gebhart/patrepeval huggingface dataset:
Abstract 4787: Targeting miR-21 in hepatocellular carcinoma (2014)

Abstract Hepatocellular carcinoma (HCC) remains a significant unmet medical need with few therapeutic options available. Micro RNA 21 (miR-21) has been shown to be upregulated in HCC, however, contribution of this onco-miR to the maintenance of tumorigenic phenotype in liver cancer remains poorly understood. We have developed potent and specific single-stranded oligonucleotide inhibitors of miR-21 (anti-miR-21) and used them to interrogate dependency on miR-21 in a panel of 20 commercially available HCC cell lines in vitro. Upon lipid-mediated transfection, anti-miR-21, but not its mismatched (MM) control, caused significant de-repression of known direct targets of miR-21 (ANKRD46, DDAH1, RECK1) and inhibited survival of a large subset of HCC cell lines. Treatment of these sensitive HCC cell lines with anti-miR-21 resulted in dose- and time-dependent induction of caspase 3/7 activity. In contrast, non-responder HCC cell lines failed to significantly upregulate caspase activity and maintained viability in the presence of anti-miR compound. Further analysis of responder cell lines revealed robust induction of cell death, inhibition of cell migration and suppression of clonogenic growth upon treatment with miR-21 inhibitor. To better understand the consequences of miR-21 suppression in HCC, we carried out global gene expression profiling of anti-miR-21 treated sensitive liver cancer cells. Striking enrichment in miR-21 targets was noted among upregulated transcripts. Gene ontology analysis identified key cellular processes affected by miR-21 inhibition, including deregulation of metabolic pathways. In addition to the induction of direct miR-21 targets, cyclin H was found to be significantly downregulated upon miR-21 inhibition in the majority of responder cell lines. We hypothesize that inhibition of cyclin H expression, while an indirect effect of miR-21 suppression, could contribute to the activity of anti-miR-21 compounds. In summary, our data suggest that inhibition of miR-21 merits further investigation in the treatment of hepatocellular carcinoma. Citation Format: Sonya Zabludoff, Timothy Wagenaar, Francisco Adrian, Charles Allerson, Heike Arlt, Raffaele Baffa, Bal Bhat, Hui Cao, Scott Davis, Carlos Garcia-Echeverria, Kathrin Heermeier, Shih-Min Huang, Lan Jiang, Eric Marcusson, Christiane Metz-Weidmann, Adam Pavlicek, Jack Pollard, Jennifer Rocnik, Sabine Scheidler, Chaomei Shi, Fangxian Sun, Tatiana Tolstykh, Qunyan Yu, Gang Zheng, Dmitri Wiederschain. Targeting miR-21 in hepatocellular carcinoma. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4787. doi:10.1158/1538-7445.AM2014-4787
Automatic Curation of Golf Highlights using Multimodal Excitement\n Features (2017)

The production of sports highlight packages summarizing a game's most\nexciting moments is an essential task for broadcast media. Yet, it requires\nlabor-intensive video editing. We propose a novel approach for auto-curating\nsports highlights, and use it to create a real-world system for the editorial\naid of golf highlight reels. Our method fuses information from the players'\nreactions (action recognition such as high-fives and fist pumps), spectators\n(crowd cheering), and commentator (tone of the voice and word analysis) to\ndetermine the most interesting moments of a game. We accurately identify the\nstart and end frames of key shot highlights with additional metadata, such as\nthe player's name and the hole number, allowing personalized content\nsummarization and retrieval. In addition, we introduce new techniques for\nlearning our classifiers with reduced manual training data annotation by\nexploiting the correlation of different modalities. Our work has been\ndemonstrated at a major golf tournament, successfully extracting highlights\nfrom live video streams over four consecutive days.\n
High Speed Research Program Structural Acoustics Multi-Year Summary Report (2013)

This report summarizes the work conducted by the Structural Acoustics Integrated Technology Development (ITD) Team under NASA's High Speed Research (HSR) Phase II program from 1993 to 1999. It is intended to serve as a reference for future researchers by documenting the results of the interior noise and sonic fatigue technology development activities conducted during this period. For interior noise, these activities included excitation modeling, structural acoustic response modeling, development of passive treatments and active controls, and prediction of interior noise. For sonic fatigue, these activities included loads prediction, materials characterization, sonic fatigue code development, development of response reduction techniques, and generation of sonic fatigue design requirements. Also included are lessons learned and recommendations for future work.
Abstract C40: αvβ6 integrin promotes a TGFβ1-mediated cancer cell autonomous osteolytic program through upregulation of matrix metalloproteinase 2 (MMP2) (2013)

