gebhart/patrepeval huggingface dataset:
Assembly of binding loops on aromatic templates as VCAM-1 mimetics (1999)

The design and synthesis of cyclic mimetics of VCAM-1 protein that reproduce the integrin-binding domain are presented. The unprotected peptide precursor 37-43, Thr-Gln-Ile-Asp-Ser-Pro-Leu, was grafted onto functional templates of type naphthalene, biphenyl and benzyl through the chemoselective formation of C- and N-terminal oximes resulting in a mixture of four isomeric forms due to syn-anti isomerism of the oxime bonds. Some isomers could be monitored by HPLC and identified by NMR. The molecule containing a naphthalene-derived template was found to inhibit the VCAM-1/VLA-4 interaction more efficiently than previously reported for sulfur-bridged cyclic peptides containing similar sequences. The finding confirms the importance of incorporating conformational constraints between the terminal ends of the peptide loop 37-43 in the design of synthetic inhibitors of the VCAM-1/integrin interaction.
Variation of Angle Parameters in Asians: An Anterior Segment Optical Coherence Tomography Study in a Population of Singapore Malays (2009)

In this Malay population, angle width measured by AS-OCT was smaller in women than in men, and in eyes with shorter axial length and shallower ACD.
Sedimentation and water electrolysis effects in electrofiltration of kaolin suspension (2004)

Abstract Filtration combined with an electric field (electrofiltration) enhances the filtration kinetics of aqueous suspensions. Although electrophoresis and electroosmosis largely contribute to electrofiltration behavior, side effects such as water electrolysis, heat production, and gravitational sedimentation of particles may be influential. A mathematical model was developed to include gravitational sedimentation of particles and electrolytic gas in electrofiltration theory. The model successfully represented electrofiltration data obtained from kaolin suspensions with a laboratory horizontal filter. Electrolytic gas contributed to an increase of 13% in electrofiltration rate. Settling particles increased cake resistance to downward electrofiltration flow and could substantially offset electrokinetic effects at high settling velocities. Because of electrolysis ionic products, a decrease of pH occurred in the filter during electrofiltration, causing the coagulation of kaolin particles and an increase in hydraulic cake permeability. Subsequent filtration could then take place rapidly without any electric field. The overall processing time was decreased by half when an electric field is applied only for 37% of the processing time. This coagulation phenomenon seems to be a promising means to accelerate the filtration kinetics without the need for full‐time electrofiltration. © 2004 American Institute of Chemical Engineers AIChE J, 50: 3120–3133, 2004
Simultaneous synthesis of FLAIR and segmentation of white matter hypointensities from T1 MRIs (2018)

Segmenting vascular pathologies such as white matter lesions in Brain magnetic resonance images (MRIs) require acquisition of multiple sequences such as T1-weighted (T1-w) --on which lesions appear hypointense-- and fluid attenuated inversion recovery (FLAIR) sequence --where lesions appear hyperintense--. However, most of the existing retrospective datasets do not consist of FLAIR sequences. Existing missing modality imputation methods separate the process of imputation, and the process of segmentation. In this paper, we propose a method to link both modality imputation and segmentation using convolutional neural networks. We show that by jointly optimizing the imputation network and the segmentation network, the method not only produces more realistic synthetic FLAIR images from T1-w images, but also improves the segmentation of WMH from T1-w images only.
MPEG-4 video transport over the Internet: a summary (2002)

With the success of the Internet and flexibility of MPEG-4, transporting MPEG-4 video over the Internet is expected to be an important component of many multimedia applications in the near future. Video applications typically have delay and loss requirements, which cannot be adequately supported by the current Internet. Thus, it is a challenging problem to design an efficient MPEG-4 video delivery system that can maximize the perceptual quality while achieving high resource utilization. This paper addresses this problem by presenting an end-to-end architecture for transporting MPEG-4 video over the Internet. The proposed MPEG-4 video transport architecture ties together a range of technologies from both signal processing and networking areas. The paper provides important experience and insights on how to harness the power of these technologies in designing protocols and mechanisms for MPEG-4 video transport over the Internet.
Reactivity of perfluoro-(cis-2,3-dialkyloxaziridines) with heteroaromatic nitrogen compounds (1996)

