gebhart/patrepeval huggingface dataset:
A Single-Chain Class II MHC-IgG3 Fusion Protein Inhibits Autoimmune Arthritis by Induction of Antigen-Specific Hyporesponsiveness (2002)

T cells play a central role in many autoimmune diseases. A method to specifically target the function of autoreactive T cell clones would avoid the global immunosuppression associated with current therapies. To develop a molecule capable of inhibiting autoreactive T cell responses in vivo, single-chain peptide-I-A-IgG3 fusion proteins were constructed and expressed in both mammalian and insect cells. The fusion proteins were designed with an IgG3 Fc moiety to make them divalent, allowing TCR cross-linking, while lacking FcR binding and costimulation. The fusion proteins stimulated T cell hybridomas in vitro in a peptide-specific, MHC-restricted manner but failed to do so in soluble form. In vivo administration of an I-A(q) fusion protein, containing an immunodominant collagen II peptide, significantly delayed the onset and reduced the severity of collagen-induced arthritis in DBA/1 mice by induction of Ag-specific hyporesponsiveness. Such fusion proteins may be useful to study novel therapeutic approaches for T cell-mediated autoimmune diseases.
Relationship of respiratory sounds to alterations in the upper airway resistance (2012)

Respiratory sound analysis is a simple and noninvasive way to study the pathophysiology of the upper airway (UA). Recently, it has been used to diagnose partial or complete UA collapse in patients with obstructive sleep apnea (OSA). In this study, we investigated whether uid accumulation in the neck alters the properties of respiratory sounds in temporal and spectral domains and whether the respiratory sounds analysis can be used to monitor variations in the physiology of the UA, as re ected by UA resistance (R(UA)). We recorded respiratory sounds and R(UA) from 19 individuals while awake. We applied lower body positive pressure (LBPP) to shift uid out of the legs and into the neck, which increased R(UA). We calculated !rst and second formants and energy of inspiratory sound segments. Our results show that during both control (no LBPP) and LBPP arms of the study, the extracted features were different for the sound segments corresponding to low and high R(UA). Also, the features were different during control and LBPP arms of the study. With the application of support vector machine (SVM) based classi!er, we were able to classify the sound segments into two groups of high/low resistance during control and LBPP arms and into two groups of control/LBPP when including all sound segments. The accuracies of non-linear SVM classi!er were 74.5 ± 19.5%, 75.0 ± 15.4% and 77.1 ± 12.3% for the control arm, LBPP arm and between the arms, respectively. We also showed that during the LBPP arm, the variations in !rst formant of the sound segments corresponding to low and high R(UA) was much less than during the control arm. This indicates that with application of LBPP and accumulation of uid in the neck, there are less variations in the morphology of the UA in response to changes in R(UA), than during the control arm. These results indicate that acoustic analysis of respiratory sounds can be used to investigate physiology of the UA and how interventions can alter UA properties.
Abstract 2875: Targeted therapy of Ewing’s sarcoma by human anti CD99 targeted hybrid polymerized liposomal nanoparticles (HPLNs) encapsulating anticancer agents (2019)

