gebhart/patrepeval huggingface dataset:
The histone deacetylase inhibitor trichostatin A alters the pattern of DNA replication origin activity in human cells (2005)

Eukaryotic chromatin structure limits the initiation of DNA replication spatially to chromosomal origin zones and temporally to the ordered firing of origins during S phase. Here, we show that the level of histone H4 acetylation correlates with the frequency of replication initiation as measured by the abundance of short nascent DNA strands within the human c-myc and lamin B2 origins, but less well with the frequency of initiation across the beta-globin locus. Treatment of HeLa cells with trichostatin A (TSA) reversibly increased the acetylation level of histone H4 globally and at these initiation sites. At all three origins, TSA treatment transiently promoted a more dispersive pattern of initiations, decreasing the abundance of nascent DNA at previously preferred initiation sites while increasing the nascent strand abundance at lower frequency genomic initiation sites. When cells arrested in late G1 were released into TSA, they completed S phase more rapidly than untreated cells, possibly due to the earlier initiation from late-firing origins, as exemplified by the beta-globin origin. Thus, TSA may modulate replication origin activity through its effects on chromatin structure, by changing the selection of initiation sites, and by advancing the time at which DNA synthesis can begin at some initiation sites.
Transforming Image Completion (2011)

Image completion is an important photo-editing task which involves synthetically filling a hole in the image such that the image still appears natural. State-of-the-art image completion methods work by searching for patches in the image that fit well in the hole region. Our key insight is that image patches remain natural under a variety of transformations (such as scale, rotation and brightness change), and it is important to exploit this. We propose and investigate the use of different optimisation methods to search for the best patches and their respective transformations for producing consistent, improved completions. Experiments on a number of challenging problem instances demonstrate that our methods outperform state-of-the-art techniques. © 2011. The copyright of this document resides with its authors.
Assembly of the Alu domain of the signal recognition particle (SRP): dimerization of the two protein components is required for efficient binding to SRP RNA. (1990)

The signal recognition particle (SRP), a cytoplasmic ribonucleoprotein, plays an essential role in targeting secretory proteins to the rough endoplasmic reticulum membrane. In addition to the targeting function, SRP contains an elongation arrest or pausing function. This function is carried out by the Alu domain, which consists of two proteins, SRP9 and SRP14, and the portion of SRP (7SL) RNA which is homologous to the Alu family of repetitive sequences. To study the assembly pathway of the components in the Alu domain, we have isolated a cDNA clone of SRP9, in addition to a previously obtained cDNA clone of SRP14. We show that neither SRP9 nor SRP14 alone interacts specifically with SRP RNA. Rather, the presence of both proteins is required for the formation of a stable RNA-protein complex. Furthermore, heterodimerization of SRP9 and SRP14 occurs in the absence of SRP RNA. Since a partially reconstituted SRP lacking SRP9 and SRP14 [SRP(-9/14)] is deficient in the elongation arrest function, it follows from our results that both proteins are required to assemble a functional domain. In addition, SRP9 and SRP14 synthesized in vitro from synthetic mRNAs derived from their cDNA clones restore elongation arrest activity to SRP(-9/14).
A Low-Power Scalable Stream Compute Accelerator for General Matrix Multiply (GEMM) (2014)

Many applications ranging from machine learning, image processing, and machine vision to optimization utilize matrix multiplication as a fundamental block. Matrix operations play an important role in determining the performance of such applications. This paper proposes a novel efficient, highly scalable hardware accelerator that is of equivalent performance to a 2 GHz quad core PC but can be used in low-power applications targeting embedded systems requiring high performance computation. Power, performance, and resource consumption are demonstrated on a fully-functional prototype. The proposed hardware accelerator is 36× more energy efficient per unit of computation compared to state-of-the-art Xeon processor of equal vintage and is 14× more efficient as a stand-alone platform with equivalent performance. An important comparison between simulated system estimates and real system performance is carried out.
Activation with CpG-A and CpG-B Oligonucleotides Reveals Two Distinct Regulatory Pathways of Type I IFN Synthesis in Human Plasmacytoid Dendritic Cells (2003)