Pyridine N-oxides 3 are exclusively formed under particularly mild conditions when perfluorinated dialkyloxaziridines 1 are reacted with pyridine derivatives 2 bearing a substituent at the 2-position. Starting from pyridines substituted at the 3- and 4-positions, the previously unreported N-perfluoroacylpyridiniumaminides 4 are also produced and isolated as solid, stable compounds. Bis(pyridinium-N-aminides) 9, which have been prepared starting from bis-pyridine substrates and pyridazine and quinoxaline starting materials, also show the same reactivity. This behaviour reveals how oxaziridines 1 can work as both aminating and oxygenating agents.
High Speed Silicon Capacitor Modulators for TM Polarisation (2019)

A 500μm long capacitive silicon electro-optical MZI modulator for TM polarization light has been proposed and experimentally demonstrated with data rate 30 Gbit/s and 2 V peak-to-peak driving voltage in a push-pull configuration.
Antithrombotics in thrombosis and cancer (2005)

Many cancer patients have a hypercoagulable state, with recurrent thrombosis due to the impact of cancer cells and chemotherapy or radiotherapy on the coagulation cascade. Studies have demonstrated that unfractionated heparin (UFH) or its low molecular weight fractions interfere with various processes involved in tumour growth and metastasis. These include fibrin formation; binding of heparin to angiogenic growth factors, such as basic fibroblast growth factor (FGF2) and vascular endothelial growth factor (VEGF); modulation of tissue factor; and perhaps other more important modulatory mechanisms, such as enhanced tissue factor pathway inhibitor (TFPI) release and inhibition of various matrix-degrading enzymes. Clinical trials have suggested a clinically relevant effect of low molecular weight heparin (LMWH), as compared to UFH, on the survival of cancer patients with deep vein thrombosis. Similarly, the impact of warfarin on the survival of cancer patients with thromboembolic disorders was demonstrated. Studies from our laboratory demonstrated a significant role for LMWH, warfarin, anti-VIIa, and LMWH-releasable TFPI on the regulation of angiogenesis, tumour growth, and tumour metastasis. Thus, modulation of tissue factor/VIIa non-coagulant activities by LMWH, warfarin, anti-VIIa, or TFPI might be a useful therapeutic method for the inhibition of angiogenesis associated with human tumour growth and metastasis. Additionally, antiplatelet drugs could have an impact on tumour metastasis, and the combination of antiplatelets and anticoagulants at adjusted doses might provide greater benefits to cancer patients.
Mutational and Structural Analysis of the Tandem Zinc Finger Domain of Tristetraprolin (2013)

Tristetraprolin (TTP), the best known member of a class of tandem (R/K)YKTELCX8CX5CX3H zinc finger proteins, can destabilize target mRNAs by first binding to AU-rich elements (AREs) in their 3'-untranslated regions (UTRs) and subsequently promoting deadenylation and ultimate destruction of those mRNAs. This study sought to determine the roles of selected amino acids in the RNA binding domain, known as the tandem zinc finger (TZF) domain, in the ability of the full-length protein to bind to AREs within the tumor necrosis factor α (TNF) mRNA 3'-UTR. Within the CX8C region of the TZF domain, mutation of some of the residues specific to TTP, not found in other members of the TTP protein family, resulted in decreased binding to RNA as well as inhibited mRNA deadenylation and decay. Evaluation of simulation solution models revealed a distinct structure in the second zinc finger of TTP that was induced by the presence of these TTP-specific residues. In addition, mutations within the lead-in sequences preceding the first C of highly conserved residues within the CX5C or CX3H regions or within the linker region between the two fingers also perturbed both RNA binding and the simulation model of the TZF domain in complex with RNA. We conclude that, although the majority of conserved residues within the TZF domain of TTP are required for productive binding, not all residues at sequence-equivalent positions in the two zinc fingers of the TZF domain of TTP are functionally equivalent.
The Effects of Intake Charge Preheating in a Gasoline-Fueled HCCI Engine (2005)

