gebhart/patrepeval huggingface dataset:
Identification of Plasmin-interactive Sites in the Light Chain of Factor VIII Responsible for Proteolytic Cleavage at Lys36 (2009)

We have recently reported that plasmin likely associates with the factor VIII light chain to proteolyze at Lys36 within the A1 domain. In this study, we determined that the rate of plasmin-catalyzed inactivation on the forms of factor VIIIa containing A1-(1-336) and 1722A3C1C2, reflecting Lys36 cleavage, was reduced by approximately 60%, compared with those containing 1649A3C1C2 and 1690A3C1C2. SDS-PAGE analysis revealed that Lys36 cleavage of factor VIIIa with 1722A3C1C2 was markedly slower than those with 1649A3C1C2 and 1690A3C1C2. Surface plasmon resonance-based assays, using active site-modified anhydro-plasmin (Ah-plasmin) showed that 1722A3C1C2 bound to Ah-plasmin with an approximately 3-fold lower affinity than 1649A3C1C2 or 1690A3C1C2 (Kd, 176, 68.2, and 60.3 nM, respectively). Recombinant A3 bound to Ah-plasmin (Kd, 44.2 nM), whereas C2 failed to bind, confirming the presence of a plasmin-binding site within N terminus of A3. Furthermore, the Glu-Gly-Arg active site-modified factor IXa also blocked 1722A3C1C2 binding to Ah-plasmin by approximately 95%, supporting the presence of another plasmin-binding site overlapping the factor IXa-binding site in A3. In keeping with a major contribution of the lysine-binding sites in plasmin for interaction with the factor VIII light chain, analysis of the A3 sequence revealed two regions involving clustered lysine residues in 1690-1705 and 1804-1818. Two peptides based on these regions blocked 1649A3C1C2 binding to Ah-plasmin by approximately 60% and plasmin-catalyzed Lys36 cleavage of factor VIIIa with A1-(1-336) by approximately 80%. Our findings indicate that an extended surface, centered on residues 1690-1705 and 1804-1818 within the A3 domain, contributes to a unique plasmin-interactive site that promotes plasmin docking during cofactor inactivation by cleavage at Lys36.
Waveguide Devices for Terahertz Signal Processing (2016)

We introduce two waveguide based devices for signal processing in future terahertz wireless communications systems: a leaky-wave antenna for frequency multiplexing and a T-junction waveguide for broadband power splitting.
Effect of Cyclic Changes in Temperature and Pressure on Permeation Properties of Composite Polyamide Seawater Reverse Osmosis Membranes (2010)

The effects of cyclic changes in feed water temperature and pressure on permeate flux, solute rejection, and compaction in spiral wound composite polyamide seawater reverse osmosis membranes were examined with pure water and 4% NaCl solutions. A membrane permeability hysteresis or memory effect due to the up and down temperature and pressure sequences was only seen with the saline water studies. However, the observed changes appeared to be reversible and were consistent with the Spiegler-Kedem/ Film Theory and the Kimura-Sourirajan Analysis/ Film Theory models. The overall results suggest that the net effect on permeance and solute rejection is the consequence of several interactions with feed/operating temperatures affecting membrane porosity and water/solute cluster size, and transmembrane pressure influencing membrane compaction.
A Novel Real-Time Deep Learning Approach for Indoor Localization Based on RF Environment Identification (2020)

Internet-of-Things (IoT) applications often require the use of sensor-based indoor tracking and positioning, for which the performance is significantly enhanced by identifying the type of the surrounding indoor environment. This letter develops a highly accurate and computationally efficient method for indoor localization based on a novel two-stage deep learning approach. In the first stage, a convolutional neural network (CNN) is designed to perform indoor environment identification by extracting the inherent features based on a real dataset obtained from radio-frequency (RF) measurements. Then, in the second stage, another CNN is designed to perform indoor localization taking into account knowledge of the environment type as obtained from the first stage. Numerical investigations demonstrate that the proposed two-stage CNN deep learning approach outperforms benchmark methods, with significant enhancements in localization accuracy and computational efficiency. The findings of this letter make the proposed CNN approach a key element for facilitating real-time deployment of efficient low-power IoT sensor networks.
2-Amino-N-pyrimidin-4-ylacetamides as A2AReceptor Antagonists: 1. Structure−Activity Relationships and Optimization of Heterocyclic Substituents (2008)