Two different CpG oligonucleotides (ODN) were used to study the regulation of type I IFN in human plasmacytoid dendritic cells (PDC): ODN 2216, a CpG-A ODN, known to induce high amounts of IFN-alpha in PDC, and ODN 2006, a CpG-B ODN, which is potent at stimulating B cells. CpG-A ODN showed higher and prolonged kinetics of type I IFN production compared with that of CpG-B ODN. In contrast, CpG-B ODN was more active than CpG-A ODN in stimulating IL-8 production and increasing costimulatory and Ag-presenting molecules, suggesting that CpG-A and CpG-B trigger distinct regulatory pathways in PDC. Indeed, CpG-A ODN, but not CpG-B ODN, activated the type I IFNR-mediated autocrine feedback loop. PDC were found to express high constitutive levels of IFN regulatory factor (IRF)7. IRF7 and STAT1, but not IRF3, were equally up-regulated by both CpG-A and CpG-B. CD40 ligand synergistically increased CpG-B-induced IFN-alpha independent of the IFNR but did not affect CpG-B-induced IFN-beta. In conclusion, our studies provide evidence for the existence of two distinct regulatory pathways of type I IFN synthesis in human PDC, one dependent on and one independent of the IFNR-mediated feedback loop. The alternate use of these pathways is based on the type of stimulus rather than the quantity of IFN-alphabeta available to trigger the IFNR. Constitutive expression of IRF7 and the ability to produce considerable amounts of IFN-alpha independent of the IFNR seem to represent characteristic features of PDC.
Combined Bone Morphogenetic Protein-2 and −7 Gene Transfer Enhances Osteoblastic Differentiation and Spine Fusion in a Rodent Model (2004)

Combined BMP2 and BMP7 gene transfer is significantly more effective in inducing osteoblastic differentiation and spine fusion than individual BMP gene transfer.
Isolation and characterization of a retinal pigment epithelial cell fluorophore: An all-trans -retinal dimer conjugate (2005)

Several lines of investigation suggest that the nondegradable fluorophores that accumulate as lipofuscin in retinal pigment epithelium (RPE) cells contribute to the etiology of macular degeneration. Despite evidence that much of this fluorescent material may originate as inadvertent products of the retinoid cycle, the enzymatic pathway by which the 11-cis-retinal chromophore of rhodopsin is generated, the only fluorophores of the RPE to be characterized as yet have been A2E and its isomers. Here, we report the isolation and structural characterization of an additional RPE lipofuscin fluorophore that originates as a condensation product of two molecules of all-trans-retinal (ATR) dimer and forms a protonated Schiff base conjugate with phosphatidylethanolamine (PE), the latter conjugate (ATR dimer-PE) having UV-visible absorbance maxima at 285 and 506 nm. ATR dimer was found to form natively in bleached rod outer segments in vitro and when rod outer segments were incubated with ATR. HPLC analysis of eye-cups that included RPE and isolated neural retina from Abcr-/- mice and RPE isolated from human donor eyes revealed the presence of a pigment with the same UV-visible absorbance and retention time as synthetic ATR dimer-PE conjugate. Evidence that ATR dimer undergoes a photooxidation process involving the addition of oxygens at double bonds as well as an aromatic demethylation also may indicate a role for this molecule, or its derivatives, in the photoreactivity of RPE lipofuscin.
Dynamic behaviour of radio channels due to trans-horizon propagation mechanisms (1993)

To study the propagation mechanisms of trans-horizon radio links, the Letter proposes an event-based approach. Data from one year captured on a trans-horizon link of 156 km are divided into different groups according to the signal amplitude signature of the chart recordings. The propagation mechanisms for each group are investigated using the cross-correlation between received signal amplitudes along the same path. These amplitudes are obtained using two different transmitter antenna heights.
Crystal Structure of a p53 Tumor Suppressor-DNA Complex: Understanding Tumorigenic Mutations (1994)

