gebhart/patrepeval huggingface dataset:
Small Molecules with Either Receptor-Selective or Pan-Receptor Activity in the Three LuxR-Type Receptors that Regulate Quorum Sensing in <i>Pseudomonas aeruginosa</i> (2022)

Quorum sensing (QS) allows bacteria to assess their local cell density using chemical signals and plays a prominent role in the ability of common pathogens to infect a host. Non-native molecules capable of attenuating bacterial QS represent useful tools to explore the role of this pathway in virulence. As individual bacterial species can have multiple QS systems and/or reside in mixed communities with other bacteria capable of QS, chemical tools that are either selective for one QS system or "pan-active" and target all QS pathways are of significant interest. Herein we outline the analysis of a set of compounds reported to target one QS system in <i>Pseudomonas aeruginosa</i> for their activity in two other QS circuits in this pathogen and the discovery of molecules with novel activity profiles, including subsets that agonize all three QS systems, agonize one but antagonize the other two, or strongly antagonize just one.
Moiré-free color halftoning using hexagonal geometry and spot functions (2012)

Hexagons are widely observed as a packing or tiling geometry in nature, yet they appear to have been avoided in conventional halftone tiling. A goal of the present study is to understand the potential barriers that have prevented their use and present new halftone geometry options that overcome the issues while offering several potential benefits. While conventional halftone geometries often include the fourth screen (e.g., yellow) in a suboptimal manner, the hexagonal geometry presented here can include a clustered-dot fourth screen moiré-free. Hexagonal screens can appear to have smoother texture. Due to differences in packing geometry and touch point geometry, hexagons have the potential to possess different tone reproduction characteristics, which may be favorable for some marking processes. We also present a parametrically controlled hexagonal halftone spot function that allows for optimization of dot touch points and provides compact growth. The controllable touch points can prevent a tone reproduction discontinuity, while the compact growth throughout the gray range ensures maximum stability. Additionally, we present a three-colorant dot-off-dot halftone configuration using hexagonal geometry. Examples are provided.
Structure of the Gene for Human Plasminogen Activator Inhibitor-2 (1989)

Plasminogen activator inhibitor-2 (PAI-2) can regulate the formation of plasmin by inhibiting urokinase and tissue plasminogen activator. PAI-2 is induced in monocytes and endothelium by inflammatory mediators, and it is made in the placenta during pregnancy. PAI-2 is a member of the serine protease inhibitor gene family, and it is particularly similar to chicken ovalbumin. Like ovalbumin, PAI-2 is secreted without cleavage of a signal peptide. To determine the structure of the PAI-2 gene, two bacteriophage lambda human genomic DNA libraries were screened with PAI-2 cDNA probes. Characterization of three positive clones shows that the human PAI-2 gene spans 16.5 kilobases and has eight exons. The 5'-untranslated sequence of the PAI-2 mRNA is 77 base pairs in length as suggested by primer extension and S1 nuclease mapping. The eukaryotic consensus sequence TATAAAA is found 22 base pairs 5' of the proposed cap site. The PAI-2 gene is on chromosome 18q21-23 as determined by hybridization to flow-sorted chromosomes and by in situ hybridization. There appear to be two common PAI-2 alleles that differ by six nucleotides in exons 1, 4, and 8. The structure of the PAI-2 gene is quite different from that of PAI-1 although these two inhibitors have common target protease specificity. In contrast, the structure of the PAI-2 gene is very similar to that of the chicken ovalbumin gene. When protein sequences are aligned to obtain maximal identity, six of the seven intron positions in the PAI-2 gene are identical to those in the chicken ovalbumin gene. We conclude that PAI-2 is the closest mammalian homologue of avian ovalbumin.
A Hierarchical Thread Scheduler and Register File for Energy-Efficient Throughput Processors (2012)

