gebhart/patrepeval huggingface dataset:
Avoiding cache thrashing due to private data placement in last-level cache for manycore scaling (2009)

Without high-bandwidth broadcast, large numbers of cores require a scalable point-to-point interconnect and a directory protocol. In such cases, a shared, inclusive last level cache (LLC) can improve data sharing and avoid three-way communication for shared reads. However, if inclusion encompasses thread-private data, two problems arise with the shared LLC. First, current memory allocators align stack bases on page boundaries, which emerges as a source of severe conflict misses for large numbers of threads on data-parallel applications. Second, correctness does not require the private data to reside in the shared directory or the LLC. This paper advocates stack-base randomization that eliminates the major source of conflict misses for large numbers of threads. However, when capacity becomes a limitation for the directory or last-level cache, this is not sufficient. We then propose non-inclusive, semi-coherent cache organization (NISC) that removes the requirement for inclusion of private data and reduces capacity misses. Our data-parallel benchmarks show that these limitations prevent scaling beyond 8 cores, while our techniques allow scaling to at least 32 cores for most benchmarks. At 8 cores, stack randomization provides a mean speedup of 1.2X, but stack randomization with 32 cores gives a speedup of 2.7X over the best baseline configuration. Comparing to conventional performance with a 2 MB LLC, our technique achieves similar performance with a 256 KB LLC, suggesting LLCs may be typically overprovisioned. When very limited LLC resources are available, NISC can further improve system performance by 1.8X.
Combining Trigram-based and feature-based methods for context-sensitive spelling correction (1996)

This paper addresses the problem of correcting spelling errors that result in valid, though unintended words (such as peace and piece, or quiet and quite) and also the problem of correcting particular word usage errors (such as amount and number, or among and between). Such corrections require contextual information and are not handled by conventional spelling programs such as Unix spell. First, we introduce a method called Trigrams that uses part-of-speech trigrams to encode the context. This method uses a small number of parameters compared to previous methods based on word trigrams. However, it is effectively unable to distinguish among words that have the same part of speech. For this case, an alternative feature-based method called Bayes performs better; but Bayes is less effective than Trigrams when the distinction among words depends on syntactic constraints. A hybrid method called Tribayes is then introduced that combines the best of the previous two methods. The improvement in performance of Tribayes over its components is verified experimentally. Tribayes is also compared with the grammar checker in Microsoft Word, and is found to have substantially higher performance.
Cord-Blood Engraftment with Ex Vivo Mesenchymal-Cell Coculture (2012)

Poor engraftment due to low cell doses restricts the usefulness of umbilical-cord-blood transplantation. We hypothesized that engraftment would be improved by transplanting cord blood that was expanded ex vivo with mesenchymal stromal cells.
Living With a Lifetime Store (2003)

Storage trends have brought us to the point where it is affordable to keep a complete digital record of one’s life. The MyLifeBits system is designed to store and manage a lifetime’s worth of data. To experiment with a lifetime store, we have digitized everything possible from Gordon Bell’s life. These are added to his existing digital assets. We also continue to add new digital capture such as web pages, telephone, radio and television. In this paper we explain the key requirements of a lifetime store. We show how typed links and database features are keys to the usefulness of such a system.
Tanezumab for the Treatment of Pain from Osteoarthritis of the Knee (2010)

In this proof-of-concept study, treatment with tanezumab was associated with a reduction in joint pain and improvement in function, with mild and moderate adverse events, among patients with moderate-to-severe osteoarthritis of the knee. (Funded by Rinat Neuroscience; ClinicalTrials.gov number, NCT00394563.).
Bifunctional cis-Abienol Synthase from Abies balsamea Discovered by Transcriptome Sequencing and Its Implications for Diterpenoid Fragrance Production (2012)