Mutations in the p53 tumor suppressor are the most frequently observed genetic alterations in human cancer. The majority of the mutations occur in the core domain which contains the sequence-specific DNA binding activity of the p53 protein (residues 102-292), and they result in loss of DNA binding. The crystal structure of a complex containing the core domain of human p53 and a DNA binding site has been determined at 2.2 angstroms resolution and refined to a crystallographic R factor of 20.5 percent. The core domain structure consists of a beta sandwich that serves as a scaffold for two large loops and a loop-sheet-helix motif. The two loops, which are held together in part by a tetrahedrally coordinated zinc atom, and the loop-sheet-helix motif form the DNA binding surface of p53. Residues from the loop-sheet-helix motif interact in the major groove of the DNA, while an arginine from one of the two large loops interacts in the minor groove. The loops and the loop-sheet-helix motif consist of the conserved regions of the core domain and contain the majority of the p53 mutations identified in tumors. The structure supports the hypothesis that DNA binding is critical for the biological activity of p53, and provides a framework for understanding how mutations inactivate it.
Enforced Expression of METCAM/MUC18 Increases Tumorigenesis of Human Prostate Cancer LNCaP Cells in Nude Mice (2011)

Enforced expression of human metastasis cell adhesion molecule/MUC18 increases prostate tumorigenesis in vivo and may affect the process by increasing proliferation, up-regulating the AKT survival pathway, and augmenting the angiogenic ability of prostate cancer cells.
State-of-Charge estimation algorithms and their implications on cells in parallel (2014)

State-of-Charge (SOC) of a battery is one of the most important parameters used by a Battery Management System (BMS). It is subsequently very important for the efficient functioning of an electric/hybrid vehicle. Since, the SOC is a derived quantity, it is important that the algorithm, on which the estimator is based, is robust and accurate. The algorithms developed thus far, for different battery chemistries are dependent mainly on the current and voltage data received from individual cells or the entire battery. It is possible that an accurate SOC-estimation algorithm could be the key to increasing the efficiency of a typical hybrid-electric vehicle and hence the real-world applicability. This accuracy should be relevant to both normal and failure cases associated with any drive cycle. This in turn depends on the current and voltage signals received, the positing of such sensors, etc. Also, as battery is comprised of a combination of series and parallel strings, it is important that the difference between the SOCs for an individual cell and that of the entire battery is negligible. The objective of this paper is to compare three SOC estimation algorithms: the current based Coulomb-Counter approach; the voltage dependent model-based approach; and the mixed algorithm that adapts the complementary behavior of the other two methods. In this, the positioning of current and voltage sensors; and the reliability of data, i.e. cell SOC and pack SOC, have been considered. Models created using MATLAB/Simulink, based on literature, have been used. It is seen that the SOC estimation algorithm that is based on both current and voltage data is the most accurate under difference cases of normal and failure cases including short-circuit, open-circuit, etc.
Patterning micron-sized features in a cross-linked poly(acrylic acid) film by a wet etching process (2006)

This paper describes a photolithographic method to create sub-micron-scale patterns of cation-cross-linked poly(acrylic acid) (CCL-PAA). PAA can be cross-linked with a wide range of metal cations-including, but not limited to, Ag, Ca, Pd, Al, La, and Ti. Upon patterning a positive photoresist (diazonaphthoquinone-novolac resin) on a film of CCL-PAA, the exposed regions of CCL-PAA were etched by either an aqueous NaOH or EDTA solution. The initial cross-linking cation could be exchanged for a second cation that could not be patterned photolithographically. We used these patterned films of CCL-PAA i) to host and template the reduction of metallic cations to metallic nanoparticles, and ii) to fabricate porous, low- dielectric substrates.
Posttranscriptional silencing of reporter transgenes in tobacco correlates with DNA methylation. (1994)

Endogenous plant genes or transgenes can be silenced on introduction of homologous gene sequences. Here we document a reporter gene-silencing event in Nicotiana tabacum that has a distinctive combination of features--i.e., (i) silencing occurs by a posttranscriptional process, (ii) silencing correlates with DNA methylation, and (iii) this de novo methylation is not restricted to cytosines located in the symmetrical motifs CG and CXG.
Local expression of antiinflammatory cytokines in cancer. (1993)

