gebhart/patrepeval huggingface dataset:
Abstract A73: Antisense oligonucleotides targeting ENO2 have selective anti-proliferative effects in glioblastoma cell with 1p36 genomic loss (2015)

Abstract Essential cellular processes are often supported by redundant genes and pathways. Cancer cells frequently harbor deletions or mutations in essential genes and survive because of this functional redundancy. Identification of recurrent events that leave cancer cells selectively sensitive to inhibition of a particular pathway or gene can provides the opportunity to develop therapeutics with a high degree of selectivity for cancer cells over normal cells. In Glioblastoma Multiform (GBM), one of the most malignant brain cancers, roughly 3-5% of tumors have loss of the chromosome locus 1p36. Among the genes lost at this locus, is enolase1 (ENO1). Loss of ENO1 is tolerated by the cancer cells and is not required for cancer initiation or progression; likely because of functional redundancy with the closely related paralog, ENO2. However, it has been recently demonstrated that cancer cells with homozygous ENO1 loss are selectively sensitive to ENO2 inhibition. Here we investigate the potential of Antisense Oligonucleotides (ASO) targeted to ENO2 as a therapeutic approach to treat GBM with 1p36 loss of ENO1.We show that constrained ethyl (cET) modified ASOs targeting ENO2 produced dose dependent inhibition of ENO2 RNA and protein levels in GBM cells when delivered by free uptake. ASO-mediated ENO2 depletion led to the selective inhibition of ENO1-null cells and not the isogenic cells engineered to express ENO1. Moreover, cell cycle analysis is demonstrated that ENO2 depletion resulted in impaired proliferation due to unsuccessful transition of cells from G1 to S phase of the cell cycle. These findings support the application of ASO to elicit synthetic lethality in GBM tumors with 1p36 loss. Citation Format: Maria Shahmoradgoli, Curt Mazur, Youngsoo Kim, Brett P Monia, A. Robert Macleod, Florian M Muller, Christopher E Hart. Antisense oligonucleotides targeting ENO2 have selective anti-proliferative effects in glioblastoma cell with 1p36 genomic loss. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr A73.
Phytobezoar des Ductus hepaticus communis – seltene Differenzialdiagnose einer Cholestase im Langzeitverlauf nach Kausch-Whipple-Operation: Fallbericht und Literaturübersicht (2012)

Obstruction of bile flow following pancreatoduodenectomy can be caused by stenosis of the hepaticojejunostomy created at the time of surgery, obstruction of the bile-draining jejunal loop, stones or, very rarely, ingested foreign bodies in the common hepatic duct. In analogy with endoscopic sphincterotomy or the once popular side-to-side-choledochduodenostomy, the creation of a hepaticojejunostomy eliminates the barrier of the sphincter Oddi, enabling intestinal content such as ingested foreign bodies or food fibers to migrate into the bile duct. We report on the case of a patient developing biliary tract obstruction due to fibrous material in the common hepatic duct 15 years after pancreatoduodenectomy. In addition, an overview of the literature on the rare phenomenon of foreign body-associated obstructive jaundice is given.
Poly(l-lactic acid), by near-ambient pressure XPS (2019)

Near ambient pressure - x-ray photoelectron spectroscopy (NAP-XPS) is a less traditional form of XPS that allows samples to be analyzed at relatively high pressures, i.e., at 2500 Pa or higher. With NAP-XPS, one can analyze moderately volatile liquids, biological samples, porous materials, and/or polymeric materials that outgas significantly. In this submission we show C 1s, O 1s, and survey NAP-XPS spectra from poly(l-lactic acid). The C 1s and O 1s envelopes were fit with three and two Gaussian-Lorentzian sum functions, respectively. Water vapor (800 Pa) was used as the residual gas for charge compensation, which was confirmed by the sharp peak at 535.0 eV in the O 1s narrow scan. The uniqueness plot corresponding to the C 1s fit shows that the fit parameters had statistical significance. C 1s and O 1s spectra of PLLA damaged by exposure to x-rays for ca. 1 hour are also included.
HAI-GEN 2021: 2nd Workshop on Human-AI Co-Creation with Generative Models (2021)

