gebhart/patrepeval huggingface dataset:
An analytical model for loop tiling and its solution (2002)

The authors address the problem of estimating the performance of loop tiling, an important program transformation for improved memory hierarchy utilization. We introduce an analytical model for estimating the memory cost of a loop nest as a rational polynomial in tile size variables. We also present a constant-time algorithm for finding an optimal solution to the model (i.e., for selecting optimal tile sizes) for the case of doubly nested loops. This solution can be applied to tiling of three loops by performing an iterative search on the value of the first tile size variable, and using the constant-time algorithm at each point in the search to obtain optimal tile size values for the remaining two loops. Our solution is efficient enough to be used in production-quality optimizing compilers, and has been implemented in the IBM XL Fortran product compilers. This solution can also be used by processor designers to efficiently predict the performance of a set of tiled loops for a range of memory hierarchy parameters.
<i>In Vivo</i> Gene Therapy of Cancer with <i>E. coli</i> Purine Nucleoside Phosphorylase (1997)

We have developed a new strategy for the gene therapy of cancer based on the activation of purine nucleoside analogs by transduced E. coli purine nucleoside phosphorylase (PNP, E.C. 2.4.2.1). The approach is designed to generate antimetabolites intracellularly that would be too toxic for systemic administration. To determine whether this strategy could be used to kill tumor cells without host toxicity, nude mice bearing human malignant D54MG glioma tumors expressing E. coli PNP (D54-PNP) were treated with either 6-methylpurine-2'-deoxyriboside (MeP-dR) or arabinofuranosyl-2-fluoroadenine monophosphate (F-araAMP, fludarabine, a precursor of F-araA). Both prodrugs exhibited significant antitumor activity against established D54-PNP tumors at doses that produced no discernible systemic toxicity. Significantly, MeP-dR was curative against this slow growing solid tumor after only 3 doses. The antitumor effects showed a dose dependence on both the amount of prodrug given and the level of E. coli PNP expression within tumor xenografts. These results indicated that a strategy using E. coli PNP to create highly toxic, membrane permeant compounds that kill both replicating and nonreplicating cells is feasible in vivo, further supporting development of this cancer gene therapy approach.
Rapid manufacturing of dental prostheses by means of selective laser sintering/melting (2005)

In recent years, digitizing and automation have gained an important place in the manufacturing of medical products. However, many dental parts are still being produced by manual and inefficient conventional methods. This paper presents a fully digital and fast procedure for the design and manufacturing of implant-supported frameworks for complex dental prostheses by means of Selective Laser Sintering (SLS) or Selective Laser Melting (SLM). Offering a digital solution to the dental profession implies a real challenge because patient and dentist set high requirements on quality, material and precision. During this study, frameworks were manufactured by SLS/SLM of stainless steel, Ti6Al4V and a dental CoCr-alloy. The accuracy of the final framework has been analyzed by studying the error accumulation of the successive steps in the proposed procedure. SLS/SLM allows an efficient and customized production of the complex biocompatible frameworks without lengthy manual pre- or post-processing and with a medically acceptable accuracy corresponding to the precision of a conventionally fabricated framework.
Film bulk acoustic resonator (FBAR) based power converters: A new trend featuring EMI reduction and high power density (2013)

In this paper, a series resonant converter and a LED driver have been implemented by using a film bulk acoustic resonators (FBAR) in place of the inductor. This MEMS device can offer very high inductance density with excellent Q factor and can be conveniently fabricated in a CMOS compatible process. FBARs are smaller in size and weight compared to an inductor offering the same inductance per volume and quality factor, and therefore,, FBAR based power converters can offer higher power density. Simulation and experimental results with zero voltage switching (ZVS) and zero current switching (ZCS) have been provided to validate the use of FBARs in power converter circuits. The EMI of a discrete inductor based converter has been compared to that of an FBAR based converter, and the FBAR based converter showed better EMI performance. To the knowledge of the authors, the use of FBAR in power converter circuits has not been reported in the literature yet.
Correlation of Pathologic Features With CpG Island Methylator Phenotype (CIMP) by Quantitative DNA Methylation Analysis in Colorectal Carcinoma (2006)

