gebhart/patrepeval huggingface dataset:
Effects of orthopedic implants with a polycaprolactone polymer coating containing bone morphogenetic protein-2 on osseointegration in bones of sheep (2009)

BMP-2 within the polycaprolactone coating did not stimulate osteogenesis. The polycaprolactone coating appeared to cause a barrier effect that prevented formation of new bone. A longer period or use of another carrier polymer may result in increased osseointegration.
A 64-Mbit, 640-MByte/s bidirectional data strobed, double-data-rate SDRAM with a 40-mW DLL for a 256-MByte memory system (1998)

A 64-Mbit bidirectional data strobed, double-data-rate SDRAM achieves a peak bandwidth of 2.56 GByte/s on a 64-bit-channel, 256-MByte memory system at V/sub cc/=3.3 V and T=25/spl deg/C. The circuit features are: (1) a bidirectional data strobing scheme to eliminate the clock-related skews of I/O data in a multimodule system, (2) a low-power delay-locked loop having a wide range of locking frequency (40-160 MHz) with fast access time and minimal variations, and (3) a twisted data bussing architecture with minimized loading difference between I/O data paths and small chip-size overhead associated with the 2-bit prefetch operation.
OFDM pilot allocation for sparse channel estimation (2012)

In communication systems, efficient use of the spectrum is an indispensable concern. Recently the use of compressed sensing for the purpose of estimating orthogonal frequency division multiplexing (OFDM) sparse multipath channels has been proposed to decrease the transmitted overhead in form of the pilot subcarriers which are essential for channel estimation. In this article, we investigate the problem of deterministic pilot allocation in OFDM systems. The method is based on minimizing the coherence of the submatrix of the unitary discrete fourier transform (DFT) matrix associated with the pilot subcarriers. Unlike the usual case of equidistant pilot subcarriers, we show that non-uniform patterns based on cyclic difference sets are optimal. In cases where there are no difference sets, we perform a greedy method for finding a suboptimal solution. We also investigate the performance of the recovery methods such as orthogonal matching pursuit (OMP) and iterative method with adaptive thresholding (IMAT) for estimation of the channel taps.
Analyzing the Uses of a Software Modeling Tool (2006)

While a lot of progress has been made in improving analyses and tools that aid software development, less effort has been spent on studying how such tools are commonly used in practice. A study into a tool's usage is important not only because it can help improve the tool's usability but also because it can help improve the tool's underlying analysis technology in a common usage scenario. This paper presents a study that explores how (beginner) users work with the Alloy Analyzer, a tool for automatic analysis of software models written in Alloy, a first-order, declarative language. Alloy has been successfully used in research and teaching for several years, but there has been no study of how users interact with the analyzer. We have modified the analyzer to log (some of) its interactions with the user. Using this modified analyzer, 11 students in two graduate classes formulated their Alloy models to solve a problem set (involving two problems, each with one model). Our analysis of the resulting logs (total of 68 analyzer sessions) shows several interesting observations; based on them, we propose how to improve the analyzer, both the performance of analyses and the user interaction. Specifically, we show that: (i) users often perform consecutive analyses with slightly different models, and thus incremental analysis can speed up the interaction; (ii) users' interaction with the analyzer is sometimes predictable, and akin to continuous compilation, the analyzer can precompute the result of a future action while the user is editing the model; and (iii) (beginner) users can naturally develop semantically equivalent models that have significantly different analysis time, so it is useful to study manual and automatic model transformations that can improve performance.
Isolation of a Highly Quiescent Subpopulation of Primitive Leukemic Cells in Chronic Myeloid Leukemia (1999)