Previously we have described a novel series of potent and selective A 2A receptor antagonists (e.g., 1) with excellent aqueous solubility. While these compounds are efficacious A 2A antagonists in vivo, the presence of an unsubstituted furyl moiety was a cause of some concern. In order to avoid the potential metabolic liabilities that could arise from an unsubstituted furyl moiety, an optimization effort was undertaken with the aim of replacing the unsubstituted furan with a more metabolically stable group while maintaining potency and selectivity. Herein, we describe the synthesis and SAR of a range of novel heterocyclic systems and the successful identification of a replacement for the unsubstituted furan moiety with a methylfuran or thiazole moiety while maintaining potency and selectivity.
Using phase space diagrams to interpret multiple frequency drive sonoluminescence (2000)

The recent experimental results of J. Holzfuss, M. Ruggeberg, and R. Mettin [Phys. Rev. Lett. 81, 1961 (1998)] in which a second harmonic drive system was used to generate sonoluminescence (SL) have been analyzed in the context of the dissociation hypothesis (DH) of D. Lohse and S. Hilgenfeldt [J. Chem. Phys. 107, 6986 (1997)]. The second harmonic introduces two more variables that are under experimental control: a phase and an additional pressure term to the acoustic drive pressure. Diffusive equilibrium curves for a fixed gas concentration were calculated as was the Mach criterion. A phase space diagram was constructed to permit the prediction of regions of stable SL, unstable SL, stable non-SL, and unstable non-SL. These were compared to Holzfuss' experimental observations, and excellent quantitative agreement was seen. The results provide further evidence that the underlying assumptions of DH are sound. They also indicate the utility of DH for determining appropriate experimental conditions to achieve SL and for optimizing an experimental system.
<title>Parametric study for increasing on-station duration via unconventional aircraft launch approach</title> (2004)

The need for better atmospheric predictions is causing the atmospheric science community to look for new ways to obtain longer, higher-resolution measurements over several diurnal cycles. The high resolution, <i>in-situ</i> measurements required to study many atmospheric phenomena can be achieved by an Autonomous Aerial Observation System (AAOS); however, meeting the long on-station time requirements with an aerial platform poses many challenges. Inspired by the half-scale drop test of the deployable Aerial Regional-scale Environmental Survey (ARES) Mars airplane, a study was conducted at the NASA Langley Research Center to examine the possibility of increasing on-station time by launching an airplane directly at the desired altitude. The ARES Mars airplane concept was used as a baseline for Earth atmospheric flight, and parametric analyses of fundamental configuration elements were performed to study their impact on achieving desired on-station time with this class of airplane. The concept involved lifting the aircraft from the ground to the target altitude by means of an air balloon, thereby unburdening the airplane of ascent requirements. The parameters varied in the study were aircraft wingspan, payload, fuel quantity, and propulsion system. The results show promising trends for further research into aircraft-payload design using this unconventional balloon-based launch approach.
ConditionalQA: A Complex Reading Comprehension Dataset with Conditional Answers (2022)

We describe a Question Answering (QA) dataset that contains complex questions with conditional answers, i.e. the answers are only applicable when certain conditions apply. Answering the questions requires compositional logical reasoning across complex context. We call this dataset ConditionalQA. In addition to conditional answers, the dataset also features:
Mechanisms of Icosahedral Virus Assembly (2010)

