gebhart/patrepeval huggingface dataset:
Measurement-based characterization of parallel i/o systems (1999)

In high-performance parallel systems, there has been an increasing gap between the computational performance of parallel subsystems (CPU, memory, and interconnection network) on the one hand and the performance of the 1/0 subsystem on the other. This performance gap necessitates a search for alternative configurations and improved system software. Understanding the overall performance of these parallel systems requires a detailed characterization of individual subsystems (hardware and software) as well as of the interactions among them. Such characterization, in turn, requires detailed performance measurements of the individual subsystems. It also requires synthetic workload generators to generate predictive workloads that can be used to exercise and stress the parallel subsystems repeatedly. 
This research addresses the issue of evaluating the performance of parallel I/O subsystems for a variety of I/O intensive workloads on massively parallel systems. First, a model-based workload specification methodology for generating parallel I/O intensive workloads is described. Second, a synthetic workload generator and a performance measurement and monitoring environment based on the synthetic workload generator is described. Finally, the performances of three different kinds of I/O configurations, based on a client/server model, are characterized on two production class parallel file systems. In light of the measurements obtained on two parallel file systems, possible extensions are suggested to improve the overall architecture as well as the parallel file system of the massively parallel systems.
Culprits in the degradation of cyclin E apprehended (1999)

Critical events in the life of a cell require that the flux through particular regulatory pathways be abruptly and irreversibly altered in response to intracellular and extracellular signals. The central role played by reversible phosphorylation in controlling signaling pathways is well established, but in the last few years, ubiquitinmediated proteolysis has emerged as an equally important, and in some cases collaborative, partner in the control of regulatory processes in the cell. Ubiquitination, typically in the form of polyubiquitination, serves as a signal for destruction of the tagged protein by the 26S proteasome. Because the proteolytic event itself is very rapid, it is the process of ubiquitination that is rate limiting and highly regulated. Protein ubiquitination involves a cascade of ubiquitin transfer reactions and requires three components: E1, E2, and E3 (Hershko and Ciechanover 1998). In the first step, a ubiquitin-activating enzyme (E1) is charged with ubiquitin through a thiol–ester linkage. This ubiquitin is then transferred to one of a dozen or so ubiquitin conjugating enzymes (E2) also as a thiol–ester. The ubiquitin is finally transferred from the E2 to one or more lysine residues in the substrate with the aid of an E3 ubiquitin ligase. Multiple rounds of ubiquitin conjugation with the initial ubiquitin as the recipient lead to polyubiquitin chain formation. In essence, E3s function as substrate-specific adaptors by simultaneously binding substrate and the E2, although in some cases, E3s may also serve as an intermediate in the ubiquitin transfer process. Given that there are a large and diverse number of proteins whose abundance in the cell is controlled by ubiquitin-mediated proteolysis, how is sufficient diversity generated such that E3s selectively recognize only one or a few substrates? The answer to this question appears to be a superfamily of multicomponent E3s that dock substrates with a core ubiquitin-conjugating system via modular, substrate-specific adaptor proteins. The core-conjugating apparatus in several E3s includes a member of the Cullin/Cdc53 family of proteins first identified in budding yeast and Caenorhabditis elegans (Kipreos et al. 1996; Mathias et al. 1996; Willems et al. 1996). New work, including a recent paper in Genes and Development, implicates two distinct members of the Cullin family—Cul3 and Cul1—in the ubiquitin-mediated destruction of mammalian cyclin E, an activator of Cdk2 and an essential regulator of the G1/S transition (Singer et al. 1999; Dealy et al. 1999; Wang et al. 1999). The work reveals an unanticipated link between Cul3 and cell cycle control, and provides the first evidence that distinct Cullin complexes function in concert to control the levels of a single target protein. The requirement of Cul3 for embryonic development (Singer et al. 1999) provides yet another reminder of the importance of ubiquitin-mediated proteolysis in coordinating crucial events in the organism.
Structural Aspects of Heparin Responsible for Interactions With von Willebrand Factor (1997)

