gebhart/patrepeval huggingface dataset:
ROMA: reliable overlay multicast with loosely coupled TCP connections (2004)

We consider the problem of architecting a reliable content delivery system across an overlay network using TCP connections as the transport primitive. We first argue that natural designs based on store-and-forward principles that tightly couple TCP connections at intermediate end-systems impose fundamental performance limitations, such as dragging down all transfer rates in the system to the rate of the slowest receiver. In contrast, the ROMA architecture we propose incorporates the use of loosely coupled TCP connections together with fast forward error correction techniques to deliver a scalable solution that better accommodates a set of heterogeneous receivers. The methods we develop establish chains of TCP connections, whose expected performance we analyze through equation-based methods. We validate our analytical findings and evaluate the performance of our ROMA architecture using a prototype implementation via extensive Internet experimentation across the PlanetLab distributed testbed.
Cell signalling pathways underlying induced pluripotent stem cell reprogramming (2014)

Induced pluripotent stem (iPS) cells present great promise, both to research and to medicine. However, we know very little regarding the mechanisms that occur throughout the iPS cell reprogramming process and thus the process remains inefficient. In this review, we discuss the 3 stages of reprogramming, initiation, maturation and stabilisation, and clarify the signalling pathways underlying each phase. We draw together the current knowledge to propose a model for the interactions between the key pathways in iPS cell reprogramming with the aim of illuminating this complex yet fascinating process.
Cost‐utility analysis of Canadian tailored prophylaxis, primary prophylaxis and on‐demand therapy in young children with severe haemophilia A (2008)

Primary prophylaxis is the emerging standard treatment for boys with severe haemophilia. Tailored (escalating-dose) prophylaxis (EscDose), beginning at a low frequency and escalating with repeated bleeding may prevent arthropathy at a lower cost than standard prophylaxis (SP). From a societal perspective, we compared the incremental cost per joint-haemorrhage that is avoided and quality-adjusted-life-year (QALY) gained of SP and EscDose to on-demand (Demand) therapy in severe haemophilia A boys treated to age 6 using a decision analytic model. Costs included factor VIII (FVIII), professional visits and tests, central venous placement/complications, hospitalization, home programmes and parents' lost work-days. Resource utilization was estimated by surveying 17 Canadian clinics. The natural history of bleeding and other probabilities were determined from a longitudinal chart review (n = 24) and published literature. EscDose costs an additional $3192 per joint-haemorrhage that was avoided compared with Demand whereas SP costs an additional $9046 per joint-haemorrhage that was avoided compared with EscDose. Clinic costs and lost wages were reduced by 60-80% for EscDose and SP compared with Demand. EscDose attained more QALYs than SP and Demand on account of less bleeding than Demand and lower need for ports than SP. The incremental cost per QALY for EscDose vs. Demand was $542 938. EscDose was less expensive with similar QALYs compared to SP. Sensitivity analysis was performed on all probability- and cost-estimates, and showed the model was sensitive to the cost of FVIII and the SP and target joint utilities. In conclusion, prophylaxis will substantially improve clinical outcomes and quality of life compared to Demand treatment, but with substantial cost.
Genes Encoding Proteins Homologous to Halobacterial Gvps N, J, K, F & L are Located Downstream ofgvpCin the CyanobacteriumAnabaena flos-aquae (1997)

Only two gas vesicle genes have been previously identified in the cyanobacteria, gvpA and gvpC, both of which encode structural gas vesicle proteins. Analysis of the nucleotide sequence immediately downstream of gvpC in the cyanobacterium Anabaena flos-aquae has revealed the presence of 4 ORFs (open reading frames) the products of which share significant homology with a number of the gene products derived from halobacterial gvp gene clusters. In halobacteria the gas vesicle gene clusters consist of 14 genes involved in gas vesicle synthesis and assembly. The product of Anabaena ORF 1, located immediately downstream of gvpC is homologous to halobacterial GvpNs. For the remaining ORFs the predicted gene products show homology to both GvpJ and GvpA for ORF 2, to GvpK and GvpA for ORF 3, and to both GvpF and GvpL for ORF 4.
Synthesis and stabilization of complex behaviors through online trajectory optimization (2012)