Recent advances in generative AI have resulted in a rapid and dramatic increase to the fidelity of created artifacts, from realistic-looking images of faces [10] to antimicrobial peptide sequences that treat diseases [5] to faked videos of prominent business leaders [4, 11]. We believe that people skilled within their creative domain can realize great benefits by incorporating generative models into their own work: as a source of inspiration, as a tool for manipulation, or as a creative partner. Our workshop will bring together researchers and practitioners from both the HCI and AI disciplines to explore and better understand the opportunities and challenges in building, using, and evaluating human-AI co-creative systems.
CCR9 inhibition does not interfere with the development of immune tolerance to oral antigens (2013)

Recent literature indicates that mice deficient in the chemokine receptor CCR9 (CCR9(-/-) mice) are unable to generate oral tolerance. The present report describes how such inability can be overcome by increasing the dose of oral antigen. Pharmacological inhibition of CCR9 did not affect the generation of oral tolerance, regardless of antigen dose. These results highlight the inadequacy of genetic deletion of CCR9 when predicting the effects of pharmacological CCR9 inhibition on intestinal biology.
Automatic Ground Truth Generation of Camera Captured Documents Using Document Image Retrieval (2013)

In this paper a novel method for automatic ground truth generation of camera captured document images is proposed. Currently, no dataset is available for camera captured documents. It is very difficult to build these datasets manually, as it is very laborious and costly. The proposed method is fully automatic, allowing building the very large scale (i.e., millions of images) labeled camera captured documents dataset, without any human intervention. Evaluation of samples generated by the proposed approach shows that 99.98% of the images are correctly labeled. Novelty of the proposed approach lies in the use of document image retrieval for automatic labeling, especially for camera captured documents, which contain different distortions specific to camera, e.g., blur, occlusion, perspective distortion, etc.
A Rationally Engineered Hyperactive Actin‐Resistant DNase1‐Fc Fusion Protein Ameliorates Autoimmune Glomerulonephritis (2019)

Loss of B cell tolerance and generation of autoreactive anti‐nuclear antibodies are hallmarks of systemic lupus erythematosus (SLE) and lupus nephritis. Lupus nephritis is characterized by glomerular and tubulointerstitial inflammation often initiated by the renal glomerular deposition of anti‐nuclear immune complexes which trigger subsequent activation of complement, macrophages/monocytes and other innate inflammatory cells. The mechanism of anti‐nuclear immunoglobulin accumulation and clearance in lupus nephritis pathogenesis remains largely uncharacterized. Here, we show that innate immune activation in the NZB/W F1 mouse model and in human lupus nephritis biopsies rapidly reduces DNase1 expression in renal cortex proximal tubular cells. To overcome the loss of endogenous DNase1, we treated lupus‐prone mice with a hyperactive actin resistant variant of DNase1 with improved catalytic activity against nucleic acid‐IgG immune complexes and acceptable in vivo pharmacokinetics. Hyperactive DNase1‐Fc fusion protein ameliorates nephritis in a murine model of lupus nephritis and reduces immune complex deposition/complement fixation. Taken together, our data suggest that the loss of renal DNase1 through TLR signaling or other innate immune activation impairs clearance of autoreactive anti‐nuclear immune complex deposits in the kidney to promote nephritis progression. Our findings provide a therapeutic rationale for using an engineered DNase1‐Fc as a potential therapeutic approach in lupus nephritis. Support or Funding Information All authors are current or previous employees of Genentech, Inc. This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .
Dual Role of Inflammatory Stimuli in Activation-induced Cell Death of Mouse Microglial Cells (2001)

We have previously shown that mouse microglial cells undergo apoptosis upon inflammatory activation and that nitric oxide (NO) is the major autocrine mediator in this process (Lee, P., Lee, J., Kim, S., Yagita, H., Lee, M. S., Kim, S. Y., Kim, H., and Suk, K. (2001) Brain Res. 892, 380-385). Here, we present evidence that interferon regulatory factor-1 (IRF-1) and caspase-11 are the essential molecules in activation-induced cell death of microglial cells. The apoptogenic action of inflammatory stimuli such as lipopolysaccharide (LPS) and interferon-gamma (IFNgamma) was mediated through the induction of IRF-1 and caspase-11 expression in two separate events. Although IRF-1 was required for NO synthesis, caspase-11 induction was necessary for NO-independent apoptotic pathway. Microglial cells from IRF-1-deficient mice showed markedly decreased NO production, and they were partially resistant to apoptosis in response to LPS/IFNgamma but were sensitive to NO donor exposure. LPS/IFNgamma treatment resulted in the induction of caspase-11 followed by activation of caspase-11, -1, and -3. Inactivation of caspase-11 by the transfection of dominant-negative mutant or treatment with the caspase inhibitors rendered microglial cells partially resistant to LPS/IFNgamma-induced apoptosis. Inhibition of both NO synthesis and caspase-11 completely blocked LPS/IFNgamma-induced cytotoxicity. These results indicated that LPS/IFNgamma not only induced the production of cytotoxic NO through IRF-1 but also initiated the NO-independent apoptotic pathway through the induction of caspase-11 expression.
Miniature Super-Directive and Super-Gain Parasitic Antenna Array Based on Far-Field Pattern Synthesis (2022)

