gebhart/patrepeval huggingface dataset:
Vaccine-induced protection against intrarectal AIDS virus transmission in the absence of anti-Env antibodies mediated by trained innate immunity (2020)

Abstract Although anti-Envelope antibodies have been viewed as the primary means of protection against SIV or SHIV acquisition, we have found in two distinct vaccine studies that protection against intrarectal SHIV or SIV acquisition in repeated low-dose challenge can be achieved in the absence of anti-Env antibodies (Vaccine efficacy = 44% in one study and 81% in the other). Specific CD8+ T cells were induced but did not correlate with protection, and in one of the studies, CD8+ depletion experiments excluded any CD8-dependence of the protection. Rather, protection correlated with protective myeloid cells and inversely with suppressive myeloid-derived suppressor cells. Trained innate immunity of monocytes lasting at least 7 weeks after vaccination was confirmed by demonstrating the ability of monocytes from vaccinated animals to produce more IL-6, TNFa and/or Mip1a when re-exposed to virus than those from control animals. This trained innate response correlated with the number of exposures required to achieve infection. Trained innate immunity has been shown to be mediated by epigenetic changes in monocytes, and indeed, we have been able to detect such epigenetic changes. Thus, vaccine protection against rectal acquisition of SHIV or SIV can be achieved in the absence of anti-Env antibodies and even of CD8+ T cells, and can be mediated by trained innate monocyte immunity. These findings suggest a new mode of vaccine protection that needs to be investigated in future AIDS vaccine clinical trials.
Symbiosis with artificial intelligence via the prism of law, robots, and society (2021)

Abstract The rapid advances in Artificial Intelligence and Robotics will have a profound impact on society as they will interfere with the people and their interactions. Intelligent autonomous robots, independent if they are humanoid/anthropomorphic or not, will have a physical presence, make autonomous decisions, and interact with all stakeholders in the society, in yet unforeseen manners. The symbiosis with such sophisticated robots may lead to a fundamental civilizational shift, with far-reaching effects as philosophical, legal, and societal questions on consciousness, citizenship, rights, and legal entity of robots are raised. The aim of this work is to understand the broad scope of potential issues pertaining to law and society through the investigation of the interplay of law, robots, and society via different angles such as law, social, economic, gender, and ethical perspectives. The results make it evident that in an era of symbiosis with intelligent autonomous robots, the law systems, as well as society, are not prepared for their prevalence. Therefore, it is now the time to start a multi-disciplinary stakeholder discussion and derive the necessary policies, frameworks, and roadmaps for the most eminent issues.
Role of aminopeptidase N (CD13) in tumor‐cell invasion and extracellular matrix degradation (1993)

We have investigated the effect of monoclonal antibodies (MAbs) specific for aminopeptidase N/CD13 on the invasion of human metastatic tumor cells into reconstituted basement membrane (Matrigel). The invasion of human metastatic tumor cells (SN12M renal-cell carcinoma, HT1080 fibrosarcoma and A375M melanoma) into Matrigel-coated filters was inhibited by an anti-CD13 MAb, WM15, in a concentration-dependent manner. However, this MAb did not have any effect on tumor-cell adhesion and migration to the extracellular matrices, which may be involved in tumor-cell invasion. MAb WM15 inhibited the degradation of type-IV collagen by tumor cells in a concentration-dependent manner. We also found that WM15 inhibited hydrolysing activities towards substrates of aminopeptidases in 3 different tumor cells. Since our previous study indicated that bestatin, an aminopeptidase inhibitor, was able to inhibit tumor-cell invasion, as well as aminopeptidase activities of murine and human metastatic tumor cells, cell-surface amino-peptidase N/CD13 may be partly involved in the activation mechanism for type-IV collagenolysis to achieve tumor-cell invasion, and anti-CD13 MAb WM15 may inhibit tumor-cell invasion through a mechanism involving its inhibitory action on the aminopeptidase N in tumor cells.
Cationic antimicrobial copolymer poly (methylmethacrylate‐co‐PHMG) decontaminates water (2016)

