gebhart/patrepeval huggingface dataset:
Design of an On-Interposer Passive Equalizer for High Bandwidth Memory (HBM) with 30Gbps Data Transmission (2016)

In this paper, a new on-interposer passive equalizer was proposed for the next generation High Bandwidth Memory (HBM) with 1024 I/O lines and 30 Gbps data rate. It is a coil-shaped shunt metal line and embedded on a ground plane to reduce area consumption on a signal layer and to maintain fine pitch of 10 um. The proposed equalizer utilizes its inductance and resistance to perform a high-pass filter. The performance of the proposed equalizer is verified using eye-diagram simulations. The target channel is a 1 mm on-interposer channel with the fine pitch of 10 μm which has completely closed eye-diagram at 30 Gbps. By applying the proposed equalizer to the target channel, eye-height was improved by 12.3 % (147 mV) of input voltage and timing jitter was reduced by 20.5 % (6.83 ps) of 1 unit interval (UI). By applying the proposed equalizers for 30 Gbps data transmission to HBM interface between 1 GPU and 1 HBM, total I/O bandwidth can be increased to 3.84 TBps with the total routing width of 10.24 mm.
Pituitary Development: Regulatory Codes in Mammalian Organogenesis (2002)

During mammalian pituitary gland development, distinct cell types emerge from a common primordium. Appearance of specific cell types occurs in response to opposing signaling gradients that emanate from distinct organizing centers. These signals induce expression of interacting transcriptional regulators, including DNA binding-dependent activators and DNA binding-independent transrepressors, in temporally and spatially overlapping patterns. Together they synergistically regulate precursor proliferation and induction of distinct cell types. Terminal cell type differentiation requires selective gene activation strategies and long-term active repression, mediated by cell type-specific and promoter-specific recruitment of coregulatory complexes. These mechanisms imply the potential for flexibility in the ultimate identity of differentiated cell types.
A common mutant epidermal growth factor receptor confers enhanced tumorigenicity on human glioblastoma cells by increasing proliferation and reducing apoptosis. (1996)

Alterations of the EGFR gene occur frequently in human gliomas where the most common is an in-frame deletion of exons 2-7 from the extracellular domain, resulting in a truncated mutant receptor (deltaEGFR or de 2-7 EGFR). We previously demonstrated that introduction of deltaEGFR into human U87MG glioblastoma cells (U87MG.deltaEGFR) conferred remarkably enhanced tumorigenicity in vivo. Here, we show by cell-mixing experiments that the enhanced tumorigenicity conferred by deltaEGFR is attributable to a growth advantage intrinsic to cells expressing the mutant receptor. We analyzed the labeling index of the proliferation markers Ki-67 and bromodeoxyuridine and found that tumors derived from U87MG.deltaEGFR cells had significantly higher labeling indexes than those of tumors derived from U87MG cells that were either naive, expressed kinase-deficient mutants of deltaEGFR, or overexpressed exogenous wild-type EGFR. We also utilized terminal deoxynucleotidyl transferase-mediated nick end-labeling assays and showed that the apoptotic index of U87MG.deltaEGFR tumors was more than 4-fold lower than that of parental U87MG tumors. This decrease in cell death was inversely correlated with the expression level of Bcl-X(L), a negative regulator of apoptosis, which was more than 3-fold higher in U87MG.deltaEGFR-derived tumors than in those derived from parental cells. Similar observations were obtained in vitro in serum-free conditions. These results suggest that deltaEGFR exerts its pronounced enhancement of glioblastoma tumorigenicity by stimulating proliferation and inhibiting apoptosis and that the effects are directly attributable to its constitutively active signal.
The Complete Book of Running (1978)

Packed with information for the beginner, the more experienced runner and the marathon winner, this book explains the many benefits to be reaped from running and advises on how to overcome the difficulties. It covers all aspects on the subject, including finding the time to run, running and weight loss, running for women and how to beat the weather, there is also a guide to nutrition, clothing and health for the runner.
ALSCRIPT: a tool to format multiple sequence alignments (1993)

