gebhart/patrepeval huggingface dataset:
A proangiogenic peptide derived from vascular endothelial growth factor receptor-1 acts through α5β1 integrin (2008)

Vascular endothelial growth factor receptor-1 (VEGFR-1) is a tyrosine kinase receptor for growth factors of the VEGF family. Endothelial cells express a membrane-bound and a soluble variant of this protein, the latter being mainly considered as a negative regulator of VEGF-A signaling. We previously reported that the soluble form is deposited in the extracellular matrix produced by endothelial cells in culture and is able to promote cell adhesion and migration through binding to alpha5beta1 integrin. In this study, we demonstrate that the Ig-like domain II of VEGFR-1, which contains the binding determinants for the growth factors, is involved in the interaction with alpha5beta1 integrin. To identify domain regions involved in integrin binding, we designed 12 peptides putatively mimicking the domain II surface and tested their ability to inhibit alpha5beta1-mediated endothelial cell adhesion to soluble VEGFR-1 and directly support cell adhesion. One peptide endowed with both these properties was identified and shown to inhibit endothelial cell migration toward soluble VEGFR-1 as well. This peptide directly binds alpha5beta1 integrin, but not VEGF-A, inducing endothelial cell tubule formation in vitro and neoangiogenesis in vivo. Alanine scanning mutagenesis of the peptide defined which residues were responsible for its biologic activity and integrin binding.
On the guaranteed error-correction of decimation-enhanced iterative decoders (2014)

Finite alphabet iterative decoders (FAIDs) proposed for LDPC codes on the binary symmetric channel are capable of surpassing the belief propagation (BP) decoder in the error floor region with lower complexity and precision, but these decoders are difficult to analyze for finite-length codes. Recently, decimation-enhanced FAIDs (DFAIDs) were proposed for column-weight-three codes. Decimation involves fixing the bit values of certain variable nodes during message-passing based on the messages they receive after some number of iterations. In this paper, we address the problem of proving the guaranteed error-correction capability of DFAIDs for column-weight-three LDPC codes. We present the methodology of the proof to derive sufficient conditions on the Tanner graph that guarantee the correction of a given error pattern in a finite number of iterations. These sufficient conditions are described as a list of forbidden graphs that must not be contained in the Tanner graph of the code. As a test case, we consider the problem of guaranteeing the correction of four errors. We illustrate the analysis for a specific 4-error pattern and provide the sufficient conditions for its correction. We also present results on the design of codes satisfying those sufficient conditions and their impact on the achievable code rate.
Algorithmic and architectural enhancements for real-time MPEG-1 decoding on a general purpose RISC workstation (1995)

Traditional video decoders require use of specially designed video decompression processors. We present novel algorithmic and architectural enhancements that allowed for the first time the real-time decompression of MPEG-1 video and audio streams on a low-end, general purpose RISC processor. For video decompression, efficient algorithmic implementations were derived by examining the Huffman decoder, the inverse quantizer and the inverse DCT as a single system. For audio decompression, a new DCT based implementation of the subband filtering operation yields 30% speed improvement in the audio decoding process and 17% speed improvement in overall audio and video decoding. Besides algorithmic enhancements, a new set of "multimedia" instructions and minor changes in the design of a traditional RISC ALU allowed increased parallelism of pixel-based operations with minimal design and control overhead. Experimental results show that with the synergistic combination of algorithmic and architectural enhancements a multimedia-enhanced RISC processor can achieve higher decoding rates than generic RISC and CISC processors, even when these processors operate at higher clock rates and have larger instruction and data caches.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Aerosol Drug Delivery During Noninvasive Positive Pressure Ventilation: Effects of Intersubject Variability and Excipient Enhanced Growth (2017)

The EEG approach enabled high-efficiency lung delivery of aerosols administered during NPPV and reduced intersubject aerosol delivery variability by an order of magnitude. Use of an in-line DPI device that connects to the NPPV mask appears to be a convenient method to rapidly administer an EEG aerosol and synchronize the delivery with inspiration.
Data from PF-06804103, A Site-specific Anti-HER2 Antibody–Drug Conjugate for the Treatment of HER2-expressing Breast, Gastric, and Lung Cancers (2023)

