gebhart/patrepeval huggingface dataset:
Cysteine proteases in Langerhans cells limits presentation of cartilage derived type II collagen for autoreactive T cells (2004)

Development of type-II collagen (CII)-induced arthritis (CIA) is dependent on activation of CII-reactive T cells. Dendritic cells (DCs) are believed to play a crucial role in antigen-specific priming of T cells but it is still unclear how the CII-reactive T cells are primed since Langerhans cells (LCs) are poor antigen-presenting cells for CII. In the present study we show that LCs, treated with cysteine protease inhibitors, are able to process and present CII to T-cell hybridomas specific for the immune-dominant glycosylated 259–270 peptide bound to the MHC class II molecule Aq. Interestingly, the self (mouse) CII peptide could also now be efficiently presented. The poor presentation by LCs is a peptide-specific effect, since both bovine CII (bCII) (presenting a different peptide on H-2r) and ovalbumin could be efficiently presented, and blockage of cysteine proteases did not enhance antigen presentation. The enhanced CII-presentation by cysteine protease inhibition is seen mainly in LCs and not in antigen-primed B cells or macrophages. B cell and macrophage presentation of CII occur even without protease inhibition and are only to a minor extent influenced by cysteine protease inhibition. These data suggest that a LC deficiency in processing of the immune-dominant CII epitope in both CIA and RA may limit the exposure of this self-antigen to T cells, but that presentation can be overcome by modulation of the peptide proteolysis during CII processing.
Procedure for Lung Engineering (2011)

Lung tissue, including lung cancer and chronic lung diseases such as chronic obstructive pulmonary disease, cumulatively account for some 280,000 deaths annually; chronic obstructive pulmonary disease is currently the fourth leading cause of death in the United States. Contributing to this mortality is the fact that lungs do not generally repair or regenerate beyond the microscopic, cellular level. Therefore, lung tissue that is damaged by degeneration or infection, or lung tissue that is surgically resected is not functionally replaced in vivo. To explore whether lung tissue can be generated in vitro, we treated lungs from adult rats using a procedure that removes cellular components to produce an acellular lung extracellular matrix scaffold. This scaffold retains the hierarchical branching structures of airways and vasculature, as well as a largely intact basement membrane, which comprises collagen IV, laminin, and fibronectin. The scaffold is mounted in a bioreactor designed to mimic critical aspects of lung physiology, such as negative pressure ventilation and pulsatile vascular perfusion. By culturing pulmonary epithelium and vascular endothelium within the bioreactor-mounted scaffold, we are able to generate lung tissue that is phenotypically comparable to native lung tissue and that is able to participate in gas exchange for short time intervals (45-120 minutes). These results are encouraging, and suggest that repopulation of lung matrix is a viable strategy for lung regeneration. This possibility presents an opportunity not only to work toward increasing the supply of lung tissue for transplantation, but also to study respiratory cell and molecular biology in vitro for longer time periods and in a more accurate microenvironment than has previously been possible.
Protein kinase CK2 interacts with and phosphorylates the <i>Arabidopsis</i> circadian clock-associated 1 protein (1998)

The circadian clock-associated 1 (CCA1) gene encodes a Myb-related transcription factor that has been shown to be involved in the phytochrome regulation of Lhcb1*3 gene expression and in the function of the circadian oscillator in Arabidopsis thaliana. By using a yeast interaction screen to identify proteins that interact with CCA1, we have isolated a cDNA clone encoding a regulatory (beta) subunit of the protein kinase CK2 and have designated it as CKB3. CKB3 is the only reported example of a third beta-subunit of CK2 found in any organism. CKB3 interacts specifically with CCA1 both in a yeast two-hybrid system and in an in vitro interaction assay. Other subunits of CK2 also show an interaction with CCA1 in vitro. CK2 beta-subunits stimulate binding of CCA1 to the CCA1 binding site on the Lhcb1*3 gene promoter, and recombinant CK2 is able to phosphorylate CCA1 in vitro. Furthermore, Arabidopsis plant extracts contain a CK2-like activity that affects the formation of a DNA-protein complex containing CCA1. These results suggest that CK2 can modulate CCA1 activity both by direct interaction and by phosphorylation of the CCA1 protein and that CK2 may play a role in the function of CCA1 in vivo.
Minimal PAM specificity of a highly similar SpCas9 ortholog (2018)