Abstract Most anticancer therapies are unspecific and therefore inevitably lead to off-target toxicity. To overcome these shortcomings, targetable hybrid polymerization liposomal nanoparticles (HPLNs) have been invented. Multiple innovative and proprietary technologies have been developed to enable creation of this unique form of nanoparticle therapy with covalent attachment of targeting molecules such as tumor specific antibodies or peptides. Human monoclonal anti-CD99 antibody-targeted HPLNs encapsulating irinotecan (CD99-HPLN/Ir) can efficiently reach implanted Ewing sarcoma tumors in xenograft mice and dramatically reduce and/or eliminate the tumor burden. Complete tumor ablation has been observed at doses as low as 1 mg irinotecan/kg, treated twice per week. In other cases, animals who failed untargeted (HPLN/Ir) treatment showed complete tumor ablation after ‘salvage’ treatment with CD99-HPLN/Ir. Our CD99 targeted HPLN/irinotecan formulation, termed NV103 showed much better efficacy than the commercial untargeted liposomal irinotecan (Onivyde™) and doxorubicin (Doxil™). Toxic side effects, normally associated with systemic administration of free irinotecan, were minimized or undetectable. Our nanoparticles showed excellent bioavailability. Even the untargeted HPLN/Ir improve drug bioavailability six-fold in a comparison experiment with the drug in liposome form (Onivyde™), with no discernable systemic toxicity. Experiments using human antiCD99 antibody targeted HPLNs demonstrated they can be used for delivery of therapeutic nucleic acids including siRNA, ASO or functional CRISPR-Cas9 systems against EWS-FLI1. Targeted HPLN/ siRNA and ASO against EWS-Fli1 reduced the protein expression of EWS-Fli1 by 35% and 65%, respectively. Our results of HPLN/CRISPR-Cas9 systems showed the high efficient delivery of CRISPR-Cas9 components and a 70% knockdown of EWS-FLI1 expression in vitro. In the initial animal study our work showed the systemic administration of human monoclonal anti-CD99 antibody-targeted HPLNs encapsulating CRISPR-Cas9 against EWS-Fli1 could reduce the tumor growth of Ewing tumor successfully. In conclusion, our targeted HPLNs can be used as a clinically viable method for the targeted delivery of varied therapeutics including chemotherapeutic agents (Doxorubicin and Irinotecan), therapeutic nucleic acids (siRNA and ASO) and CRISPR-Cas9 systems. Ultimately, after development of other tumor-specific targeting agents and varied encapsulated therapeutics, this technology can be usefully adapted for the treatment of various cancers as well. Citation Format: HyungGyoo Kang, Jon Nagy, Sheetal Mitra, Triche Triche. Targeted therapy of Ewing’s sarcoma by human anti CD99 targeted hybrid polymerized liposomal nanoparticles (HPLNs) encapsulating anticancer agents [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2875.
Impaired Lipoprotein Receptor-Mediated Peripheral Binding of Plasma Amyloid-β is an Early Biomarker for Mild Cognitive Impairment Preceding Alzheimer's Disease (2011)

Soluble circulating low density lipoprotein receptor-related protein-1 (sLRP) provides key plasma binding activity for Alzheimer's disease (AD) amyloid-β peptide (Aβ). sLRP normally binds 70-90% of plasma Aβ preventing free Aβ access to the brain. In AD, Aβ binding to sLRP is compromised by increased levels of oxidized sLRP which does not bind Aβ. Here, we determined plasma oxidized sLRP and Aβ40/42 sLRP-bound, other proteins-bound and free plasma fractions, cerebrospinal fluid (CSF) tau/Aβ42 ratios, and mini-mental state examination (MMSE) scores in patients with mild cognitive impairment (MCI) who progressed to AD (MCI-AD, n = 14), AD (n = 14) and neurologically healthy controls (n = 14) recruited from the Göteborg MCI study. In MCI-AD patients prior to conversion to AD and AD patients, the respective increases in oxidized sLRP and free plasma Aβ40 and Aβ42 levels were 4.9 and 3.7-fold, 1.8, and 1.7-fold and 4.3 and 3.3-fold (p < 0.05, ANOVA with Tuckey post-hoc test). In MCI-AD and AD patients increases in oxidized sLRP and free plasma Aβ40 and Aβ42 correlated with increases in CSF tau/Aβ42 ratios and reductions in MMSE scores (p < 0.05, Pearson analysis). A heterogeneous group of 'stable' MCI patients that was followed over 2-4 years (n = 24) had normal CSF tau/Aβ42 ratios but increased oxidized sLRP levels (p < 0.05, Student's t test). Data suggests that a deficient sLRP-Aβ binding might precede and correlate later in disease with an increase in the tau/Aβ42 CSF ratio and global cognitive decline in MCI individuals converting into AD, and therefore is an early biomarker for AD-type dementia.
Performance Analysis and Modeling of Video Transcoding Using Heterogeneous Cloud Services (2018)

