gebhart/patrepeval huggingface dataset:
Thermal annealing of implantation-induced compaction for improved silica waveguide performance (1996)

The optimum processing parameters for the fabrication of low-loss waveguides in fused silica by ion implantation and annealing have been determined through a comparison of implantation-induced physical and optical properties. The step height at an implanted/unimplanted boundary resulting from Si implantation was measured as a function of the ion dose (2×1012–6×1016/cm2) and energy (1–9 MeV) and the postimplantation annealing temperature (200–900 °C) and time (0.1–150 min). For a given ion energy (5 MeV), the step height increased for doses &lt;∼1015/cm2 and thereafter, saturated. For a given ion dose (2×1015/cm2), a near-linear trend was evident for step height as a function of ion energy. Isochronal and isothermal annealing both resulted in a nonlinear reduction in step height, typical of a thermally induced process. In contrast to the continual reduction in step height observed during isochronal annealing, the loss coefficient exhibited a distinct minimum of ∼0.15 dB/cm at an intermediate temperature of 500 °C. This feature was consistent with the removal of a specific defect or color center.
Entropic Lattice Boltzmann Method for Large Scale Turbulence Simulation (2003)

Recently, a minimal kinetic model for fluid flow, known as entropic lattice Boltzmann method, has been proposed for the simulation of isothermal hydrodynamic flows. At variance with previous Lattice Boltzmann methods, the entropic version permits to describe the non-linear dynamics of short scales in a controlled and stable way. In this paper, we provide the first numerical evidence that the entropic lattice Boltzmann scheme provides a quantitatively correct description of the large-scale structures of two-dimensional turbulence, free of numerical instabilities. This indicates that the entropic lattice Boltzmann method might provide a starting basis for the formulation of a new class of turbulence models based on genuinely kinetic principles.
Regulation of Cox-2 by Cyclic AMP Response Element Binding Protein in Prostate Cancer: Potential Role for Nexrutine (2007)

We recently showed that Nexrutine, a Phellodendron amurense bark extract, suppresses proliferation of prostate cancer cell lines and tumor development in the transgenic adenocarcinoma of mouse prostate (TRAMP) model. Our data also indicate that the anti-proliferative effects of Nexrutine are emediated in part by Akt and Cyclic AMP response element binding protein (CREB). Cyclooxygenase (Cox-2), a pro-inflammatory mediator, is a CREB target that induces prostaglandin E(2) (PGE(2)) and suppresses apoptosis. Treatment of LNCaP cells with Nexrutine reduced tumor necrosis factor alpha-induced enzymatic as well as promoter activities of Cox-2. Nexrutine also reduced the expression and promoter activity of Cox-2 in PC-3 cells that express high constitutive levels of Cox-2. Deletion analysis coupled with mutational analysis of the Cox-2 promoter identified CRE as being sufficient for mediating Nexrutine response. Immunohistochemical analysis of human prostate tumors show increased expression of CREB and DNA binding activity in high-grade tumors (three-fold higher in human prostate tumors compared to normal prostate; P = .01). We have identified CREB-mediated activation of Cox-2 as a potential signaling pathway in prostate cancer which can be blocked with a nontoxic, cost-effective dietary supplement like Nexrutine, demonstrating a prospective for development of Nexrutine for prostate cancer management.
Multiplexed Data Independent Acquisition for Comparative Proteomics (2012)

Each scan isolates and fragments five 4 m/z – wide precursor ranges randomly chosen from a predefined list of consecutive, adjacent ranges. In this example, the mass range from 500-900 m/z is sampled every 20 scan events. Step 1: Generate a list of isolation windows to be sampled (in this example, 100 4 m/z wide windows 500-900 m/z) Step 2: Build a scan by removing 5 isolation windows at random from the isolation window list, repeat until the isolation window list is empty Step 3: Repopulate the isolation window list, go to step 2. Q-Exactive Isolation Window Uniformity
Stimulus-Responsive Macromolecules and Nanoparticles for Cancer Drug Delivery (2010)