Extensive gene promoter methylation in colorectal carcinoma has been termed the CpG island methylator phenotype (CIMP). Previous studies on CIMP used primarily methylation-specific polymerase chain reaction (PCR), which, unfortunately, may detect low levels of methylation that has little or no biological significance. Utilizing quantitative real-time PCR (MethyLight), we measured DNA methylation in a panel of 5 CIMP-specific gene promoters (CACNA1G, CDKN2A (p16), CRABP1, MLH1, and NEUROG1) in 459 colorectal carcinomas obtained from 2 large prospective cohort studies. CIMP was defined as tumors that showed methylation in >or=4/5 promoters. CIMP was significantly associated with the presence of mucinous or signet ring cell morphology, marked Crohn's-like lymphoid reaction, tumor infiltrating lymphocytes, marked peritumoral lymphocytic reaction, tumor necrosis, tumor cell sheeting, and poor differentiation. All these features have previously been associated with microsatellite instability (MSI). Therefore, we divided the 459 colorectal carcinomas into 6 subtypes, namely, MSI-high (MSI-H)/CIMP, MSI-H/non-CIMP, MSI-low (MSI-L)/CIMP, MSI-L/non-CIMP, microsatellite stable/CIMP, and micro satellite sstable/non-CIMP. Compared with MSI-H/non-CIMP, MSI-H/CIMP was associated with marked tumor infiltrating lymphocytes, tumor necrosis, sheeting, and poor differentiation (all P<or=0.05). Compared with MSI-L/non-CIMP, MSI-L/CIMP was associated with tumors that had <50% signet ring cell component, marked tumor infiltrating lymphocytes, and poor differentiation (all P<0.05). In conclusion, several pathologic features that have previously been shown to be associated with MSI are also significantly associated with CIMP. Both MSI and CIMP appear to play a role in the pathogenesis of specific morphologic patterns of colorectal carcinoma.
Acceleration of Synthetic Organic Reactions Using Supercritical Water:  Noncatalytic Beckmann and Pinacol Rearrangements (2000)

A high-pressure and high-temperature FTIR was used to study noncatalytic Beckmann and pinacol rearrangements using supercritical water (scH2O). Significant acceleration of Beckmann and pinacol rearrangements can be achieved by using scH2O, especially near the critical point, even in the absence of any acid catalysts. It has been demonstrated that scH2O acts effectively in the place of conventional acid catalysts for both the rearrangements. The rate of pinacol rearrangement using scH2O is significantly larger by a factor of 28200 than that in 0.871 M HCl solution at 46.7 MPa under distillation conditions. The activation energy for the former at 25 MPa was found to be markedly reduced to about one-third of that for the latter. The accelerated rates of reaction may be attributed to a great increase in the local proton concentration around the organic reactants. In addition, the nature of scH2O can be adjustable to weak acidity in the near-critical region, and then it does not catalyze the pinacol rearrangement, but opens a new reaction pathway from pinacol through a completely dehydrated product and then to a Diels−Alder adduct between the dehydrated products.
Abstract 1000: PD-L1 binding peptide identified by phage peptide display inhibits PD-1/PD-L1 interaction and activates T cells (2018)

