gebhart/patrepeval huggingface dataset:
Chondral Resurfacing of Articular Cartilage Defects in the Knee with the Microfracture Technique (2006)

BACKGROUND: Microfracture is a frequently used technique for the repair of articular cartilage lesions of the knee. Despite the popularity of the technique, prospective information about the clinical results after microfracture is still limited. The purpose of our study was to identify the factors that affect the clinical outcome from this cartilage repair technique. METHODS: Forty-eight symptomatic patients with isolated full-thickness articular cartilage defects of the femur in a stable knee were treated with the microfracture technique. Prospective evaluation of patient outcome was performed for a minimum follow-up of twenty-four months with a combination of validated outcome scores, subjective clinical rating, and cartilage-sensitive magnetic resonance imaging. RESULTS: At the time of the latest follow-up, knee function was rated good to excellent for thirty-two patients (67%), fair for twelve patients (25%), and poor for four (8%). Significant increases in the activities of daily living scores, International Knee Documentation Committee scores, and the physical component score of the Short Form-36 were demonstrated after microfracture (p < 0.05). A lower body-mass index correlated with higher scores for the activities of daily living and SF-36 physical component, with the worst results for patients with a body-mass index of >30 kg/m2. Significant improvement in the activities of daily living score was more frequent with a preoperative duration of symptoms of less than twelve months (p < 0.05). Magnetic resonance imaging in twenty-four knees demonstrated good repair-tissue fill in the defect in thirteen patients (54%), moderate fill in seven (29%), and poor fill in four patients (17%). The fill grade correlated with the knee function scores. All knees with good fill demonstrated improved knee function, whereas poor fill grade was associated with limited improvement and decreasing functional scores after twenty-four months. CONCLUSIONS: Microfracture repair of articular cartilage lesions in the knee results in significant functional improvement at a minimum follow-up of two years. The best short-term results are observed with good fill grade, low body-mass index, and a short duration of preoperative symptoms. A high body-mass index adversely affects short-term outcome, and a poor fill grade is associated with limited short-term durability.
Reduction of CuO Butterfly Wing Scales Generates Cu SERS Substrates for DNA Base Detection (2013)

We prepare three-dimensional Cu plasmonic structures via a reduction of CuO photonic crystals replicated from butterfly wing scales. These Cu superstructures with high purity provide surface-enhanced Raman scattering (SERS) substrates for the label-free detection of DNA bases down to a micromolar level, which is achieved for the first time on Cu and even comparable to the detection-sensitivity for DNA bases on some Ag substrates. The generation of such superstructures has provided a substantial step for the biotemplated SERS substrates with high sensitivity, high reproducibility, and ultra-low cost to detect biomolecules, and presented affordable high-quality routine SERS consumables for corresponding biolaboratories.
Carbon−Nitrogen Bond-Forming Reactions of Palladacycles with Hypervalent Iodine Reagents (2007)

Palladium(II) complexes containing bidentate cyclometalated C∼N chelating ligands are shown to react with PhINTs at room temperature to insert “NTs” into the Pd−C bond. This “NTs” insertion reaction has been applied to palladacyclic complexes of azobenzene, benzo[h]quinoline, and 8-ethylquinoline. The newly aminated organic ligands can be liberated from the metal center by protonolysis with trifluoroacetic acid or HCl.
Mycobacterial Antigens Exacerbate Disease Manifestations inMycobacterium tuberculosis-Infected Mice (2002)