RNA-guided DNA endonucleases of the CRISPR-Cas system are widely used for genome engineering and thus have numerous applications in a wide variety of fields. CRISPR endonucleases, however, require a specific protospacer adjacent motif (PAM) flanking the target site, thus constraining their targetable sequence space. In this study, we demonstrate the natural PAM plasticity of a highly similar, yet previously uncharacterized, Cas9 from <i>Streptococcus canis</i> (ScCas9) through rational manipulation of distinguishing motif insertions. To this end, we report affinity to minimal 5'-NNG-3' PAM sequences and demonstrate the accurate editing capabilities of the ortholog in both bacterial and human cells. Last, we build an automated bioinformatics pipeline, the Search for PAMs by ALignment Of Targets (SPAMALOT), which further explores the microbial PAM diversity of otherwise overlooked <i>Streptococcus</i> Cas9 orthologs. Our results establish that ScCas9 can be used both as an alternative genome editing tool and as a functional platform to discover novel <i>Streptococcus</i> PAM specificities.
ChemInform Abstract: Synthesis and Antimicrobial Activities of Structurally Novel S,S′‐Bis(heterosubstituted) Disulfides. (2012)

Abstract A variety of novel title disulfides is synthesized and evaluated for antimicrobial cytostatic activity.
BGRP: A Tree-Based Aggregation Protocol for Inter-domain Reservations (1999)

Resource reservation needs to accommodate the rapidly growing size and increasing service diversity of the Internet. Recently, hierarchical architectures have been proposed that provide domain-level reservation.However, it is not clear that these proposals can set up and maintain reservations in an efficient and scalable fashion. In this paper, we describe a distributed architecture and protocol,called the Border Gateway Reservation Protocol (BGRP), for inter-domain resource reservation that can scale in terms of message processing load. state storage and bandwidth. Each stub or transit domain may use its own intra-domain resource reservation protocol. BGRP builds a sink tree for each of the stub domains. Each sink tree aggregates bandwidth reservations from all data sources in the network.Since backbone routers only maintain the sink tree information, the total number of reservation states at each router scales, in the worst case, linearly with the number of domains in the Internet. BGRP relies on differentiated services for data forwarding. As a result, the number of packet classifier entries is small, not the number of micro-flows.To reduce the protocol message traffic, routers may reserve domain bandwidth beyond the current load so that sources can join or leave the tree or change their reservation without having to send messages all the way to the root for every such change. We use``soft state'' to maintain reservations. In contrast to RSVP, refresh messages are delivered reliably, allowing us to reduce the refresh frequency.
Compact, Low-Power, High-Speed Silicon Electro-Optic Modulator (2007)

A 250 μm long, CMOS-compatible, PIN diode Mach-Zehnder modulator has been fabricated with response extending to 13 GHz. Modeling shows that precompensation enables the fabrication of ultracompact 10 GHz 3 dB-bandwidth, optically broadband modulators.
ChemInform Abstract: Facile Conversion of Red Phosphorus into Soluble Polyphosphide Anions by Reaction with Potassium Ethoxide. (2016)

Abstract Soluble polyphosphide anions P 5 ‐ , P 16 2‐ , and P 21 3‐ are identified by 31 P NMR after refluxing a 1:1 THF/DME solution containing P red and K or KOEt, with the latter requiring only 2 h reaction time.
A small CRLH-TL metamaterial antenna with a magneto-dielectric material (2008)

This paper has presented a method of size reduction of the CRLH transmission line antenna by using a magneto-dielectric material. The CRLH-TL antenna is composed of two patches and vias, and the magneto-dielectric material is constructed by split ring resonators. The resonant frequency of the antenna is reduced by using the magneto-dielectric material: 7.34% at -1st-order mode and 24.88% at zeroth-order mode. An antenna operated at zeroth-order resonant mode is fabricated and measured. It operates at 1.888 GHz and has a bandwidth of 0.48%, a gain of 0.534 dBi, and an efficiency of 51.7%.
CueFlik (2008)