Vinyl terminated poly hexamethylene guanidine hydrochloride (PHMG) and methyl methacrylate (MMA) were copolymerized and tested for surface antimicrobial activity. PHMG chains of molecular weight ~2000 were functionalized with vinyl end groups (PHMG–C = C) by reacting the PHMG amino end groups with 1,2‐epoxy‐9‐decene, or glycidyl methacrylate. PHMG–C = C was copolymerized with MMA at 10% w/w ratio to form water insoluble poly(MMA‐co‐PHMG). Films of these copolymers demonstrated strong antimicrobial activity for 3 months against Escherichia coli and heterotrophic plate count bacteria. The synthesized PHMG–MMA copolymers may be used for self‐sterilizing coatings and water decontamination. Copyright © 2016 John Wiley &amp; Sons, Ltd.
Design and Synthesis of Novel Diaminoquinazolines with in Vivo Efficacy for β-Catenin/T-Cell Transcriptional Factor 4 Pathway Inhibition (2009)

We are introducing a novel series of 2,4-diaminoquinazolines as beta-catenin/Tcf4 inhibitors which were identified by ligand-based design. Here we elucidate the SAR of this series and explain how we were able to improve key molecular properties such as solubility and cLogP leading to compound 9. Analogue 9 exhibited better biological activity and improved physical and pharmacological properties relative to the HTS hit 49. Furthermore, 9 demonstrated good cell growth inhibition against several human colorectal cancer lines such as LoVo and HT29. In addition, treatment with compound 9 led to gene expression changes that overlapped significantly with the transcriptional profile resulting from the pathway inhibition by siRNA knockdown of beta-catenin or Tcf4. Subsequently, 9 was tested for efficacy in a beta-catenin/RKE-mouse xenograft, where it led to more then 50% decrease in tumor volume.
Supplemental Figure 4 from MHC Class I Loss Is a Frequent Mechanism of Immune Escape in Papillary Thyroid Cancer That Is Reversed by Interferon and Selumetinib Treatment <i>In Vitro</i> (2023)

&lt;p&gt;Supplemental Figure 4. &lt;b&gt;Effect of Selumetinib treatment on expression of antigen processing machinery (APM), cytokines, signal transducer of activation and transcription (STAT), and MHC class I molecule genes in thyroid cancer cell lines.&lt;/b&gt; Mean fold change in gene expression in papillary thyroid cancer cell lines (A) BCPAP, (B) K-1, or (C) TPC-1 following selumetinib (10μM) treatment relative to vehicle control is shown (statistical significant difference from 1 is indicated by an asterix, p&lt;0.05). All cell lines showed up-regulation of &lt;sup&gt;TAP1, STAT1, STAT6&lt;/sup&gt;, and &lt;sup&gt;LMP2&lt;/sup&gt; with selumetinib, though these differences did not meet statistical significance. Notably, increases in expression of APM genes were greatest in K-1, the cell line showing greatest phenotypic response to selumetinib treatment. In addition, the expression of &lt;sup&gt;IFNγ, IFNα1A&lt;/sup&gt;, and &lt;sup&gt;IFNα2A&lt;/sup&gt; was down-regulated in BCPAP and TPC-1 and of &lt;sup&gt;IFNα2A&lt;/sup&gt; in K-1, supporting the additive effect of interferon and selumetinib therapy seen in these cell lines. Mean fold change increases in the gene expression of &lt;sup&gt;HLA-A, B, C&lt;/sup&gt; and &lt;sup&gt;beta-2 microglobulin (β2m)&lt;/sup&gt; for each cell line are shown for illustration purposes and paralleled phenotypic changes observed by flow cytometry for these cell lines.&lt;/p&gt;
Intraaortic Balloon Pumping for Ventricular Septal Defect or Mitral Regurgitation Complicating Acute Myocardial Infarction (1973)