Chronic myeloid leukemia (CML) is characterized by an increased proliferative activity of the leukemic progenitors that produce an elevated number of mature granulocytes. Nevertheless, cell cycle-active agents, even in very high doses, are alone unable to eradicate the leukemic clone, suggesting the presence of a rare subset of quiescent leukemic stem cells. To isolate such cells, we first used Hoechst 33342 and Pyronin Y staining to obtain viable G(0) and G(1)/S/G(2)/M fractions of CD34(+) cells by fluorescence-activated cell sorting (FACS) from 6 chronic-phase CML patients' samples and confirmed the quiescent and cycling status of the 2 fractions by demonstration of expected patterns of Ki-67 and D cyclin expression. Leukemic (Ph(+)/BCR-ABL(+)) cells with in vitro progenitor activity and capable of engrafting immunodeficient mice were identified in the directly isolated G(0) cells. Single-cell reverse transcriptase-polymerase chain reaction (RT-PCR) analysis showed that many leukemic CD34(+) G(0) cells also expressed BCR-ABL mRNA. CD34(+) from 8 CML patients were also labeled with carboxyfluorescein diacetate succinimidyl diester (CFSE) before being cultured (with and without added growth factors) to allow viable cells that had remained quiescent (ie, CFSE(+)) after 4 days to be retrieved by FACS. Leukemic progenitors were again detected in all quiescent populations isolated by this second strategy, including those exposed to a combination of flt3-ligand, Steel factor, interleukin-3, interleukin-6, and granulocyte colony-stimulating factor. These findings provide the first direct and definitive evidence of a deeply but reversibly quiescent subpopulation of leukemic cells in patients with CML with both in vitro and in vivo stem cell properties.
Molecular design of sugar recognition systems by sugar-diboronic acid macro cyclization (1996)

Abstract
Intravascular Ultrasound Guidance Improves Angiographic and Clinical Outcome of Stent Implantation for Long Coronary Artery Stenoses (2003)

Angiographic and clinical outcome up to 12 months after long stent placement guided by IVUS is superior to guidance by angiography.
Further Evidence of the Anti‐inflammatory Effects of Silver Nanoparticles (2009)

The production of pure silver in nanoparticle size has opened new dimensions in the clinical use of this precious metal. We and others have demonstrated previously that silver nanoparticles (nAg) possess efficient antimicrobial activity. Herein we show they may also have significant anti-inflammatory effects in a postoperative peritoneal adhesion model. This finding provides further insight into the biological actions of nAg as well as a potentially novel therapy for peritoneal adhesions in clinical surgery.With the advent of nanoscience, pure silver can now be made into nanometer-sized particles. As a result, we are able to explore the potentially beneficial properties of pure silver. In our previous study using a burn wound model in mice, we demonstrated that besides antibacterial action, silver nanoparticles (nAg) appear to have anti-inflammatory properties. Herein we further confirm the anti-inflammatory effects of nAg and explore their potential clinical application through a postoperative peritoneal adhesion model. We also elucidate the potential mechanism of action of silver. Our in vitro and in vivo experimental findings show that nAg are effective at decreasing inflammation in peritoneal adhesions without significant toxic effects. This study thus provides further evidence for and contributes to the understanding of the anti-inflammatory properties of nAg and may also give a novel therapeutic direction for the prevention of postoperative adhesions.
Peritoneal Dialysis for Chronic Congestive Heart Failure (2015)

Maladaptive responses between a failing heart and the kidneys ultimately lead to permanent chronic kidney disease, referred to as cardiorenal syndrome type 2. In this narrative review, we discuss the pathophysiological pathways in the progression of cardiorenal failure and review the current evidence on peritoneal dialysis as a treatment strategy in cardiorenal syndrome type 2. A patient with heart failure can present with clinical symptoms related to venous congestion even in the absence of end-stage renal disease. Diuretics remain the cornerstone for the treatment of fluid overload related to heart failure. However, with chronic use, diuretic resistance can supervene. When medical therapy is no longer able to relieve congestive symptoms, ultrafiltration might be needed. Patients with heart failure tolerate well the gentle rate of fluid removal through peritoneal dialysis. Recent publications suggest a positive impact of starting peritoneal dialysis in patients with cardiorenal syndrome type 2 on the hospitalisation rate, functional status and quality of life.
[Three (3) cases of advanced hepatocellular carcinoma (HCC) treated successfully by transcatheter arterial chemoembolization (TACE) using lipiodol and a fine- powder formulated cisplatin (DH)]. (2009)