Abstract Immune suppressive mechanism within the tumor microenvironment inhibits antitumor T cell function, leading to evasion of tumor from immune attack. One of the mechanisms is the up-regulation of programmed death-ligand 1 (PD-L1) expression on tumor cells which binds to programmed cell death protein 1 (PD-1) on activated T cells and inhibits T cell functions. Inhibiting the PD-L1/PD-1 interaction could reverse the tumor microenvironment and enhance the endogenous antitumor immune response. To identify a novel peptide that selectively binds to PD-L1, we screened a phage-displayed peptide library against cells transiently expressing PD-L1 at high levels. After multiple rounds of screening, selected phage clones were sequenced. Of these, two phage clones showed more selective binding to cells expressing PD-L1 compared to a control clone. The peptides displayed on the clones were synthesized for further study and named as PD-L1Pep-1 (9mer) and PD-L1Pep-2 (7mer). Fluorescein-conjugated PD-L1Pep-1 and PD-L1Pep-2 selectively bound to cells highly expressing PD-L1, whereas only negligible binding to cells expressing PD-L1 at low levels. The cell binding of the PD-L1-binding peptides was enhanced after treatment of cells with interferon-γ which is a potent inducer of PD-L1 in many types of cancer cells. FACS analysis showed that the pre-treatment of cells with an anti-PD-L1 antibody competed and reduced the cell binding of the PD-L1-binding peptides, suggesting the antibody and peptides bind to the same epitope on PD-L1. Co-culture experiments of CT26 mouse colon tumor cells with primary T cells isolated from a mouse spleen showed that, similar to the anti-PD-L1 antibody, the PD-L1-binding peptides increased the secretion of Interleukin-2 and interferon-γ by the T cells, indicating that the PD-L1-binding peptides can reactivate the T cells that were suppressed by the co-cultured tumor cells. In-vivo fluorescence imaging of BALB/c mice bearing subcutaneously transplanted CT26 mouse colon tumor cells showed tumor targeting ability of the PD-L1-binding peptides to PD-L1-expressing tumor. These findings suggest that PD-L1Pep-1 and PD-L1Pep-2 can inhibit PD-L1/PD-1 interaction and activate T cells in vivo and hold a potential as a cancer immunotherapeutic. Keywords: Colon tumor, immunotherapy, PD-L1, peptide, phage display Citation Format: Smriti Gurung, Fatima Khan, Soo-Woong Lee, Jaewon Yoon, Byungheon Lee. PD-L1 binding peptide identified by phage peptide display inhibits PD-1/PD-L1 interaction and activates T cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1000.
Cinema 3D: large scale automultiscopic display (2016)

While 3D movies are gaining popularity, viewers in a 3D cinema still need to wear cumbersome glasses in order to enjoy them. Automultiscopic displays provide a better alternative to the display of 3D content, as they present multiple angular images of the same scene without the need for special eyewear. However, automultiscopic displays cannot be directly implemented in a wide cinema setting due to variants of two main problems: (i) The range of angles at which the screen is observed in a large cinema is usually very wide, and there is an unavoidable tradeoff between the range of angular images supported by the display and its spatial or angular resolutions. (ii) Parallax is usually observed only when a viewer is positioned at a limited range of distances from the screen. This work proposes a new display concept, which supports automultiscopic content in a wide cinema setting. It builds on the typical structure of cinemas, such as the fixed seat positions and the fact that different rows are located on a slope at different heights. Rather than attempting to display many angular images spanning the full range of viewing angles in a wide cinema, our design only displays the narrow angular range observed within the limited width of a single seat. The same narrow range content is then replicated to all rows and seats in the cinema. To achieve this, it uses an optical construction based on two sets of parallax barriers, or lenslets, placed in front of a standard screen. This paper derives the geometry of such a display, analyzes its limitations, and demonstrates a proof-of-concept prototype.
Maternal serum unconjugated oestriol as an antenatal screening test for Down's syndrome (1988)

The median maternal serum unconjugated oestriol level between 13 and 27 weeks gestation in 77 pregnancies associated with Down's syndrome was lower than the median level in 385 unaffected control pregnancies matched for maternal age, gestational age, and duration of serum sample storage (P less than 0.001). The median level for the affected pregnancies was 73% of that in the controls. Low unconjugated oestriol levels can be used to detect fetal Down's syndrome; at cut-off levels selected to detect at least 35% of affected pregnancies, unconjugated serum oestriol was a better screening test than either maternal age or serum alpha-fetoprotein (AFP). The use of all three variables in combination to select women with a 1:250 or greater risk of a Down's syndrome term pregnancy would yield a 45% detection rate with a false-positive rate of 5.2%. The same detection rate using maternal age alone or using age and serum AFP in combination would yield higher false-positive rates, 15% and 9.8% respectively. The addition of unconjugated oestriol to a Down's syndrome screening programme would therefore be more efficient than the use of age and AFP alone; for a given detection rate fewer women would need an amniocentesis or, for a given percentage of women having an amniocentesis, more pregnancies with Down's syndrome would be detected.
Consistent prediction of absolute permeability in carbonates without upscaling (2020)