We present an online trajectory optimization method and software platform applicable to complex humanoid robots performing challenging tasks such as getting up from an arbitrary pose on the ground and recovering from large disturbances using dexterous acrobatic maneuvers. The resulting behaviors, illustrated in the attached video, are computed only 7 × slower than real time, on a standard PC. The video also shows results on the acrobot problem, planar swimming and one-legged hopping. These simpler problems can already be solved in real time, without pre-computing anything.
Assessment of Docking Poses:  Interactions-Based Accuracy Classification (IBAC) versus Crystal Structure Deviations (2004)

Six docking programs (FlexX, GOLD, ICM, LigandFit, the Northwestern University version of DOCK, and QXP) were evaluated in terms of their ability to reproduce experimentally observed binding modes (poses) of small-molecule ligands to macromolecular targets. The accuracy of a pose was assessed in two ways: First, the RMS deviation of the predicted pose from the crystal structure was calculated. Second, the predicted pose was compared to the experimentally observed one regarding the presence of key interactions with the protein. The latter assessment is referred to as interactions-based accuracy classification (IBAC). In a number of cases significant discrepancies were found between IBAC and RMSD-based classifications. Despite being more subjective, the IBAC proved to be a more meaningful measure of docking accuracy in all these cases.
Identification of 21 Genes of Infectious Laryngotracheitis Virus Using Random Sequencing of Genomic DNA (1989)

DNA from infectious laryngotracheitis virus (ILTV) was randomly sheared and cloned into the M13 bacteriophage. Clones containing ILTV DNA were sequenced and the predicted amino acid sequences were compared to the known sequences of other herpesviruses using computer analysis. Twenty-one ILTV genes were identified, 20 by comparison to varicella-zoster virus and 19 by comparison to herpes simplex virus type 1; only 12 genes, giving consistently lower homology scores, were found by comparison with the gammaherpesvirus Epstein-Barr virus, indicating that ILTV sequences bear greater similarity to other alpha- than to gammaherpesvirus sequences.
Hepatitis B Virus and Hepatocellular Carcinoma: Molecular Biology and Mechanistic Considerations (1984)

The question of whether HBV causes HCC has to date best been answered by epidemiologic studies, in particular prospective analysis such as the ongoing study in Taiwan. The mechanism whereby HBV may cause HCC by genetic or epigenetic means, acting alone or in concert with other agents, is still moot . To date, studies of HBV gene expression have not shown the presence of a transforming gene or an oncogene associated with this virus. The finding of integrated HBV DNA in most HCC of carriers is highly suggestive of a causal role of the virus in the pathogenesis of neoplasia. In order to be more certain, it will be necessary to show that expression of integrated HBV genes or of cellular genes, as a result of HBV infection, causes neoplastic transformation of cells. Failure to date to demonstrate that HBV DNA induces neoplastic transformation of eukaryotic cells in culture may be simply due to an inadequate experimental model. The majority of these experiments have used fibroblasts or monkey kidney cells as the recipient cell, whereas cultured human hepatocytes might be more suitable. Whatever role HBV eventually is shown to have in the pathogenesis of HCC, molecular biologic techniques will have in great measure contributed to that knowledge. The use of these powerful new methods will permit studies of the replication of HBV and possible elucidation of how this virus affects the hepatocyte during persistent infection and will in time lead to a better understanding of cell and molecular events leading to development of hepatic malignancy.
Engineering precision RNA molecular switches (1999)

