gebhart/patrepeval huggingface dataset:
Max: functional domains and interaction with c-Myc. (1992)

The product of the c-myc proto-oncogene is a DNA-binding protein, the deregulated expression of which is associated with a variety of malignant neoplasms. The cDNA for the max gene was recently cloned as a result of the ability of its protein product to interact with the c-Myc protein. We studied bacterially produced Max, c-Myc, and a series of truncated c-Myc proteins. Full-length c-Myc alone cannot bind DNA. However, a truncated c-Myc protein comprising the basic, helix-loop-helix, and leucine zipper regions can bind specifically to DNA bearing the sequence GGGCAC(G/A)TGCCC. Max protein, either alone or in a heteromeric complex with full-length c-Myc, binds to the same core sequence. Using a novel combination of chemical and photo-cross-linking analysis, we demonstrate that either Max or a c-Myc/Max heteromeric complex binds to DNA virtually exclusively in a dimeric structure. Using fusion proteins in cultured cells, we establish a number of functional characteristics of Max. First, we show that Max can interact with c-Myc intracellularly in a manner dependent on the integrity of the helix-loop-helix and leucine zipper motifs. Second, a nuclear localization domain that contains the sequence PQSRKKLR is mapped to the carboxy-terminal region of Max. Third, Max lacks a transcriptional activation domain that is functional in Chinese hamster ovary cells when fused to a heterologous DNA-binding domain. These data suggest that Max may serve as a cofactor for c-Myc in transcriptional activation or, by itself, as a transcriptional repressor.
Pre-execution via speculative data-driven multithreading (2001)

This dissertation introduces pre-execution, a novel technique for accelerating sequential programs. Pre-execution directly attacks the instructions that cause performance problems—mis-predicted branches and cache missing loads. In pre-execution, future branch outcomes and load addresses are computed on the side and the results are fed to the main program. In doing so, the main program is spared from having to incur the full computation latencies of these instructions. Pre-execution exploits out-of-order fetch and decoupling. Fetching and executing only critical load and branch computations while skipping over all unrelated instructions allows pre-execution to compute values faster than the main program. Decoupling, doing so in a separate thread, isolates stalls that occur in these computations so that they do not directly impact the main program thread. 
This dissertation describes speculative data-driven multithreading (DDMT), an implementation of pre-execution. DDMT implements the runtime component of pre-execution—responsible for pre-executing computations and communicating the results to the main program—as an extension to a superscalar processor. In addition to using the single cache hierarchy to allow pre-executing computations to prefetch for the main program, DDMT stores individual pre-executed instruction results in the shared physical register and then passes them one-by-one to the main program via a novel modification to register renaming called register integration. 
For DDMT's setup component—responsible for finding load and branch computations and conveying them to the runtime component—this dissertation introduces an algorithm for automatically extracting performance-enhancing computations from program traces. The algorithm evaluates a benefit-cost function over all candidate computations in a trace and chooses those that maximize benefit (latency tolerance) while minimizing cost (execution overhead). The algorithm is formulated to permit software, hardware, and hybrid implementations. 
The dissertation includes a simulation-driven performance evaluation of DDMT Our results show that DDMT achieves 10% to 15% performance improvements for general-purpose integer programs running on an aggressive baseline processor with large caches, with the potential for greater improvements on likely future processor designs. We conclude that pre-execution and DDMT are promising technologies that merit consideration for inclusion in future machines.
A multimedia synchronization protocol for multicast groups (2002)

Multicast distribution of multimedia streams is an important component of many existing and future networked services. These services are characterized by the integrated processing of different media types, such as audio and video. Often, different multimedia streams must be played out in a synchronized way. Due to the asynchronous nature of networks, some problems can disrupt synchronization such as delay jitter and different initial playback times. The author proposes a method consisting of intra-stream and inter-client synchronization mechanisms. It allows different members of a multicast group to playback media units at the same time and in a continuous manner. The mechanism can be used in networks having unknown delay bounds. It allows receivers to be synchronized for media unit playbacks. To do this, we use feedback messages for source and buffer management. However, there is no assumption about clock synchronization and messages are not time-stamped.
A Portrait of AKT Kinases: Human Cancer and Animal Models Depict a Family with Strong Individualities (2004)