To control tuberculosis worldwide, the burden of adult pulmonary disease must be reduced. Although widely used, Mycobacterium bovis BCG vaccination given at birth does not protect against adult pulmonary disease. Therefore, postexposure vaccination of adults with mycobacterial antigens is being considered. We examined the effect of various mycobacterial antigens on mice with prior M. tuberculosis infection. Subcutaneous administration of live or heat-treated BCG with or without lipid adjuvants to infected mice induced increased antigen-specific T-cell proliferation but did not reduce the bacterial load in the lungs and caused larger lung granulomas. Similarly, additional mycobacterial antigen delivered directly to the lungs by aerosol infection with viable M. tuberculosis mixed with heat-killed Mycobacterium tuberculosis (1:1) also did not reduce the bacillary load but caused increased expression of tumor necrosis factor alpha (TNF-alpha) and interleukin 6 (IL-6), which was associated with larger granulomas in the lungs. When M. tuberculosis-infected mice were treated with recombinant BCG that secreted cytokines shown to reduce disease in a preinfection vaccine model, the BCG secreting TNF-alpha, and to a lesser extent, IL-2 and gamma interferon (IFN-gamma), caused a significant increase in granuloma size in the lungs. Moreover, treatment of M. tuberculosis-infected mice with recombinant murine TNF-alpha resulted in increased inflammation in the lungs and accelerated mortality without affecting the bacillary load. Taken together, these studies suggest that administration of mycobacterial antigens to mice with prior M. tuberculosis infection leads to immune activation that may exacerbate lung pathology via TNF-alpha-induced inflammation without reducing the bacillary load.
Ontology-Based Privacy Protection in Location Commerce (2010)

Location commerce extends e-commerce through the provision of location-related activities, but this gives rise to greater concerns about privacy invasion. To encourage the smooth growth of location commerce, it is suggested that control over the sharing of intimate information be given back to the consumer. This study proposes an ontology-based privacy protection (OPP) framework that allows consumers to specify their own privacy preferences and then uses these preferences to determine whether or not a message from a merchant can be delivered to a consumer. We use ontology to structure the knowledge to simplify the framework and allow for the possibility of automation. The system is believed to be context-aware, as the location, time, service type, information type, and other contextual data are taken into consideration. We develop a prototype system for demonstration and experiment, and show that the framework design is feasible and has a reasonable performance.
NGF-mediated transcriptional targets of p53 in PC12 neuronal differentiation (2007)

Within the PC12 neuronal context, putative p53-occupied genomic loci spanned the entire Rattus norvegicus genome upon NGF treatment. We conclude that receptor-mediated p53 transcriptional activity is involved in PC12 differentiation and may suggest a contributory role for p53 in neuronal development.
Effects of Vasectomy on Gene Expression Profiling along the Human Epididymis1 (2008)

Worldwide, almost 100 million men rely on vasectomy for male contraceptive purposes. Due to changes in their personal lives, an increasing number of these men request surgical vasectomy reversal. Unfortunately, a significant proportion of these men remain infertile, despite the reestablishment of patent ducts, possibly due to epididymal damage caused by vasectomy. In animal models, vasectomy affects different epididymal physiological and biochemical parameters. However, the consequences of vasectomy on epididymal function are poorly understood. Furthermore, results obtained with animal models cannot be extrapolated to humans to understand the consequences of vasectomy on epididymal function. Gene expression along the epididymis is highly regulated. We previously showed that the human epididymal expression pattern of two genes is altered after vasectomy. To complete the list of epididymal genes affected by vasectomy, we analyzed the epididymal gene expression pattern of three vasectomized donors using the Affymetrix human GeneChip U133 Plus 2. These results were compared with the gene expression pattern of three "normal" donors. The data generated allowed the identification of many human epididymal genes for which expression is modified after vasectomy. Quantitative (Qt)-PCR and Western blot analysis of six selected genes known to be expressed in specific epididymal segments were performed. The Qt-PCR results confirmed the selected transcripts expression pattern deduced from microarray data. However, Western blot analysis revealed some differences in protein distribution along the epididymis when compared with the encoding transcripts expression pattern. These results contribute to an understanding of the reasons why fertility is not recovered in vasovasostomized men, even though spermogram values suggest surgical success of vasectomy reversal.
Monoclonal antibody M195: a diagnostic marker for acute myelogenous leukemia. (1989)

