gebhart/patrepeval huggingface dataset:
Metabolism of 2-oxoaldehyde in yeasts. Purification and characterization of NADPH-dependent methylglyoxal-reducing enzyme from Saccharomyces cerevisiae (1985)

An enzyme catalyzing the reduction of methylglyoxal was isolated from Saccharomyces cerevisiae and its enzymatic properties were analyzed. The enzyme, specifically eluted from a blue-dextran--Sepharose CL-6B column by the substrate, methylglyoxal, was homogeneous on polyacrylamide gel electrophoresis. The enzyme consisted of single polypeptide chain with a relative molecular mass of 43 000. The enzyme was glycoprotein and contained 6.6% carbohydrate. NADPH was specifically required for activity and the Km for NADPH was 2.0 X 10(-7) M. The enzyme was active on various glyoxals such as glyoxal, methylglyoxal (Km = 5.88 mM) and phenylglyoxal (Km = 1.54 mM). The reaction catalyzed by the enzyme was virtually irreversible. The activity was inhibited by sulfhydryl agents and activated by reducing agents such as glutathione. Intermediates in glycolysis, nucleosides, nucleotides, polyamines and various metal ions showed little inhibitory or activating effects on enzyme activity. Tricarboxylic acids showed a slight inhibitory effect. The activity of the enzyme was strongly inhibited by anionic detergents. The enzyme was rapidly inactivated by incubating with the substrates probably because of the non-enzymatic interaction between glyoxals and NH2 groups in arginine residues in the enzyme. NADP, one of the reaction products, also inhibited the enzyme activity and the Ki for NADP was about 0.07 mM. We tentatively designated the enzyme methylglyoxal reductase.
PageSeer: Using Page Walks to Trigger Page Swaps in Hybrid Memory Systems (2019)

Hybrid main memories composed of DRAM and NonVolatile Memory (NVM) combine the capacity benefits of NVM with the low-latency properties of DRAM. For highest performance, data segments should be exchanged between the two types of memories dynamically-a process known as segment swapping-based on the access patterns to the segments in the program. The key difficulty in hardware-managed swapping is to identify the appropriate segments to swap between the memories at the right time in the execution. To perform hardware-managed segment swapping both accurately and with substantial lead time, this paper proposes to use hints from the page walk in a TLB miss. We call the scheme PageSeer. During the generation of the physical address for a page in a TLB miss, the memory controller is informed. The controller uses historic data on the accesses to that page and to a subsequently-referenced page (i.e., its follower page), to potentially initiate swaps for the page and for its follower. We call these actions MMU-Triggered Prefetch Swaps. PageSeer also initiates other types of page swaps, building a complete solution for hybrid memory. Our evaluation of PageSeer with simulations of 26 workloads shows that PageSeer effectively hides the swap overhead and services many requests from the DRAM. Compared to a state-of-the-art hardware-only scheme for hybrid memory management, PageSeer on average improves performance by 19% and reduces the average main memory access time by 29%.
The tumor-infiltrating B cell response in medullary breast cancer is oligoclonal and directed against the autoantigen actin exposed on the surface of apoptotic cancer cells (2001)

Medullary carcinoma of the breast (MCB) is a morphologically and biologically distinct subtype of human breast cancer that, despite cytologically anaplastic features, has a more favorable prognosis than other types of breast cancer at similar stages of differentiation. It has been proposed that the improved clinical outcome is due, at least in part, to the presence of a prominent lymphoplasmacytic cell infiltrate in the tumor stroma. We studied the B lymphoplasmacytic cell infiltrates in MCB to determine the role of the antibody response produced by the local infiltrating cells. Oligoclonal predominance among tumor-infiltrating B cells in a panel of MCB patients was observed, suggesting that certain B cell clones were expanded, possibly in response to specific tumor-associated stimuli. IgG antibody phage-display libraries were generated from MCB-infiltrating lymphoplasmacytic cells of two patients, and MCB-reactive monoclonal antibodies were retrieved by selection on fresh-frozen MCB tissue sections. Analysis by mass spectrometry revealed that the antigen targeted by the dominant clones in the oligoclonal B lymphoplasmacytic response in both patients was not a cancer-specific antigen but the cytoskeletal protein beta-actin. MCB exhibits an increased rate of apoptosis, and apoptotic MCB cells were shown to expose actin on the cell surface, permitting its recognition by the humoral immune system. Further, actin fragments, similar to those observed after cleavage with the apoptotic protease granzyme B, were observed in MCB tissue. Our results indicate that the major antibody response produced by tumor-infiltrating B lymphoplasmacytic cells are autoimmune in nature and a consequence of the perturbed state of increased MCB apoptosis caused by granzyme B-induced T cell cytotoxicity and/or intrinsic cellular factors of MCB cells.
Browser-based Harnessing of Voluntary Computational Power (2017)