<div>Abstract<p>The approval of ado-trastuzumab emtansine (T-DM1) in HER2<sup>+</sup> metastatic breast cancer validated HER2 as a target for HER2-specific antibody–drug conjugates (ADC). Despite its demonstrated clinical efficacy, certain inherent properties within T-DM1 hamper this compound from achieving the full potential of targeting HER2-expressing solid tumors with ADCs. Here, we detail the discovery of PF-06804103, an anti-HER2 ADC designed to have a widened therapeutic window compared with T-DM1. We utilized an empirical conjugation site screening campaign to identify the engineered ĸkK183C and K290C residues as those that maximized <i>in vivo</i> ADC stability, efficacy, and safety for a four drug–antibody ratio (DAR) ADC with this linker–payload combination. PF-06804103 incorporates the following novel design elements: (<a href="#bib1" target="_blank">i</a>) a new auristatin payload with optimized pharmacodynamic properties, (<a href="#bib2" target="_blank">ii</a>) a cleavable linker for optimized payload release and enhanced antitumor efficacy, and (<a href="#bib3" target="_blank">iii</a>) an engineered cysteine site–specific conjugation approach that overcomes the traditional safety liabilities of conventional conjugates and generates a homogenous drug product with a DAR of 4. PF-06804103 shows (<a href="#bib1" target="_blank">i</a>) an enhanced efficacy against low HER2-expressing breast, gastric, and lung tumor models, (<a href="#bib2" target="_blank">ii</a>) overcomes <i>in vitro</i>- and <i>in vivo</i>–acquired T-DM1 resistance, and (<a href="#bib3" target="_blank">iii</a>) an improved safety profile by enhancing ADC stability, pharmacokinetic parameters, and reducing off-target toxicities. Herein, we showcase our platform approach in optimizing ADC design, resulting in the generation of the anti-HER2 ADC, PF-06804103. The design elements of identifying novel sites of conjugation employed in this study serve as a platform for developing optimized ADCs against other tumor-specific targets.</p></div>
Design of the Hollow Stabilizer (1983)

自動車の軽量化の一環として. スタビライザ (アンチロールバー) の中空化が始まっている. 本論文は中空スタビライザの設計に関するものである. 中空スタビライザに生じる応力分布の構成が実験的に求められ, 中実スタビライザにくらべて, 全く異なった応力構成をしていることが確認された. パイプ係数を適用することによって, 中空スタビライザの設計応力の予測が可能となった. また, 応力測定の実測値は有限要素法による計算値と良く一致することも確認された. ここで得られた設計法に基づいて, 疲労試験によって, 中空スタビライザに適切なパイプ材料について有益な実験結果も得られた.
Improved Monolingual Hypothesis Alignment for Machine Translation System Combination (2009)

This article presents a new hypothesis alignment method for combining outputs of multiple machine translation (MT) systems. An indirect hidden Markov model (IHMM) is proposed to address the synonym matching and word ordering issues in hypothesis alignment. Unlike traditional HMMs whose parameters are trained via maximum likelihood estimation (MLE), the parameters of the IHMM are estimated indirectly from a variety of sources including word semantic similarity, word surface similarity, and a distance-based distortion penalty. The IHMM-based method significantly outperforms the state-of-the-art, TER-based alignment model in our experiments on NIST benchmark datasets. Our combined SMT system using the proposed method achieved the best Chinese-to-English translation result in the constrained training track of the 2008 NIST Open MT Evaluation.
A Peptide-Based Positron Emission Tomography Probe for <i>In Vivo</i> Detection of Caspase Activity in Apoptotic Cells (2014)

These studies illuminate [(18)F]FB-VAD-FMK as a promising PET imaging probe to detect apoptosis in tumors and as a novel, potentially translatable biomarker for predicting response to personalized medicine.
TU‐G‐BRA‐04: Biological Optimization in Carbon Therapy (2011)