Monoclonal antibody (mAb) M195 is a mouse IgG2a reactive with a myelomonocytic differentiation antigen found on early myeloid cells and monocytes. The reactivity of M195 with fresh hematopoietic neoplasms in the blood or bone marrow from 227 patients at Memorial Hospital was determined by flow cytometry. M195 was positive on 67% of 61 myeloblastic leukemias. Seventy percent of Tdt-negative ANLL and 30% of Tdt-positive ANLL were positive; 100% of CMMOL and 100% of CML in myeloblastic crisis or accelerated phase were positive. In contrast, M195 was positive on only 8% of 51 lymphoblastic leukemias and 1% of 70 other nonmyeloid samples. M195 binding did not correlate well with FAB classification of ANLL. The pattern of reactivity of M195 was similar but not identical to that of MY9 (CD33) on the same cases (83% concordance). Cross-blocking of M195 binding by MY9 and L4F3 (CD33) was demonstrated. M195 may bind to a different epitope on the same protein antigen. The presence of both MY9 and M195 positivity on a leukemia sample had a 98% specificity of diagnosing ANLL, which was greater than MY9 alone (88%) or M195 alone (92%). Assays of granulocytic-monocytic and erythroid colony-forming units showed M195 to be present on these hematopoietic progenitors. This pattern of reactivity of M195, together with its lack of reactivity with mature granulocytic elements or with adult tissues, make it a candidate for therapy of ANLL in vivo.
Towards non-invasive cancer diagnostics and treatment based on electromagnetic fields, optomechanics and microtubules (2017)

In this paper, we discuss biological effects of electromagnetic (EM) fields in the context of cancer biology. In particular, we review the nanomechanical properties of microtubules (MTs), the latter being one of the most successful targets for cancer therapy. We propose an investigation on the coupling of electromagnetic radiation to mechanical vibrations of MTs as an important basis for biological and medical applications. In our opinion optomechanical methods can accurately monitor and control the mechanical properties of isolated MTs in a liquid environment. Consequently, studying nanomechanical properties of MTs may give useful information for future applications to diagnostic and therapeutic technologies involving non-invasive externally applied physical fields. For example, electromagnetic fields or high intensity ultrasound can be used therapeutically avoiding harmful side effects of chemotherapeutic agents or classical radiation therapy.
Use of TLS parameters to model anisotropic displacements in macromolecular refinement (2001)

An essential step in macromolecular refinement is the selection of model parameters which give as good a description of the experimental data as possible while retaining a realistic data-to-parameter ratio. This is particularly true of the choice of atomic displacement parameters, where the move from individual isotropic to individual anisotropic refinement involves a sixfold increase in the number of required displacement parameters. The number of refinement parameters can be reduced by using collective variables rather than independent atomic variables and one of the simplest examples of this is the TLS parameterization for describing the translation, libration and screw-rotation displacements of a pseudo-rigid body. This article describes the implementation of the TLS parameterization in the macromolecular refinement program REFMAC. Derivatives of the residual with respect to the TLS parameters are expanded in terms of the derivatives with respect to individual anisotropic U values, which in turn are calculated using a fast Fourier transform technique. TLS refinement is therefore fast and can be used routinely. Examples of TLS refinement are given for glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and a transcription activator GerE, for both of which there is data to only 2.0 A, so that individual anisotropic refinement is not feasible. GAPDH has been refined with between one and four TLS groups in the asymmetric unit and GerE with six TLS groups. In both cases, inclusion of TLS parameters gives improved refinement statistics and in particular an improvement in R and free R values of several percent. Furthermore, GAPDH and GerE have two and six molecules in the asymmetric unit, respectively, and in each case the displacement parameters differ significantly between molecules. These differences are well accounted for by the TLS parameterization, leaving residual local displacements which are very similar between molecules and to which NCS restraints can be applied.
Interaction Interface of Human Flap Endonuclease-1 with Its DNA Substrates (2004)