Abstract Computers connected to internet represent an immense computing power, mostly unused by their owners. One way to utilize this public resource is via world wide web, where users can share their resources using nothing more except their browsers. We survey the techniques employing the idea of browser-based voluntary computing (BBVC), discuss their commonalities, recognize recurring problems and their solutions and finally we describe a prototype implementation aiming at efficient mining of voluntary-contributed computing power.
Lymphocytic Toxicity in Patients After Peptide-Receptor Radionuclide Therapy (PRRT) with <sup>177</sup> Lu-DOTATATE and <sup>90</sup> Y-DOTATOC (2009)

Lymphocyte toxicity in PRRT is mainly due to the selective targeting on B-cells. The relative sparing of T-lymphocytes could explain the absence of clinical side-effects in these patients, such as increased risk of infections. These findings open interesting perspectives in the treatment of B-cell lymphoproliferative disorders.
A randomized comparison of balloon angioplasty versus rotational atherectomy in complex coronary lesions (COBRA study) (2000)

Complex coronary artery lesions can be treated with a high level of success and low complication rates either by PTCA with adjunctive stenting or rotablation. The long-term clinical and angiographic outcome is comparable.
Low Temperature, Selective Atomic Layer Deposition of Cobalt Metal Films Using Bis(1,4-di-<i>tert</i>-butyl-1,3-diazadienyl)cobalt and Alkylamine Precursors (2017)

The atomic layer deposition (ALD) of cobalt metal films is described using the precursor bis(1,4-di-tert-butyl-1,3-diazadienyl)cobalt and tert-butylamine or diethylamine. Platinum, copper, ruthenium, Si(100) with native oxide, thermal SiO2, hydrogen-terminated silicon, and carbon-doped oxide substrates were used with growth temperatures between 160 and 220 °C. Plots of growth rate versus pulse lengths showed saturative, self-limited behavior at ≥3.0 s for bis(1,4-di-tert-butyl-1,3-diazadienyl)cobalt and ≥0.1 s for tert-butylamine. An ALD window was observed between 170 and 200 °C, with a growth rate of 0.98 Å/cycle on platinum substrates. A plot of thickness versus the number of cycles at 200 °C on platinum substrates was linear between 25 and 1000 cycles, with a growth rate of 0.98 Å/cycle. A 98 nm thick film grown at 200 °C showed crystalline cobalt metal by X-ray diffraction. Atomic force microscopy of 10 and 98 nm thick cobalt metal films grown on platinum substrates at 200 °C showed rms roughness values that were ≤3.1% of the film thicknesses. X-ray photoelectron spectroscopy analyses were performed on 49 and 98 nm thick films grown on platinum substrates at 170 and 200 °C, respectively. Both samples showed oxidized cobalt on the film surface but revealed cobalt metal upon argon ion sputtering. The films showed >98% pure cobalt, with ≤0.9% each of oxygen, carbon, and nitrogen. On copper substrates, a plot of thickness versus the number of cycles was linear between 25 and 500 cycles, with a growth rate of 0.98 Å/cycle. In contrast, analogous growth studies on ruthenium substrates showed no films after 25 and 50 cycles, a small amount of growth at 100 cycles, and a growth rate of 0.98 Å/cycle at 200 and 500 cycles. No film growth was observed at 200 °C on Si(100) with native oxide, 100 nm thermal SiO2, hydrogen-terminated silicon, and carbon-doped oxide substrates after 500 cycles. Similarly, no growth was observed on these insulating substrates after 200 cycles at temperatures between 160 and 220 °C. Accordingly, this process affords inherently selective cobalt metal growth on metal substrates between 160 and 220 °C. Lower purity nitrogen carrier and purge gas (<99.9%) afforded a much lower growth rate, likely because of the formation of surface cobalt oxides and attendant reduced cobalt metal nucleation. A mechanism for cobalt metal growth is proposed in which 1 and tert-butylamine form an adduct, which then decomposes thermally to cobalt metal, 1,4-di-tert-butyl-1,3-diazadiene, and tert-butylamine.
Derby intramedullary nail — A biomechanical comparison (1985)