To characterize the nature of the local cytokine response to cancer, we chose to investigate cytokine patterns in biopsy specimens of basal cell carcinoma (BCC). We hypothesized that a distinct pattern of local cytokine production may be characteristic of BCC, a neoplasia of epidermis, in comparison to the pattern of seborrheic keratosis (SK), a benign growth of epidermis. We analyzed cytokine mRNAs in BCC versus SK by performing polymerase chain reaction on mRNA derived from biopsy specimens. The mRNAs encoding cytokines for IL-4, IL-5, IL-10, and granulocyte macrophage colony-stimulating factor were strongly expressed in BCC lesions and weakly expressed in SK lesions. Conversely, IL-2, IFN-gamma, and lymphotoxin mRNAs were strongly expressed in SK lesions and weakly expressed in BCC lesions. The response to malignancy, BCC, was typified by cytokines characteristic of murine TH2 cells. This cytokine pattern favors humoral immunity with concomitant immunosuppression of cell-mediated immune responses. In comparison, the response to the benign growth, SK, was typified by cytokines characteristic of murine TH1 cells that favor cell-mediated immune reactions. The findings of a distinct cytokine pattern in skin cancer provide a framework to develop strategies for immunologic intervention.
CNS-specific immunity at the choroid plexus shifts toward destructive Th2 inflammation in brain aging (2013)

The adaptive arm of the immune system has been suggested as an important factor in brain function. However, given the fact that interactions of neurons or glial cells with T lymphocytes rarely occur within the healthy CNS parenchyma, the underlying mechanism is still a mystery. Here we found that at the interface between the brain and blood circulation, the epithelial layers of the choroid plexus (CP) are constitutively populated with CD4(+) effector memory cells with a T-cell receptor repertoire specific to CNS antigens. With age, whereas CNS specificity in this compartment was largely maintained, the cytokine balance shifted in favor of the T helper type 2 (Th2) response; the Th2-derived cytokine IL-4 was elevated in the CP of old mice, relative to IFN-γ, which decreased. We found this local cytokine shift to critically affect the CP epithelium, triggering it to produce the chemokine CCL11 shown to be associated with cognitive dysfunction. Partial restoration of cognitive ability in aged mice, by lymphopenia-induced homeostasis-driven proliferation of memory T cells, was correlated with restoration of the IL-4:IFN-γ ratio at the CP and modulated the expression of plasticity-related genes at the hippocampus. Our data indicate that the cytokine milieu at the CP epithelium is affected by peripheral immunosenescence, with detrimental consequences to the aged brain. Amenable to immunomodulation, this interface is a unique target for arresting age-related cognitive decline.
Matrix Metalloproteinase-9 Pretreatment Level Predicts Intracranial Hemorrhagic Complications After Thrombolysis in Human Stroke (2003)

Baseline MMP-9 level predicts PH appearance after t-PA treatment. Therefore, we suggest that MMP determination may increase the safety profile for thrombolysis and, in the future, anti-MMP drugs might be combined with t-PA to prevent hemorrhagic complications.
Membrane Oxidative Metabolism of Human Eosinophilic Cell Line EoL-1 in Response to Phorbol Diester and Formyl Peptide: Synergistic Augmentation by Interferon-γ Tumor Necrosis Factor (1989)