The ALSCRIPT program described in this article was developed specifically to allow the easy formatting and graphical display of large multiple alignments. Although written originally for the author's use, the interface is relatively friendly, and should be easy to learn by anyone familiar with plotting graphs
DNS Complexity (2007)

DNS is a distributed, coherent, reliable, autonomous, hierarchical database, the first and only one of its kind. Created in the 1980s when the Internet was still young but overrunning its original system for translating host names into IP addresses, DNS is one of the foundation technologies that made the worldwide Internet possible. Yet this did not all happen smoothly, and DNS technology has been periodically refreshed and refined. Though it’s still possible to describe DNS in simple terms, the underlying details are by now quite sublime. This article explores the supposed and true definitions of DNS and shows some of the tension between these two definitions through the lens of the Internet protocol development philosophy.
Painting by feature (2013)

In this paper we propose a reinterpretation of the brush and the fill tools for digital image painting. The core idea is to provide an intuitive approach that allows users to paint in the visual style of arbitrary example images. Rather than a static library of colors, brushes, or fill patterns, we offer users entire images as their palette, from which they can select arbitrary contours or textures as their brush or fill tool in their own creations. Compared to previous example-based techniques related to the painting-by-numbers paradigm we propose a new strategy where users can generate salient texture boundaries by our randomized graph-traversal algorithm and apply a content-aware fill to transfer textures into the delimited regions. This workflow allows users of our system to intuitively create visually appealing images that better preserve the visual richness and fluidity of arbitrary example images. We demonstrate the potential of our approach in various applications including interactive image creation, editing and vector image stylization.
Wallage, ICT en de onuitroeibaarheid van illusies. (2001)

CTB: Cholera Toxin B; CpG: Cytosine preceding Guanosine; ODN: Oligodeoxynucleotides; Alum: Aluminum hydroxide; TRAP: Target of RNAIII-activating Protein; TLR9: Toll-like Receptor 9; TMB: 3, 3', 5, 5'-tetramethylbenzidine; mAbs: Monoclonal Antibodies; OD: Optical Densities; <i>S. aureus: Staphylococcus aureus</i>; ClfA: Clumping factor A; FnBPA: Fibronection-binding protein A; IsdB: Iron-regulated surface determinant B; SasA: <i>Staphylococcus aureus</i> Surface Protein A; GapC: Glycer-aldehyde-3-phosphate dehydrogenase-C.
332. Contributions to the chemistry of synthetic antimalarials. Part IX. Some pyrimidine derivatives (1950)

J. S. Moffatt, J. Chem. Soc., 1950, 1603 DOI: 10.1039/JR9500001603
Security policy enforcement at the file system level in the Windows NT operating system family (2001)

This paper describes the implementation of an enforcement module for file system security implemented as part of a security architecture for distributed systems which enforces a centrally administered security policy under the Windows NT operating system platform. The mechanism provides mandatory access control, encryption, and auditing on an individual file basis across distributed systems while being fully transparent to both users and application programs and functioning regardless of the type of file system or its attachment mechanism.
Mutagenesis of the putative alpha-helical domain of the Vpr protein of human immunodeficiency virus type 1: effect on stability and virion incorporation. (1995)

vpr is one of the auxiliary genes of human immunodeficiency virus type 1 (HIV-1) and is conserved in the related HIV-2/simian immunodeficiency virus lentiviruses. The unique feature of Vpr is that it is the only nonstructural protein incorporated into the virus particle. Secondary structural analysis predicted an amphipathic alpha-helical domain in the amino terminus of Vpr (residues 17-34) which contains five acidic and four leucine residues. To evaluate the role of specific residues of the helical domain for virion incorporation, mutagenesis of this domain was carried out. Substitution of proline for any of the individual acidic residues (Asp-17 and Glu-21, -24, -25, and -29) eliminated the virion incorporation of Vpr and also altered the stability of Vpr in cells. Conservative replacement of glutamic residues of the helical domain with aspartic residues resulted in Vpr characteristic of wild type both in stability and virion incorporation, as did substitution of glutamine for the acidic residues. In contrast, replacement of leucine residues of the helical domain (residues 20, 22, 23, and 26) by alanine eliminated virion incorporation function of Vpr. These data indicate that acidic and hydrophobic residues and the helical structure in this region are critical for the stability of Vpr and its efficient incorporation into virus-like particles.
Specialized Surface Protrusions of Invasive Cells, Invadopodia and Lamellipodia, Have Differential MT1‐MMP, MMP‐2, and TIMP‐2 Localization (1999)

