gebhart/patrepeval huggingface dataset:
<title>3D model acquisition, design, planning, and manufacturing of orthopaedic devices: a framework</title> (1996)

Design and manufacture of orthopedic devices using rapid prototyping technologies has been until recently a highly iterative process that involves multiple users, including doctors, design engineers and rapid prototyping experts. Existing systems for creation of orthopedic parts through rapid prototyping do not follow the principles of concurrent engineering and design for manufacture. This leads to excessive communication between parties and delays in product realization time. In this paper, we lay out the framework for a unified expert system that will enable a doctor to create quickly and easily fully functional prosthetics and orthopedic implants. Necessary components of the model acquisition process should include volumetric segmentation of objects from a CT or MRI dataset and NURBS surface fitting to the boundary points. Finite element analysis and surface model modification modules are also needed, but should be provided in an intuitive fashion for doctors who are not experienced in computer aided design. Preprocessing for rapid prototype building should be automatic, and should include optimal orientation, support structure generation and build simulation modules. Finally, the model should be passed to the rapid prototyping machine in a presliced format for speed and accuracy.
DNA from Both High-Capacity and First-Generation Adenoviral Vectors Remains Intact in Skeletal Muscle (1999)

Previous studies of the use of adenoviral vectors in animal models of gene therapy have focused on the immune response against transduced cells as the major limiting factor to long-term transgene expression. In this study we eliminated the variable of immunity induced by expression of the transgene in order to investigate vector DNA stability of both first-generation and high-capacity adenoviral vectors after gene transfer to skeletal muscle. Transgene expression from a high-capacity adenoviral vector remained at a high level for at least 20 weeks and was accompanied by persistence of intact vector genomes. In contrast, transgene expression from a first-generation adenoviral vector markedly diminished by 6 weeks after gene transfer and was accompanied by mild and variable inflammatory cell infiltrates. Surprisingly, despite this loss of transgene expression, the first-generation adenoviral vector genomes persisted like the high-capacity adenoviral vector genomes. Therefore, in the absence of immunity to transgene proteins, loss of expression from the first-generation vector was due to inhibition of transgene expression rather than to the elimination of vector-containing cells. DNA stability and persistent expression of the high-capacity adenoviral vector supports the potential of this vector for clinical applications of muscle gene transfer.
The least-squares CMA: A new technique for rapid correction of constant modulus signals (2005)

A new rapidly-converging constant modulus algorithm is presented, analyzed, and demonstrated for a two-sensor array. The algorithm is shown to be globally stable and convergent for any linearly-independent set of input data. The algorithm is also shown to converge significantly (10 to 100 times) faster than the conventional CMA, with negligible (< 1 dB.) convergent misadjustment, in the presence of moderate and severe co-channel interference.
Cancer chemotherapy: new strategies for success. (1986)

use of methotrexate to treat patients with choriocarcinoma demonstrated the important principle, in humans, that systemic chemotherapy could be used to destroy the neoplasm yet spare the patient (1). With the development ofnew chemotherapeutic agents, new strategies for their administration and combination, and more effective approaches to supportive care, it has become possible to cure patients with acute lymphoblastic leukemia (ALL),' Hodgkin's disease, diffuse histiocytic lymphoma, Burkitt's lymphoma, testicular cancer, Wilms' tumor, embryonal rhabdomyosarcoma, and Ewing's sarcoma (2, 3). Chemotherapy can also be used to achieve significant tumor regression and improve survival in patients with breast, gastric, prostatic, ovarian, and small cell lung cancers as well as for those with acute and chronic myelogenous leukemia and soft tissue sarcomas (2, 3).
Retrospective: multiscalar processors (1998)

Article Retrospective: multiscalar processors Share on Author: Gurindar Sohi Computer Sciences Department, University of Wisconsin Computer Sciences Department, University of WisconsinView Profile Authors Info & Claims ISCA '98: 25 years of the international symposia on Computer architecture (selected papers)August 1998 Pages 111–114https://doi.org/10.1145/285930.285970Online:01 August 1998Publication History 0citation404DownloadsMetricsTotal Citations0Total Downloads404Last 12 Months3Last 6 weeks0 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Synthesis and Antimalarial Activities of Several Fluorinated Artemisinin Derivatives (1995)