Abstract Metastatic prostate cancer to the bone is associated with considerable morbidity and mortality. Because the molecular basis of this process is not completely understood, current treatment is largely palliative, aiming at reducing severe bone pain, nerve compression and pathological fractures. The molecular circuitries controlling osseous prostate metastasis are known to depend on the activity of a pro-metastatic cytokine, TGFβ1, and of matrix metalloproteinases (MMPs). MMP2 is known to enhance prostate cancer-mediated bone degradation and has been reported to be induced by TGFβ1. Various studies show that the αvβ6 integrin activates and is induced by TGFβ1, thus potentiating TGFβ1 responses in the sites where it is expressed. However, a role for αvβ6 in regulating TGFβ1—induced MMP2 has not been described before. Here, we demonstrate that the αvβ6 integrin is upregulated in human prostate cancer bone metastasis and promotes osteolysis as observed by μ–computed tomography (μ–CT) in an in vivo model of metastatic bone disease. Using immunoblotting and real-time PCR analysis, we provide evidence that the αvβ6 integrin sustains TGFβ1—dependent upregulation of MMP2 mRNA and protein levels by associating with TGFβ receptor II. We also show that αvβ6 contributes to upregulation of MMP2 by TGFβ1 through a highly specific transcriptional program mediated by Smad3, and promotes osteolysis in vivo through upregulation of MMP2 in cancer cells. In conclusion, we have identified a novel role of the αvβ6 integrin in directing, in vivo, a cell-autonomous osteolytic program through activation of MMP2. These mechanistic studies will support the development of novel molecular strategies for prostate cancer bone metastasis through inhibition of the TGFβ1\αvβ6\MMP2 signaling pathway. Acknowledgments: This work was supported by the following grants: NIH — RO1 CA89720 to Dr. Lucia R. Languino and NIH — PO1 CA140043 to Drs. Lucia R. Languino, Gary S. Stein, Jane B. Lian. Drs. Dutta and Li share the first authorship. Citation Format: Anindita Dutta, Jing Li, Huimin Lu, Jacqueline Akech, Jitesh Pratap, Tao Wang, Thomas J. FitzGerald, Zhong Jiang, Shelia M. Violette, Gary S. Stein, Jane B. Lian, Lucia R. Languino. αvβ6 integrin promotes a TGFβ1-mediated cancer cell autonomous osteolytic program through upregulation of matrix metalloproteinase 2 (MMP2). [abstract]. In: Proceedings of the AACR Special Conference on Tumor Invasion and Metastasis; Jan 20-23, 2013; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2013;73(3 Suppl):Abstract nr C40.
Mechanisms and consequences of agonist-induced talin recruitment to platelet integrin αIIbβ3 (2008)

Platelet aggregation requires agonist-induced alphaIIbbeta3 activation, a process mediated by Rap1 and talin. To study mechanisms, we engineered alphaIIbbeta3 Chinese hamster ovary (CHO) cells to conditionally express talin and protease-activated receptor (PAR) thrombin receptors. Human PAR1 or murine PAR4 stimulation activates alphaIIbbeta3, which was measured with antibody PAC-1, indicating complete pathway reconstitution. Knockdown of Rap1-guanosine triphosphate-interacting adaptor molecule (RIAM), a Rap1 effector, blocks this response. In living cells, RIAM overexpression stimulates and RIAM knockdown blocks talin recruitment to alphaIIbbeta3, which is monitored by bimolecular fluorescence complementation. Mutations in talin or beta3 that disrupt their mutual interaction block both talin recruitment and alphaIIbbeta3 activation. However, one talin mutant (L325R) is recruited to alphaIIbbeta3 but cannot activate it. In platelets, RIAM localizes to filopodia and lamellipodia, and, in megakaryocytes, RIAM knockdown blocks PAR4-mediated alphaIIbbeta3 activation. The RIAM-related protein lamellipodin promotes talin recruitment and alphaIIbbeta3 activity in CHO cells but is not expressed in megakaryocytes or platelets. Thus, talin recruitment to alphaIIbbeta3 by RIAM mediates agonist-induced alphaIIbbeta3 activation, with implications for hemostasis and thrombosis.
Approach to Cataract Surgery in an Ebola Virus Disease Survivor with Prior Ocular Viral Persistence (2020)