Surface protrusions, invadopodia, and analogous lamellipodia at the leading edge of an invasive cell, which make contact with the underlying extracellular matrix (ECM), are the main motor for cellular locomotion and invasion. Previous studies have demonstrated that invadopodia, but not lamellipodia, are sites of ECM degradation on the cell surface. Such degradative activity is in part due to the localization of latent matrix metalloproteinase-2 (MMP-2) and membrane type-1 MMP (MT1-MMP) to invadopodia, where MMP activation occurs. Although lamellipodia exhibit similar structure and mobility to invadopodia, lamellipodia, by virtue of their location at the cellular periphery, are readily accessible to the soluble tissue inhibitor of matrix metalloproteinase-2 (TIMP-2) and blood-borne inhibitors. We show here that TIMP-2 co-localizes with MT1-MMP and MMP-2 at lamellipodia but not with that of invadopodia. Thus, the MMP-TIMP localization at lamellipodia may be a key mechanism for the regulation of MMP activation on the cell surface, which in turn governs expression of the cell-invasive phenotype.
Effect of Truncated Forms of the Steroidogenic Acute Regulatory Protein on Intramitochondrial Cholesterol Transfer* (1998)

It has been proposed that the steroidogenic acute regulatory (StAR) protein controls hormone-stimulated steroid production by mediating cholesterol transfer to the mitochondrial inner membrane. This study was conducted to determine the effect of wild-type StAR and several modified forms of StAR on intramitochondrial cholesterol transfer. Forty-seven N-terminal or 28 C-terminal amino acids of the StAR protein were removed, and COS-1 cells were transfected with pCMV vector only, wild-type StAR, N-47, or the C-28 constructs. Lysates from the transfected COS-1 cells were then incubated with mitochondria from MA-10 mouse Leydig tumor cells that were preloaded with [3H]cholesterol. After incubation, mitochondria were collected and fractionated on sucrose gradients into outer membranes, inner membranes, and membrane contact sites, and [3H]cholesterol content was determined in each membrane fraction. Incubation of MA-10 mitochondria with wild-type StAR containing cell lysate resulted in a significant 34.9% increase in [3H]cholesterol content in contact sites and a significant 32.8% increase in inner mitochondrial membranes. Incubations with cell lysate containing N-47 StAR protein also resulted in a 16.4% increase in [3H]cholesterol in contact sites and a significant 26.1% increase in the inner membrane fraction. In contrast, incubation with the C-28 StAR protein had no effect on cholesterol transfer. The cholesterol-transferring activity of the N-47 truncation, in contrast to that of the C-28 mutant, was corroborated when COS-1 cells were cotransfected with F2 vector (containing cytochrome P450 side-chain cleavage enzyme, ferridoxin, and ferridoxin reductase) and either pCMV empty vector or the complementary DNAs of wild-type StAR, N-47 StAR, or C-28 StAR. Pregnenolone production was significantly increased in both wild-type and N-47-transfected cells, whereas that in C-28-transfected cells was similar to the control value. Finally, immunolocalization studies with confocal image and electron microscopy were performed to determine the cellular location of StAR and its truncated forms in transfected COS-1 cells. The results showed that wild-type and most of the C-28 StAR protein were imported into the mitochondria, whereas most of N-47 protein remained in the cytosol. These studies demonstrate a direct effect of StAR protein on cholesterol transfer to the inner mitochondrial membrane, that StAR need not enter the mitochondria to produce this transfer, and the importance of the C-terminus of StAR in this process.
Pulse shaping strategies for nonlinear interferometric vibrational imaging optimized for biomolecular imaging (2005)