The carbonyl groups in several artemisinin derivatives were converted into geminal difluorinated compounds on treatment with diethylaminosulfur trifluoride. A number of other mono- and polyfluorinated artemisinin derivatives were prepared. Their in vitro antimalarial activities were all equal to or greater than the nonfluorinated analogs or precursors.
Trypanosoma cruzi trans-sialidase and neuraminidase activities can be mediated by the same enzymes. (1992)

Trans-sialidase and neuraminidase activities have been detected on the surface membrane of trypomastigotes of Trypanosoma cruzi, and both have been implicated in the parasite's invasion of host cells. We show here that these enzymes are structurally related. They are recognized by two independently derived monoclonal antibodies, are anchored to the membrane by glycosylphosphatidylinositol, copurify by ion exchange, molecular sieving, and hydrophobic chromatography, have maximal activities between pH 6.5 and 7.5, and are inactivated by heating at 56 degrees C. Furthermore, the neuraminidase and trans-sialidase reactions are coupled. An increase of the concentration of acceptors of the transfer reaction decreases the amount of free sialic acid released through the neuraminidase reaction. We conclude that a single enzyme can catalyze the transfer or the hydrolysis of macromolecular-bound sialic acid. The predominant direction of the reaction will depend on the availability of appropriate oligosaccharide acceptors of sialic acid.
The SHOOT MERISTEMLESS gene is required for maintenance of undifferentiated cells in Arabidopsis shoot and floral meristems and acts at a different regulatory level than the meristem genes WUSCHEL and ZWILLE (1996)

The function of the SHOOT MERISTEMLESS (STM) gene in shoot and floral meristems throughout Arabidopsis development has been analyzed. The results show that STM plays a major role in maintaining shoot and floral meristems. In an allelic series of stm mutants the shoot meristem was either reduced or completely absent in mature embryos and mutant seedling cotyledons showed partial fusion, indicating that the STM gene affects embryonic shoot meristem development and spacing of cotyledons. Postembryonically, stm mutants initiated adventitious shoot development at a position corresponding to the shoot meristem in wild-type. Repetitively initiated defective mutant shoot and floral meristems were consumed during primordia formation and typically terminated prematurely in fused ectopic primordia, indicating that STM is required for continuous shoot and floral meristem function. Analogous defects were observed in stm embryonic and postembryonic development suggesting that similar mechanisms are employed in embryonic and postembryonic organ primordia initiation. Allelic combination suggest different thresholds for STM requirement during plant development. STM requirement could not be bypassed by standard growth factor regimes or by shoot regeneration from calli. The results suggest that STM functions by preventing incorporation of cells in the meristem center into differentiating organ primordia and that this role can completely account for all defects observed in stm mutants. Mutations in the WUSCHEL (WUS) and ZWILLE (ZLL) genes result in defective organization and premature termination of shoot meristems. Genetic interactions between STM, WUS and ZLL were analyzed and the results indicate that STM acts upstream of WUS and ZLL. Therefore, while STM appears to function in keeping central meristem cells undifferentiated, WUS and ZLL seem to be subsequently required for proper function of these cells.
Correlative Memory Deficits, Aβ Elevation, and Amyloid Plaques in Transgenic Mice (1996)

Transgenic mice overexpressing the 695-amino acid isoform of human Alzheimer beta-amyloid (Abeta) precursor protein containing a Lys670 --> Asn, Met671 --> Leu mutation had normal learning and memory in spatial reference and alternation tasks at 3 months of age but showed impairment by 9 to 10 months of age. A fivefold increase in Abeta(1-40) and a 14-fold increase in Abeta(1-42/43) accompanied the appearance of these behavioral deficits. Numerous Abeta plaques that stained with Congo red dye were present in cortical and limbic structures of mice with elevated amounts of Abeta. The correlative appearance of behavioral, biochemical, and pathological abnormalities reminiscent of Alzheimer's disease in these transgenic mice suggests new opportunities for exploring the pathophysiology and neurobiology of this disease.
[Clinical effects of adjuvant therapy using Z-100 (Ancer 20 injection) for oral cancer--prevention of stomatitis and hematopoietic impairment]. (2000)