The application of high linear energy transfer (LET) radiation in modern radiation oncology, like carbon‐ion therapy, requires different concepts of treatment plan optimization when compared RT‐planning for photon beams. Although, by far not perfect, the standard strategy employs the concept of relative biological effectiveness (RBE), which converts the delivered physical particle dose into a radio‐biologically equivalent dose of low LET beams. In order to introduce the respective RBE models into the inverse planning process of particle therapy one directly aims to optimize the biological effect, mostly expressed in terms of a linear quadratic model (LQM) for a dose‐effect relationship. We will first introduce the general framework of biological optimization for inverse planning of intensity modulated particle therapy (IMPT). The effects of the intrinsic radiation quality on the design of treatment plans will be demonstrated for various forms of dose delivery methods, like spread‐out Bragg peaks (SOBP), distal edge‐tracking (DET) or 3D‐spot scanning and different clinical treatment sites. So far, the employed models only account for the most important radiobiological factor, the anticipated local LET distribution, while other additional factors like the oxygen enhancement ratio or the influence of different fractionation schemes are not considered explicitly. Finally, another important issue will be briefly mentioned, the robustness of biologically optimized treatment plans versus uncertainties in the dose delivery process or even the limited knowledge of the biological input parameters of the employed models that are predicting the biological effect. Some results in the framework of the worst‐case optimization will be discussed. Learning Objectives: 1. To review the framework of biological inverse planning of carbon therapy 2. To understand the potential and inherent limitations of the optimization approach
Incoherent digital holography with phase-only spatial light modulators (2015)

Today, spatial light modulators (SLMs) offer the world of digital holography a robust technology that can be incorporated into hologram recorders. This review surveys recent developments related to the role of SLMs in a family of incoherent digital hologram recorders termed Fresnel incoherent correlation holography (FINCH). Two systems branching out from FINCH, and discussed herein, are a confocal version of FINCH and a synthetic aperture FINCH-based system.
Calcium-sensing receptor as a therapeutic target for pulmonary fibrosis (2018)

<b>Introduction:</b> Pulmonary fibrosis is a symptom of chronic lung diseases characterised by excessive extracellular matrix deposition resulting in the decline of lung function. Idiopathic pulmonary fibrosis (IPF), the most notable, usually results in death within 5 years and currently has no effective treatments. <b>Aims:</b> The extracellular calcium-sensing receptor (CaSR) has been shown to play a role in pathological activation of cardiac fibroblasts and to drive inflammatory lung disease. However, the role of the CaSR in IPF remains unelucidated. This study investigates the role of CaSR in lung fibroblast activation and whether CaSR antagonists, calcilytics, attenuate this process. <b>Methods:</b> Human lung fibroblasts were treated with transforming growth factor-β1 (TGF-β1) in the presence or absence of calcilytic for 72 hours. qPCR, immunofluorescence, ELISA, histology and Western blot analyses were used to assess mRNA and protein expression of CaSR and known fibrotic markers. <b>Results:</b> CaSR is increased in human IPF lungs when compared to control. In human lung fibroblasts, mRNA levels of α-smooth muscle actin and collagen 1 were significantly reduced by calcilytics compared to control (p<0.01). Exogenous TGF-β1 supplementation increased CaSR and α-smooth muscle actin expression in control fibroblasts, but this was supressed by co-treatment with calcilytics (p<0.001). <b>Conclusions:</b> Our results are the first to report that functional CaSR is up-regulated in activated lung fibroblasts and that calcilytics reduce markers implicated in pulmonary fibrosis. Thus, CaSR may represent a novel therapeutic target in pulmonary fibrosis.
Star-branched block copolymer ionomers: synthesis, characterization, and properties (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStar-branched block copolymer ionomers: synthesis, characterization, and propertiesRobson F. Storey, Scott E. George, and Mark E. NelsonCite this: Macromolecules 1991, 24, 10, 2920–2930Publication Date (Print):May 1, 1991Publication History Published online1 May 2002Published inissue 1 May 1991https://pubs.acs.org/doi/10.1021/ma00010a044https://doi.org/10.1021/ma00010a044research-articleACS PublicationsRequest reuse permissionsArticle Views259Altmetric-Citations30LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Dynamic Word Embeddings (2017)

