gebhart/patrepeval huggingface dataset:
A Novel Minimal Script for Arabic Text Recognition Databases and Benchmarks (2009)

This paper presents a minimal Arabic text that covers the different basic shapes of Arabic alphabet (viz. standalone, initial, medial, and terminal). It is designed with minimal repetition of character shapes in the minimal text. The novelty of the suggested script could be seen from different perspectives. It enables the collection of handwritten text from different writers with minimized effort and time. It is enough for a writer to write three lines of meaningful Arabic text to cover all possible character shapes, a total of 125 shapes. The written text is designed to have even distribution of letter frequencies. This assures enough samples of all character shapes when text is collected from enough number of writers. The same is true for printed Arabic text. This is especially useful when using large number of features with classifiers that require large number of samples for each category. Hidden Markov Models and Neural networks are two examples of these classifiers. The use of the minimal text enables proper training, as all Arabic character shapes are present with adequate frequency, hence resulting in higher recognition rates. This is not the case with natural text where the frequency of some Arabic characters differ widely, where in some cases 100 folds or more. The proposed minimal text may be used to build a data base of handwritten Arabic text collected of many writers. This covers the need for a database in the research of Arabic handwritten text recognition and benchmarking. In addition, this paper presents statistical analysis of Arabic corpora for estimating the number of occurrences of the different shapes of Arabic characters in large corpora. The frequency of Arabic characters could be used in different applications. In this research work, it was utilized in enhancing the search for the minimal Arabic text.
Marangoni forces created by surface plasmon decay (2005)

We present optical microfluidic manipulation of silicone oil and glycerol via surface tension driven forces sustained by surface plasmon deexcitation energy. The phonon energy associated with the decaying optically excited surface plasmons in a thin gold foil creates thermal gradients capable of actuating fluid flows. Spectral dependence of the plasmon decay length and control of optical beam characteristics are shown to provide a means for further manipulation.
Fuel Ethanol Production from Lignocellulosic Sugars (1997)

Fermentation studies of ethanol production from lignocellulosic sugars using the genetically engineered Saccharomyces yeast 1400 (pLNH33) and its parent Saccharomyces yeast strain 1400 are reported. While the parent strain 1400 is unable to ferment xylose, the recombinant yeast 1400 (pLNH33) ferments xylose and mixtures of glucose and xylose. High ethanol yields upto 84% were obtained by fermentation of glucose-xylose mixtures using the recombinant yeast. The kinetics of ethanol inhibition of yeast cell growth on glucose and xylose are presented. Results of ethanol production from corn fiber and corn cob by the simultaneous saccharification and fermentation (SSF) process are also reported.
Optimization of 1,4-Oxazine β-Secretase 1 (BACE1) Inhibitors Toward a Clinical Candidate (2018)

In previous studies, the introduction of electron withdrawing groups to 1,4-oxazine BACE1 inhibitors reduced the p K<sub>a</sub> of the amidine group, resulting in compound 2 that showed excellent in vivo efficacy, lowering Aβ levels in brain and CSF. However, a suboptimal cardiovascular safety margin, based on QTc prolongation, prevented further progression. Further optimization resulted in the replacement of the 2-fluoro substituent by a CF<sub>3</sub>-group, which reduced hERG inhibition. This has led to compound 3, with an improved cardiovascular safety margin and sufficiently safe in GLP toxicity studies to progress into clinical trials.
Biodistribution of a Nonpeptidic Fluorescent Endothelin a Receptor Imaging Probe (2009)

Biodistribution studies are essential for understanding the biologic behavior of novel fluorochrome-based molecular imaging agents. In this study, the biodistribution of a recently developed fluorescent imaging probe with high affinity to the endothelin A (ET(A)) receptor was evaluated by fluorescence reflectance imaging (FRI). CD-1 mice were injected with 2 nmol of the probe intravenously and sacrificed at various time points. Tissue samples of the heart, spleen, lung, kidneys, liver, brain, and muscle were removed and imaged by FRI. Initially, the signal intensity (SI) was highest in lung, kidney, and liver tissue, followed by the heart, whereas spleen, muscle, and brain showed the lowest SI. In the kidneys, the SI decreased rapidly. In the heart, an initial SI increase was observed, followed by SI attenuation, whereas in the lung, the SI steadily increased. Competition experiments showed a significant (p < .005) degree of specific binding in the heart, with a reduction in SI of > 50%. In conclusion, FRI allows us to perform biodistribution studies of novel fluorescent tracers. The developed imaging probe can be exploited to image ET A receptor expression ideally 30 minutes to 3 hours after injection.
Lidar technique for adjusting aerosol model number densities to existing conditions (1989)

