages ranging from 20 mV to 250 mV while supplying a regulated 1 V output. The converter consumes 1.6 (1.1) ¿W of quiescent power, delivers up to 25 (175) ¿W of output power, and is 46 (75)% efficient for a 20 mV and 100 mV input, respectively.
The amount of newly formed bone in sinus grafting procedures depends on tissue depth as well as the type and residual amount of the grafted material (2005)

At 12 months post-augmentation, the two examined bone fillers, beta-TCP and BBM, promoted new bone formation in sinus grafting but the amount of newly formed bone was significantly greater in BBM-grafted sites. However, both exhibited similar residual grafted material area fraction at this healing period. This could imply that BBM possesses better osteoconductive properties.
The artificial gene Jazz, a transcriptional regulator of utrophin, corrects the dystrophic pathology in mdx mice (2009)

The absence of the cytoskeletal protein dystrophin results in Duchenne muscular dystrophy (DMD). The utrophin protein is the best candidate for dystrophin replacement in DMD patients. To obtain therapeutic levels of utrophin expression in dystrophic muscle, we developed an alternative strategy based on the use of artificial zinc finger transcription factors (ZF ATFs). The ZF ATF 'Jazz' was recently engineered and tested in vivo by generating a transgenic mouse specifically expressing Jazz at the muscular level. To validate the ZF ATF technology for DMD treatment we generated a second mouse model by crossing Jazz-transgenic mice with dystrophin-deficient mdx mice. Here, we show that the artificial Jazz protein restores sarcolemmal integrity and prevents the development of the dystrophic disease in mdx mice. This exclusive animal model establishes the notion that utrophin-based therapy for DMD can be efficiently developed using ZF ATF technology and candidates Jazz as a novel therapeutic molecule for DMD therapy.
New hope for old dreams: evidence that plant cellulose synthase genes have finally been identified. (1996)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
The Btk tyrosine kinase is a major target of the Bcr-Abl inhibitor dasatinib (2007)

Dasatinib is a small-molecule kinase inhibitor used for the treatment of imatinib-resistant chronic myelogenous leukemia (CML). We have analyzed the kinases targeted by dasatinib by using an unbiased chemical proteomics approach to detect binding proteins directly from lysates of CML cells. Besides Abl and Src kinases, we have identified the Tec kinases Btk and Tec, but not Itk, as major binders of dasatinib. The kinase activity of Btk and Tec, but not of Itk, was inhibited by nanomolar concentrations of dasatinib in vitro and in cultured cells. We identified the gatekeeper residue as the critical determinant of dasatinib susceptibility. Mutation of Thr-474 in Btk to Ile and Thr-442 in Tec to Ile conferred resistance to dasatinib, whereas mutation of the corresponding residue in Itk (Phe-435) to Thr sensitized the otherwise insensitive Itk to dasatinib. The configuration of this residue may be a predictor for dasatinib sensitivity across the kinome. Analysis of mast cells derived from Btk-deficient mice suggested that inhibition of Btk by dasatinib may be responsible for the observed reduction in histamine release upon dasatinib treatment. Furthermore, dasatinib inhibited histamine release in primary human basophils and secretion of proinflammatory cytokines in immune cells. The observed inhibition of Tec kinases by dasatinib predicts immunosuppressive (side) effects of this drug and may offer therapeutic opportunities for inflammatory and immunological disorders.
Shape-Memory Polymers for Biomedical Applications (2008)

Most polymers used in clinical applications today are materials that have been developed originally for application areas other than biomedicine. On the other side, different biomedical applications are demanding different combinations of material properties and functionalities. Compared to the intrinsic material properties, a functionality is not given by nature but result from the combination of the polymer architecture and a suitable process. Examples for functionalities that play a prominent role in the development of multifunctional polymers for medical applications are biofunctionality (e.g. cell or tissue specificity), degradability, or shape-memory functionality. In this sense, an important aim for developing multifunctional polymers is tailoring of biomaterials for specific biomedical applications. Here the traditional approach, which is designing a single new homo- or copolymer, reaches its limits. The strategy, that is applied here, is the development of polymer systems whose macroscopic properties can be tailored over a wide range by variation of molecular parameters. The Shape-memory capability of a material is its ability to trigger a predefined shape change by exposure to an external stimulus. A change in shape initiated by heat is called thermally-induced shape-memory effect. Thermally, light-, and magnetically induced shape-memory polymers will be presented, that were developed especially for minimally invasive surgery and other biomedical applications. Furthermore triple-shape polymers will be introduced, that have the capability to perform two subsequent shape changes. Thus enabling more complex movements of a polymeric material.
Deterministic phase retrieval: a Green’s function solution (1983)

Equations for the propagation of phase and irradiance are derived, and a Green’s function solution for the phase in terms of irradiance and perimeter phase values is given. A measurement scheme is discussed, and the results of a numerical simulation are given. Both circular and slit pupils are considered. An appendix discusses the local validity of the parabolic-wave equation based on the factorized Helmholtz equation approach to the Rayleigh–Sommerfeld and Fresnel diffraction theories. Expressions for the diffracted-wave field in the near-field region are given.
Changes of Epidermal Mu-Opiate Receptor Expression and Nerve Endings in Chronic Atopic Dermatitis (2005)

