gebhart/patrepeval huggingface dataset:
The Role of Prenylamine in the Prevention of Adriamycin-Induced Cardiotoxicity. A Review of Experimental and Clinical Findings (1988)

Experimental and clinical trials to determine the potential of prenylamine in the prevention of adriamycin-related cardiotoxicity are reviewed. In mice given 4 mg/kg body weight adriamycin, the incidence of myocardial damage after 19 days' treatment was lower than in those given adriamycin and placebo. Rabbits were given adriamycin (total dose 10.8 mg/kg body weight), adriamycin plus prenylamine (1.5 mg/kg body weight), and adriamycin plus vitamins A (250 IU) and E (40 mg) for 9-11 weeks. Adriamycin-induced electrocardiogram changes were observed to a lesser extent in animals also receiving prenylamine. Heart homogenates from adriamycin-treated animals showed enhanced hydroperoxide-initiated chemiluminescence which was not affected by the simultaneous administration of prenylamine. The extent of adriamycin-induced myocytolysis and the degree of alterations observed on electron microscopy were markedly reduced by prenylamine. In a double-blind clinical trial with 26 oncological patients, no cardiomyopathy, arrhythmia or adverse reactions were observed in the group given adriamycin plus prenylamine. In those given adriamycin plus placebo, two patients developed congestive cardiopathy and another showed severe supraventricular arrhythmias together with hypotension and dyspnoea. The mechanisms of adriamycin-related cardiotoxicity, the effects of prenylamine and the benefit from combined treatment are discussed.
Hemodialysis Access Flow Measurement—Comparison of Ultrasound Dilution and Duplex Ultrasonography (1996)

Decreased hemodialysis access flow is associated with an increased risk of access thrombosis. Duplex ultrasonography can measure access flow and select a subset of patients at increased risk for access failure. With in-line techniques (ultrasound dilution), access flow can be measured during hemodialysis. This study attempted to determine if access flow measured by ultrasound dilution (QA-T) was comparable to that measured by duplex ultrasonography (QA-S). The authors performed 66 simultaneous measurements of hemodialysis access flow in 19 patients by ultrasound dilution and duplex ultrasound with time-domain correlation during 19 hemodialysis treatments. The mean access flow was 1,086 +/- 505 ml/min by ultrasound dilution and 1,026 +/- 513 ml/min with duplex ultrasonography (NS). Regression analysis revealed a linear relationship between the two techniques described by the equation QAT = 246.14 + 0.8104(QAS) (correlation coefficient of 0.83; p < 0.0001). Measurement of hemodialysis access flow by ultrasound dilution was essentially equivalent to that obtained by duplex ultrasound. Additional studies are needed to determine if regular in-line flow measurements can predict and prevent future access thrombosis and decreased the cost of access management.
Isoprene Biosynthesis inBacillus subtilisvia the Methylerythritol Phosphate Pathway (1999)

Isoprene (2-methyl-1,3-butadiene), an abundant natural product of unknown function in plants, has recently been found to be one of the major volatiles formed by Bacillus subtilis. To understand the metabolic origins of isoprene in B. subtilis, we used (13)C- and (2)H-labeling methods with GC-MS analysis of released isoprene. The results indicate that, in this bacterium, isoprene is not formed by the mevalonate pathway or from catabolism of leucine, but, as in plant systems, it is a product of the methylerythritol phosphate pathway of isoprenoid synthesis. This work supports the idea that B. subtilis could be used as a microbial model for studying the biochemistry of isoprene formation.
Configuration-based optimization for six degree-of-freedom haptic rendering using sphere-trees (2011)

This paper presents a novel constraint-based six degree-of-freedom (6-DoF) haptic rendering algorithm for simulating both contact forces and torques between interacting rigid bodies. We represent an object using a hierarchy of spheres, i.e., a sphere-tree. Such a representation allows fast detection of multiple contacts/collisions among objects and facilitates contact constraint formulation. Given a moving graphic tool as the avatar of the haptic tool in the virtual environment, we constrain its position and orientation, i.e., its six dimensional configuration, by solving a constrained optimization problem. The constraints in the 6-D configuration space (C-space) of the graphic tool is obtained and updated through on-line mapping of the non-penetration constraint between the spheres of the graphic tool and those of the other objects in the three dimensional physical space, based on the result of collision detection. The problem is further modeled as a quadratic programming problem and solved by classic active-set methods. Our algorithm has been implemented and interfaced with a 6-DoF Phantom Premium 3.0. We demonstrate its performance in dental surgery simulations involving complex, multi-contact virtual environments. Our method enables stable operations and realistic feel of haptic sensation.
Natural Selection and Algorithmic Design of mRNA (2003)