High-quality video streaming, either in form of Video-On-Demand (VOD) or live streaming, usually requires converting (i.e., transcoding) video streams to match the characteristics of viewers' devices (e.g., in terms of spatial resolution or supported formats). Considering the computational cost of the transcoding operation and the surge in video streaming demands, Streaming Service Providers (SSPs) are becoming reliant on cloud services to guarantee Quality of Service (QoS) of streaming for their viewers. Cloud providers offer heterogeneous computational services in form of different types of Virtual Machines (VMs) with diverse prices. Effective utilization of cloud services for video transcoding requires detailed performance analysis of different video transcoding operations on the heterogeneous cloud VMs. In this research, for the first time, we provide a thorough analysis of the performance of the video stream transcoding on heterogeneous cloud VMs. Providing such analysis is crucial for efficient prediction of transcoding time on heterogeneous VMs and for the functionality of any scheduling methods tailored for video transcoding. Based upon the findings of this analysis and by considering the cost difference of heterogeneous cloud VMs, in this research, we also provide a model to quantify the degree of suitability of each cloud VM type for various transcoding tasks. The provided model can supply resource (VM) provisioning methods with accurate performance and cost trade-offs to efficiently utilize cloud services for video streaming.
Separation of Active Pharmaceutical Ingredients (APIs) from Excipients in Pharmaceutical Formulations (2015)

The active pharmaceutical ingredient (API) may be physically separated from the excipients in a pharmaceutical formulation by making use of the difference in density of the API and that of the excipients. The API may then be fully characterized by standard techniques. In the density separation process, the API is not dissolved, and the crystal form of the API is not changed. As examples, Form I fexofenadine hydrochloride is separated from Allegra Allergy 24 h Tablets, and Form I lansoprazole is separated from Equate Lansoprazole Delayed Release Capsules.
A new approach to primer design for the control of PCR bias in methylation studies (2008)

Primer design for PCR-based methylation analysis following bisulfite conversion of DNA is considerably more complex than primer design for regular PCR. The choice of the optimal primer set is critical to the performance and correct interpretation of the results. Most methodologies in methylation analysis utilize primers that theoretically amplify methylated and unmethylated templates at the same time. The proportional amplification of all templates is critical but difficult to achieve due to PCR bias favouring the amplification of the unmethylated template. The focus of this brief communication is to point out the important criteria needed for the successful choice of primers that will enable the control of PCR bias in bisulfite based methylation-screening protocols.
Prokaryotic genome editing based on the subtype I-B-Svi CRISPR-Cas system (2023)

Type I CRISPR-Cas systems are the most common among six types of CRISPR-Cas systems, however, non-self-targeting genome editing based on a single Cas3 of type I CRISPR-Cas systems has not been reported. Here, we present the subtype I-B-Svi CRISPR-Cas system (with three confirmed CRISPRs and a cas gene cluster) and genome editing based on this system found in Streptomyces virginiae IBL14. Importantly, like the animal-derived bacterial protein SpCas9 (1368 amino-acids), the single, compact, non-animal-derived bacterial protein SviCas3 (771 amino-acids) can also direct template-based microbial genome editing through the target cell's own homology-directed repair system, which breaks the view that the genome editing based on type I CRISPR-Cas systems requires a full Cascade. Notably, no off-target changes or indel-formation were detected in the analysis of potential off-target sites. This discovery broadens our understanding of the diversity of type I CRISPR-Cas systems and will facilitate new developments in genome editing tools.
Compression of hyperspectral imagery using hybrid DPCM/DCT and entropy-constrained trellis coded quantization (2002)

A system is presented for compression of hyperspectral imagery which utilizes trellis coded quantization (TCQ). Specifically, DPCM is used to spectrally decorrelate the hyperspectral data, while a 2-D discrete cosine transform (DCT) coding scheme is used for spatial decorrelation. Entropy-constrained codebooks are designed using a modified version of the generalized Lloyd algorithm. This coder achieves compression ratios of greater than 70:1 with average PSNR of the coded hyperspectral sequence exceeding 40.0 dB.
The Effect of Bit Type on Reactive Torque and Consequent Tool-Face-Control Anomalies (2016)