We present a probabilistic language model for time-stamped text data which tracks the semantic evolution of individual words over time. The model represents words and contexts by latent trajectories in an embedding space. At each moment in time, the embedding vectors are inferred from a probabilistic version of word2vec [Mikolov et al., 2013]. These embedding vectors are connected in time through a latent diffusion process. We describe two scalable variational inference algorithms--skip-gram smoothing and skip-gram filtering--that allow us to train the model jointly over all times; thus learning on all data while simultaneously allowing word and context vectors to drift. Experimental results on three different corpora demonstrate that our dynamic model infers word embedding trajectories that are more interpretable and lead to higher predictive likelihoods than competing methods that are based on static models trained separately on time slices.
PD 116,152, a new phenazine antitumor antibiotic. Structure and antitumor activity. (1986)

A new, highly substituted phenazine with antitumor activity was isolated from the culture broth of a Streptomyces sp. This compound, whose structure was determined by spectroscopic methods and verified by X-ray diffraction analysis, was found to be methyl 6-formyl-4,7,9-trihydroxy-8-methyl-1-phenazinecarboxylate.
What Are Optimal P2Y12 Inhibitor and Schedule of Administration in Patients With Acute Coronary Syndrome? (2019)

Guidelines recommend treatment with a P2Y<sub>12</sub> platelet adenosine diphosphate receptor inhibitor in patients undergoing elective or urgent percutaneous coronary intervention (PCI), but the optimal agent or timing of administration is still not clearly specified. The P2Y<sub>12</sub> inhibitor was initially used for its platelet anti-aggregatory action to block thrombosis of the recanalized coronary artery or deployed stent. It is now recognized that these agents also offer potent cardioprotection against a reperfusion injury that occurs in the first minutes of reperfusion if platelet aggregation is blocked at the time of reperfusion. But this is difficult to achieve with oral agents which are slowly absorbed and often require time-consuming metabolic activation. Patients with ST-segment elevation myocardial infarction who usually have a large mass of myocardium at risk of infarction seldom have sufficient time for upstream-administered oral agents to achieve a therapeutic P2Y<sub>12</sub> level of inhibition by the time of balloon inflation. However, optimal treatment could be assured by initiating an IV cangrelor infusion shortly prior to stenting followed by subsequent post-PCI transition to an oral agent, that is, ticagrelor, once success of the recanalization and absence of need for surgical intervention are confirmed. Not only should this sequence provide optimal protection against infarction, it should also negate bleeding if coronary artery bypass grafting should be required since stopping the cangrelor infusion at any time will quickly restore platelet reactivity. It is anticipated that cangrelor-induced myocardial salvage will help preserve myocardial function and significantly diminish postinfarction heart failure.
Genetic enhancement of palmitic acid accumulation in cotton seed oil through<scp>RNA</scp>i down‐regulation of<i>gh<scp>KAS</scp>2</i>encoding β‐ketoacyl‐<scp>ACP</scp>synthase<scp>II</scp>(<scp>KASII</scp>) (2016)

Palmitic acid (C16:0) already makes up approximately 25% of the total fatty acids in the conventional cotton seed oil. However, further enhancements in palmitic acid content at the expense of the predominant unsaturated fatty acids would provide increased oxidative stability of cotton seed oil and also impart the high melting point required for making margarine, shortening and confectionary products free of trans fatty acids. Seed-specific RNAi-mediated down-regulation of β-ketoacyl-ACP synthase II (KASII) catalysing the elongation of palmitoyl-ACP to stearoyl-ACP has succeeded in dramatically increasing the C16 fatty acid content of cotton seed oil to well beyond its natural limits, reaching up to 65% of total fatty acids. The elevated C16 levels were comprised of predominantly palmitic acid (C16:0, 51%) and to a lesser extent palmitoleic acid (C16:1, 11%) and hexadecadienoic acid (C16:2, 3%), and were stably inherited. Despite of the dramatic alteration of fatty acid composition and a slight yet significant reduction in oil content in these high-palmitic (HP) lines, seed germination remained unaffected. Regiochemical analysis of triacylglycerols (TAG) showed that the increased levels of palmitic acid mainly occurred at the outer positions, while C16:1 and C16:2 were predominantly found in the sn-2 position in both TAG and phosphatidylcholine. Crossing the HP line with previously created high-oleic (HO) and high-stearic (HS) genotypes demonstrated that HP and HO traits could be achieved simultaneously; however, elevation of stearic acid was hindered in the presence of high level of palmitic acid.
2:1 Cocrystals of Homochiral and Achiral Amino Acid Zwitterions with Li<sup>+</sup> Salts: Water-Stable Zeolitic and Diamondoid Metal–Organic Materials (2011)