Nanoparticles and macromolecular carriers have been widely used to increase the efficacy of chemotherapeutics, largely through passive accumulation provided by the enhanced permeability and retention effect. Stimulus-responsive peptide and polymer vehicles can further enhance the efficacy of antitumor therapeutics compared with the administration of free drug by three mechanisms: increasing the overall accumulation within solid tumors; providing a homogeneous spatial distribution in tumor tissues; and increasing the intracellular localization of anticancer therapeutics. This article highlights recent developments in 'smart' - stimulus-responsive - peptide, polymer and lipid drug carriers designed to enhance the localization and efficacy of therapeutic payloads as compared with free drug.
Two Catholic Libraries in Copenhagen, 1648–1962: St Andrew's Library and Niels Steensen's Library (2004)

The Catholic Church has a long tradition of viewing libraries as key resources; indeed, in the monasteries of mediaeval times the library was simply called an armarium (in the sense of a closet where treasures were stored — a spiritual and intellectual arsenal). More than a hundred Catholic libraries have existed in Denmark from the middle of the seventeenth century up to the Second Vatican Council (1962–1965). These libraries represent an almost virgin area of research. Once the new Danish Constitution (1849), which guaranteed religious liberty, allowed the Catholic Church legally to resume its work, the libraries appear to have been important resources for the Church in all its missionary, educational and pastoral activities. The history of an ancient Catholic theological research library (St Andrew's Library) and a Catholic 'public library' (Niels Steensen's Library) of more recent date, both in Copenhagen, are treated here. It is concluded that they — each in its own way — make valuable and useful supplements to the academic and public libraries in Denmark.
Crystallization Properties and Polymorphic Behavior of Isotactic Poly(1-Butene) from Metallocene Catalysts: The Crystallization of Form I from the Melt (2009)

A study of the crystallization from the melt and of the polymorphic behavior of isotactic poly(1-butene) (iPB) prepared with metallocene catalysts is presented. Samples of isotactic polybutene of different stereoregularity, containing different concentrations of stereodefects (rr triads defects) and regiodefects (4,1 units) have been prepared with different C2- and C1-symmetric metallocene catalysts. The concentration of defects and the molecular mass are controlled through a rational choice of the catalyst structure and conditions of polymerization. Highly isotactic samples with concentration of rr stereodefects lower than 2 mol %, crystallize from the melt in the metastable form II. This is a common polymorphic behavior observed in iPB samples prepared with Ziegler−Natta catalysts and extensively reported in the literature. More stereodefective iPB samples, containing concentration of stereodefects higher than 2 mol %, crystallize form the melt as mixtures of form II and form I, the fraction of crystals of form I increases with increasing concentration of defects and decreasing cooling rate from the melt, and samples with concentration of rr defects of 3−4 mol % crystallize from the melt in the pure form I at low cooling rates. This is the first experimental observation of the crystallization of the stable trigonal form I of iPB from the melt at atmospheric pressure. This result may be of interest because the crystallization of the metastable form II from the melt and the spontaneous transformation at room temperature of form II into the stable form I has been considered for long time an unavoidable problem that stands in the way of the industrial development of the Ziegler−Natta iPB.
An Operation-Based Model of Version Storage and Consistency Management for Fine-Grained Software Objects (2000)

Software documents consists of a number of objects and relationships between them, and structure of documents can be changed frequently. In this paper, we propose a version storage and consistency management model for fine-grained software objects based on operations applied to edit software objects. An object has an interface and can be updated only through operations defined in its interface. Operations applied to objects are recorded in the operation history, which is used to retrieve versions of a document and manage consistency between documents. Because versions of an object are stored and retrieved using the operation delta, it is not needed to compare versions of a document to extract delta and it is easy to identify the changes between versions in order to propagate the changes. Consistencies between documents are managed using dependencies between objects and kinds of the operations applied to the objects. Therefore unnecessary version propagation can be avoided. This paper presents a formal model of version retrieval and consistency management at the fine-grained level based on operations applied to the objects.
Abstract A19: Identification of Heregulin (HRG) expression as a driver of a difficult-to-treat cancer phenotype and development of a companion diagnostic for the HRG-ErbB3 targeting drug seribantumab (2017)