Unfractionated heparin (UFH) binds von Willebrand factor (vWF) and inhibits the vWF-platelet GP Ib interaction. For vWF, a heparin-binding domain has been identified, but for heparin, the structures that confer such activity are unknown. To investigate this, UFH was depolymerized by methods that yield structurally distinct fragments. The glycosaminoglycans (GAGs) produced were separated into five groups of homogeneous molecular weight (MW). Anti-Xa activity, vWF binding affinity, and vWF-dependent platelet agglutination were measured. Periodate oxidation but not heparinase digestion destroyed anti-Xa activity. At all MWs, periodate conferred greater vWF binding affinity and greater ability to inhibit platelet agglutination than heparinase. As an example, at MW 6100, the binding IC50 was 100+/-19 micromol/L for a periodate-derived GAG and 527+/-70 micromol/L for a heparinase-derived GAG. At the same MW, the agglutination IC50 was 17+/-5 micromol/L for periodate and 135+/-18 micromol/L for heparinase. This suggests that the disaccharide GlcNS[6S]-IdoA2S, destroyed by heparinase but not periodate, is crucial to heparin-vWF interactions. An MW dependency was also noted, with a minimum dodecasaccharide required for activity inhibition. To further investigate the heparin/vWF interaction, affinity fractionation of heparins was performed with an immobilized peptide derived from a heparin-binding domain of vWF. Disaccharide analysis of high-affinity heparins revealed an increased ratio of IdoA2S-GlcN[S/Ac]6S to IdoA2S-GlcN[S/Ac]. Affinity fractionation of oligosaccharides (MW 3500) diminished the relative content of all disaccharides except IdoA2S-GlcNS6S, which was increased. These data suggest that the disaccharide structures IdoA2S-GlcNS6S and GlcNS6S-IdoA2S are crucial to heparin/vWF interactions. Understanding the structural aspects that confer such activity may be useful in designing heparin-based antithrombotic drugs.
The Structural Basis Of Antigen-Antibody Recognition (1987)

Many bacterial clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated (Cas) systems employ the dual RNA–guided DNA endonuclease Cas9 to defend against invading phages and conjugative plasmids by introducing site-specific ...Read More
[HGF as a key molecule in cardiovascular diseases]. (2001)

Hepatocyte growth factor(HGF) is focused as a powerful endothelial growth factor in the field of cardiovascular diseases. As its physiological role in atherosclerosis, restenosis, angiogenesis etc is very important, HGF-based new treatments for various diseases are expected. Clinical gene therapy for restenosis and ischemic diseases using VEGF gene have already performed in USA, and they could show beneficial effects of such strategies. In Japan, gene therapy using HGF gene for ASO has just begun in spring 2001. In near future, powerful therapeutic effects of HGF could applied to restenosis, graft failure, cardiomyopathy, cerebral vascular diseases, renal failure and so on.
iNEMI BFR-free PCB materials evaluation project report (2008)

Brominated flame retardants, namely polybrominated diphenyl ethers (PBDEs), were one of the main materials used to reduce the flammability of consumer goods and electronics. Growing evidence shows that PBDE compounds are making their way into the environment. These chemicals may cause health effects, prompting many nations to ban or suspend their use in new consumer goods.
Merck molecular force field. V. Extension of MMFF94 using experimental data, additional computational data, and empirical rules (1996)

