gebhart/patrepeval huggingface dataset:
Present Trends in Clinical Experience with Dynamic Cardiomyoplasty (1995)

Dynamic cardiomyoplasty has been performed to reinforce the myocardium in the treatment of patients with severe cardiomyopathies. At the Heart Institute of São Paulo University Medical School, 36 patients were submitted to cardiomyoplasty between May 1988 and December 1993. The indications were idiopathic dilated cardiomyopathy in 31, ischemic cardiomyopathy in 3, and Chagas' disease cardiomyopathy in 2 patients. Twenty-eight patients were categorized in New York Heart Association (NYHA) Class III and 8 in Class IV despite the use of maximal medical therapy. There were no hospital deaths, and patients were followed up from 2 to 70 months (mean, 24 months). Besides the improvement of NYHA functional class from 3.2 +/- 0.6 to 1.6 +/- 0.9 at 6 months of follow-up, patients also presented significant changes in the left ventricular systolic and diastolic functions. Nevertheless, 16 patients died, and 2 patients were submitted to heart transplantation during late follow-up. Actuarial survival rates were 82.3% at 1 year, 61.5% at 2 years, and 38.8% at 5 years of follow-up. Otherwise, the analysis of factors influencing the outcome showed that long-term survival was significantly affected by preoperative functional class and by pulmonary vascular resistance. The 26 patients operated in NYHA functional Class III and with pulmonary vascular resistance below 4 Wood units presented survival rates of 72.7% at 2 years and of 63% at 5 years of follow-up. In conclusion dynamic cardiomyoplasty improves functional class and left ventricular function in patients with severe cardiomyopathies. However, the long-term survival after this surgical procedure may be limited by the patients' condition before the operation.
Mammary epithelial cell differentiation in vitro is regulated by an interplay of egf action and tenascin-c downregulation (1995)

Expression of the extracellular matrix glycoprotein tenascin-C in the mammary gland is associated with cellular proliferation and cell motility during organogenesis and tumorigenesis. Because the source and the regulation of tenascin-C in these tissues are unclear, we have used tenascin-C cDNA, FITC-immunofluorescence and immuno-precipitation to examine tenascin-C expression of mammary epithelial cells. Using several mammary epithelial cell lines we could show that tenascin-C can be produced and secreted by epithelial cells. However it was found that tenascin-C synthesis was inversely correlated with the polarized epithelial phenotype. Among three mouse mammary epithelial cell clones, tenascin-C expression was most abundant in HC-11 cells, the least differentiated cell type. Expression levels were high during the growth phase but were nearly abolished when cells were grown to confluence and induced to express milk proteins. Downregulation of tenascin-C by EGF apparently commits HC-11 cells to respond to lactogenic hormones and consequently, hormone induced levels of beta-casein mRNA decreased significantly when HC-11 cells were grown on a tenascin-C substrate. On the other hand, TGF-beta, another growth factor involved in coordinated growth and differentiation of the mammary gland in vivo was found to be a very potent inducer of tenascin-C. The generation of fully polarized and tight epithelium affected the levels of tenascin-C expression. In contrast to HC-11 cells, which do not form epithelial domes in vitro, highly polarized and dome forming EpH4 and Fos-ER cells nearly lacked tenascin-C. Similarly, induction of dome formation in the rat mammary stem cell line Rama 25 by the differentiation inducer dimethylsulfoxide caused a loss of TN-C-transcripts. The inability of Fos-ER cells to develop domes in the presence of soluble tenascin-C also suggests its interference with induction and maintenance of mammary epithelial cell differentiation.
Cloning of Sucrose:Sucrose 1-Fructosyltransferase from Onion and Synthesis of Structurally Defined Fructan Molecules from Sucrose1 (1998)