Abstract Heregulin (HRG) is the cognate ligand of the ErbB3 receptor and has been identified as a potent driver of a distinct tumor cell phenotype characterized by enhanced survival that appears to be inherently more resistant to standard of care therapies. Seribantumab (MM-121) is a fully human monoclonal antibody designed to block HRG from binding to ErbB3 and to prevent the establishment of HRG-driven cancer cell survival in response to cytotoxic therapies. Clinical evidence from randomized studies suggests that patients who receive standard therapy have shorter progression-free survival (PFS) when their tumors are positive for HRG RNA expression compared to patients receiving standard therapy with HRG-negative tumors. The addition of seribantumab was able to enhance the anti-tumor effect of these respective standard therapies and prolong PFS in patients with HRG-positive tumors. Profiling data indicates that positive HRG expression can be found in more than a third of most solid tumors identifying a high unmet medical need. In order to identify HRG-driven tumors with a more difficult-to-treat phenotype, an RNA in situ hybridization (ISH) diagnostic assay has been developed. Details will be presented illustrating the benefits of RNA ISH over alternate detection methods for HRG. This includes the visualization of tumor cell HRG expression with high sensitivity and specificity in small tissue specimens such as fine needle aspirates and core needle biopsies. This assay is currently being used to select patients for inclusion into diagnostic-driven clinical studies. Citation Format: Sara Mathews, Gregory Finn, Arthur J. Kudla, Victoria Rimkunas, Peter Laivins, Gavin MacBeath, Akos Czibere, Jason Baum. Identification of Heregulin (HRG) expression as a driver of a difficult-to-treat cancer phenotype and development of a companion diagnostic for the HRG-ErbB3 targeting drug seribantumab. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Targeting the Vulnerabilities of Cancer; May 16-19, 2016; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(1_Suppl):Abstract nr A19.
SoK: Keylogging Side Channels (2018)

The first keylogging side channel attack was discovered over 50 years ago when Bell Laboratory researchers noticed an electromagnetic spike emanating from a Bell 131-B2 teletype terminal. This spike, emitted upon each key press, enabled up to 75% of plaintext communications to be recovered in field conditions. Since then, keylogging attacks have come to leverage side channels emanating from the user's finger and hand movements, countless keyboard electromagnetic and acoustic emanations, microarchitectural attacks on the host computer, and encrypted network traffic. These attacks can each be characterized by the type of information the side channel leaks: a spatial side channel reveals physical key locations or the similarity between key pairs, and a temporal side channel leverages key press and release timings. We define and evaluate the performance of idealized spatial and temporal keylogging side channels and find that, under the assumption of typing English words, nontrivial information gains can be achieved even in the presence of substantial measurement error. For temporal side channels, we find that the information gained by different temporal features strongly correlates to typing speed and style. Finally, to help drive future research, we review the current state-of-the-art keylogging side channel attacks and discuss some of the mitigation techniques that can be applied.
Studies of the “Chain Reversal Regions” of the Avian Sarcoma/Leukosis Virus (ASLV) and Ebolavirus Fusion Proteins: Analogous Residues Are Important, and a His Residue Unique to EnvA Affects the pH Dependence of ASLV Entry (2010)

Most class I fusion proteins exist as trimers of dimers composed of a receptor binding and a fusion subunit. In their postfusion forms, the three fusion subunits form trimers of hairpins consisting of a central coiled coil (formed by the N-terminal helices), an intervening sequence, and a region containing the C helix (and flanking strands) that runs antiparallel to and packs in the grooves of the N-terminal coiled coil. For filoviruses and most retroviruses, the intervening sequence includes a "chain reversal region" consisting of a short stretch of hydrophobic residues, a Gly-Gly pair, a CX(6)CC motif, and a bulky hydrophobic residue. Maerz and coworkers (A. L. Maerz, R. J. Center, B. E. Kemp, B. Kobe, and P. Poumbourios, J. Virol. 74:6614-6621, 2000) proposed a model for this region of human T-cell leukemia virus type 1 (HTLV-1) Env in which expulsion of the final bulky hydrophobic residue is important for early conformational changes and specific residues in the chain reversal region are important for forming the final, stable trimer of hairpins. Here, we used mutagenesis and pseudovirus entry assays to test this model for the avian retrovirus avian sarcoma/leukosis virus (ASLV) and the filovirus ebolavirus Zaire. Our results are generally consistent with the model proposed for HTLV-1 Env. In addition, we show with ASLV EnvA that the bulky hydrophobic residue following the CX(6)CC motif is required for the step of prehairpin target membrane insertion, whereas other residues are required for the foldback step of fusion. We further found that a His residue that is unique to the chain reversal region of ASLV EnvA controls the pH at which ASLV entry occurs.
Multi-level queue NVM/DRAM hybrid memory management with language runtime support (2015)