This article describes the extension of the Merck Molecular Force Field (MMFF94) to a much broader range of organic systems. It also describes a preliminary parameterization of MMFF94 for the hydronium and hydroxide ions and for various halide, alkalai, and alkalai earth ions as well as for such “protein” metals as Zn2+, Ca2+, Cu2+, Cu+, Fe2+, and Fe3+. The extension employed computational data on charge distributions, molecular geometries, and conformational energies for a series of oxysulfur (particularly sulfonamide) and oxyphosphorous compounds and for a diverse set of small molecules and ions not covered in the core parameterization. It also employed experimental data for approximately 2800 good-quality structures extracted from the Cambridge Structural Database (CSD). Some of the additional computational data were used to extend the explicit parameterization of electrostatic interactions and to more widely define a useful additive approximation for the “bond polarity” parameters (bond charge increments) used in MMFF94. Both the experimental and computational data served to define reference bond lengths and angles that the extended force field uses in conjunction with force constants obtained from carefully calibrated empirical rules. The extended torsion parameters consist partly of explicit parameters derived to reproduce MP2/6-31G* conformational energies and partly of “default parameters” provided by empirical rules patterned after those used in DREIDING and UFF but calibrated, where possible, against computationally derived MMFF94 torsion parameters. Comparisons to experimental data show that MMFF94 reproduces crystallographic bond lengths and bond angles with relatively modest root mean square (rms) deviations of approx. 0.02 Å and 2°, respectively. © John Wiley & Sons, Inc.
Increased Eotaxin in Tears of Patients Wearing Contact Lenses (2004)

An increase of eotaxin levels in tears was measured in patients wearing contact lenses. Eotaxin levels correlated with the severity of giant papillary conjunctivitis. These data suggest that eotaxin could play a role in papilla formation.
The Art of SQL (2006)

For all the buzz about trendy IT techniques, data processing is still at the core of our systems, especially now that enterprises all over the world are confronted with exploding volumes of data. Database performance has become a major headache, and most IT departments believe that developers should provide simple code to solve immediate problems and let DBAs tune any bad SQL later. In The Art of SQL, author and expert Stephane Faroult argues that this safe only leads to disaster. His insightful book, named after Art of War by Sun Tzu, contends that writing quick inefficient code is sweeping the dirt under the rug. code may run for 5 to 10 years, surviving several major releases of the database management system and on several generations of hardware. The code must be fast and sound from the start, and that requires a firm understanding of and relational theory. The Art of offers best practices that teach experienced users to focus on strategy rather than specifics. Faroult's approach takes a page from Sun Tzu's classic treatise by viewing database design as a military campaign. You need knowledge, skills, and talent. Talent can't be taught, but every strategist from Sun Tzu to modern-day generals believed that it can be nurtured through the experience of others. They passed on their experience acquired in the field through basic principles that served as guiding stars amid the sound and fury of battle. This is what Faroult does with SQL. Like a successful battle plan, good architectural choices are based on contingencies. What if the volume of this or that table increases unexpectedly? What if, following a merger, the number of users doubles? What if you want to keep several years of data online? Faroult's way of looking at performance may be unconventional and unique, but he's deadly serious about writing good and using well. The Art of is not a cookbook, listing problems and giving recipes. The aim is to get you-and your manager-to raise good questions.
An efficient filter for approximate membership checking (2008)

We consider the problem of identifying sub-strings of input text strings that approximately match with some member of a potentially large dictionary. This problem arises in several important applications such as extracting named entities from text documents and identifying biological concepts from biomedical literature. In this paper, we develop a filter-verification framework, and propose a novel in-memory filter structure. That is, we first quickly filter out sub-strings that cannot match with any dictionary member, and then verify the remaining sub-strings against the dictionary. Our method does not produce false negatives. We demonstrate the efficiency and effectiveness of our filter over real datasets, and show that it significantly outperforms the previous best-known methods in terms of both filtering power and computation time.
Lupus anticoagulant activities of murine monoclonal antibodies to liposomal phosphatidylinositol phosphate. (1987)

Four murine monoclonal antibodies having high levels of activity against phosphatidyl-inositol phosphate (PIP) were tested for lupus anticoagulant activity. The antibodies showed different degrees of potency in a modified partial thromboplastin time test (APTT) that used dilutions of either bovine brain extract (Thrombofax) or liposomes consisting of phosphatidylcholine/phosphatidylserine (PC/PS) as the phospholipid source. The same relative order of anticoagulant potency that was observed in the APTT that used the PC/PS liposomes was maintained when the anti-PIP antibodies were tested for cross-reactivity either by induction of complement-dependent immune damage to liposomes containing PS, or in enzyme-linked immunosorbent assays that used PS, cardiolipin (CL), or phosphatidylinositol (PI) as antigens. The data indicate that monoclonal antibodies to PIP can express anticoagulant activity in a modified APTT that correlates with their different degrees of cross-reactivity against the negatively-charged phospholipids PS, CL, and PI.
[Inhibition of gastric secretion by omeprazole and efficacy of calcium carbonate in the control of hyperphosphatemia in patients on maintenance hemodialysis]. (1999)