Nonlinear interferometric vibrational imaging (NIVI) measures the temporal cross-correlation of anti-Stokes radiation from coherent anti-Stokes Raman scattering (CARS) processes to achieve increased sensitivity, stray light rejection, and nonresonant background rejection. Because the intensity of CARS radiation is proportional to the square of the molecular density of a target resonance, it is critical to maximize the recoverable signal for a given illumination level. Especially if one desires to measure several resonances, there can be a sensitivity as well as a speed advantage to measuring them simultaneously rather than serially. We discuss the methods of sample excitation that NIVI allows and their potential sensitivity advantages, as well as present experimental results demonstrating Raman signal recovery using these pulse sequences.
There’s an app for that, but it doesn’t work. Diagnosing Mobile Applications in the Wild (2010)

Abstract — There are a lot of applications that run on modern mobile operating systems. Inevitably, some of these applications fail in the hands of users. Diagnosing a failure to identify the culprit, or merely reproducing that failure in the lab is difficult. To get insight into this problem, we interviewed developers of five mobile applications and analyzed hundreds of trouble tickets. We find that support for diagnosing unexpected application behavior is lacking across major mobile platforms. Even when developers implement heavyweight logging during controlled trials, they do not discover many dependencies that are then stressed in the wild. They are also not well-equipped to understand how to monitor the large number of dependencies without impacting the phone’s limited resources such as CPU and battery. Based on these findings, we argue for three fundamental changes to failure reporting on mobile phones. The first is spatial spreading, which exploits the large number of phones in the field by spreading the monitoring work across them. The second is statistical inference, which builds a conditional distribution model between application behavior and its dependencies in the presence of partial information. The third is adaptive sampling, which dynamically varies what each phone monitors, to adapt to both the varying population of phones and what is being learned about each failure. We propose a system called MobiBug that combines these three techniques to simplify the task of diagnosing mobile applications. Categories and Subject Descriptors C.4 [Performance of systems] Reliability, availability, and serviceability D.2.5 [Testing and debugging] Distributed debugging C.2.4 [Distributed systems] Distributed applications
Anterior Cruciate Ligament Graft Tensioning in Full Extension (1995)

The purpose of this study was to determine anterior laxity and graft forces in cadaveric knees after anterior cruciate ligament reconstruction in which the graft is tensioned with the knee in full extension. We also analyzed the clinical results from a series of patients who had ligament reconstructions using this technique. We performed anterior cruciate ligament reconstructions on seven fresh cadaveric knees and then measured the anterior laxity, graft set force, and graft tension. We also did a prospective minimum 2-year followup on 57 patients who underwent anterior cruciate ligament reconstruction. The in vitro data showed average anterior laxity of 1.1 mm greater than the intact knee with an 89-N anterior force at 30 degrees of knee flexion. Average graft set force was 68 N, and graft tension in extension was 18 N. In the clinical portion of the study, knee laxity improved from 7.5 to 0.8 mm (side-to-side difference at 89 N). The patients' Lysholm and Tegner scores improved from 65 to 90 and 3.9 to 5.6, respectively. Only one patient had a postoperative contracture. The results of this study suggest that graft tensioning in full extension provides a low incidence of flexion deformity, maintaining excellent functional results and satisfactory biomechanics.
Comprehensive proteome analysis by chromatographic protein prefractionation (2004)