Flap endonuclease-1 or FEN-1 is a structure-specific and multifunctional nuclease critical for DNA replication, repair, and recombination; however, its interaction with DNA substrates has not been fully understood. In the current study, we have defined the borders of the interaction between the FEN-1 protein and its DNA substrates and identified six clusters of conserved positively charged amino acid residues, which are in direct contact with DNA substrate. To map further the corresponding interactions between FEN-1 residues and DNA substrates, we performed biochemical assays employing a series of flap DNA substrates lacking some structural components and a series of binding-deficient point mutants of FEN-1. It was revealed that Arg(47), Arg(70), and Lys(326)-Arg(327) of FEN-1 interact with the upstream duplex of DNA substrates, whereas Lys(244)-Arg(245) interact with the downstream duplex. This result indicates the orientation of the FEN-1-DNA interaction. Moreover, Arg(70) and Arg(47) were determined to interact with the sites around the 2nd nucleotide (Arg(70)) or the 5th/6th nucleotide (Arg(47)) of the template strand in the upstream duplex portion counting from the nick point of the flap substrate. Together with previously published data and the crystallographic ainformation from the FEN-1.DNA complex that we published recently (Chapados, B. R., Hosfield, D. J., Han, S., Qiu, J., Yelent, B., Shen, B., Tainer, J. A. (2004) Cell 116, 39-50) we are able to propose a reasonable model for how the human FEN-1 protein interacts with its DNA substrates.
A phase I study of bendamustine hydrochloride administered day 1+2 every 3 weeks in patients with solid tumours (2007)

The aim of the study was to determine the maximum tolerated dose (MTD), the dose limiting toxicity (DLT), and the pharmacokinetic profile (Pk) of bendamustine (BM) on a day 1 and 2 every 3 weeks schedule and to recommend a safe phase II dose for further testing. Patients with solid tumours beyond standard therapy were eligible. A 30-min intravenous infusion of BM was administered d1+d2 q 3 weeks. The starting dose was 120 mg m(-2) per day and dose increments of 20 mg m(-2) were used. Plasma and urine samples were analysed using validated high-performance liquid chromatography/fluorescence assays. Fifteen patients were enrolled. They received a median of two cycles (range 1-8). The MTD was reached at the fourth dose level. Thrombocytopaenia (grade 4) was dose limiting in two of three patients at 180 mg m(-2). One patient also experienced febrile neutropaenia. Lymphocytopaenia (grade 4) was present in every patient. Nonhaematologic toxicity including cardiac toxicity was not dose limiting with this schedule. Mean plasma Pk values of BM were tmax 35 min, t(1/2) 49.1 min, Vd 18.3 l m(-2), and clearance 265 ml min(-1) m(-2). The mean total amount of BM and its metabolites recovered in the first micturition was 8.3% (range 2.7-26%). The MTD of BM in the present dose schedule was 180 mg m(-2) on day 1+2. Thrombocytopaenia was dose limiting. The recommended dose for future phase II trials with this schedule is 160 mg m(-2) per day.
Regulation of the amplification C3 convertase of human complement by an inhibitory protein isolated from human erythrocyte membrane (1979)

An activity that is inhibitory to the properdin-stabilized amplification C3 convertase (C3b,Bb,P) was solubilized from human erythrocyte (E(hu)) membranes by Nonidet P-40 and purified to homogeneity. The inhibitory membrane glycoprotein had an apparent M(r) of 1-1.2x10(6) on gel filtration in the presence of Nonidet P-40. On sodium dodecyl sulfate/polyacrylamide gel electrophoresis it presented a single stained band with an apparent M(r) of 205,000, with or without prior reduction of disulfides. The inhibitory protein of the E(hu) membrane produced a dose-related, first-order decay of C3b,Bb,P function on sheep erythrocytes (E(s)) and released (125)I-labeled Bb from these sites, indicating a mechanism of inhibition by decay-dissociation of the amplification C3 convertase. The 50% inhibitory dose of the E(hu) membrane protein was not altered by removal of sialic acid from the E(s) bearing C3b,Bb,P sites. E(hu) membrane protein also serves as a cofactor for C3b inactivator-induced cleavage of the alpha polypeptide chain of C3b. Thus, the inhibitory membrane protein can abrogate the activity of amplification convertase sites that have formed and also can prevent generation of such sites by augmenting irreversible inactivation of C3b.Discrimination between cells by the alternative complement pathway occurs after initial deposition of C3b and is related to the modulation by surface constituents of the capacity of bound C3b to function as a subunit of the amplification C3 convertase. The existence in the E(hu) membrane of a protein that can impair the functions of membrane-bound C3b and C3b,Bb,P could represent a molecular basis for preventing inappropriate self-recognition.
L-lysine-.alpha.-ketoglutarate aminotransferase. I. Identification of a product, .DELTA.1-piperideine-6-carboxylic acid (1968)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTL-lysine-.alpha.-ketoglutarate aminotransferase. I. Identification of a product, .DELTA.1-piperideine-6-carboxylic acidKenji. Soda, Haruo. Misono, and Tatsuo. YamamotoCite this: Biochemistry 1968, 7, 11, 4102–4109Publication Date (Print):November 1, 1968Publication History Published online1 May 2002Published inissue 1 November 1968https://pubs.acs.org/doi/10.1021/bi00851a045https://doi.org/10.1021/bi00851a045research-articleACS PublicationsRequest reuse permissionsArticle Views282Altmetric-Citations77LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Simple methods for in vitro pollen germination and pollen preservation of selected species of the genus Agave (2008)