The labdanoid diterpene alcohol cis-abienol is a major component of the aromatic oleoresin of balsam fir (Abies balsamea) and serves as a valuable bioproduct material for the fragrance industry. Using high-throughput 454 transcriptome sequencing and metabolite profiling of balsam fir bark tissue, we identified candidate diterpene synthase sequences for full-length cDNA cloning and functional characterization. We discovered a bifunctional class I/II cis-abienol synthase (AbCAS), along with the paralogous levopimaradiene/abietadiene synthase and isopimaradiene synthase, all of which are members of the gymnosperm-specific TPS-d subfamily. The AbCAS-catalyzed formation of cis-abienol proceeds via cyclization and hydroxylation at carbon C-8 of a postulated carbocation intermediate in the class II active site, followed by cleavage of the diphosphate group and termination of the reaction sequence without further cyclization in the class I active site. This reaction mechanism is distinct from that of synthases of the isopimaradiene- or levopimaradiene/abietadiene synthase type, which employ deprotonation reactions in the class II active site and secondary cyclizations in the class I active site, leading to tricyclic diterpenes. Comparative homology modeling suggested the active site residues Asp-348, Leu-617, Phe-696, and Gly-723 as potentially important for the specificity of AbCAS. As a class I/II bifunctional enzyme, AbCAS is a promising target for metabolic engineering of cis-abienol production.
[Inhibitory effect of knocking down microRNA-221 and microRNA-222 on glioma cell growth in vitro and in vivo]. (2009)

There is a significant inhibitory effect of antisense miR-221/222 on the growth of human glioma U251 cells. miR-221/222 may be considered as a candidate target for gene therapy of human gliomas.
SMOOTHING OVER THE CRACKS (1989)

In this article, the state of repair of britain's concrete motorway and major road bridges is briefly discussed. A random survey of 200 concrete bridges carried out in 1986 by g maunsell and ptnrs, on behalf of the Department of Transport, revealed widespread problems of deterioraton, and estimates of 800 million were given for maintenance and repair work for the next decade. Much of the deterioration is caused by the ingress of chlorides present in de-icing salts used for winter maintenance work. Access and support equipment to carry out repair work is reviewed, including scaffolding, platforms and powered cradles. (for the maunsell report see IRRD no 821905).
Mesenchymal stem cells produce Wnt isoforms and TGF-β1 that mediate proliferation and procollagen expression by lung fibroblasts (2009)

Studies have been carried out previously to determine whether mesenchymal stem cells (MSC) influence the progression of pulmonary fibrosis. Here, we asked whether MSC (derived from mouse bone marrow and human umbilical cord blood) produce factors that mediate lung fibroblast (LF) growth and matrix production. MSC-conditioned media (CM) were found by ELISA to contain significant amounts of PDGF-AA and transforming growth factor-beta1 (TGF-beta1). Proliferation was increased in a concentration-dependent manner in LF cell lines and primary cells cultured in MSC-CM, but neither anti-PDGF antibodies nor PDGF receptor-specific antibodies affected proliferation, nor did a number of other antibodies to well-known mitogenic factors. However, proliferation was significantly inhibited by the Wnt signaling antagonist, secreted frizzled related protein-1 (sFRP-1). In addition, anti-Wnt1 and anti-Wnt2 antibodies attenuated MSC-CM-induced proliferation, and increased expression of Wnt7b was identified. As would be expected in cells activated by Wnt, nuclear beta-catenin was increased. The amount of TGF-beta1 in MSC-CM and its biological activity were revealed by activation at acidic pH. The stem cells synthesized and released TGF-beta1 that increased alpha1-procollagen gene expression by LF target cells. Addition of anti-TGF-beta to the MSC-CM blocked upregulation of collagen gene expression. These data demonstrate that MSC from mice and humans produce Wnt proteins and TGF-beta1 that respectively stimulate LF proliferation and matrix production, two hallmarks of fibroproliferative lung disease. It will be essential to determine whether these factors can play a role in attempts to use MSC for therapeutic approaches.
Cryptanalysis of an efficient certificateless two-party authenticated key agreement protocol. (2012)