In this paper, a generalized far-field pattern synthesis technique is presented. This technique is used to design an electrically small directive parasitic antenna array with end-fire radiation characteristic, having an electrical size ka=0.9 and driven with a single feeding port. The CST-MWS simulated super-directivity condition shows 10.1 dBi directivity for a three-element parasitic array with a 28.6% radiation efficiency, resulting in a 4.7 dBi gain. For gain and radiation efficiency enhancement, the way to achieve a super-gain condition is demonstrated, with CST-MWS simulated gain showing 6.6 dBi and 99.7% radiation efficiency for a three-element parasitic array.
Revitalization Efforts [President's Message] (2016)

Presents the President's message for this issue of the publication.
Compressed Ultrasound Imaging: From Sub-Nyquist Rates to Super Resolution (2021)

Medical ultrasound imaging is an ongoing research field for digital signal processing. Following decades of developement in the analogue domain, the introduction of high power computation has led to increased activity and research in the fields of digital signal processing, and, most recently, in machine learning, for the sake of delivering higher quality imaging, while reducing the size of the data required to acquire, process, display and, recently, wirelessly transmit the data to remote devices. An overview of the basics of ultrasound acquisition and imaging is given, followed by a presentation of its limitations and challenges. An in-depth explanation about the development and algorithmics of the methods designed to address each of these challenges follows, with an introduction of the outstanding tasks and issues posed in each field, and their potential applications and benefits to modern healthcare.
Expansion of the genetic code for the biosynthesis of useful alloproteins (2003)

非天然型アミノ酸を導入することによって, 蛋白質に新規な性質や機能を付加したり, 機能や構造の解明に役立てたりすることができる. 非天然型アミノ酸を特定のコドンに対応付けるシステム(人工遺伝暗号システム)によって, 無細胞蛋白質合成系や生きた細胞において, 非天然型アミノ酸を組み込んだ蛋白質(アロ蛋白質)が生産できるようになっている. 近年, 利用可能なアミノ酸のレパートリーも拡大し, 部位特異的な組み込みも可能であることで有用性が増してきている.
The enlarging spectrum of Nav1.7 mutations associated with neurological pain syndromes. (P2.022) (2015)

OBJECTIVE: To identify Nav1.7 mutations in neurological pain syndromes. BACKGROUND: Nav1.7 is a voltage-gated sodium-channel (gene SCN9A) instrumental in neurological pain syndromes including primary erythermalgia (PE), paroxysmal extreme pain disorder (PEPD), and idiopathic painful small fiber neuropathies (I-SFN). Some mutations of SCN9A gene have been associated with a gain of function of the rapid Nav1.7 sodium channels resulting in impair inactivation of NaV1.7 and a persistent current. DESIGN/METHODS: In order to investigate the clinical spectrum of patients with neuropathies associated with Nav1.7 mutations, we included patients with sensory symptoms suggestive of either SFN, or PE, or PEPD between 2013 and 2014. All patients had a neurological examination with clinical assessment, neurophysiological tests with laser evoked potentials (LEPs), quantitative sensory testing and suddoscan, a skin biopsy for quantification of intraepidermal nerve fiber density (IENFD/mm). A genomic screening of SCN9A was performed for all patients. No causes for neuropathies could be identified in the series of patients. RESULTS: We included 35 patients with neuropathic pain, burning pain and/or redness focused on the distal extremities. The patients were 20 men, 15 women, of 63.1±12.9 age. Twenty-nine patients had small fiber neuropathy, three had primary erythermalgia and three paroxysmal extreme pain disorder. No one had familial history of neurological pain syndromes. 9/35 (26[percnt]) patients had genetics abnormalities in the SCN9A gene. Of those, six patients (5 SFN and 1 PEPD) had similar deletion on exon 25, two SFN with mutation in exon 20 and one erythermalgia in exon 13. These mutations have never been reported in the investigated conditions. The mutations were associated with either neurophysiological or histological abnormalities or both, however one patient had both normal results. CONCLUSIONS: The physiological consequences of these three new mutations remains to be investigated through alternative splicing studies and functional analysis. Study Supported by:
A fast response full bridge power factor corrector (2002)