The intraaortic balloon pump (IABP) has been employed in the management of five patients with ventricular septal rupture (VSD) and six patients with acute mitral regurgitation (AMR) following myocardial infarction. All patients were in cardiogenic shock which responded poorly to medical therapy including pressor and inotropic agents. IABP resulted in significant clinical and hemodynamic improvement in all cases. In patients with VSD, IABP produced a fall in wedge (PCW) pressure from 17 ± 4 ( sd ) to 13 ± 4 mm Hg ( P &lt; 0.01) while mean arterial pressure increased from 68 to 73 mm Hg. Systemic A-V O 2 difference fell from 9.7 ± 2.4 to 8.1 ± 2.4 vol % ( P &lt; 0.05) while pulmonary A-V O 2 difference was unchanged. Thus the pulmonic/systemic flow ratio (P/S) declined in all patients. In patients with AMR, PCW fell from 25 ± 4 to 20 ± 4 mm Hg ( P &lt; 0.02) with a significant diminution in "V"-wave amplitude. Cardiac output (CO) rose from 3.1 ± 0.9 to 3.7 ± 1.0 liters/min ( P &lt; 0.01). All patients underwent coronary angiography without complication in preparation for emergency surgery. IABP reduces AMR following acute myocardial infarction and reduces the P/S in VSD by a selective augmentation of systemic CO. Such direct therapy acutely stabilizes these severely ill patients. Detailed angiography may then be performed safely.
Model-assisted complementary double exposure with source optimization (2004)

Source optimization techniques fall into two contrasting categories: The first and most common category includes methods to minimize OPC complexity and maximize process window for a specific pattern, without guaranteeing adequate image quality for the rest of the layout. The second category includes methods which optimize source and mask concurrently to deliver the largest process window and maximum resolution. This approach however, provides minimum control in the manufacturability of the mask. Our formulation is a hybrid combination of both categories. We apply a model-assisted double exposure decomposition using pre-optimized sources. By adding a second exposure we minimize possible negative impacts that the pattern specific source may have over the whole layout, while providing control over the area of interest and taking into account realistic mask constraints. We applied this technique to an SRAM design and the surrounding logic. Because of the general formulation of the model-assisted decomposition, we do not explicitly select memory or periphery logic, since by construction this method determines which feature segments correspond to each of the available exposures. We quantify the lithographic performance of this technique against other RET options via a statistical analysis of CD control and ILS behavior.
HARK-Bird-Box: A Portable Real-time Bird Song Scene Analysis System (2018)

This paper addresses real-time bird song scene analysis. Observation of animal behavior such as communication of wild birds would be aided by a portable device implementing a real-time system that can localize sound sources, measure their timing, classify their sources, and visualize these factors of sources. The difficulty of such a system is an integration of these functions considering the real-time requirement. To realize such a system, we propose a cascaded approach, cascading sound source detection, localization, separation, feature extraction, classification, and visualization for bird song analysis. Our system is constructed by combining an open source software for robot audition called HARK and a deep learning library to implement a bird song classifier based on a convolutional neural network (CNN). Considering portability, we implemented this system on a single-board computer, Jetson TX2, with a microphone array and developed a prototype device for bird song scene analysis. A preliminary experiment confirms a computational time for the whole system to realize a real-time system. Also, an additional experiment with a bird song dataset revealed a trade-off relationship between classification accuracy and time consuming and the effectiveness of our classifier.
Design issues related to pie menus for 5-way joysticks (2007)

Although linear textual menus are a widely adopted solution in the mobile phone user interfaces, alternatives that would take smaller amount of screen real estate exist, e.g. toolbars and pie menus. Pie menus also provide access to functions with fewer key presses than traditional Options menu but are best suited for expert users. We compared toolbars and pie menus as a way to access most often used functions of a mobile media player. Based on user test results, we selected pie menus for implementation into a prototype and made another user test to see what kind of design considerations are related to pie menus for digital joysticks. The user feedback was positive and six design issues were identified.
Tangelo: An Open-source Python Package for End-to-end Chemistry Workflows on Quantum Computers (2022)

Tangelo [link: https://github.com/goodchemistryco/Tangelo] is an open-source Python software package for the development of end-to-end chemistry workflows on quantum computers, released under Apache 2.0 license. It aims to support the design of successful experiments on quantum hardware, and to facilitate advances in quantum algorithm development. The software enables quick exploration of different approaches by assembling reusable building blocks and algorithms, with the flexibility to let users introduce their own. Tangelo is backend-agnostic and enables switching between various backends (Braket, Qiskit, Qulacs, Azure Quantum, QDK, Cirq...) with minimal changes in the code. The package can be used to explore quantum computing applications such as open-shell systems, excited states, or more industrially-relevant systems by leveraging problem decomposition at scale. This paper outlines the design choices, philosophy, and main features of Tangelo.
Terahertz-Driven Luminescence and Colossal Stark Effect in CdSe–CdS Colloidal Quantum Dots (2017)