Modern graphics processing units (GPUs) employ a large number of hardware threads to hide both function unit and memory access latency. Extreme multithreading requires a complex thread scheduler as well as a large register file, which is expensive to access both in terms of energy and latency. We present two complementary techniques for reducing energy on massively-threaded processors such as GPUs. First, we investigate a two-level thread scheduler that maintains a small set of active threads to hide ALU and local memory access latency and a larger set of pending threads to hide main memory latency. Reducing the number of threads that the scheduler must consider each cycle improves the scheduler’s energy efficiency. Second, we propose replacing the monolithic register file found on modern designs with a hierarchical register file. We explore various trade-offs for the hierarchy including the number of levels in the hierarchy and the number of entries at each level. We consider both a hardware-managed caching scheme and a software-managed scheme, where the compiler is responsible for orchestrating all data movement within the register file hierarchy. Combined with a hierarchical register file, our two-level thread scheduler provides a further reduction in energy by only allocating entries in the upper levels of the register file hierarchy for active threads. Averaging across a variety of real world graphics and compute workloads, the active thread count can be reduced by a factor of 4 with minimal impact on performance and our most efficient three-level software-managed register file hierarchy reduces register file energy by 54%.
GaAsP Top Solar Cells for Increased Solar Conversion Efficiency (1989)

Abstract : The development of multijunction solar cells is the key to achieving large increases in solar power conversion efficiency over current state-of-the- art technology. In the optimal multijunction design, the top solar cell is the most critical since, by itself, it generates two-thirds of the total power generated by the solar cell stack. There are two viable technical approaches for the top solar cell for the mechanically-stacked tandem solar cell: GaAsP/GaP and AlGaAs/AlGaAs. Both top solar cell approaches have demonstrated good device properties. No other approach has made acceptable devices. Gallium arsenide phosphide, Multijunction solar cells, Solar energy conversion, Tandem solar cells, Photovoltaic devices, Space power.
Timing of Treatment with the Flavonoid 7,8-DHF Critically Impacts on Its Effects on Learning and Memory in the Ts65Dn Mouse (2019)

No therapies currently exist for intellectual disability in Down syndrome (DS). In view of its similarities with DS, including learning and memory (L&M) defects, the Ts65Dn mouse model of DS is widely used for the design of therapy. 7,8-dihydroxyflavone (7,8-DHF), a flavonoid that targets the tropomyosin-related kinase B (TrkB) receptor of brain-derived neurotrophic factor (BDNF), exerts positive effects in various brain disease models. Based on previous demonstration that administration of 7,8-DHF in the postnatal period P3-P15 restores hippocampal neurogenesis and spinogenesis, we sought to establish whether these effects translate into behavioral benefits after treatment cessation. We found that Ts65Dn mice treated with 7,8-DHF (5.0 mg/kg/day) during postnatal days P3-P15 did not show any L&M improvement at one month after treatment cessation, indicating that the effects of 7,8-DHF on the brain are ephemeral. Based on evidence that chronic treatment with 7,8-DHF in juvenile Ts65Dn mice restores L&M, we sought to establish whether a similar effect is elicited in adulthood. We found that Ts65Dn mice treated with 7,8-DHF (5.0 mg/kg/day) for about 40 days starting from 4 months of age did not show any improvement in L&M. The results suggest that timing of therapy with 7,8-DHF is a critical issue for attainment of positive effects on the brain.
Watermelon (<i>Citrullus lanatus</i>) Hydroperoxide Lyase Greatly Increases C<sub>6</sub>Aldehyde Formation in Transgenic Leaves (2005)

Fatty acid hydroperoxide lyase (HL) is the key enzyme for the production of the "green note"compounds, leaf aldehyde [(2E)-hexenal] and leaf alcohol [(3Z)-hexenol], in plant tissues. A cDNA encoding HL was cloned from leaves of watermelon (Citrullus lanatus) and expressed in Nicotiana tabacum. The enzyme is 3 times more active with 13-hydroperoxylinolenic acid than with 13-hydroperoxylinoleic acid. The activity against 9-hydroperoxides of polyunsaturated fatty acids is minimal. Enzyme activity of the watermelon HL in the transgenic leaves was approximately 50 times higher than endogenous HL activity in the wild-type N. tabacum plants. When compared with Arabidopsis HL also expressed in N. tabacum, the highest HL activity is 10 times higher in watermelon HL overexpressing leaves than in Arabidopsis HL overexpressers.
Developing a Therapeutic Anti - Dendritic Cell Antibody to Prevent Graft Versus Host Disease. (2009)