More than a decade after their discovery, the three AKT kinase family members have emerged as central players in the signaling cascades that regulate cell growth, proliferation, survival and various aspects of intermediary metabolism. The mechanisms of activation of AKT kinases have been defined in relatively precise terms and new substrates are currently being validated in vivo. However, it is presently unclear whether AKT1, AKT2 and AKT3 are functionally redundant or whether each one performs specific functional role(s). In this review, we will summarize the signaling properties and highlight the specificities of AKT kinases that have emerged from the study of human cancer and animal models. While AKT kinases are an attractive target for pharmacological intervention, knowledge of the precise individual roles of AKT family members will improve the design of highly specific AKT-based therapeutics having reduced toxicity and improved efficacy.
Differential Frequencies of p16INK4a Promoter Hypermethylation, p53 Mutation, and K-ras Mutation in Exfoliative Material Mark the Development of Lung Cancer in Symptomatic Chronic Smokers (2000)

p16(INK4a) promoter hypermethylation and p53 mutations can occur in chronic smokers before any clinical evidence of neoplasia and may be indicative of an increased risk of developing lung cancer or of early disease. K-ras mutations occur exclusively in the presence of clinically detectable neoplastic transformation. Molecular analysis of sputum for such markers may provide an effective means of screening chronic smokers to enable earlier detection and therapeutic intervention of lung cancer.
Ardisiacrispin A and B, Two Utero-Contracting Saponins fromArdisia crispa (1987)

The main utero-contracting activity of an aqueous extract of Ardisia crispa (Thunb.) A. DC. is due to two new triterpenic saponins called ardisiacrispin A and B, respectively. The saponins were isolated by extraction with n-butanol, followed by chromatography on silica gel columns. Final purification was obtained by reversed phase HPLC. 13C-NMR identified the aglycone of both saponins as cyclamiretin A. The structure of the ardisiacrispins was deduced by sugar and methylation analysis in combination with 1H- and 13C-NMR spectral data.
Characterization of the two intracellular lipases of Y. lipolytica encoded by TGL3 and TGL4 genes: New insights into the role of intracellular lipases and lipid body organisation (2013)

Eukaryotes store lipids in a specialised organelle, the lipid body (LB), mainly as triglycerides (TAGs). Both the rates of synthesis and degradation contribute to the control of the accumulation of TAGs. The synthesis of TAGs in yeasts has been well documented, especially in the model yeast Saccharomyces cerevisiae and in the oleaginous yeast Yarrowia lipolytica. However, descriptions of the processes involved in TAG degradation are more scarce and mostly for S. cerevisiae. Here, we report the characterisation of two Y. lipolytica genes, YlTGL3 and YlTGL4, encoding intracellular lipases involved in TAG degradation. The two proteins are localised in lipid bodies, and YlTgl4 was mainly found at the interface between LBs. Surprisingly, the spatial organisation of YlTgl3 and YlTgl4 depends on the culture medium and on the physiological phase of the cell. Inactivation of one or both genes doubles the lipid accumulation capacity of Y. lipolytica, increasing the cell's capacity to accumulate TAGs. The amino acid sequence of YlTgl4 contains the consensus sequence motif (G/A)XSXG, typical of serine hydrolases, whereas YlTgl3 does not. Single and double mutants are unable to degrade TAGs, and higher expression of YlTgl4 correlates with TAG degradation. Therefore, we propose that YlTgl4 is the main lipase responsible for TAG degradation and that YlTgl3 may act as a positive regulator of YlTgl4 rather than a functional lipase. Thus, contrary to S. cerevisiae, Y. lipolytica possesses two intracellular lipases with distinct roles and with distinct localisations in the LB.
The extracellular processing of HIV‐1 envelope glycoprotein gp160 by human plasmin (1999)

Cleavage of the envelope glycoprotein precursor gp160 of HIV-1 is a prerequisite for the infectivity of HIV-1, and occurs at least in part before gp160 reaches the cell surface. Kexin/subtilisin-related endopeptidases are proposed enzyme candidates for this intracellular processing. In this study, we reveal the possibility that plasminogen binds to the cell surface and part of gp160 escaping intracellular processing is cleaved by plasmin extracellularly. Plasmin cleaves gp160 precisely at the C-terminal arginine residue of gp120, and the processing is effectively inhibited by an analogue peptide of the cleavage motif (RXK/RR) and by plasmin inhibitors.
Combining structure search and content search for the World-Wide Web (1998)