In the simplest icosahedral virus assembly systems, morphogenesis is a function of a single viral coat protein. The simplicity of these systems may be a direct consequence of the evolutionary niche that these viruses occupy. Many of these systems are small plant and enveloped animal viruses, systems...
Circulating endothelial cells in preclinical models of cancer (2006)

A49 Circulating endothelial cells (CEC) are detected at elevated concentrations in cancer patients. Endothelial cells contribute to tumor angiogenesis by incorporation into newly forming blood vessels to support tumor growth and metastasis. A set of flow cytometry reagents for murine models has been established. The enumerated mouse CEC, demonstrate the following phenotype CD31 + /CD34 + /CD45 - and nucleated. A positive relationship between CEC concentration and tumor volume was determined for 11/12 murine models including the PC3 xenograft model of prostate cancer and the HT1080 sarcoma xenograft model. CEC concentrations have been characterized in normal, tumor bearing and tumor-bearing compound-treated mice using HT1080 (human fibrosarcoma), B16 (murine melanoma) and bEND.3 (murine hemangioma) tumor models and indicate that an elevated number of CEC are detected in tumor-bearing mice when compared to normal mice.We are conducting systematic CEC analysis in preclinical models of cancer to study changes in this biomarker in relationship to tumor type, tumor burden, compound dose, dose regimen, and class of compound. Preliminary data from tumor growth inhibition studies using angiogenisis inhibitors, including TSP mimetic peptides and tyrosine kinase inhibitors, demonstrate a decrease in the number of CEC detected at the treatment endpoints in drug-treated animals vs. vehicle-treated controls. Time-course analyses of these changes in CEC concentration have been performed in several models including HT-1080 and B16. Further, having shown that CEC number is elevated in tumor bearing mice and reduced in tumor bearing mice treated with anti-angiogenic agents, experiments to explore the characteristics of the CEC, specifically, the activation status demonstrated by co-expression of CD105 in the CEC and the apoptotic status of the cells by measuring the annexin V positivity has been explored. Using the HT1080 model, correlations between CEC concentration, activation status and apoptotic state with tumor volume has been observed. CEC will be monitored in patients undergoing clinical trials with our angiogenesis inhibitors.
Proceedings of the 2nd international conference on Virtual execution environments (2006)

It is our great pleasure to welcome you to the Second International Conference on Virtual Execution Environments -- VEE'06. Interest in virtual execution environments spans the programming language, operating system, and computer architecture communities. The goal of the VEE conference is to provide a single venue to bring together researchers and practitioners from all three of these communities to share their perspectives with others interested in the various aspects of virtual execution environments. This year's VEE is co-located with PLDI 2006 in Ottawa, Ontario and, for the first time, is equally co-sponsored by ACM SIGOPS and ACM SIGPLAN. VEE'07 will be held as part of FCRC in June 2007 and we hope VEE'08 will be co-located with a leading operating systems conference.The call for papers attracted 44 submissions, which was a significant decline from the 65 papers submitted to VEE'05. However, the average quality of the submissions was quite high. We believe that the decision to move the submission deadline significantly earlier (and before the PLDI notification date) was the primary cause of the decline in the number of submissions. The steering committee is reconsidering this decision for future conferences.Every submitted paper was reviewed by three program committee members. Program committee members had the option of asking for input from additional external reviewers when preparing their reviews; 20% of the PC reviews were prepared with the help of external reviewers. The program committee met at IBM Research in Hawthorne, NY on February 14, 2006 -- two days after the largest snowfall in the history of New York City. As a result, only half of the committee was able to successfully travel to New York and attend the meeting in person. However, all of the committee members who were not physically present participated in the meeting via an all day teleconference. The committee accepted 17 excellent papers that cover a wide spectrum of topics related to virtual execution environments. In addition to the technical papers, the program includes keynote talks by James Larus and Leendert van Doorn.
Comparison of Engraftment Syndrome with G-CSF Versus GM-CSF after Autologous Hematopoietic Progenitor Cell Transplantation for Multiple Myeloma (2015)