A combination of radiotherapy and chemotherapy is a usual treatment method for malignant head and neck tumors, however chemoradiotherapy is associated with hematopoietic impairment and serious stomatitis in patients. The clinical effects and evaluation of hematopoietic activity (e.g., leukocyte count) and the degree of stomatitis under adjuvant therapy using Z-100 (Ancer 20 injection) for oral cancer were investigated for preoperative cancer therapy. In order to evaluate the clinical effects of Ancer 20 injection with regard to hematopoietic activity and the degree of stomatitis, a clinical study was performed for 18 patients with oral cancer in our department. The 18 patients, who had oral squamous cell carcinomas (5 of the tongue, 4 of the mandibular gingiva, 3 of the maxillary gingiva, 1 of the floor of the mouth, 3 of the buccal mucosa, and 2 others), were treated with this combination of adjuvant therapy with Ancer 20 injection, from March, 1991 to March, 1997. They were injected with Ancer 20 (twice a week, 40 micrograms) during the cancer treatment period. We investigated hematopoietic activity, (e.g., leukocyte and platelet counts) and the degree of stomatitis periodically, before and after the combined radiotherapy and chemotherapy treatment period. It was found that in the patients who were treated with Ancer 20 injection, the decrease in leukocyte and platelet counts was prevented and the condition of stomatitis was improved. These results suggest that Ancer 20 injection may generally improve various dysfunctions due to hematopoietic impairment by radiotherapy combined with chemotherapy, and improve immunological factors. We conclude that Ancer 20 injection is a useful adjuvant treatment for oral cancer.
DenseReg: Fully Convolutional Dense Shape Regression In-the-Wild (2017)

In this paper we propose to learn a mapping from image pixels into a dense template grid through a fully convolutional network. We formulate this task as a regression problem and train our network by leveraging upon manually annotated facial landmarks "in-the-wild". We use such landmarks to establish a dense correspondence field between a three-dimensional object template and the input image, which then serves as the ground-truth for training our regression system. We show that we can combine ideas from semantic segmentation with regression networks, yielding a highly-accurate quantized regression architecture. Our system, called DenseReg, allows us to estimate dense image-to-template correspondences in a fully convolutional manner. As such our network can provide useful correspondence information as a stand-alone system, while when used as an initialization for Statistical Deformable Models we obtain landmark localization results that largely outperform the current state-of-the-art on the challenging 300W benchmark. We thoroughly evaluate our method on a host of facial analysis tasks, and demonstrate its use for other correspondence estimation tasks, such as the human body and the human ear. DenseReg code is made available at http://alpguler.com/DenseReg.html along with supplementary materials.
Droplet‐Based DNA Purification in a Magnetic Lab‐on‐a‐Chip (2006)

Merge, mix, split, and transport are the main manipulation steps used for on-chip droplet-based DNA purification (see figure). The system is able to extract genomic material from dilute raw cell samples by using the actuation of magnetic microparticles within the droplets through a matrix of coils.
Robust De-anonymization of Large Sparse Datasets (2008)

We present a new class of statistical de- anonymization attacks against high-dimensional micro-data, such as individual preferences, recommendations, transaction records and so on. Our techniques are robust to perturbation in the data and tolerate some mistakes in the adversary's background knowledge. We apply our de-anonymization methodology to the Netflix Prize dataset, which contains anonymous movie ratings of 500,000 subscribers of Netflix, the world's largest online movie rental service. We demonstrate that an adversary who knows only a little bit about an individual subscriber can easily identify this subscriber's record in the dataset. Using the Internet Movie Database as the source of background knowledge, we successfully identified the Netflix records of known users, uncovering their apparent political preferences and other potentially sensitive information.
Restoration of MAGI-1 Expression in Human Papillomavirus-Positive Tumor Cells Induces Cell Growth Arrest and Apoptosis (2014)