Although great advances have been made in therapies for patients with hepatocellular carcinoma(HCC), the prognosis for advanced HCC remains poor because liver transplantation is not applicable. We report three(3)cases of HCC treated successfully by transcatheter arterial chemoembolization(TACE)using a suspension of Lipiodol and a fine powder formulation of cisplatin(DDPH). Case No. 1 was a 64-year-old man with multiple HCCs who had undergone several sessions of TACE using doxorubicin(ADM). During the course of the treatment, the HCC became intractable and residual tumors were observed repeatedly within a short period. He was then treated by TACE using DDPH instead of ADM. The tumor marker levels decreased in response to this treatment and no recurrence of HCC has been observed. Case No. 2 was a 71-year-old man who had been diagnosed with multiple HCCs in 2004. He was treated by TACE with ADM, but the procedure had to be repeated more than three(3)times due to residual tumors. Despite the treatment, the tumor grew gradually and a formation of tumor thrombus was observed in the inferior vena cava. Both the tumor and tumor thrombus reduced in size after TACE with DDPH. Case No. 3 was a 52-year-old man who had been monitored diabetes mellitus and chronic hepatitis at our hospital. Multiple HCCs were diagnosed in 2006. TACE with DDPH was performed as an initial therapy. The tumors shrank or disappeared in response to this treatment. These results propose that TACE with DDHP against advanced HCC is effective.
Improved applications of the tetracycline-regulated gene depletion system. (2009)

Tightly controlled expression of transgenes in mammalian cells is an important tool for biological research, drug discovery, and future genetic therapies. The tetracycline-regulated gene depletion (Tet-Off) system has been widely used to control gene activities in mammalian cells, because it allows strict regulation of transgenes but no pleiotropic effects of prokaryotic regulatory proteins. However, the Tet-Off system is not compatible with every cell type and this is the main remaining obstacle left for this system. Recently, we overcame this problem by inserting an internal ribosome entry site (IRES) to drive a selectable marker from the same tetracycline-responsive promoter for the transgene. We also employed a CMV immediate early enhancer/beta-actin (CAG) promoter to express a Tet-controlled transactivator. Indeed, the Tet-Off system with these technical modifications was applied successfully to the human pre-B Nalm-6 cell line in which conventional Tet-Off systems had not worked efficiently. These methodological improvements should be applicable for many other mammalian proliferating cells. In this review we give an overview and introduce a new method for the improved application of the Tet-Off system.
Using impedance-based approaches for measuring cell-mediated cytotoxicity and antibody-dependent cell-mediated cytotoxicity (ADCC) (2015)

Meeting abstracts The most common method for measuring cell-mediated cytotoxicity is the release assay. Effector cell-mediated disruption of the target cell membrane results in leakage of its cytoplasmic contents into the culture medium. Endogenous biomolecules (such as lactate dehydrogenase) or
An unusual pectate lyase from a Bacillus sp. with high activity on pectin: cloning and characterization The EMBL accession number for the nucleotide sequence determined in this work is AJ237980. (2000)

The gene pelA encoding a pectate lyase from the strain Bacillus sp. BP-23 was cloned and expressed in Escherichia coli. The nucleotide sequence of a 1214 bp DNA fragment containing pelA gene was determined, revealing an ORF of 666 nucleotides that encoded a protein of 23233 Da. The deduced amino acid sequence of the encoded enzyme showed homology to pectate lyases A, B, C and D from Fusarium solani, Pel-3 and PelB from Erwinia carotovora and Pell from Erwinia chrysanthemi. Homology was also found to the protein deduced from the Bacillus subtilis yvpA gene, the function of which is unknown. The heterologous expressed enzyme depolymerized polygalacturonate and pectins of methyl esterification degree from 22 to 89%, and exhibited similar activity on polygalacturonate and on 89% esterified citrus pectin. Optimum temperature and pH for enzymic activity were 50 degrees C and pH 10, respectively. Ca2+ was required for activity on pectic substrates, while the enzyme was strongly inhibited by Ba2+.
Introduction to WordNet: An On-line Lexical Database* (1990)

WordNet is an on-line lexical reference system whose design is inspired by current psycholinguistic theories of human lexical memory. English nouns, verbs, and adjectives are organized into synonym sets, each representing one underlying lexical concept. Different relations link the synonym sets.
1α,25-Dihydroxyvitamin D3upregulates FGF23 gene expression in bone: the final link in a renal-gastrointestinal-skeletal axis that controls phosphate transport (2005)