&lt;div class="htmlview paragraph"&gt;Experiments were performed on a homogeneously fueled compression ignition gasoline-type engine with a high degree of intake charge preheating. It was observed that fuels that contained lower end and/or non-branched hydrocarbons (gasoline and an 87 octane primary reference fuel (PRF) blend) exhibited sensitivity to thermal conditions in the surge tanks upstream of the intake valves. The window of intake charge temperatures, measured near the intake valve, that provided acceptable combustion was shifted to lower values when the upstream surge tank gas temperatures were elevated. The same behavior, however, was not observed while using isooctane as a fuel. Gas chromatograph mass spectrometer analysis of the intake charge revealed that oxygenated species were present with PRF 87, and the abundance of the oxygenated species appeared to increase with increasing surge tank gas temperatures. No significant oxygenated species were detected when running with isooctane. The presence of the oxygenated species for PRF 87 fueling indicated that reactions were occurring in the intake surge tanks which resulted in needing lower intake charge temperatures to achieve autoignition.&lt;/div&gt;
Imaging birefringent crystals using micro optical coherence tomography (Conference Presentation) (2017)

Background: Uric acid crystals have recently been identified as a possible therapeutic target for coronary artery disease. Being subcellular in size, it is difficult to identify these crystals in situ. Micro optical coherence tomography (Micro-OCT) allows one to image subcellular structures with 1–micron resolution. Even though Micro-OCT should be capable of resolving urate crystals, it’s difficult to differentiate these structures from other scattering particles within tissue. In this work we developed a novel polarization sensitive micro OCT (ps-Micro-OCT) system for identification of uric acid crystals. Methods: A spectrometer based ps-Micro-OCT system was developed using a broadband light source. The broadband input light was divided into reference and sample signals using a beam splitter. The reference signal was further divided into two polarized signals with different polarization states. Reflected reference and sample signals were combined and sent to a spectrometer that recorded the interference signal. Results: To test the performance of system, a mirror was used as sample and a quarter wave-plate was placed in the sample path. The measured quarter wave-plate angle values matched closely to actual angle values. Next we prepared uric acid crystals in our lab and imaged them using this system.We were able to image and identify these crystals based on polarization measurements. Conclusion: In this work we imaged and identified uric acid crystals using a newly developed ps-Micro-OCT system. The proposed technique will enable imaging uric acid crystals in coronary artery.
Organosilica Cages Target Hepatic Sinusoidal Endothelial Cells Avoiding Macrophage Filtering (2021)

Over the last years, advancements in the use of nanoparticles for biomedical applications have clearly showcased their potential for the preparation of improved imaging and drug-delivery systems. However, compared to the vast number of currently studied nanoparticles for such applications, only a few successfully translate into clinical practice. A common "barrier" that prevents nanoparticles from efficiently delivering their payload to the target site after administration is related to liver filtering, mainly due to nanoparticle uptake by macrophages. This work reports the physicochemical and biological investigation of disulfide-bridged organosilica nanoparticles with cage-like morphology, OSCs, assessing in detail their bioaccumulation <i>in vivo</i>. The fate of intravenously injected 20 nm OSCs was investigated in both healthy and tumor-bearing mice. Interestingly, OSCs exclusively colocalize with hepatic sinusoidal endothelial cells (LSECs) while avoiding Kupffer-cell uptake (less than 6%) under both physiological and pathological conditions. Our findings suggest that organosilica nanocages hold the potential to be used as nanotools for LSECs modulation, potentially impacting key biological processes such as tumor cell extravasation and hepatic immunity to invading metastatic cells or a tolerogenic state in intrahepatic immune cells in autoimmune diseases.
Realizing A Composable Enterprise Microservices Fabric with AI-Accelerated Material Discovery API Services (2020)

The complexity of building, deploying, and managing cross-organizational enterprise computing services with self-service, security, and quality assurances has been increasing exponentially in the era of hybrid multiclouds. AI-accelerated material discovery capabilities, for example, are desirable for enterprise application users to consume through business API services with assurance of satisfactory nonfunctional properties, e.g., enterprise-compliant self-service management of sharable sensitive data and machine learning capabilities at Internet scale. This paper presents a composable microservices based approach to creating and continuously improving enterprise computing services. Moreover, it elaborates on several key architecture design decisions for Navarch, a composable enterprise microservices fabric that facilitates consuming, managing, and composing enterprise API services. Under service management model of individual administration, every Navarch microservice is a managed composable API service that can be provided by an internal organization, an enterprise partner, or a public service provider. This paper also illustrates a Navarch-enabled systematic and efficient approach to transforming an AI-accelerated material discovery tool into secure, scalable, and composable enterprise microservices. Performance of the microservices can be continuously improved by exploiting advanced heterogeneous microservice hosting infrastructures. Factual comparative performance analyses are provided before the paper concludes with future work.
Bevacizumab-Associated Pancreatitis: Cases Reported to the Adverse Event Reporting System of the Food and Drug Administration (2014)