Sucrose (Suc):Suc 1-fructosyltransferase (1-SST) is the key enzyme in plant fructan biosynthesis, since it catalyzes de novo fructan synthesis from Suc. We have cloned 1-SST from onion (Allium cepa) by screening a cDNA library using acid invertase from tulip (Tulipa gesneriana) as a probe. Expression assays in tobacco (Nicotiana plumbaginifolia) protoplasts showed the formation of 1-kestose from Suc. In addition, an onion acid invertase clone was isolated from the same cDNA library. Protein extracts of tobacco protoplasts transformed with this clone showed extensive Suc-hydrolyzing activity. Conditions that induced fructan accumulation in onion leaves also induced 1-SST mRNA accumulation, whereas the acid invertase mRNA level decreased. Structurally different fructan molecules could be produced from Suc by a combined incubation of protein extract of protoplasts transformed with 1-SST and protein extract of protoplasts transformed with either the onion fructan:fructan 6G-fructosyltransferase or the barley Suc:fructan 6-fructosyltransferase.
Towards Optimal Active Learning for Matrix Factorization in Recommender Systems (2011)

Recommender systems help web users to address information overload. However their performance depends on the number of provided ratings by users. This problem is amplified for a new user because he/she has not provided any rating. To address this problem, active learning methods have been proposed to acquire those ratings from users, that will help most in determining their interests. The optimal active learning selects a query that directly optimizes the expected error for the test data. This approach is applicable for prediction models in which this question can be answered in closed-form given the distribution of test data is known. Unfortunately, there are many tasks and models for which the optimal selection cannot efficiently be found in closed-form. Therefore, most of the active learning methods optimize different, non-optimal criteria, such as uncertainty. Nevertheless, in this paper we exploit the characteristics of matrix factorization, which leads to a closed-form solution and by being inspired from existing optimal active learning for the regression task, develop a method that approximates the optimal solution for recommender systems. Our results demonstrate that the proposed method improves the prediction accuracy of MF.
The reality of negative refraction (2003)

One of the most fundamental phenomena in optics is refraction. When a beam of light crosses the interface between two different materials, its path is altered depending on the difference in the refractive indices of the materials. The greater the difference, the greater the refraction of the beam. For all known naturally occurring materials the refractive index assumes only positive values. But does this have to be the case?
Weight loss on low‐fat vs. low‐carbohydrate diets by insulin resistance status among overweight adults and adults with obesity: A randomized pilot trial (2015)

Substantial weight loss was achieved overall, but a significant diet × IR status interaction was not observed. Opportunity to detect differential response may have been limited by the focus on high diet quality for both diet groups and sample size.
The Domestication of <i>ortho</i>-Quinone Methides (2014)

CONSPECTUS: An ortho-quinone methide (o-QM) is a highly reactive chemical motif harnessed by nature for a variety of purposes. Given its extraordinary reactivity and biological importance, it is surprising how few applications within organic synthesis exist. We speculate that their widespread use has been slowed by the complications that surround the preparation of their precursors, the harsh generation methods, and the omission of this stratagem from computer databases due to its ephemeral nature. About a decade ago, we discovered a mild anionic triggering procedure to generate transitory o-QMs at low temperature from readily available salicylaldehydes, particularly OBoc derivatives. This novel reaction cascade included both the o-QM formation and the subsequent consumption reaction. The overall transformation was initiated by the addition of the organometallic reagent, usually a Grignard reagent, which resulted in the formation of a benzyloxy alkoxide. Boc migration from the neighboring phenol produced a magnesium phenoxide that we supposed underwent β-elimination of the transferred Boc residue to form an o-QM for immediate further reactions. Moreover, the cascade proved controllable through careful manipulation of metallic and temperature levers so that it could be paused, stopped, or restarted at various intermediates and stages. This new level of domestication enabled us to deploy o-QMs for the first time in a range of applications including diastereocontrolled reactions. This sequence ultimately could be performed in either multipot or single pot processes. The subsequent reaction of the fleeting o-QM intermediates included the 1,4-conjugate additions that led to unbranched or branched ortho-alkyl substituted phenols and Diels-Alder reactions that provided 4-unsubstituted or 4-substituted benzopyrans and chroman ketals. The latter cycloadducts were obtained for the first time with outstanding diastereocontrol. In addition, the steric effects of the newly created stereocenters in subsequent reactions of chroman ketals and acetals were studied and proved predictable. Through the use of a chiral auxiliary, Diels-Alder products were deployed in numerous enantioselective reactions including several complex natural products syntheses. In this Account, we summarize our efforts, which we hope have contributed to the synthetic renaissance for this venerable species.
A Prodrug Resistance Mechanism Is Involved in Colibactin Biosynthesis and Cytotoxicity (2013)