Fibroblast growth factor (FGF)23 is a phosphaturic hormone that decreases circulating 1alpha,25-dihydroxyvitamin D(3) [1,25(OH)(2)D(3)] and elicits hypophosphatemia, both of which contribute to rickets/osteomalacia. It has been shown recently that serum FGF23 increases after treatment with renal 1,25(OH)(2)D(3) hormone, suggesting that 1,25(OH)(2)D(3) negatively feedback controls its levels by inducing FGF23. To establish the tissue of origin and the molecular mechanism by which 1,25(OH)(2)D(3) increases circulating FGF23, we administered 1,25(OH)(2)D(3) to C57BL/6 mice. Within 24 h, these mice displayed a dramatic elevation in serum immunoreactive FGF23, and the expression of FGF23 mRNA in bone was significantly upregulated by 1,25(OH)(2)D(3), but there was no effect in several other tissues. Furthermore, we treated rat UMR-106 osteoblast-like cells with 1,25(OH)(2)D(3), and real-time PCR analysis revealed a dose- and time-dependent stimulation of FGF23 mRNA concentrations. The maximum increase in FGF23 mRNA was 1,024-fold at 10(-7) M 1,25(OH)(2)D(3) after 24-h treatment, but statistically significant differences were observed as early as 4 h after 1,25(OH)(2)D(3) treatment. In addition, using cotreatment with actinomycin D or cycloheximide, we observed that 1,25(OH)(2)D(3) regulation of FGF23 gene expression occurs at the transcriptional level, likely via the nuclear vitamin D receptor, and is dependent on synthesis of an intermediary transfactor. These results indicate that bone is a major site of FGF23 expression and source of circulating FGF23 after 1,25(OH)(2)D(3) administration or physiological upregulation. Our data also establish FGF23 induction by 1,25(OH)(2)D(3) in osteoblasts as a feedback loop between these two hormones that completes a kidney-intestine-bone axis that mediates phosphate homeostasis.
A common pharmacophore for epothilone and taxanes: Molecular basis for drug resistance conferred by tubulin mutations in human cancer cells (2000)

The epothilones are naturally occurring antimitotic drugs that share with the taxanes a similar mechanism of action without apparent structural similarity. Although photoaffinity labeling and electron crystallographic studies have identified the taxane-binding site on beta-tubulin, similar data are not available for epothilones. To identify tubulin residues important for epothilone binding, we have isolated two epothilone-resistant human ovarian carcinoma sublines derived in a single-step selection with epothilone A or B. These epothilone-resistant sublines exhibit impaired epothilone- and taxane-driven tubulin polymerization caused by acquired beta-tubulin mutations (beta274(Thr-->Ile) and beta282(Arg-->Gln)) located in the atomic model of alphabeta-tubulin near the taxane-binding site. Using molecular modeling, we investigated the conformational behavior of epothilone, which led to the identification of a common pharmacophore shared by taxanes and epothilones. Although two binding modes for the epothilones were predicted, one mode was identified as the preferred epothilone conformation as indicated by the activity of a potent pyridine-epothilone analogue. In addition, the structure-activity relationships of multiple taxanes and epothilones in the tubulin mutant cells can be fully explained by the model presented here, verifying its predictive value. Finally, these pharmacophore and activity data from mutant cells were used to model the tubulin binding of sarcodictyins, a distinct class of microtubule stabilizers, which in contrast to taxanes and the epothilones interact preferentially with the mutant tubulins. The unification of taxane, epothilone, and sarcodictyin chemistries in a single pharmacophore provides a framework to study drug-tubulin interactions that should assist in the rational design of agents targeting tubulin.
Mfold web server for nucleic acid folding and hybridization prediction (2003)

The abbreviated name, 'mfold web server', describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large. By making use of universally available web GUIs (Graphical User Interfaces), the server circumvents the problem of portability of this software. Detailed output, in the form of structure plots with or without reliability information, single strand frequency plots and 'energy dot plots', are available for the folding of single sequences. A variety of 'bulk' servers give less information, but in a shorter time and for up to hundreds of sequences at once. The portal for the mfold web server is http://www.bioinfo.rpi.edu/applications/mfold. This URL will be referred to as 'MFOLDROOT'.
Cleavage of full-length βAPP mRNA by hammerhead ribozymes (1993)