Web image search is difficult in part because a handful of keywords are generally insufficient for characterizing the visual properties of an image. Popular engines have begun to provide tags based on simple characteristics of images (such as tags for black and white images or images that contain a face), but such approaches are limited by the fact that it is unclear what tags end users want to be able to use in examining Web image search results. This paper presents CueFlik, a Web image search application that allows end users to quickly create their own rules for re ranking images based on their visual characteristics. End users can then re rank any future Web image search results according to their rule. In an experiment we present in this paper, end users quickly create effective rules for such concepts as "product photos", "portraits of people", and "clipart". When asked to conceive of and create their own rules, participants create such rules as "sports action shot" with images from queries for "basketball" and "football". CueFlik represents both a promising new approach to Web image search and an important study in end user interactive machine learning.
Development of a No-till Transplanter for Walk-behind Tractors (2022)

Highlights Walk-behind tractor. No-till vegetable transplanter. Small local garden type farming. Transplanting precision. Abstract. A no-till vegetable transplanter powered by a walk-behind tractor was developed to reduce heavy physical labor, that is often required on small scale farming operations. Currently, there are no existing commercially available no-till transplanters made for walk-behind tractors. This concept can be an important factor in improving field transplanting operations by reducing time and human labor. The original patented concept was heavy (103 kg) and included complex mechanical assemblies to be powered by the tractor’s PTO (power-take-off). It was designed for walk-behind tractors not equipped with a battery and alternator to charge the battery in which newer walk-behind tractors are equipped. Therefore, the original functional idea of the transplanter did not change, but the transplanter’s components were modified and simplified by substituting mechanical drives and control mechanisms with a single 12-V electric motor allowing variable rpm (infinitely variable spacing) and reversible direction of rotation. The improved version of the transplanter has fewer components and weighs only 83 kg, a decrease of 20 kg. Powering the transplanter electrically (not mechanically) reduced overall weight by 19%. This new version of a modular design allows easier and faster transplanter fabrication, giving farmers an option to fabricate their own transplanter to reduce costs and increase adoption of no-till vegetable systems with cover crops. Keywords: 12-V DC variable speed reversible electric motor, No-till transplanter, Power take-off (PTO), Walk-behind two-wheel tractor.
WE‐C‐103‐12: Individually Optimized Contrast Injection in CT Angiography for the Diagnosis of Pulmonary Thromboembolic Disease (2013)

Purpose: To improve the diagnostic quality of CT angiography (CTPA) for pulmonary thromboembolic disease by individually optimizing a bi‐phasic contrast injection function to achieve uniform target contrast enhancement. To compare the results against a previously reported discrete Fourier transform (DFT) approach. Methods: This simulation study uses a retrospective dataset of 27 consecutive patients. We developed an optimization approach consists of two steps: 1. Compute the impulse enhancement function (IEF) based on the test bolus scan; 2. Optimize the contrast injection function using the IEF in order to achieve uniform target enhancement. We chose a bi‐phasic contrast injection function in which the injection rates and durations are optimized by minimizing the difference between its contrast enhancement curve and the uniform target enhancement curve. The contrast volume is limited either to the clinical standard of 65 mL or to the same amount used in the DFT approach. The optimization approach is compared against the DFT approaches in terms of the root mean square errors (RMSE) from the uniform target contrast enhancement curve and the contrast volume used. Results: When the contrast volume is limited to 65 mL, the optimization approach produces contrast enhancement significantly (p<.00001) closer to the uniform target contrast enhancement (mean RMSE 17 HU) than the DFT approach (mean RMSE 56 HU), for which the contrast volume is not even limited. When the contrast volume is limited to be the same amount used in the DFT approach, the optimization approach still generate significantly improved contrast enhancement than the DFT approach (RMSE 44 HU vs. 56 HU, p<.0099). Conclusion: The optimization approach generates individually optimized bi‐phasic injection functions yielding significantly improved contrast enhancement than the DFT approach. Its implementation in clinic has great potential to improve the diagnostic quality of CTPA. This work is supported in part by Philips Healthcare, Inc.
Stem cells for investigation and treatment of inherited retinal disease (2014)