It is clear that the targeting of PDZ-containing substrates by E6 is important for the normal viral life cycle and for the progression to malignancy. Nevertheless, which of these PDZ domain-containing proteins is relevant for HPV pathology is still elusive. In a previous study, we provided evidence that MAGI-1 is a sensitive proteolytic substrate for both the HPV-16 and HPV-18 E6 oncoproteins; however, the biological consequences associated with loss of MAGI-1 expression in HPV-positive cervical cancer cells are still poorly understood. Using a mutant MAGI-1, resistant to E6-mediated degradation, we show that its expression in cervical cancer cells promotes membrane recruitment of the tight junction-associated proteins ZO-1 and PAR3, represses cell proliferation, and promotes apoptosis. These findings suggest that E6-mediated inhibition of MAGI-1 function contributes to HPV pathology by perturbing tight junction assembly with concomitant stimulation of proliferation and inhibition of apoptosis.
Molecular cloning, characterization and functional expression of the rat liver interleukin 6 receptor. (1990)

A series of cDNA clones coding for the rat liver interleukin 6 receptor (IL6-R) were isolated from an acute-phase library. The identity of the clones was established (a) by DNA sequence analysis and comparison with the known human leukocyte IL6-R and (b) by demonstrating that the clones generated specific IL6 ligand binding activity and IL6-dependent regulation of acute-phase gene control elements after transfection into appropriate recipient cells. Two types of cDNA clones were obtained corresponding to two mRNA species of different length, both encoding an identical protein of 462 amino acid residues. The two prototype clones, pRIL6RC.21 and pRIL6RC.6 contained 3'-untranslated regions of 550 and 3100 nucleotides, respectively. The sequence motifs TTATTTAT and ATTTA associated with the regulation of mRNA stability and translation efficiency were present only in the longer mRNA species. The deduced amino acid sequence of the rat liver IL6-R was 53% identical with the human leukocyte IL6-R. Both receptors contained conserved structural features in their extracellular domains, including the signal peptide, a C2 domain characteristic of the immunoglobulin superfamily, and two domains shared among members of a family of cytokine and growth factor receptors. The strongly conserved intracellular portion of the rat liver IL6-R lacked recognizable signal transduction domains. The cDNA clones were used to demonstrate that rat liver IL6-R mRNA concentrations were increased 4.2-fold at 12 h after the induction of an experimental acute-phase response. Clone pRIL6R.21ex, but not clone pRIL6RC.6ex, generated specific IL6 ligand binding activity after transfection into human Jurkat cells that lack the endogenous IL6-R. By contrast, only pRIL6RC.6ex reconstituted a response of human Hep3B-2 and HepG2 hepatoma cells to mouse IL6. These human hepatoma cells were highly responsive to human IL6 but did not respond to physiologic concentrations of murine IL6. After cotransfection with pRIL6RC.6ex and plasmids containing the chloramphenicol acetyltransferase reporter gene under the control of IL6 response elements of acute-phase plasma protein genes, these cells showed a strong stimulation of the reporter gene by recombinant mouse IL6. Thus, both cell surface ligand binding activity and the complete IL6 signal cascade terminating in the transcriptional induction of IL6-dependent promoters were successfully reconstituted. Therefore, both IL6-R mRNA species code for functionally active receptor, depending on the target cell, but only the longer mRNA species coded for significant receptor levels in human hepatoma cell lines.
Glutamine Restores Tight Junction Protein Claudin‐1 Expression in Colonic Mucosa of Patients With Diarrhea‐Predominant Irritable Bowel Syndrome (2015)

Glutamine increased claudin-1 expression in the colonic mucosa of patients with IBS-D. In addition, glutamine effect seems to be dependent on basal expression of tight junction proteins.
Oxaziridine‐Mediated Oxyamination of Indoles: An Approach to 3‐Aminoindoles and Enantiomerically Enriched 3‐Aminopyrroloindolines (2010)

A radical solution: A highly regioselective copper(II)-catalyzed oxyamination of N-acyl indoles with oxaziridines gave aminal products that could be converted in a single step into 3-aminoindoles and 3-aminopyrroloindolines (see scheme). When a chiral N-acyl group was used, the core fragment of some architecturally fascinating pyrroloindoline alkaloids was formed with 91 % ee. Bs=benzenesulfonyl, Moc=methoxycarbonyl.
Anti-angiogenic cues from vascular basement membrane collagen. (2000)