Summary The oil-and-gas drilling industry has developed a large body of knowledge about methods for drilling directional wells with steerable motors. Experience indicates that more-aggressive drill bits are harder to steer. This is commonly attributed to the fact that bits with higher aggressivity produce larger torque changes for a given change in bit weight. The actual mechanics, however, of tool-face disorientation during slide events is poorly understood. This paper reports on tests conducted on a full-size drill rig aimed at understanding the mechanics of tool-face control. Tool-face orientation and other data were measured downhole at 100 Hz. Nine different bits ranging from polycrystalline diamond compact (PDC) to hybrid to roller-cone bits were tested on an adjustable-kick-off (AKO) motor bottomhole assembly (BHA) in slide mode. These tests confirm the common industry notions about the effect of aggressivity on tool-face control. They also show that angular motion of the BHA while sliding is overdamped. Tool-face orientation consequently follows the average of the torque signal generated by the bit. Furthermore, the tool-face orientation is more easily disoriented by a torque signal at a frequency near to or less than the torsional natural frequency of the drillstring. PDC bits excite this more readily than bits with rolling cones. We also identify a tool-face disorientation anomaly that we call a fast torque anomaly (FTA). FTAs occur because the bent motor/AKO has a preferred angular orientation in the borehole. FTAs have not been previously recognized, probably because they are not identifiable in mud-pulse signals. A BHA suffering FTAs would simply appear as a chaotic and profound loss of tool-face control in mud-pulse data. Hybrid and roller-cone bits caused fewer FTAs than PDC bits.
Emergency and quick operational radio communications in Utah Power and Light Company's Deer Creek Coal Mine (2003)

An underground radio communications system has been developed and installed in the Deer Creek Coal Mine near Huntington, Utah. The minewide radio communications system provides emergency communications to mine personnel working along the face, belt lines, man and material entries, returns and designated escapeways. The system also provides quick communications between the surface monitoring center and key personnel throughout the mining complex. The radio system utilizes two robust radio signal propagation modes to provide communications throughout the mine. In the first mode, low-conductivity seams of coal, trona, potash, quartzite and gilsonite surrounded by more conductive rock layers form natural waveguides for low-attenuation-rate transmission of radio signals. In the second mode, conductors, AC power distribution cable, conveyer belt structures, steel pipe, rail, etc. form low-attenuation-rate waveguides for distribution of radio signals. The entire radio system meets intrinsic safety requirements and is composed of three basic elements: a base unit (with remote audio capability), transceivers (with different housings which are specific to the application), and repeaters.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Design and Benefits of Dynamic Skip Fire Strategies for Cylinder Deactivated Engines (2013)

<div class="section abstract"><div class="htmlview paragraph">Cylinder deactivation is a fuel consumption reduction technology for throttled internal combustion engines and other engines with thermal efficiency loss at part cylinder load. Recent production implementations, deactivating fixed sets of cylinders under part-load operating conditions, have had limited “fly zones” due to issues with drivability and noise, vibration and harshness (NVH). Dynamic skip firing, which in its ultimate form incorporates anytime, any-cylinder deactivation, continuously varies the number of firing cylinders, along with cylinder load, obtaining flexible control of acoustic and vibrational excitations from the engine, and allowing an expanded operational envelope with fewer drive ability/NVH issues. This paper outlines design considerations of dynamic skip fire operational strategies, discusses implementation of the system on a vehicle, and presents benefits to fuel economy and NVH.</div></div>
<title>Integrated Optics Rotation Sensor (IORS)</title> (1997)

The Integrated Optics Rotation SEnsor (IORS) is a rugged, lightweight, and low cost gyro instrument which is currently being sponsored by the Defense Advanced Research Projects Agency under funding from Small Business Innovative Research/Technology Reinvestment Program. It uses glass-on- silicon optical waveguide technology. The design of the IORS is quite simple, and can potentially be adapted to a number of military and commercial applications, including yaw rate sensing for an anti-skid safety device in automobiles, rotation rate sensing for robotics, weapon aiming,and guidance of smart munitions. The basic design is presented, along with preliminary performance specifications for an IORS prototype. The characteristics of the IORS is also compared to other gyros in terms of performance, size, weight, and price.
Expression of the <i>Arabidopsis</i> histone <i>H2A‐1</i> gene correlates with susceptibility to <i>Agrobacterium</i> transformation (2002)