This paper describes the design and function of the Derby intramedullary nail and its biomechanical testing, comparing it with the K nail and reamed unfractured femurs. The Derby nail is designed to transmit torsional loads and apply compression to the fracture site using a sliding proximal collar and distal extendable 'wings'. Femurs fixed with Derby, K and Zickel nails and AO plates were tested in torsion and the rotation and torsional load at failure recorded and compared with unfractured control femurs. The results show that the strength of the Derby nail in torsion is approximately equal to 4 times and the energy to failure 2.3 times that of the K nail.
Optimal whole-body PET scanner configurations for different volumes of LSO scintillator: a simulation study (2012)

The axial field of view (AFOV) of the current generation of clinical whole-body PET scanners range from 15-22 cm, which limits sensitivity and renders applications such as whole-body dynamic imaging or imaging of very low activities in whole-body cellular tracking studies, almost impossible. Generally, extending the AFOV significantly increases the sensitivity and count-rate performance. However, extending the AFOV while maintaining detector thickness has significant cost implications. In addition, random coincidences, detector dead time, and object attenuation may reduce scanner performance as the AFOV increases. In this paper, we use Monte Carlo simulations to find the optimal scanner geometry (i.e. AFOV, detector thickness and acceptance angle) based on count-rate performance for a range of scintillator volumes ranging from 10 to 93 l with detector thickness varying from 5 to 20 mm. We compare the results to the performance of a scanner based on the current Siemens Biograph mCT geometry and electronics. Our simulation models were developed based on individual components of the Siemens Biograph mCT and were validated against experimental data using the NEMA NU-2 2007 count-rate protocol. In the study, noise-equivalent count rate (NECR) was computed as a function of maximum ring difference (i.e. acceptance angle) and activity concentration using a 27 cm diameter, 200 cm uniformly filled cylindrical phantom for each scanner configuration. To reduce the effect of random coincidences, we implemented a variable coincidence time window based on the length of the lines of response, which increased NECR performance up to 10% compared to using a static coincidence time window for scanners with a large maximum ring difference values. For a given scintillator volume, the optimal configuration results in modest count-rate performance gains of up to 16% compared to the shortest AFOV scanner with the thickest detectors. However, the longest AFOV of approximately 2 m with 20 mm thick detectors resulted in performance gains of 25-31 times higher NECR relative to the current Siemens Biograph mCT scanner configuration.
Binding of Cyt1Aa and Cry11Aa Toxins of <i>Bacillus thuringiensis</i> Serovar <i>israelensis</i> to Brush Border Membrane Vesicles of <i>Tipula paludosa</i> (Diptera: Nematocera) and Subsequent Pore Formation (2007)