Commensal Escherichia coli residing in the human gut produce colibactin, a small-molecule genotoxin of unknown structure that has been implicated in the development of colon cancer. Colibactin biosynthesis is hypothesized to involve a prodrug resistance strategy that entails initiation of biosynthesis via construction of an N-terminal prodrug scaffold and late-stage cleavage of this structural motif during product export. Here we describe the biochemical characterization of the prodrug synthesis, elongation, and cleavage enzymes from the colibactin biosynthetic pathway. We show that nonribosomal peptide synthetases ClbN and ClbB assemble and process an N-acyl-D-asparagine prodrug scaffold that serves as a substrate for the periplasmic D-amino peptidase ClbP. In addition to affording information about structural features of colibactin, this work reveals the biosynthetic logic underlying the prodrug resistance strategy and suggests that cytotoxicity requires amide bond cleavage.
Biomarkers that Discriminate Multiple Myeloma Patients with or without Skeletal Involvement Detected Using SELDI‐TOF Mass Spectrometry and Statistical and Machine Learning Tools (2006)

Multiple Myeloma (MM) is a severely debilitating neoplastic disease of B cell origin, with the primary source of morbidity and mortality associated with unrestrained bone destruction. Surface enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) was used to screen for potential biomarkers indicative of skeletal involvement in patients with MM. Serum samples from 48 MM patients, 24 with more than three bone lesions and 24 with no evidence of bone lesions were fractionated and analyzed in duplicate using copper ion loaded immobilized metal affinity SELDI chip arrays. The spectra obtained were compiled, normalized, and mass peaks with mass-to-charge ratios (m/z) between 2000 and 20,000 Da identified. Peak information from all fractions was combined together and analyzed using univariate statistics, as well as a linear, partial least squares discriminant analysis (PLS-DA), and a non-linear, random forest (RF), classification algorithm. The PLS-DA model resulted in prediction accuracy between 96-100%, while the RF model was able to achieve a specificity and sensitivity of 87.5% each. Both models as well as multiple comparison adjusted univariate analysis identified a set of four peaks that were the most discriminating between the two groups of patients and hold promise as potential biomarkers for future diagnostic and/or therapeutic purposes.
The response of articular cartilage to weight-bearing against metal. A study of hemiarthroplasty of the hip in the dog (1984)

Hemiarthroplasty of the hip and some other joints has been used for many years with satisfactory results, but the fate of articular cartilage when weight-bearing against metal has not been reported. Replacement of the head of the femur was carried out in one hip of each of 26 dogs, and the changes in acetabular cartilage studied at intervals of up to 24 weeks. There was early loss of proteoglycan, followed by surface damage to the cartilage, progressive degenerative changes, and growth of pannus from the articular margins. At 24 weeks after operation there was little remaining articular cartilage, while intense subchondral activity suggested that the bony skeleton was being remodelled to conform to the shape of the prosthesis. This study is not intended to suggest that hemiarthroplasty does not help patients.
Approaching a complete repository of sequence-verified protein-encoding clones for <i>Saccharomyces cerevisiae</i> (2007)

The availability of an annotated genome sequence for the yeast Saccharomyces cerevisiae has made possible the proteome-scale study of protein function and protein-protein interactions. These studies rely on availability of cloned open reading frame (ORF) collections that can be used for cell-free or cell-based protein expression. Several yeast ORF collections are available, but their use and data interpretation can be hindered by reliance on now out-of-date annotations, the inflexible presence of N- or C-terminal tags, and/or the unknown presence of mutations introduced during the cloning process. High-throughput biochemical and genetic analyses would benefit from a "gold standard" (fully sequence-verified, high-quality) ORF collection, which allows for high confidence in and reproducibility of experimental results. Here, we describe Yeast FLEXGene, a S. cerevisiae protein-coding clone collection that covers over 5000 predicted protein-coding sequences. The clone set covers 87% of the current S. cerevisiae genome annotation and includes full sequencing of each ORF insert. Availability of this collection makes possible a wide variety of studies from purified proteins to mutation suppression analysis, which should contribute to a global understanding of yeast protein function.
A <i>Vibrio cholerae</i> Relaxed ( <i>relA</i> ) Mutant Expresses Major Virulence Factors, Exhibits Biofilm Formation and Motility, and Colonizes the Suckling Mouse Intestine (2005)