Abstract : A technique is introduced by which the total number density of the LOWTRAN 7 Navy Maritime Aerosol Model is adjusted to represent existing atmospheric conditions. Measurements of the vertical profile of relative humidity and surface wind speeds are used with the model to determine the aerosol extinction and backscatter coefficients variations with altitude. Using the single-scatter lidar (light detection and ranging) equation, these parameters are then used to calculate a range compensated power, S(h), from an airborne system. An iterative method is used by which the calculated S(h) values are adjusted to agree with corresponding measured values. Examples are presented of extinction and backscatter coefficients variations with range from the lidar calculated using adjusted size distribution. Also presented are the computer program and operating instructions for adjusting the size distributions at each altitude. Keywords: Aerosol extinction; Backscatter coefficients variations; Extinction coefficients variations; Single scatter lidar equation; Backscattered power.
Genetically simpler bovine leukemia virus derivatives can replicate independently of Tax and Rex (1995)

Retrovirus genomes have a conserved modular organization that consists of trans-acting gag, pol, and env genes that function through cis-acting sequences to replicate the RNA genome to the DNA provirus. Genetically more complex retroviruses also encode regulatory genes and cis-acting sequences that are essential for their replication. We sought to convert a more complex retrovirus into a simpler retrovirus derivative that can replicate. We constructed novel, hybrid retrovirus vectors to replicate the gag, pol, and env genes of the more complex bovine leukemia virus (BLV) in the absence of regulatory genes and cis-acting response sequences. Most of the cis-acting sequences involved in the replication and regulation of BLV were replaced by the cis-acting transcriptional control sequences of a simpler retrovirus, spleen necrosis virus. We found that the resulting hybrid BLV derivatives can replicate independently of BLV Tax and Rex and the Tax and Rex cis-acting response sequences, as measured by successive passages of virus on target cells, detection of provirus sequences, and analyses of provirus and encapsidated RNAs.
C/EBP homologous protein expression regulates immunosuppressive activity in myeloid derived suppressor cells (TUM6P.1006) (2015)

Abstract Myeloid-derived suppressor cell (MDSC) suppression of anti-tumor T cell responses is a significant barrier in cancer immunotherapy. Although pathways controlling MDSC regulatory activity have been characterized, therapies to globally and specifically inhibit MDSC function are limited. Targeting central mediators of MDSC-regulatory activity may overcome T cell suppression and increase the efficacy of T cell-based immunotherapy. We investigated the role of the stress sensor C/EBP homologous protein (Chop) on MDSC function. Elevated Chop expression in tumor-bearing mice was restricted to malignant cells and tumor MDSCs. Chop elevation was also detected in tumor MDSCs from colon carcinoma patients. Interestingly, increased CD8+ T cell-mediated anti-tumor effects were found in both systemic Chop -/- and Chop -/- bone marrow chimeric mice bearing s.c. Chop-competent tumors, suggesting the importance of MDSC-Chop in tumor-induced T cell anergy. MDSCs from Chop -/- mice showed a decreased expression of major MDSC-inhibitory pathways, reduced inhibitory activity on T cells, and a surprising ability to prime T cell proliferation and induce anti-tumor effects. The reduced regulatory activity in Chop -/- MDSCs was caused by decreased IL-6 production, resulting from decreased C/EBPb activity. Altogether the results demonstrate a central role of Chop in MDSC inhibitory activity and suggest targeting Chop to restore protective immunity in cancer.
739. rAAV Delivered MicroRNA Therapeutics Towards Efficacious Treatment of Corneal Neovascularization (2016)