Engraftment syndrome (ES) is a complication of autologous hematopoietic progenitor cell transplantation (AHPCT) characterized by fever, rash, pulmonary, liver, and/or renal dysfunction. GM-CSF has been previously shown to be associated with a higher risk of ES as compared to G-CSF after AHPCT in heterogeneous patient cohort. We compared the risk of ES with GM-CSF vs. G-CSF after AHPCT exclusively in multiple myeloma (MM) patients who received the same conditioning regimen.
Broadband Light Harvesting and Fast Charge Separation in Ordered Self-Assemblies of Electron Donor–Acceptor-Functionalized Graphene Oxide Layers for Effective Solar Energy Conversion (2015)

Three-dimensionally (3D) ordered assemblies of GO layers functionalized with tetrakis(1-methylpyridinium-4-yl)porphyrin p-toluenesulfonate (Por), N,N′-di(2-(trimethylammonium iodide)ethylene) perylenediimide (PDI), and Zn(II) phthalocyanine tetrasulfonic acid (ZnPc) were obtained in water. Proper molar ratio is essential between the cationic dyes, Por and PDI, acting as the “glue” molecules to combine the GO layers and the anionic ZnPc, acting as dispersant of GO layers to (i) construct the 3D assemblies and (ii) the proportional absorption distribution of dye-functionalized GO assemblies. Resulting 3D structures effectively harvest the light from ultraviolet to near-infrared (NIR) regions. Dye molecules are arranged in mainly lateral order on the GO layers with partial stacking, which allows direct interactions with the π-conjugations of the GO surface in 3D architecture. Ultrafast charge separation upon the photoexcitation of the dyes at various wavelengths in the visible/NIR region was observed in these assemblies, in which ZnPc and PDI were the ultimate electron donor and acceptor, respectively. Lateral charge migration among the partially stacked dye molecules was inferred from the decay characteristics of the radical ion pair. Triggered by the charge separation processes in the 3D ordered self-assemblies, significantly higher photocurrent density in the OTE/SnO2 electrode deposited with self-assemblies of (GO–Por–PDI–ZnPc)n was generated compared to those deposited with only GO or dye components.
A Cu3BHT-Graphene van der Waals Heterostructure with Strong Interlayer Coupling (2023)

Two dimensional van der Waals heterostructures (2D are of significant interest due to their intriguing physical properties that are critically defined by the constituent monolayers and their interlayer coupling . However, typical inorganic 2 D vdWhs fall into the weakly coupled region, limiting efficient interfacial charge flow crucial for developing high performance quantum opto electronics. Here, we demonstrate strong interlayer coupling in Cu3 BHT (BHT = benzenehexathiol) graphene vdWhs an organic inorganic bilayer characterized by prominent interlayer charge transfer Monolayer Cu3 BHT with a Kagome lattice is synthesized on the water surface and then coupled with graphene to produce a cm2 scale 2D vdWh. Spectroscopic and electrical studies, along with theoretical calculation s show significant hole transfer from monolayer Cu3 BHT to graphene upon contact , being characteristic fingerprints for strong interlayer coupling This study unveils the great potential of integrating highly pi-conjugated 2D coordination polymers (2DCPs) into 2D vdWhs to explor e intriguing physical phenomena.
Use of Polyethylene Glycol-based Colonoscopy Preparations Before Rectal Argon Plasma Coagulation (2012)

Deepak, Parakkal MD*; Devi, Radha MD†; Sifuentes, Humberto MD‡; Ehrenpreis, Eli Daniel MD§,∥,¶ Author Information
Regionalized Loss of Parvalbumin Interneurons in the Cerebral Cortex of Mice with Deficits in GFRα1 Signaling (2009)