Article Combining structure search and content search for the World-Wide Web Share on Authors: Hermann Kaindl Siemens AG Austria, Geusaug. 17, A-1030 Vienna, Austria Siemens AG Austria, Geusaug. 17, A-1030 Vienna, AustriaView Profile , Stefan Kramer Siemens AG Austria, Geusaug. 17, A-1030 Vienna, Austria Siemens AG Austria, Geusaug. 17, A-1030 Vienna, AustriaView Profile , Luis Miguel Afonso Rua de Campolide, 51-5, 1070 Lisboa, Portugal Rua de Campolide, 51-5, 1070 Lisboa, PortugalView Profile Authors Info & Claims HYPERTEXT '98: Proceedings of the ninth ACM conference on Hypertext and hypermedia : links, objects, time and space---structure in hypermedia systems: links, objects, time and space---structure in hypermedia systemsMay 1998 Pages 217–224https://doi.org/10.1145/276627.276651Published:01 May 1998 3citation558DownloadsMetricsTotal Citations3Total Downloads558Last 12 Months0Last 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
Differentiated biological activity of Vero cytotoxins (VT) released by human and porcine Escherichia coli strains (1983)

We have investigated the biological activity in the filtered culture supernatants from 9 VT-producing Escherichia coli strains.The filtrates from 4 strains (3 of human and one of bovine origin), were cytotoxic on Vero and HeLa cells, and caused death in intraperitoneally injected adult mice.The 5 strains of porcine origin showed cytotoxic activity on Vero and Y-1 cells but not on HeLa cells.Filtrates of these latter strains were not lethal for adult mice.VT-cytotoxins produced by all strains were inactive in the infant mouse test and the filtrates from 7 of 8 VT-producing strains assayed in rabbit ileal loops caased fluid accumulation in at least one of the 3 rabbits employed.
Connectionist Learning for Control: An Overview (1991)

THIS REPORT IS AN INTRODUCTORY OVERVIEW OF LEARNING BY CONNECTIONIST NETWORKS, ALSO CALLED ARTIFICIAL NEURAL NETWORKS, WITH A FOCUS ON THE IDEAS AND METHODS MOST RELEVANT TO THE CONTROL OF DYNAMICAL SYSTEMS. IT IS INTENDED BOTH TO PROVIDE AN OVERVIEW OF CONNECTIONIST IDEAS FOR CONTROL THEORISTS AND TO PROVIDE CONNECTIONIST RESEARCHERS WITH AN INTRODUCTION TO CERTAIN ISSUES IN CONTROL. THE PERSPECTIVE TAKEN EMPHASIZES THE CONTINUITY OF THE CURRENT CONNECTIONIST RESEARCH WITH MORE TRADITIONAL RESEARCH IN CONTROL, SIGNAL PROCESSING, AND PATTERN CLASSIFICATION. CONTROL THEORY IS A WELL-DEVELOPED FIELD WITH A LARGE LITERATURE, AND MANY OF THE LEARNING METHODS BEING DESCRIBED BY CONNECTIONISTS ARE CLOSELY RELATED TO METHODS THAT ALREADY HAVE BEEN INTENSIVELY STUDIED BY ADAPTIVE CONTROL THEORISTS. ON THE OTHER HAND, THE DIRECTIONS THAT CONNECTIONISTS ARE TAKING THESE METHODS HAVE CHARACTERISTICS THAT ARE ABSENT IN THE TRADITIONAL ENGINEERING APPROACHES. THIS REPORT DESCRIBES THESE CHARACTERISTICS AND DISCUSSES THEIR POSITIVE AND NEGATIVE ASPECTS. IT IS ARGUED THAT CONNECTIONISTS APPROACHES TO CONTROL ARE SPECIAL CASES OF MEMORY--INTENTIVE APPROACHES, PROVIDED A SUFFICIENTLY GENERALIZED VIEW OF MEMORY IS ADOPTED. BECAUSE ADAPTIVE CONNECTIONIST NETWORKS CAN COVER THE RANGE BETWEEN STRUCTURELESS LOOKUP TABLES AND HIGHLY CONSTRAINED MODEL-BASED PARAMETER ESTIMATION, THEY SEEM WELL-SUITED FOR THE ACQUISITION AND STORAGE OF CONTROL INFORMATION. AD
Cdk9 regulates neural differentiation and its expression correlates with the differentiation grade of neuroblastoma and PNET tumors (2005)