Non-volatile memory devices (NVM) devices, such as PCM, STT-MRAM, and ReRAM, enable the integration of secondary storage into main memory. This integration reduces I/O access to slow block devices; however, it is currently unrealistic to construct a large capacity main memory with a single NVM, because such devices have certain write access limitations. Combining NVM and other memory devices is necessary to overcome such disadvantages. Several researches discussed NVM/DRAM hybrid memory, combining NVM and DRAM. To use NVM/DRAM hybrid memory, the placement of data between NVM and DRAM must be determined. In particular, write-hot data should be allocated to DRAM and write-cold data to NVM. For data placement, programming language runtime supports are useful because they possess more detailed information about write access than the operating systems. A previous research proposed the individual counting method to manage NVM/DRAM hybrid memory with programming language runtime support that determine data placement based on the number of write accesses to each object. However, it is difficult to determine dynamically threshold values for data placements using the individual counting method. Here we propose a multi-level queue method to distinguish between write-hot and write-cold data. Experimental results show that the proposed method resolves the limitations of the individual counting method.
Application of systems biology principles to protein biomarker discovery: Urinary exosomal proteome in renal transplantation (2012)

The terms and candidate biomarkers identified make rational connections to pathophysiological mechanisms, suggesting that the described bioinformatic approach will be useful in advancing large-scale biomarker identification studies toward a validation phase.
Thymidine Kinase-Independent Intracellular Delivery of Bioactive Nucleotides by Aryl Phosphate Derivatives of Bromo-Methoxy Zidovudine (Compounds WHI-05 and WHI-07) in Normal Human Female Genital Tract Epithelial Cells and Sperm1 (2001)

The compounds WHI-05 (5-bromo-6-methoxy-5, 6-dihydro-3'-azidothymidine-5'-[p-methoxyphenyl] methoxyalaninyl phosphate) and WHI-07 (5-bromo-6-methoxy-5, 6-dihydro-3'-azidothymidine-5'-[p-bromophenyl] methoxyalaninyl phosphate) are aryl phosphate derivatives of zidovudine (ZDV) with dual-function anti-human immunodeficiency virus and contraceptive activity. These drugs were rationally designed to bypass the thymidine kinase (TK) dependency of ZDV activation as well as to achieve spermicidal activity. We investigated the TK activity and intracellular metabolism of WHI-05 and WHI-07 in normal human vaginal and cervical epithelial cells as well as sperm. The time- and concentration-dependent intracellular formation of ZDV metabolites following addition of WHI-05 and WHI-07 to normal human vaginal, ectocervical, and endocervical epithelial cells as well as motile sperm was studied by analytical HPLC. Thymidine kinase activity in these cells was determined by the flow cytometric method based on intracellular phosphorylation of the fluorescent nucleoside, 5-amino-2-deoxyuridine-dansyl chloride and by the ability of cell-free extracts to convert [(3)H]thymidine to thymidine monophosphate in comparison to NALM-6, a pre-B leukemia cell line. TK activity of genital tract epithelial cells and sperm was found to be relatively low or lacking. Addition of WHI-05 and WHI-07 to vaginal and cervical epithelial cells resulted in their concentration- and time-dependent conversion to alaninyl ZDV monophosphate (Ala-ZDV-MP) and 5'-ZDV monophosphate as the major metabolites. Studies using motile human sperm also demonstrated the conversion of WHI-05 and WHI-07 to Ala-ZDV-MP. These results demonstrate that human female genital tract epithelial cells and sperm efficiently convert WHI-05 and WHI-07 to bioactive ZDV metabolites despite their TK deficiency.
A metallic buried interconnect process for through-wafer interconnection (2008)