We describe a study focused on the absolute permeability of reservoir carbonate rocks from the Middle East and involving comparison of experimental data and numerical estimates obtained by combining digital-rock and Lattice-Boltzmann Methods (LBM). The question of the “representativeness” of the site at which the simulation is performed is addressed as follows. First, a low-resolution, CT X-ray scan of the core plug is performed to identify regions of large porosity (millimeter-sized vugs, etc.). These regions are then avoided to postselect smaller sites (site volume ~ 1 mm 3 ) which are to be scanned at higher resolutions (voxel size < dominant pore-throat size of the core plug). A “representativeness” criterion based on an empirically-inspired “representativeness” measure ( R -measure) is used to eliminate those sites for which R > b , where b is an upper bound (typically, b = 1). Essentially, the measure estimates how well the postselected sites capture the experimental porosity and the dominant pore-throat size of the core plug. This leads to a small set of sites for which the simulations are both computationally manageable and yield a reasonable estimate of the permeability: the experimental and predicted values differ by a factor of about 3 on average, which is a particularly significant result given the challenging heterogeneous pore space of carbonate samples. We believe the suggested methodology to be an adequate and practical way to circumvent upscaling.
Recent Advances in the Controlled Design of One-dimensional Carbon Nitrides for Thermal CO Oxidation Reaction (2021)

Graphitic carbon nitrides (gCNs) are promising materials for multidisciplinary catalytic applications due to their inimitable physicochemical merits, thermal-physical-chemical stability, and rich electron density. The catalytic properties of gCNs are determined by their structure and composition; therefore, various methods have been developed for the rational synthesis of gCNs with different morphologies and compositions. Unlike other gCN nanostructures, one-dimensional (1D) nanostructures possess an outstanding accessible surface area, multiple adsorption sites, active catalytic sites, aspect ratio, and short electron-diffusion that enable their utilization in various gas conversion reactions. The thermal CO oxidation reaction (CO OR) on either gCNs or other catalysts is important in industrial, fundamental, and environmental issues; however, the reviews on 1D gCNs for CO oxidation is not yet reported. This chapter highlights the fabrication methods of 1D gCN nanostructures (i.e., nanotubes, nanorods, nanofibers, and needles) and their mechanisms and utilization in thermal CO ORs. Lastly, the current challenges and future prospects on gCNs for CO ORs are also discussed.
Analysis of the Physical Behavior of Viruses Using the Integrated Virus Detection System (IVDS) (2004)

In this work the morphological types of the nervous receptors in the pulmonary vessels of the Wistar rat are studied with the Koelle-Friedenwall, Champy-Maillet and Jabonero techniques. Different types of corpuscules are described. Some are simple and some are more complex (tree-like terminals of Seto type). The localization of these corpuscules is variable. Sometimes they are located in the pulmonary vessels and sometimes in the conjunctive tissue. These receptors are interpreted as baro-receptors i.e. receptors of change of pressure.
How dynamic are IP addresses? (2007)

This paper introduces a novel algorithm, UDmap, to identify dynamically assigned IP addresses and analyze their dynamics pattern. UDmap is fully automatic, and relies only on application-level server logs. We applied UDmap to a month-long Hotmail user-login trace and identified a significant number of dynamic IP addresses - more than 102 million. This suggests that the fraction of IP addresses that are dynamic is by no means negligible. Using this information in combination with a three-month Hotmail email server log, we were able to establish that 95.6% of mail servers setup on the dynamic IP addresses in our trace sent out solely spam emails. Moreover, these mail servers sent out a large amount of spam - amounting to 42.2% of all spam emails received by Hotmail. These results highlight the importance of being able to accurately identify dynamic IP addresses for spam filtering. We expect similar benefits to arise for phishing site identification and botnet detection. To our knowledge, this is the first successful attempt to automatically identify and understand IP address dynamics.
Purification and Characterization of Tissue Plasminogen Activator Secreted by Human Embryonic Lung Diploid Fibroblasts, IMR-90 Cells (1991)