Vision is the most important human sense. It facilitates every major activity of daily living ranging from basic communication, mobility and independence to an appreciation of art and nature. Heritable diseases of the retina, such as age-related macular degeneration and retinitis pigmentosa, are the leading cause of blindness in the developed world, collectively affecting as many as one-third of all people over the age of 75, to some degree. For decades, scientists have dreamed of preventing vision loss or of restoring the vision of patients affected with retinal degeneration through some type of drug, gene or cell-based transplantation approach. In this review, we will discuss the current literature pertaining to retinal transplantation. We will focus on the use of induced pluripotent stem cells for interrogation of disease pathophysiology, analysis of drug and gene therapeutics and as a source of autologous cells for cell replacement.
Nickel based superalloy with improved weldability and oxidation resistance. Fifth quarterly report for the period November 1999 - January 2000 (2000)

This program is part of the US Department of Energy (DOE) Energy Related Inventions Program (ERIP). The purpose of ERIP is to promote and facilitate the development of energy saving technologies that may not otherwise be developed solely by commercial enterprises. The program has been highly successful in achieving its mission. The aim of this project is to determine and provide technical and economic data to a commercial end user of the alloy so that a full-scale alloy qualification program can be defined and implemented. The object of this project is to define the compositional range for a new alloy that is suitable for evaluation and qualification by a commercial enterprise. Alloy properties that will need to be determined include weldability, oxidation resistance, creep strength, resistance to thermo-mechanical fatigue, microstructure stability, and cost. Test results will be used to finalize the compositional range of an alloy that will undergo a rigorous qualification process.
Introduction to Perfusion Quantification using Arterial Spin Labelling (2017)

Arterial spin labeling (ASL) magnetic resonance imaging (MRI) is unique in being a completely non-invasive method for imaging perfusion in the brain. Relying upon a blood-borne tracer that is created by the MRI scanner itself, ASL is becoming a popular tool to study cerebral perfusion, as well as how this perfusion changes in response to neuronal activity or in disease. This primer provides an introduction to perfusion quantification using ASL MRI, focusing both on the methods needed to extract perfusion-weighted images and on how to quantify perfusion and other hemodynamic parameters. Starting with the simplest implementation of ASL, the primer details all the common acquisition methods, as well as the subsequent analysis steps required to quantify perfusion in an individual, detect changes in perfusion in response to neural activity or pharmacological intervention, and examine perfusion variations across groups of individuals. This is supported with examples from real data illustrating all the major steps in the analysis process, linked to online material where the reader can undertake the same analysis for themselves.
Identification of chicken enterovirus-like viruses, duck hepatitis virus type 2 and duck hepatitis virus type 3 as astroviruses (2009)

Earlier work identified and biologically characterized antigenically distinct enterovirus-like viruses (ELVs) of chickens. Three of these ELVs can now be identified as astroviruses. Characterization involved the use of a hitherto undescribed, degenerate primer-based reverse transcription-polymerase chain reaction (RT-PCR) to amplify astrovirus open reading frame (ORF) 1b-specific cDNA fragments followed by nucleotide sequence determination and analysis of the amplified fragments. ELV-1 was confirmed as an isolate of the astrovirus avian nephritis virus (ANV). ELV-4 (isolate 612) and ELV-3 (isolates FP3 and 11672) were antigenically and genetically related to the second characterized astrovirus of chickens, namely chicken astrovirus (CAstV). Using indirect immunofluorescence, the FP3 and 11672 ELV-3 isolates were very closely related to one another, and less closely related to ELV-4 and the previously described CAstV (P22 18.8.00 reference isolate). Comparative analyses based on the ORF 1b amplicon sequences showed that the FP3 and 11672 ELV-3 isolates shared high nucleotide (95%) and amino acid (98%) identities with one another, and lower nucleotide (76% to 79%) and amino acid (84% to 85%) identity levels with ELV-4 and the reference CAstV P22 18.8.00 isolates. The combined degenerate primer RT-PCR and sequencing methods also provided a nucleotide sequence specific to duck hepatitis virus type 2 (DHV-2) (renamed duck astrovirus) and duck hepatitis virus type 3 (DHV-3), which, for the first time, can also be identified as an astrovirus. Phylogenetic analyses based on the amplified ORF 1b sequences showed that ANV was the most distantly related avian astrovirus, with DHV-3 being more closely related to turkey astrovirus type 2 than DHV-2.
Lists that are smaller than their parts: A coding approach to tunable secrecy (2012)