Eight 2:1 cocrystals of amino acid zwitterions and Li(+) salts were crystallized from hot water to afford cationic networks based on tetrahedral lithium cations: square grids, an ABW topology net, and diamondoid nets.
A Soft Output Viterbi Algorithm (SOVA) Demodulator for Pre-Coded Binary CPM Signals (2002)

A soft output demodulator based on the Viterbi algorithm is presented for a binary pre-coded continuous phase modulation communication system. This soft output demodulator is as simple to implement as the Maximum Likelihood Sequence Estimator (MLSE) demodulator but requires less storage elements. Simulation results for a rate Ω convolution-coded GMSK signal with Viterbi decoding show that this demodulator can provide a 2 to 2.5 dB advantage over that of hard decision decoding using the MLSE demodulator.
Controlling the Motion of Total Knee Replacements using Intercondylar Guide Surfaces (2000)

Total knee replacements using intercondylar cams, such as posterior stabilized types, have been in use for many years. In a previous study, software was written to analyze an alternative shape of the intercondylar cams. The goal of the current study was to investigate in a more general way the potential of intercondylar cams, or guide surfaces, for reproducing the anterior-posterior motion of the natural knee throughout the flexion range. Typical sagittal outlines for the femoral and tibial bearing surfaces were defined, and a parametrized shape for the femoral guide surface was defined to produce a wide range of shapes. Software was written in which the femoral component was flexed in increments, with the posterior translation defined as a function of the flexion angle. The shape of the tibial guide surface was derived from the locus of the femoral guide surface at its multiple flexion positions. By iterating methodically through possible shapes of femoral guide surfaces, several types of total knee replacement components in common use today were identified, as well as other configurations of potential interest. For quantification of a given design, the software calculated the anterior and posterior laxity at each flexion angle. Laxity was defined as the motion before the femoral guide surface impacted the tibial guide surface or until the contact point of the bearing surfaces reached a specified slope. Convex femoral and concave saddle-shaped tibial guide surfaces produced small laxities in both directions over most of the flexion range. A saddle design with small laxities in the first half of flexion, combined with a posterior stabilized feature, was an interesting combination. Potential improvements to the currently used designs were shown in this study, and new shapes of intercondylar guide surfaces were derived that could be considered for application.
Anti–Prostate Stem Cell Antigen Monoclonal Antibody 1G8 Induces Cell Death <i>In vitro</i> and Inhibits Tumor Growth <i>In vivo</i> via a Fc-Independent Mechanism (2005)

Prostate stem cell antigen (PSCA), a 123-amino acid cell surface glycoprotein, is highly expressed in both local and metastatic prostate cancers as well as in a large proportion of bladder and pancreatic cancers. PSCA overexpression correlates with a high risk of recurrence after primary therapy for prostate cancer. We have reported previously that anti-PSCA monoclonal antibody (mAb) 1G8 inhibits tumor growth, prevents metastasis, and prolongs the survival of mice inoculated with human prostate cancer cell lines and xenografts. The current study was undertaken to elucidate the mechanism of action of anti-PSCA antibody therapy. In particular, we asked whether antitumor activity resulted from recruitment of an immune response or a direct effect on the tumor cell itself. In vitro assays show that both intact 1G8 and F(ab')2 fragments of 1G8 induce prostate cancer cell death. The anti-PSCA antibody-induced cell death is caspase independent and requires antigen cross-linking. These results were confirmed in in vivo models in which both 1G8 and F(ab')2 fragments were able to inhibit prostate tumor formation and growth equally. These results suggest that the anti-PSCA mAb 1G8 acts by a direct, Fc-independent mechanism to inhibit prostate tumor growth both in vitro and in vivo.