The anti-urokinase-IgG-resistant plasminogen activator secreted by human embryonic lung diploid fibroblasts, IMR-90 cells (ATCC, CCL186) was purified to homogeneity from serum-free conditioned medium by a four-step procedure. The fibroblast plasminogen activator was identified as tissue plasminogen activator (t-PA) by the N-terminal sequence of the purified material and the complete amino acid sequence deduced from its complementary DNA (cDNA). The apparent molecular weight was the range of 64,000 to 68,000 by SDS-PAGE and was in the range of 69,000 to 72,000 by gel filtration. The fibroblast t-PA showed a stricter substrate specificity than urokinase in enzymatic hydrolysis of various chromogenic substrates. Compared to urokinase, the fibrobrast t-PA was more stable by heating at 95 degrees C for five min and was stable from pH 5 to 10. The fibrorast t-PA had a higher affinity for fibrin than urokinase.
Characterization of cationic dextrin prepared by ultra high pressure (UHP)-assisted cationization reaction (2013)

Cationic dextrins were prepared through substitution reaction of dextrin with low and high addition levels of 2,3-epoxypropyltrimethylammonium chloride (ETMAC), respectively. Conventional cationization reactions were carried out for 5h under continued stirring. UHP-assisted cationization reactions were conducted at three pressurization levels of 100, 300 and 500 MPa for a pressure holding time of 30 min. Degree of substitution (DS) of UHP-assisted cationic dextrins ranged from 0.58 to 1.51, and in general, their DS values were enhanced with increasing pressure levels. FT-IR and (13)C NMR spectra indicated the presence of CN bond, which provided clear evidence about incorporation of cationic moieties onto dextrin molecules. In flocculation test, UHP-assisted cationic dextrin revealed higher flocculating activity. Overall results suggested that UHP-assisted cationization reaction could modulate reactivity and flocculating activity of dextrin by controlling pressure levels and reaction mixture compositions, and cationic dextrins likely possessed a higher potential to replace synthetic polymer-based flocculants.
Training dependency parsers by jointly optimizing multiple objectives (2011)

We present an online learning algorithm for training parsers which allows for the inclusion of multiple objective functions. The primary example is the extension of a standard supervised parsing objective function with additional loss-functions, either based on intrinsic parsing quality or task-specific extrinsic measures of quality. Our empirical results show how this approach performs for two dependency parsing algorithms (graph-based and transition-based parsing) and how it achieves increased performance on multiple target tasks including reordering for machine translation and parser adaptation. 1
Three-dimensional total internal reflection microscopy (2001)

We investigate the inverse-scattering problem that arises in total internal reflection microscopy. An analytic solution to this problem within the weak-scattering approximation is used to develop a novel form of three-dimensional microscopy with subwavelength resolution.
Development of a multifrequency ultrasonic transducer using PZT/polymer 1–3 composite (1989)

Abstract In a number of clinical examinations using ultrasound, it is advantageous to be able to examine a patient at different frequencies. Low frequency is used to obtain images with adequate penetration and high frequency is used to obtain images with fine resolution. In this paper the feasibility of constructing a multiple-frequency transducer using piezoelectric composite is examined. The transducer is comprised of piezoelectric ceramic rods embedded in a polymer matrix. By selecting the appropriate thickness and width of ceramic rod, the transducer assembly can be made to resonate at a number of frequencies as predicted by the mode coupling theory. One of the resonance frequencies is determined by the width of the ceramic rod; other resonance frequencies are determined by the width-to-thickness ratio of the ceramic rods. A number of multiple-frequency transducers were constructed and the results correlate well with the theoretical prediction.
Cancer-Associated SF3B1 Hotspot Mutations Induce Cryptic 3′ Splice Site Selection through Use of a Different Branch Point (2015)

Recurrent mutations in the spliceosome are observed in several human cancers, but their functional and therapeutic significance remains elusive. SF3B1, the most frequently mutated component of the spliceosome in cancer, is involved in the recognition of the branch point sequence (BPS) during selection of the 3' splice site (ss) in RNA splicing. Here, we report that common and tumor-specific splicing aberrations are induced by SF3B1 mutations and establish aberrant 3' ss selection as the most frequent splicing defect. Strikingly, mutant SF3B1 utilizes a BPS that differs from that used by wild-type SF3B1 and requires the canonical 3' ss to enable aberrant splicing during the second step. Approximately 50% of the aberrantly spliced mRNAs are subjected to nonsense-mediated decay resulting in downregulation of gene and protein expression. These findings ascribe functional significance to the consequences of SF3B1 mutations in cancer.
Method and apparatus for monitoring the shaft vibration of a rotary machine (1984)

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