Transformation of plant cells by Agrobacterium tumefaciens involves both bacterial virulence proteins and host proteins. We have previously shown that the Arabidopsis thaliana gene H2A-1 (RAT5), which encodes histone H2A-1, is involved in T-DNA integration into the plant genome. Mutation of RAT5 results in a severely decreased frequency of transformation, whereas overexpression of RAT5 enhances the transformation frequency (Mysore et al., 2000b). We show here that the expression pattern of RAT5 correlates with plant root cells most susceptible to transformation. As opposed to a cyclin-GUS fusion gene whose expression is limited to meristematic tissues, the H2A-1 gene is expressed in many non-dividing cells. Under normal circumstances, the H2A-1 gene is expressed in the elongation zone of the root, the region that is most susceptible to Agrobacterium transformation. In addition, when roots are incubated on medium containing phytohormones, a concomitant shift in H2A-1 expression and transformation susceptibility to the root base is observed. Inoculation of root segments with a transfer-competent, but not a transformation-deficient Agrobacterium strain induces H2A-1 expression. Furthermore, pre-treatment of Arabidopsis root segments with phytohormones both induces H2A-1 expression and increases the frequency of Agrobacterium transformation. Our results suggest that the expression of the H2A-1 gene is both a marker for, and a predictor of, plant cells most susceptible to Agrobacterium transformation.
Quinolizidinone Carboxylic Acids as CNS Penetrant, Selective M<sub>1</sub> Allosteric Muscarinic Receptor Modulators (2010)

Positive allosteric modulation of the M1 muscarinic receptor represents an approach to treat the cognitive decline in patients with Alzheimer's disease. Replacement of a quinolone ring system in a quinolone carboxylic acid series of M1 modulators with a quinolizidinone bearing a basic amine linkage led to a series of compounds with higher free fraction, enhanced CNS exposure, and improved efficacy in rodent in vivo models of cognition.
ChemInform Abstract: Synthesis and Biological Activity of 3‐Amino‐5‐(3,5‐diamino‐6‐chloropyrazin‐2‐yl)‐1,2,4‐oxadiazole: An Amiloride Prodrug. (1987)

Abstract The synthesis of the pyrazinyl‐oxadiazoles (Va) und (Vb) from the aminopyrazines (I) or (VI) is described.
Understanding the Effect of Preparative Approaches in the Formation of “Flower-like” Li<sub>4</sub>Ti<sub>5</sub>O<sub>12</sub>—Multiwalled Carbon Nanotube Composite Motifs with Performance as High-Rate Anode Materials for Li-Ion Battery Applications (2017)

Herein we highlight the significance of nanoscale attachment modality as an important determinant of observed electrochemical performance. Specifically, controlled loading ratios of multi-walled carbon nanotubes (MWNTs) have been successfully anchored onto the surfaces of a unique “flower-like” Li<sub>4</sub>Ti<sub>5</sub>O<sub>12</sub> (LTO) micro-scale sphere motif, for the first time, using a number of different and distinctive preparative approaches, including (i) a sonication method, (ii) an in situ direct-deposition approach, (iii) a covalent attachment protocol, as well as (iv) a π-π interaction strategy. In terms of structural characterization, the composites generated by physical sonication as well as non-covalent π-π interactions retained the intrinsic hierarchical “flower-like” morphology and exhibited a similar crystallinity profile as compared with that of pure LTO. By comparison, the composite prepared by an in situ direct deposition approach yielded not only a fragmented LTO structure, likely due to the possible interfering presence of the MWNTs themselves during the relevant hydrothermal reaction, but also a larger crystallite size, owing to the higher annealing temperature associated with its preparation. Finally, the composite created via covalent attachment was covered with an amorphous insulating linker, which probably led to a decreased contact area between the LTO and the MWNTs and hence, a lower crystallinity in the resulting composite. In addition electrode tests suggested that the composite generated by π-π interactions out-performed the other three analogous heterostructures, due to a smaller charge transfer resistance as well as a faster Li-ion diffusion. In particular, the LTO-MWNT composite, produced by π-π interactions, exhibited a reproducibly high rate capability as well as a reliably solid cycling stability, delivering 132 mA h g<sup>-1</sup> at 50 C, after 100 discharge/charge cycles, including 40 cycles at a high (>20 C) rate. To conclude, such data denote the highest electrochemical performance measured to date as compared with any LTO-carbon nanotube-based composite materials previously reported, under high discharge rate conditions, and tangibly underscore the correlation between preparative methodology and the resulting performance metrics.
Recent progress in phosphorescent white organic light-emitting devices for displays and lighting (2007)

A phosphorescent white organic light-emitting device (WOLED™) with 14%η <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ege</sub> at 1,000 cd/m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> (25% EQE with outcoupling enhancements), CIE coordinates (0.46±0.01, 0.46±0.01) and a 50% lifetime 21,000 hours at an initial luminance of 1,000 cd/m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> has been demonstrated.