Protein copy number is distributed from 7 to 8 orders of magnitude in cells and probably up to 12 orders of magnitude in plasma. Classical silver-stained two-dimensional electrophoresis (2-DE) can only display up to four orders of magnitude. This is a major drawback since it is assumed that most of the regulatory proteins are low-abundance gene products. It is thus clear that the separation of low copy number proteins in amounts sufficient for postseparation analysis is an important issue in proteome studies to complete the comprehensive description of the proteome of any given cell type. The visualization of a polypeptide on a 2-DE gel will depend on the copy number, on the quantity loaded onto the gel and on the method of detection. As the amount of protein that can be loaded onto a gel is limited, one efficient solution is to fractionate the sample prior to 2-DE analysis. Several approaches exist including subcellular fractionation, affinity purification and chromatographic and electrophoretic protein prefractionation. The chromatographic step adds a new dimension in the protein separation using specific protein properties. It allows proteins to be adsorbed to a surface and eluted differentially under certain conditions. This review article presents studies combining chromatography-based methods to 2-DE analysis and draws general conclusions on this strategy.
Sperm-mediated gene transfer (2005)

Since 1989, a new method for the production of transgenic animals has been available, namely sperm-mediated gene transfer (SMGT), based on the intrinsic ability of sperm cells to bind and internalise exogenous DNA molecules and to transfer them into the oocyte at fertilisation. We first described the SMGT procedure in a small animal model, with high efficiency reported in the mouse. In addition, we successfully adapted and optimised the technique for use in large animals; it was, in fact, highly efficient in the generation of human decay accelerating factor transgenic pig lines, as well as multigene transgenic pigs in which three different reporter genes, namely enhanced green fluorescent protein, enhanced blue fluorescent protein and red fluorescent protein, were introduced. The major benefits of the SMGT technique were found to be its high efficiency, low cost and ease of use compared with other methods. Furthermore, SMGT does not require embryo handling or expensive equipment. Sperm-mediated gene transfer could also be used to generate multigene transgenic pigs that would be of benefit as large animal models for medical research, for agricultural and pharmaceutical applications and, in particular, for xenotransplantation, which requires extensive genetic manipulation of donor pigs to make them suitable for grafting to humans.
Nonlinear Plasma Waves Resonantly Driven by Optimized Laser Pulse Trains (1994)

A method for generating large-amplitude plasma waves, which utilizes an optimized train of independently adjustable, intense laser pulses, is discussed and analyzed. Both the pulse widths and interpulse spacings are optimally determined such that resonance is maintained and the plasma wave amplitude is maximized. By mitigating the effects of both phase and resonant detuning, and by reducing laser-plasma instabilities, the use of appropriately tailored multiple laser pulses is a highly advantageous technique for accelerating electrons. Practical methods of producing the required pulse trains are suggested.
Amino acids 1–20 of the hepatitis C virus (HCV) core protein specifically inhibit HCV IRES-dependent translation in HepG2 cells, and inhibit both HCV IRES- and cap-dependent translation in HuH7 and CV-1 cells (2003)

A self-modulating mechanism by the hepatitis C virus (HCV) core protein has been suggested to influence the level of HCV replication, but current data on this subject are contradictory. We examined the effect of wild-type and mutated core protein on HCV IRES- and cap-dependent translation. The wild-type core protein was shown to inhibit both IRES- and cap-dependent translation in an in vitro system. This effect was duplicated in a dose-dependent manner with a synthetic peptide representing amino acids 1–20 of the HCV core protein. This peptide was able to bind to the HCV IRES as shown by a mobility shift assay. In contrast, a peptide derived from the hepatitis B virus (HBV) core protein that contained a similar proportion of basic residues was unable to inhibit translation or bind the HCV IRES. A recombinant vaccinia–HCV core virus was used to examine the effect of the HCV core protein on HCV IRES-dependent translation in cells and this was compared with the effects of an HBV core-recombinant vaccinia virus. In CV-1 and HuH7 cells, the HCV core protein inhibited translation directed by the IRES elements of HCV, encephalomyocarditis virus and classical swine fever virus as well as cap-dependent translation, whereas in HepG2 cells, only HCV IRES-dependent translation was affected. Thus, the ability of the HCV core protein to selectively inhibit HCV IRES-dependent translation is cell-specific. N-terminal truncated (aa 1–20) HCV core protein that was expressed from a novel recombinant vaccinia virus in cells abrogated the inhibitory phenotype of the core protein in vivo, consistent with the above in vitro data.