There is increasing evidence that neuropeptides such as a substance P, neurotrophins or beta-endorphin, an endogenous agonist for mu-opioid receptor, are involved in the pathogenesis of atopic dermatitis in which mental stress and scratching deteriorate the disease. mu-Opioid receptor, a G-protein-coupled receptor, can be downregulated and internalized by agonists and other factors in vitro. In this study, we investigated the regulation of mu-opioid receptor and nerve endings in atopic dermatitis patients. Skin biopsies from atopic dermatitis patients revealed a significant downregulation of mu-opiate receptor expression in epidermis of atopic dermatitis. Permeabilization of the skin showed that the receptor in keratinocytes from atopic dermatitis is internalized. The mRNA expression pattern of the mu-opiate receptor is different in epidermis taken from patients with chronic atopic dermatitis compared to normal skin. In atopic dermatitis, the mRNA is concentrated in the subcorneal layers of the epidermis and in normal skin in the suprabasal layers. Staining of the nerve endings using protein gene product 9.5 shows a different pattern of epidermal nerve endings in normal skin compared to atopic dermatitis. In normal skin, the epidermal nerve endings are rather thick. However, in atopic dermatitis, the epidermal nerve endings are thin and run straight through the epidermis. Based on these observations and combining the 'intensity' and 'pattern' hypothesis, we propose a new theory especially for histamine-unrelated, peripheral induction of chronic pruritus. We suggest that 'itch' is elicited in the epidermal unmyelinated nerve C-fibers and 'pain' in the dermal unmyelinated nerve fibers. The downregulation of the opioid receptor in the epidermis contributes to the chronic itching. We call this new hypothesis the 'layer hypothesis'.
Single-Agent Paclitaxel in the Treatment of Advanced Non-Small Cell Lung Cancer (1999)

Paclitaxel was the first identified member of a new class of anticancer drugs known as the taxanes. This compound has significant single-agent activity against a number of solid tumors including nonsmall cell lung cancer (NSCLC). In the first-line setting, single-agent paclitaxel has been studied on a number of different schedules and dose levels. Initial studies were done on the 24-h infusion schedule with doses of 200-250 mg/m2. Response rates were 21%-24%. Median survival ranged from six to nine months with one-year survival rates of 38%-42%. The major toxicity of this infusion schedule was myelosuppression, mainly neutropenia. Subsequent single-agent studies employed shorter infusion durations (three hours), with doses ranging from 175-225 mg/m2. The cumulative experience of the 3-h infusion schedule shows an overall response rate of 28.5% with median survival of 6-11 months and a one-year survival of 37.5%. Similar results were obtained in the one study examining the 1-h infusion schedule with doses ranging from 135-200 mg/m2. The major toxicities of the shorter infusion schedule include neutropenia, neuropathy, and myalgia/arthralgia syndrome. Weekly administration of paclitaxel also showed significant activity in advanced, metastatic NSCLC. Overall response rates have ranged from 30%-56% in the phase I/II setting with one-year survival rates of 42%-53%. A recently completed phase III trial comparing single-agent paclitaxel at 200 mg/m2 over three hours every three weeks to best supportive care (BSC) in advanced or metastatic NSCLC has shown a survival advantage for the single-agent paclitaxel arm (median survival 6.8 months for paclitaxel versus 4.8 months for BSC, p = 0.045). An ongoing phase III trial is comparing single-agent paclitaxel to the combination of carboplatin and paclitaxel (CALGB 9730) in advanced, metastatic NSCLC. Paclitaxel has also been studied in the second-line setting. Infusion schedules have ranged from 1 h, 24 h and 96 h on an every-three-week schedule. Weekly paclitaxel has also been evaluated in the second-line setting. Although the overall experience is limited, response rates have ranged from 0%-38%. The overall role of single-agent paclitaxel in prolonging survival and improving quality of life remains uncertain in this setting. The cumulative experience of single-agent paclitaxel in advanced, metastatic NSCLC suggests that it is a highly active cytotoxic agent in this setting. The consistent finding of a 35%-40% one-year survival rate is notable. The major toxicities include neutropenia, neuropathy, and myalgia/arthralgia syndrome. Given the overall activity and impact on survival along with an acceptable toxicity profile, single-agent paclitaxel warrants comparison to other active agents and combination regimens in advanced, metastatic NSCLC.
Pterins. VII. Preparation of 6,6-dimethyl-5,6,7,8-tetrahydropterin hydrochloride (1981)

The preparation of 6,6-dimethyl-5,6,7,8-tetrahydropterin (5) hydrochloride, a possible substrate for the phenylalanine hydroxylating system, has been achieved by trimethylsilylating 6-methyl-7,8- dihydropterin, reacting with methyllithium and removing the trimethylsilyl groups. Attempts to prepare this pterin by intramolecular cyclization of 2,5-diamino-6-(2'-hydroxy-2'-methylpropyl)-aminopyrimidin-4(3 H )-one (17) gave the isomeric 5,8-diamino-3,3-dimethyl-2,3-dihydroimidazo- [1,2-clpyrimidin-7(1 H )-one (20).
Review (1998)

It is now generally accepted that the presence of 5-methylcytosine (5mC) in human DNA has both a genetic and an epigenetic effect on cellular development, differentiation and transformation. First, 5mC is more unstable than its unmethylated counterpart cytosine. Hydrolytic deamination of 5mC leads to a G/T mismatch and subsequently, if unrepaired, to a C-->T transition mutation. Sites of DNA methylation are mutational hotspots in many human tumors. Second, DNA methylation of promoter regions is often correlated with the down regulation of the corresponding gene. Both of these effects have fundamental consequences for basic functions of the cell like cellular differentiation, the development of cancer and possibly other diseases, and on the evolutionary process. Recent hypotheses also propose a role for methylation in the process of aging. In this review we will describe recent findings and hypotheses about the function of 5mC in DNA with the focus on its involvement in human carcinogenesis.