Optical properties of colloidal semiconductor quantum dots (QDs), arising from quantum mechanical confinement of charge, present a versatile testbed for the study of how high electric fields affect the electronic structure of nanostructured solids. Studies of quasi-DC electric field modulation of QD properties have been limited by electrostatic breakdown processes under high externally applied electric fields, which have restricted the range of modulation of QD properties. In contrast, here we drive CdSe-CdS core-shell QD films with high-field THz-frequency electromagnetic pulses whose duration is only a few picoseconds. Surprisingly, in response to the THz excitation, we observe QD luminescence even in the absence of an external charge source. Our experiments show that QD luminescence is associated with a remarkably high and rapid modulation of the QD bandgap, which changes by more than 0.5 eV (corresponding to 25% of the unperturbed bandgap energy). We show that these colossal energy shifts can be explained by the quantum confined Stark effect even though we are far outside the regime of small field-induced shifts in electronic energy levels. Our results demonstrate a route to extreme modulation of material properties and to a compact, high-bandwidth THz detector that operates at room temperature.
2-C-Hydroxymethyl-2,3-O-isopropylidene-D-ribono-1,5-lactam (2004)

C 9 H 14 NO 5 , was formed by catalytic hydrogenation of an azidolactone using Pd-black in 1,4dioxane.
Surface Enhanced Raman Scattering (SERS) on-an-optofluidic chip using roof collapse method (2010)

Here we demonstrate a SERS optofluidic device using a nanochannel fabrication method developed by our group. This device consists of nanochannels and a SU-8 waveguide. As a test, we demonstrate the detection of SERS-active Rhodamine6G.
Pass-thoughts: Authenticating With Our Minds. (2005)

We present a novel idea for user authentication that we call pass-thoughts. Recent advances in Brain-Computer Interface (BCI) technology indicate that there is potential for a new type of human-computer interaction: a user transmitting thoughts directly to a computer. The goal of a pass-thought system would be to extract as much entropy as possible from a user&amp;apos;s brain signals upon &amp;quot;transmitting&amp;quot; a thought. Provided that these brain signals can be recorded and processed in an accurate and repeatable way, a passthought system might provide a quasi two-factor, changeable, authentication method resistant to shoulder-surfing. The potential size of the space of a pass-thought system would seem to be unbounded in theory, although in practice it will be finite due to system constraints. In this paper, we discuss the motivation and potential of pass-thought authentication, the status quo of BCI technology, and outline the design of what we believe to be a currently feasible pass-thought system. We also briefly mention the need for general exploration and open debate regarding ethical considerations for such technologies.
Haemoglobin(βK120C)–albumin trimer as an artificial O2carrier with sufficient haemoglobin allostery (2020)

The allosteric O<sub>2</sub> release of haemoglobin (Hb) allows for efficient O<sub>2</sub> delivery from the lungs to the tissues. However, allostery is weakened in Hb-based O<sub>2</sub> carriers because the chemical modifications of the Lys- and Cys-β93 residues prevent the quaternary transition of Hb. In this paper, we describe the synthesis and O<sub>2</sub> binding properties of a recombinant Hb [rHb(βK120C)]-albumin heterotrimer that maintains sufficient Hb allostery. The rHb(βK120C) core, with two additional cysteine residues at the symmetrical positions on its protein surface, was expressed using yeast cells. The mutations did not influence either the O<sub>2</sub> binding characteristics or the quaternary transition of Hb. Maleimide-activated human serum albumins (HSAs) were coupled with rHb(βK120C) at the two Cys-β120 positions, yielding the rHb(βK120C)-HSA<sub>2</sub> trimer, in which the Cys-β93 residues were unreacted. Molecular dynamics simulation demonstrated that the HSA moiety does not interact with the amino acid residues around the haem pockets and the α<sub>1</sub>β<sub>2</sub> surfaces of the rHb(βK120C) core, the alteration of which retards Hb allostery. Circular dichroism spectroscopy demonstrated that the quaternary transition between the relaxed (R) state and the tense (T) state of the Hb core occurred upon both the association and dissociation of O<sub>2</sub>. In phosphate-buffered saline solution (pH 7.4) at 37 °C, the rHb(βK120C)-HSA<sub>2</sub> trimer exhibited a sigmoidal O<sub>2</sub> equilibrium curve with the O<sub>2</sub> affinity and cooperativity identical to those of native Hb (<i>p</i> <sub>50</sub> = 12 Torr, <i>n</i> = 2.4). Moreover, we observed an equal Bohr effect and 2,3-diphosphoglycerate response in the rHb(βK120C)-HSA<sub>2</sub> trimer compared with naked Hb.
Características Químicas y nutricionales de variedades de maicillo: desarrollado de productos alimentarios... (2014)