Vascular basement membrane is an important structural component of blood vessels and has been shown to interact with and modulate vascular endothelial behavior during angiogenesis. During the inductive phase of tumor angiogenesis, this membrane undergoes many degradative and structural changes and reorganizes to a native state around newly formed capillaries in the resolution phase. Such matrix changes are potentially associated with molecular modifications that include expression of matrix gene products coupled with conformational changes, which expose cryptic protein modules for interaction with the vascular endothelium. We speculate that these interactions provide important endogenous angiogenic and anti-angiogenic cues. In this report, we identify an important antiangiogenic vascular basement membrane-associated protein, the 26-kDa NC1 domain of the alpha1 chain of type IV collagen, termed arresten. Arresten was isolated from human placenta and produced as a recombinant molecule in Escherichia coli and 293 embryonic kidney cells. We demonstrate that arresten functions as an anti-angiogenic molecule by inhibiting endothelial cell proliferation, migration, tube formation, and Matrigel neovascularization. Arresten inhibits the growth of two human xenograft tumors in nude mice and the development of tumor metastases. Additionally, we show that the anti-angiogenic activity of arresten is potentially mediated via mechanisms involving cell surface proteoglycans and the alpha1beta1 integrin on endothelial cells. Collectively, our results suggest that arresten is a potent inhibitor of angiogenesis with a potential for therapeutic use.
Catalytic synthesis of n-butyl cinnamate with Fe_2O_3/SO_4~(2-) (2005)

n-Butyl cinnamate is synthesized by cinnamic acid and n-butyl alcohol using Fe_2O_3/SO_4~(2-) as catalyst.The optimum conditions are as follows: the mole ratio of n-butanol to cinnamic acid is 2∶1,reaction time is 1.5 h,temperature is 130℃,the amount of the catalyst is 0.8 g/0.5 mol acid,the yield may up to 98.7%.
Repression of Clostridium difficile toxin gene expression by CodY (2007)

CodY, a global regulator of gene expression in low G + C Gram-positive bacteria, was found to repress toxin gene expression in Clostridium difficile. Inactivation of the codY gene resulted in derepression of all five genes of the C. difficile pathogenicity locus during exponential growth and stationary phase. CodY was found to bind with high affinity to a DNA fragment containing the promoter region of the tcdR gene, which encodes a sigma factor that permits RNA polymerase to recognize promoters of the two major toxin genes as well as its own promoter. CodY also bound, but with low affinity, to the toxin gene promoters, suggesting that the regulation of toxin gene expression by CodY occurs primarily through direct control of tcdR gene expression. Binding of CodY to the tcdR promoter region was enhanced in the presence of GTP and branched-chain amino acids, suggesting a link between nutrient limitation and the expression of C. difficile toxin genes.
A Correlation-Based Transition Model Using Local Variables: Part II — Test Cases and Industrial Applications (2004)

A new correlation-based transition model has been developed, which is built strictly on local variables. As a result, the transition model is compatible with modern CFD methods using unstructured grids and massive parallel execution. The model is based on two transport equations, one for the intermittency and one for the transition onset criteria in terms of momentum thickness Reynolds number. The proposed transport equations do not attempt to model the physics of the transition process (unlike e.g. turbulence models), but form a framework for the implementation of correlation-based models into general-purpose CFD methods. Part I of this paper gives a detailed description of the mathematical formulation of the model and some of the basic test cases used for model validation. Part II (this part) of the paper details a significant number of test cases that have been used to validate the transition model for turbomachinery and aerodynamic applications, including the drag crisis of a cylinder, separation induced transition on a circular leading edge and natural transition on a wind turbine airfoil. Turbomachinery test cases include a highly loaded compressor cascade, a low-pressure turbine blade, a transonic turbine guide vane, a 3-D annular compressor cascade and unsteady transition due to wake impingement. In addition, predictions are shown for an actual industrial application, namely a GE Low-Pressure turbine vane. In all cases good agreement with the experiments could be achieved and the authors believe that the current model is a significant step forward in engineering transition modeling.