These data do not support that CaCO3 efficiency as phosphate binder is decreased with inhibition of the gastric secretion by omeprazole.
Virtual personalised channels: video conducting of future TV broadcasting (2005)

Television is undergoing a historical change.Interactive Digital Broadcasting will be reality in 2010+.Heaps of video material will be produced by TV broadcasters, which will overwhelm both the producers as well as the consumers.Current TV formats and forms of broadcasting do not satisfy the personal moods and interests of the consumer.We hence propose the development of a TV environment which allows for the establishment of 'virtual personalised channels'.To do so, (live) semantic annotation of video material as well as methods for live staging of media events have to be designed.The resulting drastically different process of content production and consuming will lead to the satisfaction of individual human needs.The approaches outlined in this extended abstract are the basis for our upcoming IST research project LIVE.
TheBuccaneersoftware for automated model building. 1. Tracing protein chains (2006)

A new technique for the automated tracing of protein chains in experimental electron-density maps is described. The technique relies on the repeated application of an oriented electron-density likelihood target function to identify likely C(alpha) positions. This function is applied both in the location of a few promising ;seed' positions in the map and to grow those initial C(alpha) positions into extended chain fragments. Techniques for assembling the chain fragments into an initial chain trace are discussed.
Performance and scalability of EJB applications (2002)

We investigate the combined effect of application implementation method, container design, and efficiency of communication layers on the performance scalability of J2EE application servers by detailed measurement and profiling of an auction site server.We have implemented five versions of the auction site. The first version uses stateless session beans, making only minimal use of the services provided by the Enterprise JavaBeans (EJB) container. Two versions use entity beans, one with container-managed persistence and the other with bean-managed persistence. The fourth version applies the session fasade pattern, using session beans as a fasade to access entity beans. The last version uses EJB 2.0 local interfaces with the session fasade pattern. We evaluate these different implementations on two popular open-source EJB containers with orthogonal designs. JBoss uses dynamic proxies to generate the container classes at run time, making an extensive use of reflection. JOnAS pre-compiles classes during deployment, minimizing the use of reflection at run time. We also evaluate the communication optimizations provided by each of these EJB containers.The most important factor in determining performance is the application implementation method. EJB applications with session beans perform as well as a Java servlets-only implementation and an order-of-magnitude better than most of the implementations based on entity beans. The fine-granularity access exposed by the entity beans limits scalability. Use of session fasade beans improves performance for entity beans, but only if local communication is very efficient or EJB 2.0 local interfaces are used. Otherwise, session fasade beans degrade performance.For the implementation using session beans, communication cost forms the major component of the execution time on the EJB server. The design of the container has little effect on performance. With entity beans, the design of the container becomes important. In particular, the cost of reflection affects performance. For implementations using session fasade beans, local communication cost is critically important. EJB 2.0 local interfaces improve the performance by avoiding the communication layers for local communications.
Chemokines and the Homing of Dendritic Cells to the T Cell Areas of Lymphoid Organs (1999)

A quarter of a century ago, it was proposed that veiled cells in the lymph were antigen-bearing Langerhans' cells (LCs) en route to the LN T cell area (([1][1]), ([2][2])). Extensive investigations have since established that LCs are immature dendritic cells (DCs) and that insults to the skin—
The Multiubiquitin-Chain-Binding Protein Mcb1 Is a Component of the 26S Proteasome in Saccharomyces cerevisiae and Plays a Nonessential, Substrate-Specific Role in Protein Turnover (1996)