We have constructed a relaxed mutant of El Tor biotype Vibrio cholerae strain C7258 by disruption of the RelA catalytic domain. The ability of the V. cholerae relaxed mutant to biosynthesize guanosine tetraphosphate and pentaphosphate was severely affected; the mutant showed a reduced growth rate in minimal medium that could be reversed by the addition of Casamino Acids, and it was thermosensitive. Contrary to published findings, the new relA mutant still produced significant cholera toxin and toxin-coregulated pilus. The V. cholerae relA mutant was motile, produced normal biofilms, and colonized the suckling mouse intestine. Our data suggest that levels of basal guanosine nucleotides pppGpp and ppGpp, rather than the availability of a stringent response, could influence expression of virulence factors, depending on strain and culture conditions. Production of hemagglutinin (HA)/protease, which requires HapR, RpoS, and the cyclic AMP receptor protein, was not strongly affected. Nevertheless, overexpression of RelA protein from an isopropyl-beta-d-thiogalactopyranoside-inducible promoter posttranscriptionally diminished production of HA/protease.
Selective Wittig Reactions for the Synthesis of Variously Substituted 2-Vinylindoles (1989)

Three selective variants of the Wittig reaction for the syntheses of 2-vinylindoles are described. The reactions are relatively easy to perform, exhibit E-selectivity, and are characterized by a good flexibility with regard to the functional groups present in the vinyl moiety.
Large Linear Magnetoresistance and Shubnikov-de Hass Oscillations in Single Crystals of YPdBi Heusler Topological Insulators (2013)

We report the observation of a large linear magnetoresistance (MR) and Shubnikov-de Hass (SdH) quantum oscillations in single crystals of YPdBi Heusler topological insulators. Owning to the successfully obtained the high-quality YPdBi single crystals, large non-saturating linear MR of as high as 350% at 5K and over 120% at 300 K under a moderate magnetic field of 7 T is observed. In addition to the large, field-linear MR, the samples exhibit pronounced SdH quantum oscillations at low temperature. Analysis of the SdH data manifests that the high-mobility bulk electron carriers dominate the magnetotransport and are responsible for the observed large linear MR in YPdBi crystals. These findings imply that the Heusler-based topological insulators have superiorities for investigating the novel quantum transport properties and developing the potential applications.
Mechanical properties of epitaxial 3C silicon carbide thin films (2005)

Microscale tensile specimens of epitaxial 3C silicon carbide (3C-SiC) thin films were fabricated on Si substrates and tested to provide measurements of strength and elastic modulus. Samples were fabricated using both micromolding and reactive ion etching (RIE) processes to pattern the 3C-SiC films. All specimens were on the (100) plane with a <110> tensile direction. Testing was performed on a microsample tensile testing machine previously used on other materials. The samples had a thickness of 0.5 to 2 /spl mu/m, a gauge length of 4 mm, and a minimum width of 600 /spl mu/m. Testing results show an average strength of 1.19 /spl plusmn/ 0.53 GPa and 1.65 /spl plusmn/ 0.39 GPa for micromolded and RIE patterned specimens, respectively. The elastic modulus was measured to be 424 /spl plusmn/ 44 GPa, which was consistent with but slightly lower than the elastic modulus calculated with single crystal elastic constants found by ab initio calculations.
Targeted disruption of the plastid RNA polymerase genes <i>rpoA</i>, <i>B</i> and <i>C1</i>: molecular biology, biochemistry and ultrastructure (1999)