Human eosinophilic cell line EoL-1 was studied using luminol-dependent chemiluminescence (CL) for the ability to produce a respiratory burst upon stimulation with 12-O-tetradecanoylphorbol-13-acetate (TPA) and N-formyl-L-methionyl-L-leucyl-L-phenylalanine (fMLP). TPA, a potent activator of protein kinase C, induced a biphasic CL response in EoL-1. Treatment of EoL-1 with interferon-gamma (IFN-gamma) for 5 days dramatically enhanced TPA-inducible CL, and IFN-alpha A had a similar effect. Neither IFN-gamma nor IFN-alpha A strongly inhibited EoL-1 cell growth. Tumor necrosis factor (TNF) also enhanced TPA-inducible CL response of EoL-1 and, furthermore, was quite inhibitory to EoL-1 cell growth. The effects of IFN-gamma and TNF were synergistic, whereas those of IFN-alpha A and TNF were additive. Superoxide dismutase completely abrogated TPA-induced CL, but sodium azide suppressed only the late phase of CL. EoL-1 pretreated with IFN-gamma, IFN-alpha A, or TNF also became capable of producing CL response to a chemotactic peptide (fMLP). The effects of IFN-gamma and TNF were again synergistic. EoL-1 cells treated with IFN-gamma, IFN-alpha A, or TNF had abundant cytoplasm, but only TNF increased cells having distinct eosinophilic granules. IFN-gamma but not IFN-alpha A enhanced the cytological effect of TNF. It was further demonstrated that treatment of EoL-1 with IFN-gamma and TNF strongly increased the binding sites for phorbol diesters and also dramatically induced the surface expression of fMLP receptors. IFN-gamma had, however, little effect on the number or the ligand-binding affinity of TNF receptors on EoL-1. Thus, EoL-1 may provide a useful experimental model for the study of differentiation and regulation of human eosinophils.
Clustering Billions of Images with Large Scale Nearest Neighbor Search (2007)

The proliferation of the Web and digital photography have made large scale image collections containing billions of images a reality. Image collections on this scale make performing even the most common and simple computer vision, image processing, and machine learning tasks nontrivial. An example is nearest neighbor search, which not only serves as a fundamental subproblem in many more sophisticated algorithms, but also has direct applications, such as image retrieval and image clustering. In this paper, we address the nearest neighbor problem as the first step towards scalable image processing. We describe a scalable version of an approximate nearest neighbor search algorithm and discuss how it can be used to find near duplicates among over a billion images
Alteration of nuclear lamin organization inhibits RNA polymerase II–dependent transcription (2002)

Regulation of gene activity is mediated by alterations in chromatin organization. In addition, chromatin organization may be governed in part by interactions with structural components of the nucleus. The nuclear lamins comprise the lamina and a variety of nucleoplasmic assemblies that together are major structural components of the nucleus. Furthermore, lamins and lamin-associated proteins have been reported to bind chromatin. These observations suggest that the nuclear lamins may be involved in the regulation of gene activity. In this report, we test this possibility by disrupting the normal organization of nuclear lamins with a dominant negative lamin mutant lacking the NH2-terminal domain. We find that this disruption inhibits RNA polymerase II activity in both mammalian cells and transcriptionally active embryonic nuclei from Xenopus laevis. The inhibition appears to be specific for polymerase II as disruption of lamin organization does not detectably inhibit RNA polymerases I and III. Furthermore, immunofluorescence observations indicate that this selective inhibition of polymerase II-dependent transcription involves the TATA binding protein, a component of the basal transcription factor TFIID.
A 140-Mb/s, 32-state, radix-4 Viterbi decoder (1992)

A 140-Mb/s, 32-state, radix-4, R=1/2, eight-level soft-decision Viterbi decoder has been designed and fabricated using 1.2- mu m double-metal CMOS. The architecture of the add-compare-select (ACS) array is based on a restructuring of the conventional radix-2 trellis into a radix-4 trellis. Radix-4 units, consisting of four 4-way ACS units, process two stages of the constituent radix-2 trellis per iteration. A four-way ACS circuit achieves an iteration delay 17% longer than comparable two-way ACS circuits, resulting in a factor of 1.7 increase in throughput. A ring-based ACS placement and state metric routing topology achieves an area efficiency comparable to radix-2 designs. In a process referred to as pretrace-back, one stage of lookahead is applied to the trace-back recursion, combining two radix-4 trace-back iterations into a single radix-16 iteration based on 4-b decisions. This allows implementation of trace-back using one compact, single-ported decision memory, organized as a cyclic buffer. A 7.30-mm*8.49-mm chip containing 146000 transistors achieves a radix-4 iteration rate of 70 MHz.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
DUET: an agent-based personal communications network (1995)

The authors propose a network architecture that provides access to resources on different networks in a manner that is transparent to the user. They named this network distributed user-assistant for easy telecommunications (DUET). Personal agents manage resources for the users and allow each user to customize his/her communication services. This architecture is especially suitable to advanced personal communications integrating real-time voice and non-real-time messaging services.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>