We present a new information-theoretic definition and associated results, based on list decoding in a source coding setting. We begin by presenting list-source codes, which naturally map a key length (entropy) to list size. We then show that such codes can be analyzed in the context of a novel information-theoretic metric, ϵ-symbol secrecy, that encompasses both the one-time pad and traditional rate-based asymptotic metrics, but, like most cryptographic constructs, can be applied in nonasymptotic settings. We derive fundamental bounds for ϵ-symbol secrecy and demonstrate how these bounds can be achieved with MDS codes when the source is uniformly distributed. We discuss applications and implementation issues of our codes.
Synthesis and Biological Evaluation of the First Triple Inhibitors of Human Topoisomerase 1, Tyrosyl–DNA Phosphodiesterase 1 (Tdp1), and Tyrosyl–DNA Phosphodiesterase 2 (Tdp2) (2017)

Tdp1 and Tdp2 are two tyrosyl-DNA phosphodiesterases that can repair damaged DNA resulting from topoisomerase inhibitors and a variety of other DNA-damaging agents. Both Tdp1 and Tdp2 inhibition could hypothetically potentiate the cytotoxicities of topoisomerase inhibitors. This study reports the successful structure-based design and synthesis of new 7-azaindenoisoquinolines that act as triple inhibitors of Top1, Tdp1, and Tdp2. Enzyme inhibitory data and cytotoxicity data from human cancer cell cultures establish that modification of the lactam side chain of the 7-azaindenoisoquinolines can modulate their inhibitory potencies and selectivities vs Top1, Tdp1, and Tdp2. Molecular modeling of selected target compounds bound to Top1, Tdp1, and Tdp2 was used to design the inhibitors and facilitate the structure-activity relationship analysis. The monitoring of DNA damage by γ-H2AX foci formation in human PBMCs (lymphocytes) and acute lymphoblastic leukemia CCRF-CEM cells documented significantly more DNA damage in the cancer cells vs normal cells.
Development of synthetic lung surfactants. (1988)

We have previously reported the development of a reconstituted lung surfactant consisting of an organic solvent extract of natural bovine lung surfactant supplemented with synthetic lipids. This "artificial" surfactant was used successfully to treat surfactant deficiency states both in animals and humans. We now report on the successful testing of a synthetic lung surfactant consisting of a lipid-bound protein isolated from natural lung surfactant and the lipids present in the "artificial" lung surfactant and now used in the same concentration but in a synthetic, commercially available form. The synthetic lung surfactant possessed the in vitro and in vivo surface properties characterizing the "artificial" lung surfactant. In order to identify the components of the synthetic lung surfactant that are responsible for the required surface properties, a series of 25 simple mixtures was prepared. Of these, three possessed surface properties very similar to those of the "artificial" lung surfactant and the synthetic lung surfactant, in vitro as well as in vivo. These three mixtures had four components in common. Besides dipalmitoyl phosphatidylcholine and the lipid-bound protein, they each had a saturated fatty acid, palmitic or stearic, and they each had an acidic phospholipid, phosphatidylglycerol or phosphatidylserine.
Circularly Symmetric Light Scattering from Nanoplasmonic Spirals (2011)

In this paper, we combine experimental dark-field imaging, scattering, and fluorescence spectroscopy with rigorous electrodynamics calculations in order to investigate light scattering from planar arrays of Au nanoparticles arranged in aperiodic spirals with diffuse, circularly symmetric Fourier space. In particular, by studying the three main types of Vogel's spirals fabricated by electron-beam lithography on quartz substrates, we demonstrate polarization-insensitive planar light diffraction in the visible spectral range. Moreover, by combining dark-field imaging with analytical multiparticle calculations in the framework of the generalized Mie theory, we show that plasmonic spirals support distinctive structural resonances with circular symmetry carrying orbital angular momentum. The engineering of light scattering phenomena in deterministic structures with circular Fourier space provides a novel strategy for the realization of optical devices that fully leverage on enhanced, polarization-insensitive light-matter coupling over planar surfaces, such as thin-film plasmonic solar cells, plasmonic polarization devices, and optical biosensors.