The plastid encoded RNA polymerase subunit genes rpoA, B and C1 of tobacco were disrupted individually by PEG-mediated plastid transformation. The resulting off-white mutant phenotype is identical for inactivation of the different genes. The mutants pass through a normal ontogenetic cycle including flower formation and production of fertile seeds. Their plastids reveal a poorly developed internal membrane system consisting of large vesicles and, occasionally, flattened membranes, reminiscent of stacked thylakoids. The rpo- material is capable of synthesising pigments and lipids, similar in composition but at lower amounts than the wild-type. Western analysis demonstrates that plastids contain nuclear-coded stroma and thylakoid polypeptides including terminally processed lumenal components of the Sec but not of the DeltapH thylakoid translocation machineries. Components using the latter route accumulate as intermediates. In striking contrast, polypeptides involved in photosynthesis encoded by plastid genes could not be detected by Western analysis, although transcription of plastid genes, including the rrn operon, by the plastid RNA polymerase of nuclear origin is found as expected. Remarkably, ultrastructural, sedimentation and Northern analyses as well as pulse experiments suggest that rpo- plastids contain functional ribosomes. The detection of the plastid-encoded ribosomal protein Rpl2 is consistent with these results. The findings demonstrate that the consequences of rpo gene disruption, and implicitly the integration of the two plastid polymerase types into the entire cellular context, are considerably more complex than presently assumed.
Superconducting properties of a 27-A<i></i>phase of Ba-Y-Cu-O (1988)

High-purity (97%) samples of 27-A\r{} phase of Y-Ba-Cu-O have been prepared in superconducting thin films on (100) ${\mathrm{SrTiO}}_{3}$. The possibility that the observed superconductivity might arise from a residual 3% ${\mathrm{Ba}}_{2}$${\mathrm{YCu}}_{3}$${\mathrm{O}}_{7}$ impurity in this sample is ruled out using transmission electron microscopy which shows that it is present only as isolated particles. This allows for an unambiguous determination that the 27-A\r{} phase is superconducting with an onset ${T}_{c}$ of 82 K and ${T}_{c}$(R=0) of 79 K.
Computer-aided recloser applications for distribution systems (1992)

The computer-aided application of reclosers in distribution systems is detailed. An expert system (with coordination macros) built into a coordination program can help distribution engineers establish a functional protection system. The coordination program featured is the V-PRO package. Recloser characteristics and modeling of these characteristics during overcurrent protection studies using the package are discussed. The coordination of reclosers and fuse-links is described. Examples illustrating how the package is used for recloser and fuse-link coordination are given.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Detection of vasopressin mRNA in cells of the medial amygdala but not the locus coeruleus by in situ hybridization. (1990)

Vasopressin (AVP)-immunoreactive cells have been previously reported in the medial amygdala (AME) and in the locus coeruleus (LC). The present study was designed to verify the presence of AVP-synthesizing neurons in these areas using in situ hybridization histochemistry. A 35S-labelled oligonucleotide probe, complementary to the glycopeptide portion of the vasopressin-encoding mRNA, was used to label cells expressing the AVP gene in brain sections from male Wistar rats. AVP mRNA-positive cells were identified in the AME and were located throughout the anterodorsal and posterodorsal aspect of the nucleus. Cells in the LC, however, did not exhibit labelling for the glycopeptide portion of the AVP gene. The highest density of labelled cells in the medial amygdala occurred 2.30 to 2.80 mm caudal to bregma. The labelling intensity of the cells averaged 53.8 +/- 3.9 grains/cells and was constant throughout the rostro-caudal extent of the AME. These data demonstrate the presence of AVP-synthesizing cells in the AME and provide a method for quantifying their activity. In addition, these data suggest that the cells in the LC may not synthesize vasopressin.
Relaxin in sera during the luteal phase of in‐vitro fertilization cycles (1990)

To identify the time when relaxin can first be detected in peripheral sera after in-vitro fertilization (IVF) and embryo transfer, blood samples were collected from 20 women up to 14 days after oocyte retrieval. Sixteen women did not become pregnant and in eight of them relaxin (but not beta-human chorionic gonadotrophin, beta-hCG) was measurable for the first time at days 6 to 12. Concentrations of other hormones measured were also different in these eight women compared with the remaining eight non-pregnant women; their serum concentrations of 17 alpha-OH progesterone, progesterone and oestradiol were higher but concentrations of luteinizing hormone and follicle-stimulating hormone were lower. Three women became pregnant; relaxin and beta-hCG were first detected on the same day (10 to 12). The remaining woman had increased beta-hCG levels but did not develop a clinical pregnancy. Measurement of serum relaxin during IVF cycles may allow assessment of corpora luteal function before its identification by levels of steroid hormones.