Abstract. Recently, He et al. (Computers and Mathematics with Applications, 2012, 64(6): 1914-1926) proposed a new efficient certificateless two-party authenticated key agreement protocol. They claimed their protocol was provably secure in the extended Canetti-Krawczyk (eCK) model. In this paper, we will show that their protocol is insecure. A type I adversary, who obtains one party’s ephemeral private key, can impersonate the party to cheat the other party and compute the shared session key successfully. For overcoming this weakness, we also propose a simple countermeasure.
High-speed method for computing the exact solution for the pressure variations in the nearfield of a baffled piston (1973)

A method is presented whereby the pressure variations at any point in the field of a baffled piston may be efficiently calculated. If a solution for the impulse response of a piston of a given geometry is known, then for harmonic excitation the steady-state field may be computed by evaluating the driving-frequency component of the Fourier transform of the impulse response. This method involves a single integration, whereas the direct numerical solution requires a double numerical integration. An exact, closed-form solution for the impulse response of a rectangular piston is derived. With this solution and the known solution for the impulse response of a circular piston the steady-state solutions for these two geometries are obtained. Three-dimensional and contour plots of data obtained for a circular piston and for a plane of symmetry of a rectangular piston field are presented. The plots for the circular piston compare favorably with previously published plots of data calculated by a double integration.
Microwave‐Assisted Synthesis of 4′‐Azaflavones and Their N‐Alkyl Derivatives with Biological Activities (2008)

4'-Azaflavone (=2-(pyridin-4-yl)-4H-1-benzopyran-4-one; 4) and 3-[(pyridin-4-yl)methyl]-4'-azaflavone (5) were synthesized by a simple environmentally friendly microwave-assisted one-pot method through the cyclization of 3-hydroxy-1-(2-hydroxyphenyl)-3-(pyridin-4-yl)propan-1-one (1), (E)-2'-hydroxy-4-azachalcone (2; chalcone=1,3-diphenylprop-2-en-1-one), and 2'-hydroxy-2-[(hydroxy)(pyridin-4-yl)methyl]-4''-azachalcone (3) under solventless conditions using silica-supported NaHSO(4), followed by treatment with base. In addition, N-alkyl-substituted 4'-azaflavonium bromides 6 and 7 were prepared from compounds 4 and 5, respectively. The antimicrobial and antioxidant activities of compounds 1-7 were tested. The N-alkyl-substituted 4'-azaflavonium bromides 6 and 7 showed high antimicrobial activity against the Gram-positive bacteria and the fungus tested, with MIC values close to those of reference antimicrobials ampicilline and fluconazole. The alkylated compounds 6 and 7 also showed a good antioxidant character in the two antioxidant methods, DPPH (=1,1-diphenyl-2-picrylhydrazyl) radical-scavenging and ferric reducing/antioxidant power (FRAP) tests.
De Novo Design of an Enzyme (2004)

Enzymes catalyze biological reactions with amazing efficiency, and years of biochemical research have been directed at understanding how they work. In their Perspective,
 Sterner and Schmid
 describe recent work (
 Dwyer
 et al.) that brings us closer to the ultimate goal of designing enzymes with tailored activities by using computer design to build catalytic activity onto an inert protein scaffold.
Humoral immune response to citrullinated collagen type II determinants in early rheumatoid arthritis (2005)

Collagen type II (CII) is a relevant joint-specific autoantigen in the pathogenesis of rheumatoid arthritis (RA). Whereas the reasons for the breakage of self tolerance to this major cartilage component are still enigmatic, T cell responses to glycosylated CII determinants in RA patients indicate that post-translational modifications play a role. Since the conversion of arginine into citrulline by peptidylarginine deiminases (PAD) in some non-joint-specific antigens such as filaggrin or fibrin has been shown to give rise to RA-specific humoral immune responses, we investigated whether PAD modification of cartilage-specific CII might affect its recognition by circulating autoantibodies in early RA. In vitro treatment with purified PAD led to arginine deimination of native CII or of synthetic CII peptides as evidenced by amino acid analysis. The citrullination resulted in modified recognition of the immunodominant CII epitope C1(III) (amino acid residues 359-369) by murine and human antibodies. In a cohort of early RA patients (n=286), IgG antibodies directed toward a synthetic citrullinated C1(III) peptide (citC1(III)-P) were detectable with a prevalence of 40.4%. The partial autoantibody cross-reactivity between citC1(III)-P and citrullinated peptides mimicking epitopes of the cytoskeletal autoantigen filaggrin suggests that autoimmunity to cartilage-specific modified self might be a critical intermediate bridging recognition of PAD-modified extra-articular autoantigens with the disruption of tolerance to native cartilage constituents.
In-System Silicon Validation and Debug (2008)