A fast response full-bridge power factor corrector (FBPFC) is presented in this paper. The power converter is combined by two interleaved boost cells and a conventional full bridge power converter. As the interleaving technique is applied, the input ripple current of the FBPFC is reduced. Experimental result shows that the maximum power factor is 0.98, even without an input filter.
Induction of the Endoplasmic-Reticulum-Stress Response: MicroRNA-34a Targeting of the IRE1α-Branch (2020)

Neurodegenerative disorders such as Alzheimer's disease (AD) and Parkinson's disease (PD) are characterized by the accumulation of misfolded proteins in the endoplasmic reticulum (ER) and the unfolded protein response (UPR). Modulating the UPR is one of the major challenges to counteract the development of neurodegenerative disorders and other diseases with affected UPR. Here, we show that miR-34a-5p directly targets the IRE1α branch of the UPR, including the genes <i>BIP</i>, <i>IRE1α</i>, and <i>XBP1</i>. Upon induction of ER stress in neuronal cells, miR-34a-5p overexpression impacts the resulting UPR via a significant reduction in IRE1α and XBP1s that in turn leads to decreased viability, increased cytotoxicity and caspase activity. The possibility to modify the UPR signaling pathway by a single miRNA that targets central genes of the IRE1α branch offers new perspectives for future therapeutic approaches against neurodegeneration.
Genetic modification of T-cell clones for therapy of human viral and malignant diseases. (1998)

Our laboratory has pursued T cell therapy withantigen-specific T cell clones as means to treat humandisease. Our studies in the prevention of CMV disease
Evaluating the locality benefits of active messages (1995)

A major challenge in fine-grained computing is achieving locality without excessive scheduling overhead. We built two J-Machine implementations of a fine-grained programming model, the Berkeley Threaded Abstract Machine. One implementation takes an Active Messages approach, maintaining a scheduling hierarchy in software in order to improve data cache performance. Another approach relies on the J-Machine's message queues and fast task switch, lowering the control costs at the expense of data locality. Our analysis measures the costs and benefits of each approach, for a variety of programs and cache configurations. The Active Messages implementation is strongest when miss penalties are high and for the finest-grained programs. The hardware-buffered implementation is strongest in direct-mapped caches, where it achieves substantially better instruction cache performance.
Integrated 155M-10Gbps Framer with 22.5Gbps Low/High Order Cross Connect SoC (2006)

The advent of broadband services requires multi service provisioning platforms (MSPP) to achieve >10Gbps capacity with 1-4 rack unit footprint, power <200W and cost <$10K. Highly integrated SoC using 0.13mu CMOS 19.3times19.3mm die packaged in a 1517 FCBGA affords a unique MSPP solution consisting of 155M-10Gbps SONET/SDH framing, low/high order path processing, grooming, cross-connection up to 22.5Gbps and an embedded processor. A rigorous methodology enabled a production-worthy SoC comprising 9Mgates/14Mbit memory
Evaluation of Shotgun Sequencing for Proteomic Analysis of Human Plasma Using HPLC Coupled with Either Ion Trap or Fourier Transform Mass Spectrometry (2003)

This paper reports on studies directed to the characterization of the proteome of human plasma by the shotgun sequencing approach, namely the use of HPLC coupled to mass spectrometry (MS). The report will present data from two laboratories that allows the comparison of peptide and protein identifications by either accurate mass measurement on a Fourier transform mass spectrometry or MS/MS fragmentation on an ion trap mass spectrometer. Because the dynamic range of the protein components of plasma is one of the largest for a biological sample, the analysis of such a challenging sample was aided by the use of these two MS approaches. The major classes of proteins observed were transport proteins, enzymes, and enzyme inhibitors, blood-clotting factors, membrane-associated proteins including soluble forms of receptors, hormones, immunoglobulins, and other glycoproteins. The protein identifications were also highly consistent with results obtained from 2D gel studies, although a larger number of additional proteins were observed with the shotgun sequencing approach. The quantitation of low to medium level proteins was explored in the ion trap with an add-back of a known amount of human growth hormone (hGH) at a clinically relevant level (5 ug/L). The isotope coded affinity tag (ICAT) approach was used to quantitate successfully different levels of hGH in replicate analysis via the disulfide linked tryptic peptide (T6-T16). These studies suggest that the shotgun sequencing approach can be used to characterize part of the plasma proteome and serve as a starting point for the use of multidimensional analytical approaches for the analysis of complex biological samples.
Impact of innovative and sea-shell amendments in Bradyrhizobium and soybean symbiotic relationship (2019)