Corneal diseases are the second major cause of blindness worldwide. Corneal neovascularization (NV) is one of the most common pathologies in corneal diseases, leading to vision loss or even blindness. However, even though different treatments for corneal NV are available, a safe and effective therapy remains to be an unmet medical challenge. MicroRNAs (miRNAs) play roles in regulating more than half of all protein-coding genes in mammals including those involved with angiogenesis. We hypothesize that modulating expression of angiogenesis related miRNAs might be an effective approach for treating corneal NV. To this end, we first set out to identify target miRNAs that play roles in corneal NV using Nanostring technologies and the classic alkali-burn induced corneal NV mouse model. Among 618 mouse miRNAs profiled, we found 35 up-regulated and 3 down-regulated miRNAs in the neovascularized corneas, which were confirmed by qRT-PCR. We selected miR-184 and miR-204, two miRNAs that were down-regulated > 10-folds in neovascularized corneas, as our candidate targets to test the concept of in vivo gene delivery for therapeutic miRNA to treat corneal NV. As recombinant adeno-associated virus (rAAV) holds promise for highly efficient and safe in vivo gene delivery to different target tissues in a serotype dependent manner, we opted to evaluate 14 serotypes of rAAV.EGFP for gene transfer efficiency in mouse corneas by eye drops (ED), intra-stromal (IS) and subconjunctival (SC) injections to search for the suitable vector(s) for delivering miRNA therapeutics to the corneas. Among the 4 leading serotype vectors (i.e. rAAVrh.8, rh.10, rh.39 and rh.43) identified, we chose rAAVrh.10 for overexpressing pri miR-184 and pri miR-204 in the corneas with alkali-burn induced corneal NV. rAAVrh.10-mediated overexpression of miR-184 or miR-204 by IS and SC injections but not ED efficiently inhibited angiogenesis and was efficacious and safe for either prevention (IS) or treatment (SC) of corneal NV. We further invested potential target genes and pathways to elucidate the anti-angiogenic mechanism of these two miRNA therapeutics. We revealed that the anti-angiogenic effect of rAAV.pri-miR-184 was achieved by targeting Fzd4 gene, thus suppressing the canonical Wnt signaling, a well-known pathway playing vital roles in angiogenesis; while rAAV.pri-miR-204 exerted its anti-angiogenic effect by targeting angiopoietin-1 gene (Angpt1), a well-acknowledged pro-angiogenic factor. Meanwhile, the transcriptome analysis is under the way to search for novel gene targets of the miRNA therapeutics. Our study has great clinical relevance and demonstrated, for the first time, that miRNA-targeted novel therapeutics that can be delivered as either rAAV or synthetic nucleic acid drugs (i.e. miRNA mimics and antagomir) might offer an additional efficacious and safe clinical option for treating corneal NV and other angiogenesis-related diseases including age-related macular edema (AMD) and cancer.
Editing of Glutamate Receptor B Subunit Ion Channel RNAs by Four Alternatively Spliced DRADA2 Double-Stranded RNA Adenosine Deaminases (1997)

Double-stranded (ds) RNA-specific adenosine deaminase converts adenosine residues into inosines in dsRNA and edits transcripts of certain cellular and viral genes such as glutamate receptor (GluR) subunits and hepatitis delta antigen. The first member of this type of deaminase, DRADA1, has been recently cloned based on the amino acid sequence information derived from biochemically purified proteins. Our search for DRADA1-like genes through expressed sequence tag databases led to the cloning of the second member of this class of enzyme, DRADA2, which has a high degree of sequence homology to DRADA1 yet exhibits a distinctive RNA editing site selectivity. There are four differentially spliced isoforms of human DRADA2. These different isoforms of recombinant DRADA2 proteins, including one which is a human homolog of the recently reported rat RED1, were analyzed in vitro for their GluR B subunit (GluR-B) RNA editing site selectivity. As originally reported for rat RED1, the DRADA2a and -2b isoforms edit GluR-B RNA efficiently at the so-called Q/R site, whereas DRADA1 barely edits this site. In contrast, the R/G site of GluR-B RNA was edited efficiently by the DRADA2a and -2b isoforms as well as DRADA1. Isoforms DRADA2c and -2d, which have a distinctive truncated shorter C-terminal structure, displayed weak adenosine-to-inosine conversion activity but no editing activity tested at three known sites of GluR-B RNA. The possible role of these DRADA2c and -2d isoforms in the regulatory mechanism of RNA editing is discussed.
Energy-Efficient Communication in the Presence of Synchronization Errors (2015)