Introduction: Bevacizumab binds to and inhibits vascular endothelial growth factor (VEG-F). In theory, blocking of VEG-F could enhance the severity of acute pancreatitis. We searched the FDA Adverse Event Reporting System (FAERS) database for cases of pancreatitis potentially related to bevacizumab use. Methods: Using the FAERS database, 3,171,655 individual adverse event reports between January 2003 and June 2012 were downloaded and analyzed using SPSS 20 (IBM Co, Armonk, NY, USA). A search was undertaken for reactions of “pancreatitis” with bevacizumab, regardless of indication. All reports were then limited to “primary suspect” cases for bevacizumab, meaning the reporter believed that bevacizumab was the main cause of drug-induced pancreatitis. The identified cases were organized with respect to indication for bevacizumab use, age, gender, and type of pancreatitis. In addition, a PubMed search was conducted using the MESH terms “pancreatitis” and “bevacizumab”, separated by the Boolean operator “AND”. Results: Total of 116 cases of pancreatitis were identified in FAERS, including 22 cases of acute pancreatitis, 1 case of hemorrhagic pancreatitis, and 2 cases of necrotizing pancreatitis. The average age of patients reported was 54.6 years, with females accounting for 55%. The most common indication for bevacizumab use in this patient group was colorectal cancer (44 cases). Deaths were reported in 11 cases (9.5%). No previously described cases of bevacizumab-associated pancreatitis were found in the medical literature. Conclusion: A small number of cases describing the association of bevacizumab with pancreatitis have been reported to FAERS. Despite the use of bevacizumab in patients with underlying cancer, mortality from pancreatitis in this setting appears to be uncommon.Table 1
Reflections on Cyanobacterial Chromatic Acclimation: Exploring the Molecular Bases of Organismal Acclimation and Motivation for Rethinking the Promotion of Equity in STEM (2022)

Cyanobacteria are photosynthetic organisms that exhibit characteristic acclimation and developmental responses to dynamic changes in the external light environment. Photomorphogenesis is the tuning of cellular physiology, development, morphology, and metabolism in response to external light cues. The tuning of photosynthetic pigmentation, carbon fixation capacity, and cellular and filament morphologies to changes in the prevalent wavelengths and abundance of light have been investigated to understand the regulation and fitness implications of different aspects of cyanobacterial photomorphogenesis. Chromatic acclimation (CA) is the most common form of photomorphogenesis that has been explored in cyanobacteria. Multiple types of CA in cyanobacteria have been reported, and insights gained into the regulatory pathways and networks controlling some of these CA types. I examine the recent expansion of CA types that occur in nature and provide an overview of known regulatory factors involved in distinct aspects of cyanobacterial photomorphogenesis. Additionally, I explore lessons for cultivating success in scientific communities that can be drawn from a reflection on existing knowledge of and approaches to studying CA.
Second and Third Harmonic Generation at ε-Near-Zero Crossing Point in Arrays of Plasmonic Nanoshells (2012)

We theoretically investigate harmonic generation at ε=0 crossing points where losses are compensated through the inclusion of active photonic materials in metallic nanoshells. This singularity-driven process lowers the thresholds for a plethora of nonlinear optical phenomena.
Macroautophagy and ERK phosphorylation counteract the anti-proliferative effect of proteasome inhibitor in gastric cancer cells (2010)

The ubiquitin-proteasome system and macroautophagy are two complementary pathways for protein degradation. Emerging evidence suggests that proteasome inhibition might be a promising approach for the treatment of cancer. In this study, we show that proteasome inhibitor MG-132 suppressed gastric cancer cell proliferation and induced macroautophagy. The induction of macroautophagy was evidenced by the formation of LC3(+) autophagosomes and the accumulation of acidic vesicular organelles and autolysosomes and was accompanied by the suppression of mammalian target of rapamycin complex 1 activity. Abolition of macroautophagy by knockdown of Class III phosphatidylinositol-3 kinase Vps34 or ATG5/7 sensitized gastric cancer cells to the antiproliferative effect of MG-132 by promoting G(2)/M cell cycle arrest. In addition, MG-132 increased ERK phosphorylation whose inhibition by MEK inhibitor significantly enhanced the antiproliferative effect of proteasome inhibition. To conclude, this study demonstrates that macroautophagy and ERK phosphorylation serve as protective mechanisms to counteract the antiproliferative effect of proteasome inhibition. This discovery may have implications for the application of proteasome-directed therapy for the treatment of cancer.
Insight into metal-enhanced oxidation using barium on 4H-SiC surfaces (2016)