In this paper, we present the design, fabrication process and experimental results of electroplated metal interconnects buried at the bottom of deep silicon trenches with vertical sidewalls. A manual spray-coating process along with a unique trench-formation process has been developed for the electroplating of a metal interconnection structure at the bottom surface of the deep trenches. The silicon etch process combines the isotropic dry etch process and conventional Bosch process to fabricate a deep trench with angled top-side edges and vertical sidewalls. The resulting trench structure, in contrast to the trenches fabricated by wet anisotropic etching, enables spray-coated photoresist patterning with good sidewall and top-side edge coverage while maintaining the ability to form a high-density array of deep trenches without excessive widening of the trench opening. A photoresist spray-coating process was developed and optimized for the formation of electroplating mold at the bottom of 300 µm deep trenches having vertical sidewalls. A diluted positive tone photoresist with relatively high solid content and multiple coating with baking between coating steps has been experimentally proven to provide high quality sidewall and edge coverage. To validate the buried interconnect approach, a three-dimensional daisy chain structure having a buried interconnect as the bottom connector and traces on the wafer surface as the top conductor has been designed and fabricated.
Characterization of particle size and its distribution during the crystallization of organic fine chemical products as measured <i>in situ</i> using ultrasonic attenuation spectroscopy (2001)

The potential application of ultrasonic attenuation spectroscopy to the in situ examination of solution phase crystallization processes is examined through studies carried out on two organic compounds: urea and (L)-glutamic acid. For this study a commercial ultrasonic spectrometer [Ultrasizer by Malvern Instruments Ltd., F. Alba, U.S. Patent 5,121,629 (1992)] was used. A particle size analysis was carried out in an attempt to monitor the crystal size distributions of the crystals growing within the mother liquor. While this technique was found to be of limited effectiveness for the monitoring of the crystallization of urea, due to the formation of high aspect ratio needle crystals, whose long axial size is beyond the range of the technique (0.01 μm–1000 μm), good results were obtained with prismatic (L)-glutamic acid crystals. The size evolution of the latter during crystal growth was successfully monitored throughout the crystallization process.
The role of complement in experimental bullous pemphigoid. (1995)

Bullous pemphigoid (BP) is a blistering skin disease associated with an IgG autoimmune response directed against the ectodomain of the hemidesmosomal protein, BP180. An animal model of BP has recently been developed by our laboratory based on the passive transfer of rabbit antimurine BP180 antibodies into neonatal BALB/c mice. The experimental animals develop a blistering disease that reproduces all of the key immunopathological features of BP. In the present study we have investigated the role of complement in the pathogenesis of subepidermal blistering in the mouse model of BP. We demonstrate the following. (a) Rabbit anti-murine-BP180 IgG was effective in inducing cutaneous blisters in a C5-sufficient mouse strain, but failed to induce disease in the syngeneic C5-deficient strain; (b) neonatal BALB/c mice, pretreated with cobra venom factor to deplete complement, became resistant to the pathogenic effects of the anti-BP180 IgG; (c) F(ab')2 fragments generated from the anti-BP180 IgG exhibited no pathogenic activity in the mouse model; and (d) histologic evaluation of the skin of mice described in points b and c above showed minimal or no neutrophilic cell infiltration in the upper dermis. Thus, anti-BP180 antibodies trigger subepidermal blistering in this BP model via complement activation. This experimental model of BP should greatly facilitate future studies on the pathophysiology of autoantibody-mediated diseases of the dermal-epidermal junction.
A Multi‐Dimensional Microporous Silicate That Is Isomorphous to Zeolite MCM‐68 (2007)

Hot and steamy cages: The gel composition for MCM-68 typically obtained by hydrothermal methods is changed by steam-assisted crystallization and results in the formation of the highly crystalline pure silica analogue YNU-2P (see picture). The crystal structure of this compound indicates the presence of significant site defects.
Clustering the Users of Large Web Sites into Communities (2000)

In this paper we analyze the performance of clustering methods on the task of constructing community models for the users of large Web sites.