Bacillus thuringiensis serovar israelensis (B. thuringiensis subsp. israelensis) produces four insecticidal crystal proteins (ICPs) (Cry4A, Cry4B, Cry11A, and Cyt1A). Toxicity of recombinant B. thuringiensis subsp. israelensis strains expressing only one of the toxins was determined with first instars of Tipula paludosa (Diptera: Nematocera). Cyt1A was the most toxic protein, whereas Cry4A, Cry4B, and Cry11A were virtually nontoxic. Synergistic effects were recorded when Cry4A and/or Cry4B was combined with Cyt1A but not with Cry11A. The binding and pore formation are key steps in the mode of action of B. thuringiensis subsp. israelensis ICPs. Binding and pore-forming activity of Cry11Aa, which is the most toxic protein against mosquitoes, and Cyt1Aa to brush border membrane vesicles (BBMVs) of T. paludosa were analyzed. Solubilization of Cry11Aa resulted in two fragments, with apparent molecular masses of 32 and 36 kDa. No binding of the 36-kDa fragment to T. paludosa BBMVs was detected, whereas the 32-kDa fragment bound to T. paludosa BBMVs. Only a partial reduction of binding of this fragment was observed in competition experiments, indicating a low specificity of the binding. In contrast to results for mosquitoes, the Cyt1Aa protein bound specifically to the BBMVs of T. paludosa, suggesting an insecticidal mechanism based on a receptor-mediated action, as described for Cry proteins. Cry11Aa and Cyt1Aa toxins were both able to produce pores in T. paludosa BBMVs. Protease treatment with trypsin and proteinase K, previously reported to activate Cry11Aa and Cyt1Aa toxins, respectively, had the opposite effect. A higher efficiency in pore formation was observed when Cyt1A was proteinase K treated, while the activity of trypsin-treated Cry11Aa was reduced. Results on binding and pore formation are consistent with results on ICP toxicity and synergistic effect with Cyt1Aa in T. paludosa.
Separating Trojan horses, viruses, and worms - a proposed taxonomy of software weapons (2003)

The terms used today to categorise different types of software weapons are not really suitable, because there exist several different definitions of each term, many of them contradicting each other. Therefore we present some methods for solving the problem. All the methods are based on a technical description's model of IT weapons (TEBIT), which is a proposed taxonomy of software weapons. Two methods, a weapon-based and a definition-based, are evaluated empirically and the results and experiences are discussed, leading to the recommendation of the weapon-based method.
Preparation and structure of platinum group metal colloids: without solvent (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPreparation and structure of platinum group metal colloids: without solventLarry N. Lewis and N. LewisCite this: Chem. Mater. 1989, 1, 1, 106–114Publication Date (Print):January 1, 1989Publication History Published online1 May 2002Published inissue 1 January 1989https://pubs.acs.org/doi/10.1021/cm00001a021https://doi.org/10.1021/cm00001a021research-articleACS PublicationsRequest reuse permissionsArticle Views622Altmetric-Citations73LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Cloud API support for self-service Virtual Network Function (VNF) deployment (2015)

The emphasis today in Network Functions Virtualization (NFV) is on moving existing monolithic telecommunications services like the IP Multimedia Subsystem (IMS) as a unit to a virtualized infrastructure platform. Yet the next step will involve breaking down the monolithic services into smaller, more modular units called Virtualized Network Functions (VNFs) that can be quickly combined into cloud-based innovative service offerings. Current cloud Infrastructure as a Service (IaaS) API support for NFV deployments requires extensive configuration despite virtualization, exactly the antithesis of the cloud "as a service" model. This won't support the innovative combination of services envisioned for the next step. Our approach involves enhancing the cloud IaaS networking API to support more dynamic network services. We illustrate this approach with an API for L2 services deployment. We describe a new VNF service, JiffyVPN, which allows a customer to provision an IPsec VPN with Layer-2 (L2) service between data centers or from branch offices to the data center, through a few clicks on a self-serve customer portal. We developed an enhancement to the OpenStack Neutron API, called the Gateway API, that supports stitching virtual L2 networks together, and deployed JiffyVPN on top of it. We conclude with a discussion regarding developing API support for VNFs, and the need for a well-designed set of abstractions and their API implementation.
Etoposide-induced cytotoxicity in two human T-cell leukemic lines: delayed loss of membrane permeability rather than DNA fragmentation as an indicator of programmed cell death. (1993)