Simple methods to evaluate the viability and to preserve Agave tequilana Weber var. azul and A. angustifolia Haw pollen were established. Pollen viability was assessed by improving a growing media and evaluating three common pollen germination media components: sucrose, boric acid, and calcium ion. Optimal germination of pollen was obtained at 0.300 M sucrose, 0.324 mM boric acid, and 1.219 mM calcium nitrate and incubated at a temperature of 25°C. Agave pollen was preserved in olive oil and organic solvents. Olive oil, which is immiscible with water, provides an anhydrous environment and limits available oxygen, conditions similar to those provided by some organic solvents. Fresh pollen was put into eppendorf tubes containing n-butanol, n-propanol, isopropanol, extra virgin olive oil and preserved at -20, 4, and 25°C. The germination of the preserved pollen was scored at different time periods during preservation employing the optimal germination medium. The viability of pollen grains preserved at -20°C in olive oil, proved olive oil as an efficient medium for agave pollen preservation for at least 6 months.
Vibrational energy pooling in CO on NaCl(100): Methods (2002)

Vibrational states as high as n=15 have been experimentally observed in CO molecules adsorbed in a monolayer on the NaCl(100) surface after pumping the n=0→1 vibrational transition with a short (5 μs) infrared laser pulse. These high states become populated from successive single vibrational quantum exchanges between CO molecules on the surface, CO(m)+CO(n)→CO(m−1)+CO(n+1), mediated by dipole–dipole interactions and driven by the anharmonicity of the CO bond vibration. The rates for all of the possible channels of vibrational energy flow in the CO/NaCl(100) system, exchange, relaxation, and fluorescence, were calculated using perturbation theory for a model in which the CO bond vibration is treated as a Morse oscillator and is coupled to a bath of harmonic oscillators with a Debye density of states representing the underlying NaCl substrate. These rates form a Master equation that governs the overall vibrational population dynamics of CO molecules in the monolayer, and was solved using kinetic Monte Carlo (KMC) techniques. Time-dependent vibrational population distributions, Pn(t), representing the probability of finding a CO molecule in the monolayer in vibrational state n at time t, were obtained from the KMC simulations. The results are in good accord with experiment. The maximum achievable excitation is found to be limited by a crossover in the vibrational relaxation and excitation transfer rates with increasing quantum number.
Electron transfer and protein engineering studies of the soluble methane monooxygenase from Methylococcus capsulatus (Bath) (2003)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2003.
Pertuzumab plus Trastuzumab plus Docetaxel for Metastatic Breast Cancer (2011)

The combination of pertuzumab plus trastuzumab plus docetaxel, as compared with placebo plus trastuzumab plus docetaxel, when used as first-line treatment for HER2-positive metastatic breast cancer, significantly prolonged progression-free survival, with no increase in cardiac toxic effects. (Funded by F. Hoffmann-La Roche/Genentech; ClinicalTrials.gov number, NCT00567190.).