Ligand-specific molecular switches composed of RNA were created by coupling preexisting catalytic and receptor domains via structural bridges. Binding of ligand to the receptor triggers a conformational change within the bridge, and this structural reorganization dictates the activity of the adjoining ribozyme. The modular nature of these tripartite constructs makes possible the rapid construction of precision RNA molecular switches that trigger only in the presence of their corresponding ligand. By using similar enzyme engineering strategies, new RNA switches can be made to operate as designer molecular sensors or as a new class of genetic control elements.
Synergistic action of nikkomycins X and Z with papulacandin B on whole cells and regenerating protoplasts of Candida albicans (1986)

Combinations of nikkomycin X (NX) or nikkomycin Z (NZ), known inhibitors of chitin synthesis in fungi, together with papulacandin B (PB), an inhibitor of beta-glucan synthesis, were tested for synergistic activity against four isolates of Candida albicans by using the broth microdilution checkerboard technique and a method to assess the regeneration of cell wall material in protoplasts. The construction of isobolograms from the data generated by the checkerboard determinations revealed a synergistic effect for the two classes of compounds against all strains. The combination of NX and PB was more effective than the combination of NZ and PB, perhaps reflecting the lower Ki value of NX. While the presence of NX and NZ reduced chitin synthesis, as determined by staining with calcofluor white and assaying with a microfluorimeter, cells treated with PB demonstrated an increased synthesis of chitin. Protoplast regeneration experiments using similar concentrations of the two classes of compounds resulted in comparable findings. The combination of NX and PB resulted in a greater inhibition of chitin synthesis than did equivalent combinations of NZ and PB. These data suggest that combinations of agents active against cell wall synthesis in fungi may prove more useful as chemotherapeutic agents than such compounds used singly.
Auditory filter bank design using masking curves (2001)

It is very difficult and costly to experimentally observe the motion of the basilar membrane in a fully functional cochlea with the view to obtaining amplitude response at points along the membrane. This paper presents an inexpensive method of generating psychoacoustic tuning curves from the well-known masking curves in critical band rate. We present a method for designing critical band auditory filters from the tuning curves. It is also known that the auditory filter frequency response becomes broader with increasing input signal levels and becomes narrower with decreasing signal levels. We also propose a method for designing level dependent auditory filters. The proposed filter bank is applicable to various types of signal processing required to model human auditory filtering.
A parallel LSI architecture for LDPC decoder improving message-passing schedule (2006)

This paper proposes a parallel LSI architecture for LDPC decoder which improves a message-passing schedule. The proposed LDPC decoder is characterized as follows: (i) the column operations follow the row operations in a pipelined architecture to ensure that the row and column operations are performed concurrently; and (ii) the proposed parallel pipelined bit functional unit enables the decoder to perform every column operation using the messages which is updated by the row operations. These column operations can be performed without extending the single iterative decoding delay. Hardware implementation and simulation results show that the proposed decoder improves the decoding throughput and bit error performance with a small hardware overhead
Urokinase receptor is a multifunctional protein: influence of receptor occupancy on macrophage gene expression. (1995)

Binding of urokinase to the glycolipid-anchored urokinase receptor (uPAR) has been implicated in macrophage differentiation. However, no biochemical markers of differentiation have yet been directly linked to uPAR occupancy. As extensive changes in proteolytic profile characterize monocytic differentiation, we have examined the role of uPAR occupancy on protease expression by differentiating phagocytes. Antibodies to either urokinase or to uPAR that prevent receptor binding inhibited induction of cathepsin B in cultured monocytes and both cathepsin B and 92-kD gelatinase mRNA and protein in phorbol diester-stimulated myeloid cells. Mannosamine, an inhibitor of glycolipid anchor assembly, also blocked protease expression. Anti-catalytic urokinase antibodies, excess inactive urokinase, or aprotinin had no effect, indicating that receptor occupancy per se regulated protease expression. Antibodies to the integrins CD11a and CD29 or to the glycolipid-anchored proteins CD14 and CD55 also had no effect. Protease induction was independent of matrix attachment. Antibodies to urokinase or uPAR affected neither the decrease in cathepsin G nor the increase in tumor necrosis factor-alpha in phorbol ester-stimulated cells. These data establish that uPAR is a multifunctional receptor, not only promoting pericellular proteolysis and matrix attachment, but also effecting cysteine- and metallo-protease expression during macrophage differentiation.
Rapid Vapor Deposition of Highly Conformal Silica Nanolaminates (2002)