The 26S proteasome is an essential proteolytic complex that is responsible for degrading proteins conjugated with ubiquitin. It has been proposed that the recognition of substrates by the 26S proteasome is mediated by a multiubiquitin-chain-binding protein that has previously been characterized in both plants and animals. In this study, we identified a Saccharomyces cerevisiae homolog of this protein, designated Mcb1. Mcb1 copurified with the 26S proteasome in both conventional and nickel chelate chromatography. In addition, a significant fraction of Mcb1 in cell extracts was present in a low-molecular-mass form free of the 26S complex. Recombinant Mcb1 protein bound multiubiquitin chains in vitro and, like its plant and animal counterparts, exhibited a binding preference for longer chains. Surprisingly, (delta)mcb1 deletion mutants were viable, grew at near-wild-type rates, degraded the bulk of short-lived proteins normally, and were not sensitive to UV radiation or heat stress. These data indicate that Mcb1 is not an essential component of the ubiquitin-proteasome pathway in S.cerevisiae. However, the (delta)mcb1 mutant exhibited a modest sensitivity to amino acid analogs and had increased steady-state levels of ubiquitin-protein conjugates. Whereas the N-end rule substrate, Arg-beta-galactosidase, was degraded at the wild-type rate in the (delta)mcb1 strain, the ubiquitin fusion degradation pathway substrate, ubiquitin-Pro-beta-galactosidase, was markedly stabilized. Collectively, these data suggest that Mcb1 is not the sole factor involved in ubiquitin recognition by the 26S proteasome and that Mcb1 may interact with only a subset of ubiquitinated substrates.
Polymorphism in the β 1 -Adrenergic Receptor Gene and Hypertension (2001)

Our data suggest that individuals homozygous for the Arg389 allele of the beta(1)-adrenergic receptor gene are at increased risk to develop hypertension.
Facile Construction of the Pentacyclic Framework of Subincanadine B. Synthesis of 20-Deethylenylated Subincanadine B and 19,20-Dihydrosubincanadine B (2005)

[reaction: see text] We describe a facile approach for effectively constructing the pentacyclic framework of subincanadine B. The seven-step assembly of tetracyclic ketone 14 featured Michael addition, Pictet-Spengler cyclization, and Dieckmann condensation. From this key ketone intermediate, two analogues of subincanadine B, i.e., 20-deethylenylated subincanadine B (27) and 19,20-dihydrosubincanadine B (31), were synthesized in four steps, respectively.
Activities of Monomeric Insulin Analogs at Position A8 Are Uncorrelated with Their Thermodynamic Stabilities (2001)

Previous studies have demonstrated that the potency and thermodynamic stability of human insulin are enhanced in concert by substitution of Thr(A8) by arginine or histidine. These surface substitutions stabilize the N-terminal alpha-helix of the A chain, a key element of hormone-receptor recognition. Does enhanced stability necessarily imply enhanced activity? Here, we test by structure-based mutagenesis the relationship between the stability and activity of the hormone. To circumvent confounding effects of insulin self-association, A chain analogs were combined with a variant B chain (Asp(B10), Lys(B28), and Pro(B29) (DKP)) to create a monomeric template. Five analogs were obtained by chain combination; disulfide pairing proceeded in each case with native yield. CD and (1)H NMR spectra of the DKP analogs are essentially identical to those of DKP-insulin, indicating a correspondence of structures. Receptor binding affinities were determined by competitive displacement of (125)I-insulin from human placental membranes. Thermodynamic stabilities were measured by CD titration; unfolding was monitored as a function of guanidine concentration. In this broader collection of analogs receptor binding affinities are uncorrelated with stability. We suggest that receptor binding affinities of A8 analogs reflect local features of the hormone-receptor interface rather than the stability of the free hormone or the intrinsic C-capping propensity of the A8 side chain.
Genome‐wide array‐based copy number profiling in human placentas from unexplained stillbirths (2011)

We describe the potential of whole-genome placental profiling to identify small genomic imbalances, which might contribute to a small proportion of well-characterized, unexplained stillbirths.