Abstract Metal-enhanced oxidation (MEO) using ultrathin Ba layers on 4H-SiC surfaces was investigated by physical and electrical characterizations. We found that while comparable oxidation rates were enhanced for Si- and C-face surfaces even at a low temperature, significant surface and interface roughness were induced by initial MEO termed the incubation period. Depth profiling revealed that although most Ba atoms aggregated on the oxide surface, a tiny amount (∼10 14 cm −2 ) remaining at the oxide interface was responsible for the following stable MEO reaction and the reduced interface state density with the drawbacks of degraded leakage current and breakdown characteristics of SiC-MOS devices.
Design and Parametric Study of Microfluidic Cooling Manifold for 2.5D-SICs with Dielectric Coolant (2018)

2.5 dimensional stacked integrated circuits (2.5D-SICs) with through-silicon vias (TSVs), as next generation silicon technologies, are promising to go beyond Moore's law for compact, high-performance, energy-efficient microsystems. 2.5D-SICs with closely placed heterogeneous dies are considered a first step towards full 3D integration. In this paper, a novel micro-channel dielectric coolant manifold for 2.5D-SICs with multiple high-power dies, has been investigated. Five active dies are modeled with power maps of one 50 W, 25 mm×25 mm field programmable gate array (FPGA), and four high heat flux transceivers (30 W/each, 6 mm×6 mm/each). In order to provide thermal management to this heterogeneous chip system, micro-fin-bridges and micropins have been implemented in the manifold. In addition, all dies have been immersed in the micro-channel with dielectric coolant to isolate the thermal interaction between dies. Effects of chips' placement, dimensions of micro-fin-bridges and micro-pins, and dielectric coolant supply and removal locations within the manifold on pressure drop and heat transfer have been parametrically studied by full-scale computational fluid mechanics/heat transfer simulations.
Biological properties of a specific Gαq/11 inhibitor, YM‐254890, on platelet functions and thrombus formation under high‐shear stress (2006)

1 The effects of YM-254890, a specific Galpha(q/11) inhibitor, on platelet functions, thrombus formation under high-shear rate condition and femoral artery thrombosis in cynomolgus monkeys were investigated. 2 YM-254890 concentration dependently inhibited ADP-induced intracellular Ca(2+) elevation, with an IC(50) value of 0.92+/-0.28 microM. 3 P-selectin expression induced by ADP or thrombin receptor agonist peptide (TRAP) was strongly inhibited by YM-254890, with IC(50) values of 0.51+/-0.02 and 0.16+/-0.08 microM, respectively. 4 YM-254890 had no effect on the binding of fibrinogen to purified GPIIb/IIIa, but strongly inhibited binding to TRAP-stimulated washed platelets. 5 YM-254890 completely inhibited platelet shape change induced by ADP, but not that induced by collagen, TRAP, arachidonic acid, U46619 or A23187. 6 YM-254890 attenuated ADP-, collagen-, TRAP-, arachidonic acid- and U46619-induced platelet aggregation with IC(50) values of <1 microM, whereas it had no effect on phorbol 12-myristate 13-acetate-, ristocetin-, thapsigargin- or A23187-induced platelet aggregation. 7 High-shear stress-induced platelet aggregation and platelet-rich thrombus formation on a collagen surface under high-shear flow conditions were concentration dependently inhibited by YM-254890. 8 The antithrombotic effect of YM-254890 was evaluated in a model of cyclic flow reductions in the femoral artery of cynomolgus monkeys. The intravenous bolus injection of YM-254890 dose dependently inhibited recurrent thrombosis without affecting systemic blood pressure or prolonging template bleeding time. 9 YM-254890 is a useful tool for investigating Galpha(q/11)-coupled receptor signaling and the physiological roles of Galpha(q/11).