Highly uniform and conformal coatings can be made by the alternating exposures of a surface to vapors of two reactants, in a process commonly called atomic layer deposition (ALD). The application of ALD has, however, been limited because of slow deposition rates, with a theoretical maximum of one monolayer per cycle. We show that alternating exposure of a surface to vapors of trimethylaluminum and tris(tert-butoxy)silanol deposits highly conformal layers of amorphous silicon dioxide and aluminum oxide nanolaminates at rates of 12 nanometers (more than 32 monolayers) per cycle. This process allows for the uniform lining or filling of long, narrow holes. We propose that these ALD layers grow by a previously unknown catalytic mechanism that also operates during the rapid ALD of many other metal silicates. This process should allow improved production of many devices, such as trench insulation between transistors in microelectronics, planar waveguides, microelectromechanical structures, multilayer optical filters, and protective layers against diffusion, oxidation, or corrosion.
Overexpression of Transforming Growth Factor-β1 and Insulin-Like Growth Factor-I in Patients With Idiopathic Hypertrophic Cardiomyopathy (1997)

Gene expression of TGF-beta1 and IGF-I was enhanced in idiopathic hypertrophic cardiomyopathy and may be associated with its development.
Noisy Splicing Drives mRNA Isoform Diversity in Human Cells (2010)

While the majority of multiexonic human genes show some evidence of alternative splicing, it is unclear what fraction of observed splice forms is functionally relevant. In this study, we examine the extent of alternative splicing in human cells using deep RNA sequencing and de novo identification of splice junctions. We demonstrate the existence of a large class of low abundance isoforms, encompassing approximately 150,000 previously unannotated splice junctions in our data. Newly-identified splice sites show little evidence of evolutionary conservation, suggesting that the majority are due to erroneous splice site choice. We show that sequence motifs involved in the recognition of exons are enriched in the vicinity of unconserved splice sites. We estimate that the average intron has a splicing error rate of approximately 0.7% and show that introns in highly expressed genes are spliced more accurately, likely due to their shorter length. These results implicate noisy splicing as an important property of genome evolution.
Synthesis of cyclic carbonates from carbon dioxide and epoxides in the presence of organoantimony compounds as novel catalysts (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of cyclic carbonates from carbon dioxide and epoxides in the presence of organoantimony compounds as novel catalystsRyoki Nomura, Akira Ninagawa, and Haruo MatsudaCite this: J. Org. Chem. 1980, 45, 19, 3735–3738Publication Date (Print):September 1, 1980Publication History Published online1 May 2002Published inissue 1 September 1980https://pubs.acs.org/doi/10.1021/jo01307a002https://doi.org/10.1021/jo01307a002research-articleACS PublicationsRequest reuse permissionsArticle Views643Altmetric-Citations116LEARN 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
Identification and validation of suitable endogenous reference genes for gene expression studies in human peripheral blood (2009)

The reference genes identified in this study are stably expressed in whole blood of humans of both genders with multiple disease conditions and ages 2 to 78. Importantly, they also have different functions within cells and thus should be expressed independently of each other. These genes should be useful as normalization genes for microarray and RT-PCR whole blood studies of human physiology, metabolism and disease.
The role of CXC chemokines in the regulation of angiogenesis in non-small cell lung cancer (1997)