Features of the apoptotic response evident in glucocorticoid-treated thymocytes are not uniformly observed in cell lines exposed to anticancer drugs. The significance of such variation has been assessed by monitoring molecular and cellular processes induced by etoposide (VP-16) in the human lymphoblastoid T-cell lines CCRF-CEM (CEM) and MOLT-4 contrasted, where appropriate, with those induced by necrotizing injury. Cytotoxic concentrations of the drug were determined to be 5-100 microM on the basis of tetrazolium reduction assay. The two lines were equally sensitive to VP-16; no difference in concentration of drug which inhibited cell growth by 50% with respect to control (i.e., drug free) cultures was apparent irrespective of exposure times from 3-72 h. DNA strand breaks were evident in both populations within 3 h of exposure to VP-16. Morphological change, assessed microscopically, involving nuclear condensation and cell shrinkage was qualitatively and quantitatively similar in VP-16-treated CEM and MOLT-4 cells. Flow cytometric analysis indicated that the G2/M fraction of the randomly dividing MOLT-4 population was approximately one-third that of CEM cells, but each line exhibited a decrease in this fraction 3-6 h after treatment. Despite these similarities, marked differences in the response to VP-16 were evident in the two populations. Internucleosomal fragmentation, detected electrophoretically 3 h after treatment in DNA isolated from CEM cells, was not detected under any condition in MOLT-4 DNA. Apoptotic bodies, also evident within 3 h of VP-16 treatment of CEM cells, were not readily apparent in MOLT-4 cells under the same conditions. Treatment causing necrosis resulted in trypan blue uptake within 1 h in a similar high proportion of cells from both lines. Exposure to VP-16 resulted in such a loss of membrane integrity by 6 h in CEM cells, while change in this parameter occurred only after 24 h in the case of MOLT-4 cells. The findings indicate a wide scope of difference in apoptotic response and suggest delayed loss of membrane permeability, rather than DNA fragmentation, as the clearest indicator of programmed cell death in these populations.
Why does file system prefetching work (1999)

Most file systems attempt to predict which disk blocks will be needed in the near future and prefetch them into memory; this technique can improve application throughput as much as 50%. But why? The reasons include that the disk cache comes into play, the device driver amortizes the fixed cost of an I/O operation over a larger amount of data, total disk seek time can be decreased, and that programs can overlap computation and I/O. However, intuition does not tell us the relative benefit of each of these causes, or techniques for increasing the effectiveness of prefetching. To answer these questions, we constructed an analytic performance model for file system reads. The model is based on a 4.4BSD-derived file system, and parameterized by the access patterns of the files, layout of files on disk, and the design characteristics of the file system and of the underlying disk. We then validated the model against several simple workloads; the predictions of our model were typically within 4...
Model-based image matching using location (pattern, recognition) (1984)

An approach to model-based image matching using only location of pattern features is described. The computer vision task of recognizing and locating rigid shapes in the plane can be posed as this search problem: (1) Given two sets of feature points in the plane (a model pattern and a noisy, misregistered pattern), and worst-case constraints on pointwise noise, (2) find all total matchings (mapping the model into the instance), (3) such that there exists a registration (transformation of the plane combining translation, rotation, and scaling) superimposing matched point within the noise constraints.
Noise constraints are described flexibly by arbitrary convex polygons enclosing the feature points. Search among a potentially exponential number of matchings is pruned by testing feasibility of systems of linear inequalities. The Soviet ellipsoid algorithm is shown to be efficient for these tests. We focus on the case where there are no missing or spurious instance points. Under zero noise, only a low-order polynomial total number of matchings must be examined in the worst case, even for highly regular and symmetric patterns. For random patterns under moderate noise, the expected number of feasible partial matchings examined to find m successful matchings is proved to be O(m n), where n is the number of points in the patterns. Monte Carlo trials, supported by a partial complexity analysis, show that the expected runtime to find one successful matching is O(n('2)). In practice, for n < 100, expected runtime should appear linear in n, since less than 5% is due to non-linear effects. The approach extends to non-singular affine registrations in higher dimensions.
[Comet assay of DNA fragmentation: modification of silver staining for obtaining permanent preparations]. (2005)

Modification of comet analysis is proposed for obtaining permanent preparations by DNA staining with silver compounds. The sensitivity of staining is similar to that observed at the treatment by ethidium bromide and other fluorochromes. The advantages of the method are stability of slides and possibility of their reinvestigation by light microscopy. The method does not need expensive fluorescent microscope and lacks contacting with carcinogenic compounds and UV light irradiation.