A 46-year-old patient with previously documented Ebola virus persistence in his ocular fluid, associated with severe panuveitis, developed a visually significant cataract. A multidisciplinary approach was taken to prevent and control infection. Ebola virus persistence was assessed before and during the operation to provide safe, vision-restorative phacoemulsification surgery.
Picosecond response times in GaAs/AlGaAs core/shell nanowire-based photodetectors (2011)

High-speed metal-semiconductor-metal (MSM) photodetectors based on Schottky-contacted core/shell GaAs/AlGaAs and bare GaAs nanowires were fabricated and characterized. The measured core/shell temporal response has a ∼10 ps full-width at half-maximum and an estimated corrected value less than 5 ps. The bare GaAs devices exhibit a slower response (∼35 ps) along with a slow decaying persistent photocurrent (∼80 s). The core/shell devices exhibit significantly improved dc and high-speed performance over bare nanowires and comparable performance to planar MSM photodetectors. The picosecond temporal response, coupled with picoampere dark current, demonstrate the potential for core/shell nanowires in high-speed imaging arrays and on-chip optical interconnects.
Investigation of Phase Noise Compensation Methods for 43 Gbit/s RZ-DQPSK Multi-Span Transmission with Direct Detection (2008)

This paper investigates the performance of different phase noise compensation options for a 43 Gbit/s RZDQPSK multi-span transmission system with distributed inline under-compensation and direct detection. The efficiency of different phase noise compensation methods, namely (i) the compensation of the mean nonlinear phase shift (MEAN), (ii) the multi-symbol phase estimation (MSPE) and (iii) the combination of both methods is examined by Monte-Carlo simulations for varying pre- and post-compensation. Furthermore, the performance of these three strategies for different average fibre input powers is investigated. Not only the optimum phase noise compensation strategy is identified, also the impact of the dispersion map is considered and compared to the conventional receiver. For the best noise tolerant receiver option a maximum Q-gain of up to 2.7 dB can be achieved for a wide range of values for the fibre input power.
Assessment of Wheelchair Technology in Tanzania (2006)

The purpose of this assessment was to determine the current state of wheelchair technology in Tanzania and the factors that prevent Tanzania’s disabled from utilizing wheelchair technology. Ninety-nine interviews of wheelchair and tricycle users, wheelchair and tricycle manufacturers, and advocacy groups for the disabled were conducted throughout Tanzania during the summer of 2005. Technical issues identified included: tricycles are more popular and much less expensive than wheelchairs; most disabled people rely on donations to buy a mobility aid; production costs can be decreased by using bicycle components and outsourcing tasks; bicycle components are available in rural areas and are attractive for use in wheelchairs; and donated wheelchairs are often irresponsibly distributed and poorly designed for their operating environment. The assessment was conducted under the supervision of the Tanzania Training Center for Orthopedic Technologists and Whirlwind Wheelchair International.
Picorna-Like Virus Discovered in Wild Lime Psyllid Leuronota fagarae Burckhardt (Hemiptera: Psylloidea) (2021)

As of March 2021, the Family: Picornaviridae contained 158 species grouped into 68 different genera. We report the identification of a new Picornaviridae-like viral species isolated from the Wild Lime Psyllid (WLP), Leuronota fagarae. Extraction and sequencing of nucleic acid from WLP adult salivary glands identified a 5554 nt sequence with 52.75% identity to Diaphorina citri (Asian Citrus Psyllid) picorna-like virus polyprotein and 59.61% identity to Bemisia tabaci (Silverleaf Whitefly) polyprotein, NCBI BlastX and Blastp analysis. Sequence comparisons of amino acids and nucleotides showed consistent similarity and motifs with picorna-like virus polyproteins across 8 known species, having significant E-values of 7e-116 or less. Polyproteins are around 2100-2400 in length, are cleaved into multiple active peptides to allow for viral replication. Phylogenetic comparisons using amino acid and nucleic acid polyprotein sequences shows a diverse radiant group of insect hosts. The discovery of a picorna-like virus in WLP that is related to the D. citri Picorna-like virus, whose niches overlap, may provide new insight into management of psyllid vectors that transmit crop pathogens, like the bacterium causing Huanglongbing in citrus.
Dioxygen Insertion into the Axial Si-C Bonds of Organosilicon Porphyrins (1998)