Silicon validation - proving a chip works correctly at speed and in system under different operating conditions - is always necessary, even for a "perfect" design. Silicon debug - finding the root cause of a malfunction - is necessary whenever a design is not flawless. First-silicon validation and debug require a labor-intensive engineering effort of several months and have become the least predictable and most time-consuming part of a new 90-nm chip's development cycle. Lack of adequate tools and automatic procedures is a big factor in this bottleneck. The difficulty of silicon validation will increase at 65 nm and below because existing ad hoc methodologies don't scale with the unprecedented levels of SoC device complexity. Even the most sophisticated SoC design methodology cannot fully account for all the parameters that affect silicon behavior, or for all logic corner cases occurring in the life of a chip working at speed and in system. For example, the simultaneous occurrence of two unlikely events might not be anticipated pre- silicon, so it is never simulated or analyzed; however, when it occurs in system, it can cause unexpected behavior. Presilicon verification methods - simulation, emulation, FPGA prototyping, timing analysis, and formal verification - don't address many deep-submicron problems that occur in the actual device.
Carrier Generation and Recombination in P-N Junctions and P-N Junction Characteristics (1957)

For certain p-n junctions, it has been observed that the measured current-voltage characteristics deviate from the ideal case of the diffusion model. It is the purpose of this paper to show that the current due to generation and recombination of carriers from generation-recombination centers in the space charge region of a p-n junction accounts for the observed characteristics. This phenomenon dominates in semiconductors with large energy gap, low lifetimes, and low resistivity. This model not only accounts for the nonsaturable reverse current, but also predicts an apparent exp (qV/nkT) dependence of the forward current in a p-n junction. The relative importance of the diffusion current outside the space charge layer and the recombination current inside the space charge layer also explains the increase of the emitter efficiency of silicon transistors with emitter current. A correlation of the theory with experiment indicates that the energy level of the centers is a few kT from the intrinsic Fermi level.
HMPAO SPECT Study of Regional Cerebral Blood Flow in Dissociative Identity Disorder (2001)

Abstract The aim of the study was to in ves ti gate if there were any char ac ter is tics of re gional c e re bral blood flow (rCBF) in dissociative iden tity dis or der. Fif teen pa tients with dissociative iden tity dis or der and eight healthy vol un teers par tic i pated in the study. The clin i cal di ag no sis of dissociative iden tity dis or der was con firmed us ing the Struc tured Clin i cal In ter view for DSM-IV Dissociative Dis or ders. The Struc tured Clin i cal In ter view for DSM-III-R was also ad min is tered to all pa tients in or der to screen comorbid psy chi at ric con di tions. Re gional ce re bral blood flow was stud ied us ing a SPECT sys tem with Tc99m-hexamethyl -propylenamine (HMPAO) as a tracer. The rCBF ra tio was de creased in orbito-fron tal re gion bi lat er ally and in creased in left (dom i nant hemisphere) lat eral tem po ral re gion among pa tients with dissociative iden tity dis or der when com pared to the con trol group. The struc tured in ter view di ag no ses of con cur rent or life time ma jor de pres sion, PTSD, psy chotic dis or der, or on go ing drug treat ment were not sig nif i cantly re lated to perfu sion in these re gions. There was no sta tis ti cally mean ing ful dif fer ence in rCBF ra tios be tween host and al ter per son al ity states. Our find ings sug gest that orbitofron tal and left (dom i nant hemi sphere) lat eral tem poral re gions are af fected in dissociative iden tity dis or der. A rep li ca tion of this study on a larger group of drugfree dissociative pa tients and var i ous psy chi at ric con trol groups would lead to more de fin i tive find ings. Key Words: SPECTdissociative iden tity dis or derim ag ingre gional ce re bral blood flow
RORα, a Potential Tumor Suppressor and Therapeutic Target of Breast Cancer (2012)