Cdk9 is a member of the Cdc2-like family of kinases. Its cyclin partners are members of the family of cyclin T (T1, T2a and T2b) and cyclin K. The Cdk9/Cyclin T complex appears to be involved in regulating several physiological processes. Recently, Cdk9 has been identified as a regulator of the differentiation program of several cell types, such as muscle cells, monocytes and lymphocytes, suggesting that it may have a function in controlling specific differentiative pathways. We analyzed whether Cdk9 and Cyclin T1 may be involved in the regulation of neuron and astrocyte differentiation. Cdk9 and Cyclin T1 expression levels were monitored during the differentiation program of neuroblastoma and astrocytoma cell lines. Our results suggest that Cdk9/Cyclin T1 complex may be required for neuron differentiation induced by retinoic acid, because the expression level of the complex varies during differentiation, but no significant changes were observed in its expression in the astrocytoma cell line. In addition, the expression of Cdk9 and Cyclin T1 was evaluated by immunohistochemistry in samples of neuroblastoma, PNET (Primary Neuroectodermal Tumor) and astrocytoma tumors of different grades, in order to assess whether there was a correlation between Cdk9 expression and tumor grading. Our results show that in neuroblastoma and PNET tumor samples Cdk9 is more expressed the more differentiated the tumor is. Conversely, no significant alteration of Cdk9 expression was observed in astrocytoma tumor samples of different grades, thus confirming the results obtained for the cell lines.
Saliva secretion and oral flora in prolonged nasogastric tube-fed elderly patients. (2003)

These findings suggest that prolonged nasogastric tube feeding is associated with pathologic colonization of the oroparynx and with alterations in the saliva that are related to the risk of aspiration pneumonia. Further research is called for, as well as a thorough revision of the existing oral cleansing procedures in these patients.
Ultra-morphological study of the interaction of dental adhesives with carbamide peroxide-bleached enamel. (1998)

Vital bleaching with 10% carbamide peroxide caused no significant changes in relative oxygen concentration of enamel. For calcium and phosphorus, bleaching resulted in significant decreased relative concentrations. Bleaching also resulted in morphological alterations in the most superficial enamel crystallites. Some altered crystallites exhibited electron-lucent cores and reduced thickness of material around the core.
<title>Comparison Of Coherent And Incoherent Imaging In The Location Of Point Sources</title> (1982)

The position location accuracy of a point source in the fields of view of two telescopes with the same focal plane is considered. It is shown that for detectors sized to equal the distance to the first zero of the coherently added system, there is little practical difference in accuracy between a system that adds the flux coherently as opposed to a system that adds it incoherently.
Pure Red Cell Aplasia Induced by Erythropoiesis-Stimulating Agents (2008)

Pure red cell aplasia in patients who are treated for anemia of chronic kidney disease with erythropoiesis-stimulating agents such as epoetin was first reported in 1998. Although the incidence of pure red cell aplasia peaked in 2002, it remains important for nephrologists to know how to investigate a suspected case of pure red cell aplasia and how to identify other causes of hyporesponsiveness to erythropoiesis-stimulating agents, which account for the vast majority of such cases. The authors reviewed the current status of information in the literature and drew on their personal experiences with patients regarding the diagnosis and management of epoetin-induced pure red cell aplasia. The mechanism for development of epoetin-induced pure red cell aplasia remains unconfirmed. It generally occurs after the production of neutralizing anti-erythropoietin antibodies. Elucidation of a suspected pure red cell aplasia case requires a systematic approach, beginning with simple measurements such as blood cell counts, because most cases of erythropoiesis-stimulating agent hyporesponsiveness are attributable to other causes. If these criteria indicate that the patient's response to erythropoiesis-stimulating agent therapy is very poor, then bone marrow examination and measurement of anti-erythropoietin antibodies is justified. If pure red cell aplasia is confirmed, then cessation of erythropoiesis-stimulating agent therapy and initiation of immunosuppressive therapy are recommended. Continued study of epoetin-induced pure red cell aplasia is needed to help nephrologists prevent or manage future cases and will have implications for the use of other protein-based therapeutic agents.
Potential strategies to reduce medial compartment loading in patients with knee osteoarthritis of varying severity: Reduced walking speed (2004)

Patients with less-severe OA adapt a walking style that differs from that of patients with more-severe OA and controls. This walking style is associated with the potential to reduce the adduction moment when walking at slower speeds and could be linked to decreased disease severity.
A Model for the Core Structure of the Escherichia coli RecA Protein (1984)