The sequences surrounding the first 5'GUC3' in the mRNA encoding the Alzheimer amyloid peptide precursor (beta APP) were used to construct a pair of transacting hammerhead ribozymes. Each ribozyme contained the conserved core bases of the hammerhead motif found in the positive strand of satellite RNA of tobacco ringspot virus [(+)sTRSV] and two stems, 7 and 8 bases long, complementary to the target, beta APP mRNA. However, one of the ribozyme cleaving strands was lengthened at its 3' end to include the early splicing and polyadenylation signal sequences of SV40 viral RNA. This RNA, therefore, more closely mimics transcripts produced by RNA polymerase II from eucaryotic expression vectors in vivo. RNA, prepared by run-off transcription of cDNA oligonucleotide or plasmid constructs containing a T7 RNA polymerase promoter was used to characterize several properties of the cleavage reaction. In the presence of both ribozyme cleaving strands magnesium-ion dependent cleavage of a model 26 base beta APP substrate RNA or full-length beta APP-751 mRNA was observed at the hammerhead consensus cleavage site. Neither ribozyme was active against non-message homologs of beta APP mRNA, nor was cleavage detected when point mutations were made in the conserved core sequences. However, the kcat/Km at 37 degrees C in 10 mM Mg+2 of the longer ribozyme was reduced twenty-fold when model and full-length substrates were compared. The use of short deoxyoligonucleotides (13-17 mers) that bind upstream of the ribozyme was found to enhance the rate of cleavage of the full-length but not beta APP model substrate RNAs. The rate of enhancement depended on both the length of the deoxyoligonucleotide used as well as its site of binding with respect to the ribozyme. These data demonstrate the utility of ribozymes to cleave target RNAs in a catalytic, site-specific fashion in vitro. Direct comparison of the efficiency of different ribozyme constructs and different modulating activities provide an experimental strategy for designing more effective ribozymes for therapeutic purposes.
Tragedy in Athens: performance space and theatrical meaning (1998)

1. The problem of space 2. The theatre of Dionysus 3. Focus on the centre point 4. The mimetic action of the chorus 5. The chorus: its transformation of space 6. Left and right, east and west 7. Inside/outside 8. The vertical axis 9. The iconography of sacred space 10. Orchestra and theatron Select bibliography Index.
Isolation of a lipopolysaccharide-binding acute phase reactant from rabbit serum. (1986)

This report describes the purification of an acute phase reactant from acute phase rabbit serum, which endows normal serum with the properties of acute phase serum, insofar as LPS is concerned. The acute phase reactant is referred to as LPS-binding protein, or LBP. LBP was purified approximately 2,000-fold by chromatography of acute phase serum on Bio-Rex 70 and Mono-Q resins. The resulting preparation consisted of two glycoproteins having molecular weights of 60,500 and 58,000; the two were obtained in a variable ratio, usually near 10:1, respectively. After separation by SDS-PAGE, the N-terminal 36 amino acid sequences of the two proteins were identical. From the N-terminal sequence, as well as other properties of LBP, LBP appears to be unrelated to any known acute phase reactants. The direct interaction of LPS and LBP was inferred from two types of evidence: first, immunoprecipitation of [3H]LPS from APRS by anti-LBP sera; and second, by the 125I-labeling of LBP when APRS-containing 125I-labeled 2-(p-azidosalicylamido)ethyl 1,3'-dithiopropionyl-LPS was photolysed. The data presented here support the concept that the 60-kD glycoprotein we have termed LBP is a newly recognized acute phase reactant that may modulate the biochemical and biologic properties of LPS in vivo.
TOPLESS Mediates Auxin-Dependent Transcriptional Repression During Arabidopsis Embryogenesis (2008)

The transcriptional response to auxin is critical for root and vascular development during Arabidopsis embryogenesis. Auxin induces the degradation of AUXIN/INDOLE-3-ACETIC ACID (AUX/IAA) transcriptional repressors, freeing their binding partners, the AUXIN RESPONSE FACTOR (ARF) proteins, which can activate transcription of auxin response genes. We show that TOPLESS (TPL) can physically interact with IAA12/BODENLOS (IAA12/BDL) through an ETHYLENE RESPONSE FACTOR (ERF)-associated amphiphilic repression (EAR) motif. TPL can repress transcription in vivo and is required for IAA12/BDL repressive activity. In addition, tpl-1 can suppress the patterning defects of the bdl-1 mutant. Direct interaction between TPL and ARF5/MONOPTEROS, which is regulated by IAA12/BDL, results in a loss-of-function arf5/mp phenotype. These observations show that TPL is a transcriptional co-repressor and further our understanding of how auxin regulates transcription during plant development.