Messenger RNA (mRNA) sequences serve as templates for proteins according to the triplet code, in which each of the 43 = 64 different codons (sequences of three consecutive nucleotide bases) in RNA either terminate transcription or map to one of the 20 different amino acids (or residues) which build up proteins. Because there are more codons than residues, there is inherent redundancy in the coding. Certain residues (e.g., tryptophan) have only a single corresponding codon, while other residues (e.g., arginine) have as many as six corresponding codons. This freedom implies that the number of possible RNA sequences coding for a given protein grows exponentially in the length of the protein. Thus nature has wide latitude to select among mRNA sequences which are informationally equivalent, but structurally and energetically divergent. In this paper, we explore how nature takes advantage of this freedom and how to algorithmically design structures more energetically favorable than have been built through natural selection. In particular: (1) Natural Selection - we perform the first large-scale computational experiment comparing the stability of mRNA sequences from a variety of organisms to random synonymous sequences which respect the codon preferences of the organism. This experiment was conducted on over 27,000 sequences from 34 microbial species with 36 genomic structures. We provide evidence that in all genomic structures highly stable sequences are disproportionately abundant, and in 19 of 36 cases highly unstable sequences are disproportionately abundant. This suggests that the stability of mRNA sequences is subject to natural selection. (2) Artificial Selection - motivated by these biological results, we examine the algorithmic problem of designing the most stable and unstable mRNA sequences which code for a target protein. We give a polynomial-time dynamic programming solution to the most stable sequence problem (MSSP), which is asymptotically no more complex than secondary structure prediction. We show that the corresponding least stable sequence problem (LSSP) is NP-complete, and develop two heuristics for the construction of such sequences. We have implemented these algorithms, and present experimental results placing the high/low stability sequences in context with both wildtype and random encodings. Our implementation has already been applied to the design of RNA "code-words" creating little or no secondary structure in RNA computing (Brenneman and Condon, 2001; Marathe et al., 2001), and we anticipate a variety of other applications of this work to sequence design problems (Skiena, 2001).
Hind III genomic polymorphism of the C3b receptor (CR1) in patients with SLE: Low erythrocyte CR1 expression is an acquired phenomenon (1995)

Expression of the human erythrocyte C3b receptor (CR1-CD35) and its Hind III RFLP was studied in a group of 37 patients with SLE, 15 consanguineous relatives of the patients and 48 healthy normal subjects. The CR1 number on erythrocytes was quantitated by ELISA using a mAb to CR1. Serum levels of complement proteins (C3, C4, C3d) and circulating immune complexes (CIC) were estimated simultaneously in controls and relatives. The patients were followed up during the course of the treatment. The CR1/erythrocyte (CR1/E) in patients were found to be significantly low in comparison to controls. The gene frequencies for the alleles H and L (7.4 and 6.9 kb Hind III restriction fragments) in the patients were 0.75 and 0.25, respectively, which did not differ significantly from the controls (0.77 and 0.23 in normal subjects and 0.79 and 0.21 in consanguineous relatives of the patients). However, patients expressed fewer CR1/E within each genotype than their relatives and healthy subjects. CR/E was found to be stable in consecutive samples in controls. In patients, the numbers varied between low and high during the course of the treatment. The variation in the numbers was significantly correlated with C3d and CIC as well as with the severity of the disease. Our results suggest that low levels of CR1 on erythrocytes in SLE patients are required during the course of the disease and that the 6.9 kb restriction fragment does not play a role in causing susceptibility to the disease.
Distribution of tumor‐infiltrating dendritic cells in human non‐small cell lung carcinoma in relation to apoptosis (2004)

Host defense mechanisms play important roles in suppressing the development and growth of tumors. It is known that S-100 protein-positive immature dendritic cells (S100DC), as antigen presenting cells (APC), and macrophages have roles in the immune responses to tumor growth. Mediators such as nitric oxide are also important in the surveillance against cancer. We examined the distribution of S100DC and CD68-positive macrophages (CD68MØ) immunohistochemically to compare the condition of apoptotic tumor cells in 69 patients with human non-small cell lung carcinoma. The expression of inducible nitric oxide synthases (iNOS) in tumors was also studied. Unlike macrophages, S100DC were distributed predominantly in cancer nests. In the areas with infiltration of 'many' S100DC (i.e. more than 10 DC/HPF), we found two distinct patterns of tumor infiltration: scattered and aggregated infiltration of DC in tumor nests. In areas of scattered S100DC distribution, only a few apoptotic tumor cells could be detected. However, in the areas of DC aggregations, apoptotic tumor cells were significantly more abundant (P = 0.0491). In contrast to S100DC, the distribution and density of CD68MØ were associated with iNOS expression of tumor cells (P < 0.0001), but not with distribution of apoptotic tumor cells. These findings reveal differences in the in vivo condition between S100DC and CD68MØ in tumors, and suggest there is a relationship between tumor-infiltrating S100DC aggregation and apoptosis in in vivo non-small cell lung cancers.
HUPO Plasma Proteome Project specimen collection and handling: Towards the standardization of parameters for plasma proteome samples (2005)