Trabajo presentado en el 8th International Symposium of Interactions of Soil Minerals with Organic Components and Microorganisms (ISMOM), celebrado en Sevilla (España), del 23 al 28 de abril de 2019
WBSDF for simulating wave effects of light and audio (2010)

Diffraction is a common phenomenon in nature when dealing with small scale occluders. It can be observed on biological surfaces, such as feathers and butterfly wings, and man--made objects like rainbow holograms. In acoustics, the effect of diffraction is even more significant due to the much longer wavelength of sound waves. In order to simulate effects such as interference and diffraction within a ray--based framework, the phase of light or sound waves needs to be integrated.
Investment Incentives in Near-Optimal Mechanisms (2021)

In many real-world resource allocation problems, optimization is computationally intractable, so any practical allocation mechanism must be based on an approximation algorithm. We study investment incentives in strategy-proof mechanisms that use such approximations. In sharp contrast with the Vickrey-Clark-Groves mechanism, for which individual returns on investments are aligned with social welfare, we find that some algorithms that approximate efficient allocation arbitrarily well can nevertheless create misaligned investment incentives that lead to arbitrarily bad overall outcomes. However, if a near-efficient algorithm "excludes bossy negative externalities," then its outcomes remain near-efficient even after accounting for investments. A weakening of this "XBONE" condition is necessary and sufficient for the result.
Learning Power Grid Topologies (2021)

Identifying arbitrary topologies of power networks in real time is a computationally hard problem due to the number of hypotheses that grows exponentially with the network size. The potential of recovering the topology of a grid using only the publicly available data (e.g., market data) provides an effective approach to learning the topology of the grid based on the dynamically changing and up-to-date data. This enables learning and tracking the changes in the topology of the grid in a timely fashion. A major advantage of this method is that the labeled data used for training and inference is available in an arbitrarily large amount fast and at very little cost. As a result, the power of offline training is fully exploited to learn very complex classifiers for effective real-time topology identification.
Oligonucleotide-Modified Gold Nanoparticles for Intracellular Gene Regulation* (2020)

The authors describe the use of gold nanoparticle (NP)-oligonucleotide complexes as intracellular gene regulation agents for the control of protein expression in cells. Nucleic acid-based methods for controlling gene expression have had a considerable impact on research involving gene pathways and function. In initial experiments, the authors targeted mRNA sequences coding for enhanced green fluorescent protein expressed in C166, a mouse endothelial cell line. Gold NPs have a high affinity for biomolecules and have been used as non-viral vectors for DNA delivery. Glutathione has been used as a reagent to effect DNA release from NPs in the context of gene delivery. Although these systems have not yet been optimized for maximum efficacy, the ability to systematically control the oligonucleotide loading on the NP surface has allowed us to identify several features that make them attractive candidates for antisense studies and therapies.
Self-Sorting in the Formation of Metal–Organic Nanotubes: A Crucial Role of 2D Cooperative Interactions (2016)

A mixture of ferrocene-based tetratopic pyridyl ligands FcL1 and FcL2 undergoes self-sorting upon competitive coordination with AgBF4, affording homomeric nanotubes FcNT1 and FcNT2 as a mixture. No mutual interference for the nanotubular growth occurred between FcNT1 and FcNT2 even when one of these ligands was used in large excess with respect to the other. 2D X-ray diffraction analysis of unidirectionally oriented nanotube samples, prepared by using the capillary technique, revealed that although FcL1 as reported previously stacks helically in the resulting nanotube FcNT1 FcL2 prefers to stack with no discernible helical twist in FcNT2. Such a difference in their stacking geometries is most likely a major reason for why mixed-ligand metal–organic nanotubes are not constructed upon competitive coordination of FcL1 and FcL2 with AgBF4.