Abstract A dialkylsilicon porphyrin Si(TPP)(CH2CH3)2 (1) (TPP=5,10,15,20-tetraphenylporphinato) reacted with dioxygen in the dark to give a bis(ethylperoxide) complex (5), from which a dihydroxysilicon porphyrin (Si(TPP)(OH)2, (6) was obtained upon reduction and hydrolysis. In contrast with the phosphorous analogue [P(TPP)(OH)2]OH, the crystal structure of 6 showed an almost planar conformation of the porphyrin ligand.
Identification of Optimal Electrocardiographic Criteria for the Diagnosis of Unrecognized Myocardial Infarction: A Population‐Based Study (2005)

The prevalence estimates of UMI vary widely and are strongly dependent on the ECG-MI and MI recognition criteria. Future studies of UMI should explicitly recognize this variation and select the ECG-MI criteria that match their study aims.
Facile, Fmoc-Compatible Solid-Phase Synthesis of Peptide C-Terminal Thioesters (2000)

A short route to peptide C-terminal thioesters was developed that does not require the use of special linkers or resins and is compatible with standard Fmoc chemistry. Following conventional solid-phase peptide synthesis, an excess of Me(2)AlCl and EtSH in dichloromethane cleaves peptides from Wang or Pam resins to give the corresponding thioesters directly in good yield and purity.
Inhibition of NF‐κB activation by the histone deacetylase inhibitor 4‐Me2N‐BAVAH induces an early G1 cell cycle arrest in primary hepatocytes (2007)

The authors would like to draw the readers’ attention to the fact that in the above article, an incorrect version of Table 1 was published. The correct version of Table 1 is printed below:
Low interface state densities at Al2O3/GaN interfaces formed on vicinal polar and non-polar surfaces (2020)

Ni/Al2O3/GaN structures with vicinal GaN surfaces from the c- or m-plane were formed. Then, electrical interface properties of the structures were systematically investigated. It was found that interface state density (Dit) at the Al2O3/GaN interface for the c-plane is higher than that for the m-plane, and post-metallization annealing is quite effective to reduce Dit for both c- and m-planes. As a result, the low Dit value of ∼ 3 × 1010 eV−1 cm−2 was demonstrated for both planes.
Nanomaterials in Sensors (2013)

This Special Issue of <i>Nanomaterials</i> is focused on the continuing implementation of nanomaterials and nanostructures in the development of more sensitive and more specific sensing devices. As a result, these new devices employ smaller sensing elements and provide more "real time" capability. Often, the inclusion of nanomaterials leads to sensing elements for targets that were previously inaccessible. [...].
High-Speed Real-Time Resting-State fMRI Using Multi-Slab Echo-Volumar Imaging (2013)

We recently demonstrated that ultra-high-speed real-time fMRI using multi-slab echo-volumar imaging (MEVI) significantly increases sensitivity for mapping task-related activation and resting-state networks (RSNs) compared to echo-planar imaging (Posse et al., 2012). In the present study we characterize the sensitivity of MEVI for mapping RSN connectivity dynamics, comparing independent component analysis (ICA) and a novel seed-based connectivity analysis (SBCA) that combines sliding-window correlation analysis with meta-statistics. This SBCA approach is shown to minimize the effects of confounds, such as movement, and CSF and white matter signal changes, and enables real-time monitoring of RSN dynamics at time scales of tens of seconds. We demonstrate highly sensitive mapping of eloquent cortex in the vicinity of brain tumors and arterio-venous malformations, and detection of abnormal resting-state connectivity in epilepsy. In patients with motor impairment, resting-state fMRI provided focal localization of sensorimotor cortex compared with more diffuse activation in task-based fMRI. The fast acquisition speed of MEVI enabled segregation of cardiac-related signal pulsation using ICA, which revealed distinct regional differences in pulsation amplitude and waveform, elevated signal pulsation in patients with arterio-venous malformations and a trend toward reduced pulsatility in gray matter of patients compared with healthy controls. Mapping cardiac pulsation in cortical gray matter may carry important functional information that distinguishes healthy from diseased tissue vasculature. This novel fMRI methodology is particularly promising for mapping eloquent cortex in patients with neurological disease, having variable degree of cooperation in task-based fMRI. In conclusion, ultra-high-real-time speed fMRI enhances the sensitivity of mapping the dynamics of resting-state connectivity and cerebro-vascular pulsatility for clinical and neuroscience research applications.
Can Negligihle Cooperation Increase Capacity? The Average-Error Case (2018)