Communication systems are traditionally designed to have tight transmitter-receiver synchronization. This requirement has negligible overhead in the high-signal-to-noise ratio (SNR) regime. However, in many applications, such as wireless sensor networks, communication needs to happen primarily in the energy-efficient regime of low SNR, where requiring tight synchronization can be highly suboptimal. In this paper, we model the noisy channel with synchronization errors as a duplication/deletion/substitution channel. For this channel, we propose a new communication scheme that requires only loose transmitter-receiver synchronization. We show that the proposed scheme is asymptotically optimal for the Gaussian channel with synchronization errors in terms of energy efficiency as measured by the rate per unit energy. In the process, we also establish that the lack of synchronization causes negligible loss in energy efficiency. We further show that, for a general discrete memoryless channel with synchronization errors and a general input cost function admitting a zero-cost symbol, the rate per unit cost achieved by the proposed scheme is within a factor two of the information-theoretic optimum.
Ionic Self-Assembled Multilayers Adsorbed onLongPeriod FiberGratings forUseasBiosensors (2005)

Wedemonstrate that ionic self-assembled multilayers (ISAM) adsorbed onlong period gratings (LPG) function effectively asbiosensors. Theoretical simulations andexperimental measurements cmftrm that ISAM-coated-LPGs provide athermally-stable, reusable platform forbuilding efficient optical sensors. OCIScodes: 060.2340, 350.2770, 310.1620, 060.4510, 060.2280. Longperiod fiber gratings (LPG)havebeenextensively investigated foruseaschemical (1)andbiological sensors aswellasother index-modulating fiber devices (2,3). Recently, Rees(4)andwe(5)havereported the resonant wavelength shift ofanLPGtoathin-film coating ofsub-wavelength thickness byutilizing theLangmuir- Blodgett (LB)technique andionic self-assembled multilayers (ISAM) technique, respectively. Because LBthin- films haverelatively poormechanical andthermal stability, theISAMtechnique ismoresuitable forpractical devices duetoitsenhanced reliability, tunability andfilm quality. TheISAMtechnique (6,7) provides ahighly controllable meanstobuild precise, nm-thick films onanysurface withaminimum charge density, including glass, silicon, metal etc. Furthermore, adiverse array ofmaterials (e.g. clay platelets, proteins, virus particles etc.) canbe incorporated into ISAMfilms. Therefore, ISAMsonLPGsprovide arobust platform forbuilding efficient sensors. Inthis paper wedemonstrate that ISAM-coated LPGscanfunction effectively asbiosensors. Biotin, streptavidin andanti-streptavidi n weredeposited ontotheISAM-coated LPGinsequence, eachinducing a measurable resonant wavelength shift oftheLPG.Inaddition, byusing weakly-guiding scalar modetheory andLPG theory, wetheoretically confirm that theresonant wavelength oftheLPGcanbeshifted bycoating theLPGwith nm-thick ISAMfilms. Theresonant wavelength shift canresult fromthevariation ofthethickness ofthefilm and/or thevariation oftherefractive index ofthefilm. Goodthermal stability andtheability toremove andreplace the ISAMfilm enhance theflexibility andcost-efficiency ofLPG-based sensors ordevices. Polycation n3 -&Wash ->
BlueShield: A Layer 2 Appliance for Enhanced Isolation and Security Hardening among Multi-tenant Cloud Workloads (2012)

Enhanced Isolation and Security (EIS) in a cloud are of significant concern. Many organizations are hesitant in migrating to a cloud based infrastructure due to the perceived limitations with EIS. Earlier, we had presented the quantitative risk and impact assessment framework (QUIRC) [1]. QUIRC can be used to assess the security risks associated with the cloud computing platforms. In the present work, design and implementation of Blue Shield is presented. Blue Shield is a Layer2 appliance for an EIS hardening among multi-tenant cloud workloads. Blue Shield architecture provides EIS, significantly reducing the threats faced by the tenants in a cloud environment. EIS provided by Blue Shield is validated using a proof of concept implementation. Then shortcomings of the various present approaches in addressing the identified security threats are explained. It is shown that the present security applications, deployed in a non-cloud environment, do not require modification during migration to Blue Shield based clouds. Furthermore, the proposed design provides high level of protection among the VMs in the same VLAN.
Applying the Difference Term Approach for Low Frequency Biomedical Filter (2012)

Low frequency continuous time filters are essential analog blocks for biomedical applications. Integrating such filters having large time constants is difficult as it requires large component values. A novel approach to scale down the pole frequency is presented. A 5-bit reduction in the cut off frequency is achieved. This is made possible through adding a passive resistor in the forward path of the op-amp based integrator introducing a difference term of the pole frequency. Also, the filter topology is modified to avoid changing the quality factor. As an example, a 2 nd order low pass filter is designed and simulated. Simulation results show that the pole frequency is scaled down from 1.43 MHz to 4.97 kHz while maintaining tuning of 30% around the nominal value by controlling only one resistor.
End-to-End Joint Learning of Natural Language Understanding and Dialogue Manager (2016)