Inhibitory interneurons are crucially important for cerebral cortex function and behavior. The mechanisms controlling inhibitory interneuron diversification and allocation to distinct cortical areas remain poorly understood. GDNF (glial cell line-derived neurotrophic factor) and its receptor GFRalpha1 have been implicated in the development of GABAergic precursors but, because of the early lethality of null mutants, their roles in postnatal maturation and function of cortical interneurons are unknown. "cis-only" mutant mice lack GFRalpha1 only in cells that do not express the RET signaling receptor subunit and survive to adulthood. At birth, both null mutants and cis-only mice showed a specific loss of GABAergic interneurons in rostro- and caudolateral cortical regions but not in more medial areas. Unexpectedly, the adult cortex of cis-only mice displayed a complete loss of parvalbumin (PV)-expressing GABAergic interneurons in discrete regions (PV holes) interspersed among areas of normal PV cell density. PV holes predominantly occurred in the visual and frontal cortices, and their size could be affected by neuronal activity. Consistent with deficits in cortical inhibitory activity, these mice showed enhanced cortical excitability, increased sensitivity to epileptic seizure, and increased social behavior. We propose that GFRalpha1 signaling guides the development of a subset of PV-expressing GABAergic interneurons populating discrete regions of the cerebral cortex and may thus contribute to the diversification and allocation of specific cortical interneuron subtypes.
FemtoCaching: Wireless Video Content Delivery through Distributed\n Caching Helpers (2011)

Video on-demand streaming from Internet-based servers is becoming one of the\nmost important services offered by wireless networks today. In order to improve\nthe area spectral efficiency of video transmission in cellular systems, small\ncells heterogeneous architectures (e.g., femtocells, WiFi off-loading) are\nbeing proposed, such that video traffic to nomadic users can be handled by\nshort-range links to the nearest small cell access points (referred to as\n"helpers"). As the helper deployment density increases, the backhaul capacity\nbecomes the system bottleneck. In order to alleviate such bottleneck we propose\na system where helpers with low-rate backhaul but high storage capacity cache\npopular video files. Files not available from helpers are transmitted by the\ncellular base station. We analyze the optimum way of assigning files to the\nhelpers, in order to minimize the expected downloading time for files. We\ndistinguish between the uncoded case (where only complete files are stored) and\nthe coded case, where segments of Fountain-encoded versions of the video files\nare stored at helpers. We show that the uncoded optimum file assignment is\nNP-hard, and develop a greedy strategy that is provably within a factor 2 of\nthe optimum. Further, for a special case we provide an efficient algorithm\nachieving a provably better approximation ratio of $1-(1-1/d)^d$, where $d$ is\nthe maximum number of helpers a user can be connected to. We also show that the\ncoded optimum cache assignment problem is convex that can be further reduced to\na linear program. We present numerical results comparing the proposed schemes.\n
Beta-caryophyllene enhances wound healing through multiple routes (2019)

Beta-caryophyllene is an odoriferous bicyclic sesquiterpene found in various herbs and spices. Recently, it was found that beta-caryophyllene is a ligand of the cannabinoid receptor 2 (CB2). Activation of CB2 will decrease pain, a major signal for inflammatory responses. We hypothesized that beta-caryophyllene can affect wound healing by decreasing inflammation. Here we show that cutaneous wounds of mice treated with beta-caryophyllene had enhanced re-epithelialization. The treated tissue showed increased cell proliferation and cells treated with beta-caryophyllene showed enhanced cell migration, suggesting that the higher re-epithelialization is due to enhanced cell proliferation and cell migration. The treated tissues also had up-regulated gene expression for hair follicle bulge stem cells. Olfactory receptors were not involved in the enhanced wound healing. Transient Receptor Potential channel genes were up-regulated in the injured skin exposed to beta-caryophyllene. Interestingly, there were sex differences in the impact of beta- caryophyllene as only the injured skin of female mice had enhanced re-epithelialization after exposure to beta-caryophyllene. Our study suggests that chemical compounds included in essential oils have the capability to improve wound healing, an effect generated by synergetic impacts of multiple pathways.