La composicion quimica del grano de sorgo es muy similar a las que son reportados en la literatura por otros autores. Esto sugiere que la conbinacion del sorgo y maiz, no danaria la calidad individual de ninguno de los dos. Por lo tanto las mezclas de granos simples, como el maiz el sorgo y el frijol, se pueden utilizar para el desarrollo de un alimento complementario de alta calidad.
Developing silicon photonics technologies with a wafer-level test station (2018)

Imec and FormFactor present a unique wafer-level test solution that enables semi-automatic testing of passive and active silicon photonics components and circuits.
Cellulose nanoparticles: photoacoustic contrast agents that biodegrade to simple sugars (2014)

In photoacoustic imaging, nanoparticle contrast agents offer strong signal intensity and long-term stability, but are limited by poor biodistribution and clearance profiles. Conversely, small molecules offer renal clearance, but relatively low photoacoustic signal. Here we describe a cellulose-based nanoparticle with photoacoustic signal superior to gold nanorods, but that undergoes enzymatic cleavage into constituent glucose molecules for renal clearance. Cellulose nanoparticles (CNPs) were synthesized through acidic cleavage of cellulose linters and purified with centrifugation. TEM indicated that the nanoparticles were 132 &plusmn; 46 nm; the polydispersity index was 0.138. Ex vivo characterization showed a photoacoustic limit of detection of 0.02 mg/mL CNPs, and the photoacoustic signal of CNPs was 1.5- to 3.0-fold higher than gold nanorods (also at 700 nm resonance) on a particle-to-particle basis. Cell toxicity assays suggested that overnight doses below 0.31 mg/mL CNPs produced no significant (p&gt;0.05) impact on cell metabolism. Intravenous doses up to 0.24 mg were tolerated well in nude mice. Subcutaneous and orthotopic tumor xenografts of the OV2008 ovarian cancer cell line were then created in nude mice. Data was collected with a Nexus128 scanner from Endra LifeSciences. Spectral data used a LAZR system from Visualsonics both at 700 nm excitation. We injected CNPs (0.024 mg, 0.048 mg, and 0.80 mg) via tail vein and showed that the tumor photoacoustic signal reached maximum increase between 10 and 20 minutes. All injected concentrations were statistically (p&lt;0.05) elevated relative to the control group with n=3 mice in each group, and dose and signal had a linear relationship at R<sup>2</sup>&gt;0.96 suggesting quantitative signal. CNP biodegradation was demonstrated ex vivo with a glucose assay. CNPs in the presence of cellulase were reduced to free glucose in under than four hours. The glucose concentration before addition of cellulase was not detectable, but increased to 92.1 &mu;g/mL in four hours. CNPs in the absence of cellulase did not produce glucose. Small fragments of nanoparticle in the treated cohort were observed with electron microscopy. There are few photoacoustic contrast agents that offer both high signal intensity and obvious clearance/biodegradation profiles. To the best of our knowledge, this is the first example of a sugar-based photoacoustic contrast agent with important implications for clinical translation of this emerging molecular imaging modality.
Algorithm for three-dimensional control of needle steering via duty-cycled rotation (2013)

Proportional control of curvature of a flexible bevel-tipped needle can be accomplished by rotating the needle shaft with a duty cycle. Using this technique, an algorithm for image-guided path-following control in two dimensions, based on an autonomous vehicle controller, has been previously demonstrated. This paper describes a computationally simple algorithm that extends the path-following control to three dimensions. Results from simulation are presented.