Natural language understanding and dialogue policy learning are both essential in conversational systems that predict the next system actions in response to a current user utterance. Conventional approaches aggregate separate models of natural language understanding (NLU) and system action prediction (SAP) as a pipeline that is sensitive to noisy outputs of error-prone NLU. To address the issues, we propose an end-to-end deep recurrent neural network with limited contextual dialogue memory by jointly training NLU and SAP on DSTC4 multi-domain human-human dialogues. Experiments show that our proposed model significantly outperforms the state-of-the-art pipeline models for both NLU and SAP, which indicates that our joint model is capable of mitigating the affects of noisy NLU outputs, and NLU model can be refined by error flows backpropagating from the extra supervised signals of system actions.
Expression of biologically active human interleukin 1 subpeptides by transfected simian COS cells. (1986)

"Interleukin 1" (IL-1) is a term used to describe the family of macrophage-derived proteins that mediate many immune and inflammatory reactions. We have previously described the molecular cloning and sequencing of the cDNA encoding the predominant (neutral) form of human IL-1, which has been designated IL-1 beta. We report here that transfection of simian COS cells with this cDNA clone results in the transcription of IL-1 mRNA and the synthesis of antibody-neutralizable intracellular IL-1 biological activity. In addition, selective deletion of regions of the IL-1 cDNA judged not to be essential for function, on the basis of conserved sequence homology, resulted in localization of a "core" region responsible for a majority of the biological activity. These results permit mapping the active site of IL-1 to a peptide of 6970 molecular weight located within the carboxyl third (between Met-136 and Gln-197) of the IL-1 precursor.
Will Diverse Tat Interactions Lead to Novel Antiretroviral Drug Targets? (2006)

More than fifteen years following the description of Tat as a critical HIV gene expression regulatory protein, additional roles for Tat in HIV replication have been described, including reverse transcription. Tat achieves function through direct interaction with viral proteins, including reverse transcriptase, and numerous cellular proteins including cyclin T1, RNA polymerase II, protein kinase R (PKR), p300/CBP, and P/CAF. Despite our advanced knowledge of how Tat operates, this has not yet resulted in the discovery of effective agents capable of targeting various Tat functions. Nevertheless, Tat remains an attractive, virus-specific molecule and detailed understanding of specific protein interaction holds promise for future drug discovery.
Adeno‐associated virus type 5–mediated intraarticular administration of tumor necrosis factor small interfering RNA improves collagen‐induced arthritis (2010)

Our data present the first proof-of-concept for the application of rAAV5-mediated RNAi-based gene therapy for local blockade of inflammation in experimental arthritis.
Antimicrobial hydrogels formed by crosslinking polyallylamine with aldaric acid derivatives (2010)

Abstract Aqueous dispersions (0.1 wt %) of hydrogels 1 and 5 —formed by crosslinking polyallylamine hydrochloride (MW 60,000) with aldaric acid derivatives, diethyl L ‐tartrate and N , N′ ‐bis(methoxycarbonylmethyl)‐ D ‐glucaramide, respectively—exhibited complete (log 5) kill within 4 h of Escherichia coli , Pseudomonas aeruginosa , Staphylococcus aureus , and Candida albicans suspended in culture medium. This antimicrobial activity was much higher than that of uncrosslinked polyallylamine (1 wt % killed only 75% of E. coli in 24 h). When dispersed at 10 and 100 ppm, hydrogel 5 displayed complete (log 5) kill of E. coli within 30–60 and 15 min, respectively. Hydrogels 1 and 5 were active against S. aureus and Salmonella choleraesuis dried on hard stainless steel surfaces and accelerated the deaths of E. coli , P. aeruginosa , S. aureus , and C. albicans in a model skin cream formulation. A 0.8% aqueous dispersion of hydrogel 5 was also effective as a hand sanitizer, killing 99.7% of Serratia marcescens on human hands within 5 min. Hydrogels 1 and 5 caused no dermal irritation or allergic contact sensitization under the conditions of a human repeat insult patch test. © 2010 Wiley Periodicals, Inc. J Appl Polym Sci, 2011