There is a substantial list of pre-analytical variables that can alter the analysis of blood-derived samples. We have undertaken studies on some of these issues including choice of sample type, stability during storage, use of protease inhibitors, and clinical standardization. As there is a wide range of sample variables and a broad spectrum of analytical techniques in the HUPO PPP effort, it is not possible to define a single list of pre-analytical standards for samples or their processing. We present here a compendium of observations, drawing on actual results and sound clinical theories and practices. Based on our data, we find that (1) platelet-depleted plasma is preferable to serum for certain peptidomic studies; (2) samples should be aliquoted and stored preferably in liquid nitrogen; (3) the addition of protease inhibitors is recommended, but should be incorporated early and used judiciously, as some form non specific protein adducts and others interfere with peptide studies. Further, (4) the diligent tracking of pre-analytical variables and (5) the use of reference materials for quality control and quality assurance, are recommended. These findings help provide guidance on sample handling issues, with the overall suggestion being to be conscious of all possible pre-analytical variables as a prerequisite of any proteomic study.
Clinical Responses in a Phase II Study Using Adoptive Transfer of Short-term Cultured Tumor Infiltration Lymphocytes in Metastatic Melanoma Patients (2010)

We showed that lympho-depleting chemotherapy followed by transfer of short-term cultured TIL can mediate tumor regression in 50% of metastatic melanoma with manageable toxicity. The convincing clinical results combined with the simplification of the process may thus have a major effect on cell therapy of cancer.
Stereospecific syntheses of the four diastereomeric 2-amino-5-phenoxycyclopentanols (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStereospecific syntheses of the four diastereomeric 2-amino-5-phenoxycyclopentanolsJames R. McCarthy, Paul E. Wiedeman, Albert J. Schuster, Jeffrey Whitten, Robert J. Barbuch, and John C. HuffmanCite this: J. Org. Chem. 1985, 50, 17, 3095–3103Publication Date (Print):August 1, 1985Publication History Published online1 May 2002Published inissue 1 August 1985https://pubs.acs.org/doi/10.1021/jo00217a017https://doi.org/10.1021/jo00217a017research-articleACS PublicationsRequest reuse permissionsArticle Views687Altmetric-Citations14LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Evaluation of a Tree-based Pipeline Optimization Tool for Automating Data Science (2016)

As the field of data science continues to grow, there will be an ever-increasing demand for tools that make machine learning accessible to non-experts. In this paper, we introduce the concept of tree-based pipeline optimization for automating one of the most tedious parts of machine learning--pipeline design. We implement an open source Tree-based Pipeline Optimization Tool (TPOT) in Python and demonstrate its effectiveness on a series of simulated and real-world benchmark data sets. In particular, we show that TPOT can design machine learning pipelines that provide a significant improvement over a basic machine learning analysis while requiring little to no input nor prior knowledge from the user. We also address the tendency for TPOT to design overly complex pipelines by integrating Pareto optimization, which produces compact pipelines without sacrificing classification accuracy. As such, this work represents an important step toward fully automating machine learning pipeline design.
Selecting the best artificial neural network model from a multi-objective Differential Evolution Pareto front (2011)

The objective of this work is to select artificial neural network models (ANN) automatically with sigmoid basis units for multiclassification tasks. These models are designed using a Memetic Pareto Differential Evolution Neural Network algorithm (MPDENN) based on the Pareto dominance concept. We propose different methodologies to obtain the best model from the Pareto front obtained with the MPDENN algorithm. These methodologies are based on choosing the best models for training in both objectives, the Correct Classification Rate and Minimum Sensitivity, and the two models closest to the centroids of two clusters formed with the models of the first and second Pareto fronts. These methodologies are compared with three standard ensembles methodologies with very competitive results.
Optical Bloch waves in a semiconductor photonic lattice (1992)

We have observed multiple optical Bloch waves in a semiconductor photonic lattice. This photonic lattice comprises epitaxial quarter-wave periodic layers surrounding a periodic quantum-well region. After growth, the layers are structured laterally into periodic square unit cells by reactive-ion-beam etching. When photoexcited, the lattice emits a complex angular distribution of photons that reflects its periodic structure. Scattered light is distributed according to the Laue conditions in analogy with x-ray diffraction from a bulk crystal. Optical Bloch waves photostimulated in the lattice are analogous to electron Bloch waves in an atomic lattice. These optical Bloch waves exhibit long-range translational symmetry and local symmetry due to the shape of the unit cell. Interestingly, the far-field pattern of stimulated emission gives a direct mapping of the allowed Bloch wave vectors in the Brillouin zone. The mapping exhibits a wave-vector gap at the Bragg condition and may be associated with a photonic energy gap. In addition to measuring the intensity distribution of these Bloch waves, we directly measure the phase of the wave by polarization shearing interferometry.
Recent developments in myelodysplastic syndromes (2014)