Angiogenesis is a critical component of tumor biology. In recent years newer techniques of cell and molecular biology have led to important advances in our understanding of this process. The regulation of angiogenesis depends on a balance between the activity of local factors that promote (angiogenic factors) or inhibit (angiostatic factors) neovascularization. Nowhere is this paradigm of a balance more apparent than in the study of tumor-associated angiogenesis. Tumors promote angiogenesis through a combination of overexpression of angiogenic factors and local inhibition of angiostatic factors. This strategy leads to an angiogenic environment that promotes tumor growth and metastases. Our laboratory has focused studies on the role of the CXC chemokine family in the regulation of angiogenesis by non-small cell lung cancer (NSCLC). In this article, we review our findings that the CXC chemokine family is composed of members that are either angiogenic or angiostatic. We have found that in NSCLC an imbalance exists in the expression of these factors that favors tumor-derived angiogenesis, and therefore tumor growth and metastases. Furthermore, when this imbalance is corrected to reduce the presence of angiogenic factors or increase the presence of angiostatic factors, tumor growth and metastases are reduced.
Comprehensive exploration of novel chimeric transcripts in clear cell renal cell carcinomas using whole transcriptome analysis (2014)

The aim of this study was to clarify the participation of expression of chimeric transcripts in renal carcinogenesis. Whole transcriptome analysis (RNA sequencing) and exploration of candidate chimeric transcripts using the deFuse program were performed on 68 specimens of cancerous tissue (T) and 11 specimens of non-cancerous renal cortex tissue (N) obtained from 68 patients with clear cell renal cell carcinomas (RCCs) in an initial cohort. As positive controls, two RCCs associated with Xp11.2 translocation were analyzed. After verification by reverse transcription (RT)-PCR and Sanger sequencing, 26 novel chimeric transcripts were identified in 17 (25%) of the 68 clear cell RCCs. Genomic breakpoints were determined in five of the chimeric transcripts. Quantitative RT-PCR analysis revealed that the mRNA expression levels for the MMACHC, PTER, EPC2, ATXN7, FHIT, KIFAP3, CPEB1, MINPP1, TEX264, FAM107A, UPF3A, CDC16, MCCC1, CPSF3, and ASAP2 genes, being partner genes involved in the chimeric transcripts in the initial cohort, were significantly reduced in 26 T samples relative to the corresponding 26 N samples in the second cohort. Moreover, the mRNA expression levels for the above partner genes in T samples were significantly correlated with tumor aggressiveness and poorer patient outcome, indicating that reduced expression of these genes may participate in malignant progression of RCCs. As is the case when their levels of expression are reduced, these partner genes also may not fully function when involved in chimeric transcripts. These data suggest that generation of chimeric transcripts may participate in renal carcinogenesis by inducing dysfunction of tumor-related genes.
Fast and Efficient Compression of Floating-Point Data (2006)

Large scale scientific simulation codes typically run on a cluster of CPUs that write/read time steps to/from a single file system. As data sets are constantly growing in size, this increasingly leads to I/O bottlenecks. When the rate at which data is produced exceeds the available I/O bandwidth, the simulation stalls and the CPUs are idle. Data compression can alleviate this problem by using some CPU cycles to reduce the amount of data needed to be transfered. Most compression schemes, however, are designed to operate offline and seek to maximize compression, not throughput. Furthermore, they often require quantizing floating-point values onto a uniform integer grid, which disqualifies their use in applications where exact values must be retained. We propose a simple scheme for lossless, online compression of floating-point data that transparently integrates into the I/O of many applications. A plug-in scheme for data-dependent prediction makes our scheme applicable to a wide variety of data used in visualization, such as unstructured meshes, point sets, images, and voxel grids. We achieve state-of-the-art compression rates and speeds, the latter in part due to an improved entropy coder. We demonstrate that this significantly accelerates I/O throughput in real simulation runs. Unlike previous schemes, our method also adapts well to variable-precision floating-point and integer data.
Real‐time three‐dimensional imaging of macroscopic structures (1998)

We describe an extremely simple method of obtaining optically sectioned images with conventional low-power imaging systems in real time. A single spatial frequency grid pattern is projected onto an object. Images taken at three spatial positions of the grid projection are processed to provide 3D images of macroscopic structures.