In communication networks, cooperative strategies are coding schemes where network nodes work together to improve network performance metrics such as sum-rate. This work studies encoder cooperation in the setting of a discrete multiple access channel with two encoders and a single decoder. A node in the network that is connected to both encoders via rate-limited links, referred to as the cooperation facilitator (CF), enables the cooperation strategy. Previously, the authors presented a class of multiple access channels where the average-error sum-capacity has an infinite derivative in the limit where CF output link capacities approach zero. The authors also demonstrated that for some channels, the maximal-error sum-capacity is not continuous at the point where the output link capacities of the CF equal zero. This work shows that the average-error sum-capacity is continuous when CF output link capacities converge to zero; that is, the infinite derivative of the average-error sum-capacity is not a result of its discontinuity as in the maximal-error case.
Concepts and requirements for the Ethernet-based evolved fronthaul (2017)

The use of Ethernet in the fronthaul permits convergence and exploitation of statistical multiplexing gains of the new interfaces, but minimum latency and latency variation requirements may become challenging. The techniques proposed to meet these challenges are summarized.
gFinder: A Web-Based Bioinformatics Tool for the Analysis of N-Glycopeptides (2016)

Glycoproteins influence numerous indispensable biological functions, and changes in protein glycosylation have been observed in various diseases. The identification and characterization of glycoprotein and glycosylation sites by mass spectrometry (MS) remain challenging tasks, and great efforts have been devoted to the development of proteome informatics tools that facilitate the MS analysis of glycans and glycopeptides. Here we report on the development of gFinder, a web-based bioinformatics tool that analyzes mixtures of native N-glycopeptides that have been profiled by tandem MS. gFinder not only enables the simultaneous integration of collision-induced dissociation (CID) and high-energy collisional dissociation (HCD) fragmentation but also merges the spectra for high-throughput analysis. These merged spectra expedite the identification of both glycans and N-glycopeptide backbones in tandem MS data using the glycan database and a proteomic search tool (e.g., Mascot). These data can be used to simultaneously characterize peptide backbone sequences and possible N-glycan structures using assigned scores. gFinder also provides many convenient functions that make it easy to perform manual calculations while viewing the spectrum on-screen. We used gFinder to detect an additional protein (Q8N9B8) that was missed from the previously published data set containing N-linked glycosylation. For N-glycan analysis, we used the GlycomeDB glycan structure database, which integrates the structural and taxonomic data from all of the major carbohydrate databases available in the public domain. Thus, gFinder is a convenient, high-throughput analytical tool for interpreting the tandem mass spectra of N-glycopeptides, which can then be used for identification of potential missing proteins having glycans. gFinder is available publicly at http://gFinder.proteomix.org/ .
Matrix Methods for Estimating Odds Ratios with Misclassified Exposure Data: Extensions and Comparisons (1999)

Misclassification of exposure variables is a common problem in epidemiologic studies. This paper compares the matrix method (Barron, 1977, Biometrics 33, 414-418; Greenland, 1988a, Statistics in Medicine 7, 745-757) and the inverse matrix method (Marshall, 1990, Journal of Clinical Epidemiology 43, 941-947) to the maximum likelihood estimator (MLE) that corrects the odds ratio for bias due to a misclassified binary covariate. Under the assumption of differential misclassification, the inverse matrix method is always more efficient than the matrix method; however, the efficiency depends strongly on the values of the sensitivity, specificity, baseline probability of exposure, the odds ratio, case-control ratio, and validation sampling fraction. In a study on sudden infant death syndrome (SIDS), an estimate of the asymptotic relative efficiency (ARE) of the inverse matrix estimate was 0.99, while the matrix method's ARE was 0.19. Under nondifferential misclassification, neither the matrix nor the inverse matrix estimator is uniformly more efficient than the other; the efficiencies again depend on the underlying parameters. In the SIDS data, the MLE was more efficient than the matrix method (ARE = 0.39). In a study investigating the effect of vitamin A intake on the incidence of breast cancer, the MLE was more efficient than the matrix method (ARE = 0.75).
ChemInform Abstract: Rational Design of a New Series of Mixed Anti‐HIV Pronucleotides. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.