The RecA protein of Escherichia coli is essential for homologous recombination (Clark and Margulies 1965). The recA+ gene has been sequenced and has been shown to encode a 352-amino-acid protein of 37,800 daltons (Horii et al. 1980; Sancar et al. 1980). For its size, the RecA protein exhibits a remarkable variety of reactions in vitro. The protein can induce D-loops and effect strand transfer of DNA (Cox and Lehman 1981; DasGupta et al. 1981; Kahn et al. 1981; West et al. 1981), partially unwind duplex DNA (Dunn et al. 1982; Flory and Radding 1982; Iwabuchi et al. 1983), perform a cofactor-dependent, highly specific proteolytic function (McEntee and Weinstock 1981; Little et al. 1980), and catalyze DNA-dependent ATP hydrolysis (Ogawa et al. 1979; Weinstock et al. 1981). All of these activities of RecA protein depend on its binding to ATP.
Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM (2005)

Domain boundary prediction is an important step in both experimental and computational protein structure characterization. We have developed two fully automated domain parsing methods: the first, Ginzu, which we have described previously, utilizes information from homologous sequences and structures, while the second, RosettaDOM, which has not been described previously, uses only information in the query sequence. Ginzu iteratively assigns domains by homology to structures and sequence families using successively less confident methods. RosettaDOM uses the Rosetta de novo structure prediction method to build three-dimensional models, and then applies Taylor's structure based domain assignment method to parse the models into domains. Domain boundaries observed repeatedly in the models are predicted to be domain boundaries for the protein. Interestingly, RosettaDOM produced quite good domain predictions for proteins of a size typically considered to be beyond the reach of de novo structure prediction methods. For remote fold recognition targets and new folds, both Ginzu and RosettaDOM produced promising results, and in some cases where one method failed to detect the correct domain boundary, it was correctly identified by the other method. We describe here the successes and failures using both methods, and address the possibility of incorporating both protocols into an improved hybrid method.
Dialkylcyclopentadithiophene Polymers and Copolymers (2001)

Poly(2,6-(4,4-dialkyl)-4H-cyclopenta[2,1-b:3,4-b′]dithiophene) (PCPDT) homopolymers and poly[(2,7-(9,9-dialkyl)fluorene)-co-(2,6-(4,4-dialkyl)-4H-cyclopenta[2,1-b:3,4-b′]dithiophene)] (PF/PCPDT) copolymers have been synthesized according to Yamamoto with Ni(COD)2 (or NiCl2/Zn in the case of the homopolymer). PCPDT is characterized by a red-shifted long wavelength absorption maximum (565 nm) when compared to that of polyfluorene (PF, 378 nm). In contrast to PF, its heteroaromatic analogue PCPDT does not form thermotropic LC phases. The PF/PCPDT copolymers show clear indications for a block copolymer character (two separated π-π* absorption maxima, two glass transitions).
2D CSI proton MR spectroscopy of human spinal vertebra: Feasibility studies (2000)

This report focuses on proton magnetic resonance spectroscopy (1H MRS) of spine vertebra acquired with two-dimensional chemical shift imaging (2D CSI), utilizing the stimulated echo acquisition mode (STEAM) sequence. Both validity and reproducibility studies were performed. To validate the 2D CSI method, its spectra were compared with those obtained with the single-voxel (SV) method. Five normal volunteers were scanned. The reproducibility of 2D CSI was examined by performing spectroscopy on two different occasions, on three normal volunteers. Data show that the STEAM 2D CSI technique results in MRI spectra comparable to those obtained with the STEAM SV method. 2D CSI offers significant time savings and convenient multi-voxel spectral analysis at a substantially higher signal-to-noise ratio. The 2D CSI method was then applied to a patient with a small vertebral hemangioma. The results demonstrated that the voxels containing the hemangioma exhibit different spectra than the neighboring voxels of the same vertebra. Additionally, a case of vertebral osteoporosis was investigated. Results showed a significant increase in the lipid-to-water ratio (LWR). It is suggested that 2D CSI may be powerful in identifying physiological as well as pathological changes of the bone marrow. Furthermore, covering a more extensive area of the vertebral body will maximize the chances of depicting a small focus of pathologic tissue. A more detailed bone marrow pattern was noticed in on one subject whose spectra show more lipid peaks.