Once thought to be rare disorders, the myelodysplastic syndromes (MDS) are now recognized as among the most common hematological neoplasms, probably affecting >30 000 patients per year in the United States. US regulatory approval of azacitidine, decitabine, and lenalidomide between 2004 and 2006 seemed to herald a new era in the development of disease-modifying therapies for MDS, but there have been no further drug approvals for MDS indications in the United States in the last 8 years. The available drugs are not curative, and few of the compounds that are currently in development are likely to be approved in the near future. As a result, MDS diagnoses continue to place a heavy burden on both patients and health care systems. Incomplete understanding of disease pathology, the inherent biological complexity of MDS, and the presence of comorbid conditions and poor performance status in the typical older patient with MDS have been major impediments to development of effective novel therapies. Here we discuss new insights from genomic discoveries that are illuminating MDS pathogenesis, increasing diagnostic accuracy, and refining prognostic assessment, and which will one day contribute to more effective treatments and improved patient outcomes.
CYR61 and αVβ5 Integrin Cooperate to Promote Invasion and Metastasis of Tumors Growing in Preirradiated Stroma (2008)

Radiotherapy is widely used to treat human cancer. Patients locally recurring after radiotherapy, however, have increased risk of metastatic progression and poor prognosis. The clinical management of postradiation recurrences remains an unresolved issue. Tumors growing in preirradiated tissues have an increased fraction of hypoxic cells and are more metastatic, a condition known as tumor bed effect. The transcription factor hypoxia inducible factor (HIF)-1 promotes invasion and metastasis of hypoxic tumors, but its role in the tumor bed effect has not been reported. Here, we show that tumor cells derived from SCCVII and HCT116 tumors growing in a preirradiated bed, or selected in vitro through repeated cycles of severe hypoxia, retain invasive and metastatic capacities when returned to normoxia. HIF activity, although facilitating metastatic spreading of tumors growing in a preirradiated bed, is not essential. Through gene expression profiling and gain- and loss-of-function experiments, we identified the matricellular protein CYR61 and alphaVbeta5 integrin as proteins cooperating to mediate these effects. The anti-alphaV integrin monoclonal antibody 17E6 and the small molecular alphaVbeta3/alphaVbeta5 integrin inhibitor EMD121974 suppressed invasion and metastasis induced by CYR61 and attenuated metastasis of tumors growing within a preirradiated field. These results represent a conceptual advance to the understanding of the tumor bed effect and identify CYR61 and alphaVbeta5 integrin as proteins that cooperate to mediate metastasis. They also identify alphaV integrin inhibition as a potential therapeutic approach for preventing metastasis in patients at risk for postradiation recurrences.
Detection of enteroviruses from clinical specimens by spin amplification shell vial culture and monoclonal antibody assay (1996)

Conventional tube cell culture was compared with a 72-h, spin-amplified shell vial indirect immunofluorescence assay for the detection of enterovirus from clinical specimens. The sensitivity for the shell vial assay after resolution of discrepant results were 93 and 100%, respectively. The shell vial assay detected 93% of the positive cultures within 72 h of incubation while conventional tube culture detected only 51% of the positive cultures within the same time interval. The data suggest that a spin-amplified shell vial indirect immunofluorescence assay may be useful for the detection of enterovirus from clinical specimens.
Lava: A Reality Check of Network Coding in Peer-to-Peer Live Streaming (2007)

In recent literature, network coding has emerged as a promising information theoretic approach to improve the performance of both peer-to-peer and wireless networks. It has been widely accepted and acknowledged that network coding can theoretically improve network throughput of multicast sessions in directed acyclic graphs, achieving their cut-set capacity bounds. Recent studies have also supported the claim that network coding is beneficial for large-scale peer-to-peer content distribution, as it solves the problem of locating the last missing blocks to complete the download. We seek to perform a reality check of using network coding for peer-to-peer live multimedia streaming. We start with the following critical question: How helpful is network coding in peer-to-peer streaming? To address this question, we first implement the decoding process using Gauss-Jordan elimination, such that it can be performed while coded blocks are progressively received. We then implement a realistic testbed, called Lava, with actual network traffic to meticulously evaluate the benefits and tradeoffs involved in using network coding in peer-to-peer streaming. We present the architectural design challenges in implementing network coding for the purpose of streaming, along with a pull-based peer-to-peer live streaming protocol in our comparison studies. Our experimental results show that network coding makes it possible to perform streaming with a finer granularity, which reduces the redundancy of bandwidth usage, improves resilience to network dynamics, and is most instrumental when the bandwidth supply barely meets the streaming demand.