The function of the nuclear receptor (NR) in breast cancer progression has been investigated for decades. The majority of the nuclear receptors have well characterized natural ligands, but a few of them are orphan receptors for which no ligand has been identified. RORα, one member of the retinoid orphan nuclear receptor (ROR) subfamily of orphan receptors, regulates various cellular and pathological activities. RORα is commonly down-regulated and/or hypoactivated in breast cancer compared to normal mammary tissue. Expression of RORα suppresses malignant phenotypes in breast cancer cells, in vitro and in vivo. Activity of RORα can be categorized into the canonical and non-canonical nuclear receptor pathways, which in turn regulate various breast cancer cellular function, including cell proliferation, apoptosis and invasion. This information suggests that RORα is a potent tumor suppressor and a potential therapeutic target for breast cancer.
Understanding the connectivity of heap objects (2002)

Modern garbage collectors partition the set of heap objects to achieve the best performance. For example, generational garbage collectors partition objects by age and focus their efforts on the youngest objects. Partitioning by age works well for many programs because younger objects usually have short lifetimes and thus garbage collection of young objects is often able to free up many objects. However, generational garbage collectors are typically much less efficient for longer-lived objects, and thus prior work has proposed many enhancements to generational collection.Our work explores whether the connectivity of objects can yield useful partitions or improve existing partitioning schemes. We look at both direct (e.g., object A points to object B) and transitive (e.g., object A is reachable from object B) connectivity. Our results indicate that connectivity correlates strongly with object lifetimes and deathtimes and is therefore likely to be useful for partitioning objects.
Treatment of B-lymphoproliferative disorder with a monoclonal anti-interleukin-6 antibody in 12 patients: a multicenter phase 1-2 clinical trial (2001)

Severe T-cell immunodeficiency after solid organ or bone marrow transplantation may result in the uncontrolled outgrowth of latently Epstein-Barr virus-infected B cells, leading to B-lymphoproliferative disorder (BLPD). Given the potentially important pathogenic role of IL-6 in BLPD, it was tested whether the in vivo neutralization of IL-6 by a monoclonal anti-IL-6 antibody could contribute to the control of BLPD. Safety and efficacy were assessed in 12 recipients of transplanted organs who had BLPD refractory to the reduction of immunosuppression over 8 days. Five patients received 0.4 mg/kg per day. The next 7 patients received 0.8 mg/kg per day. Treatment was scheduled to last 15 days. It was completed in 10 patients, and in the other 2 patients was discontinued early (days 10 and 13, respectively) because of disease progression. Treatment tolerance was good, and no major side effects were observed. High C-reactive protein levels were found in 9 patients before treatment but were normalized under treatment in all patients, demonstrating efficient IL-6 neutralization. Complete remission (CR) was observed in 5 patients and partial remission (PR) in 3 patients. Relapse was observed in 1 of these 8 patients in whom remission was observed. This relapse was unresponsive to treatment. Disease was stable in 1 patient, but it progressed in 3 patients. Seven patients are alive and well. Two patients died because of disease progression, and 3 patients died while in CR (chronic rejection in 2 patients and BLPD sequelae in 1 patient). These data suggest that the anti-IL-6 antibody is safe and should be further explored in the treatment of BLPD.
Improving energy efficiency of personal sensing applications with heterogeneous multi-processors (2012)

The availability of multiple sensors on mobile devices offers a significant new capability to enable rich user and context aware applications. Many of these applications run in the background to continuously sense user context. However, running these applications on mobile devices can impose a significant stress on the battery life, and the use of supplementary low-power processors has been proposed on mobile devices for continuous background activities. In this paper, we experimentally and analytically investigate the design considerations that arise in the efficient use of the low power processor and provide a thorough understanding of the problem space. We answer fundamental questions such as which segments of the application are most efficient to be hosted on the low power processor, and how to select an appropriate low power processor. We discuss our measurements, analysis, and results using multiple low power processors and existing phone platforms.