Abstract Abstract 3554 Poster Board III-491 Introduction Host and donor dendritic cells (DC) stimulate alloreactive donor T lymphocytes, and initiate GVHD. We have shown that polyclonal antibody to the DC surface activation marker human CD83 (anti hCD83), which depletes activated DC, can prevent human DC and T cell induced lethal xenogeneic GVHD in SCID mice without impairing T cell mediated anti-leukaemic and anti-viral (CMV and influenza) immunity (J Exp Med 2009; 206: 387). Therefore, we made and tested a polyclonal anti mouse CD83 (RAM83) antibody in murine HSCT models and developed a human mAb against hCD83 as a potential new therapeutic immunosuppressive agent. Methods RAM83 specificity and function was tested by flow cytometry and allogeneic MLRs. It was administered as a single dose on day -1 of murine syngeneic and allo HSCT. Human and mouse single chain variable fragment (scFv) phage libraries were panned on recombinant human CD83 extracellular domain. After screening for specificity and affinity, the clones were reformatted to human IgG1 and expressed by transfected CHO cells. The purified mAb were tested for their ability to block a mixed leucocyte reaction (MLR). Results Lin-,Sca1+,Kit+ murine stem or progenitor cells were CD83-ve. RAM83 treated mice receiving syngeneic HSCT survived >35days (normal day 14 WBC). Full MHC mismatched (2× 60mg/kg cyclophosphamide + 2× 500cGy conditioned), B6 [H-2b] into BALB/c [H-2d]) recipient mice treated with a single dose of RAM83 developed GVHD later and survived longer (mean 26.9 days ±3.3) compared to controls (RAneg 12.3±1.3days, p=0.001; Nil antibody 7.7±1.5 days, p=0.0008). Daily high dose (50mg/kg) cyclosporin A delayed GVHD by a mean 18.2±3.3 days. Four phage clones that bind to human CD83 have been reformatted. Of the two tested to date, one mouse/human chimeric mAb has lost binding affinity, probably as a result of immunoglobulin variable region glycosylation. The other reformatted fully human anti-CD83 (3C12) mAb blocked a MLR, by an ADCC mechanism. Conclusions mAb targeting of activated DC is a promising novel approach to immunosuppression. The 3C12 clone and others will be subjected to preclinical testing in the xenogeneic SCID mouse model. The human mAb, which prevents GVHD without impairing the desired graft versus leukaemia effect will be developed for phase 1 clinical trials in clinical alloHSCT. Disclosures: Hart: CRC-BT: Consultancy.
Efficient Differentiation of Human Pluripotent Stem Cells to Endothelial Progenitors via Small-Molecule Activation of WNT Signaling (2014)

Human pluripotent stem cell (hPSC)-derived endothelial cells and their progenitors may provide the means for vascularization of tissue-engineered constructs and can serve as models to study vascular development and disease. Here, we report a method to efficiently produce endothelial cells from hPSCs via GSK3 inhibition and culture in defined media to direct hPSC differentiation to CD34(+)CD31(+) endothelial progenitors. Exogenous vascular endothelial growth factor (VEGF) treatment was dispensable, and endothelial progenitor differentiation was β-catenin dependent. Furthermore, by clonal analysis, we showed that CD34(+)CD31(+)CD117(+)TIE-2(+) endothelial progenitors were multipotent, capable of differentiating into calponin-expressing smooth muscle cells and CD31(+)CD144(+)vWF(+)I-CAM1(+) endothelial cells. These endothelial cells were capable of 20 population doublings, formed tube-like structures, imported acetylated low-density lipoprotein, and maintained a dynamic barrier function. This study provides a rapid and efficient method for production of hPSC-derived endothelial progenitors and endothelial cells and identifies WNT/β-catenin signaling as a primary regulator for generating vascular cells from hPSCs.
Vasostatin, a Calreticulin Fragment, Inhibits Angiogenesis and Suppresses Tumor Growth (1998)

An endothelial cell inhibitor was purified from supernatant of an Epstein-Barr virus-immortalized cell line and identified as fragments of calreticulin. The purified recombinant NH2-terminal domain of calreticulin (amino acids 1-180) inhibited the proliferation of endothelial cells, but not cells of other lineages, and suppressed angiogenesis in vivo. We have named this NH2-terminal domain of calreticulin vasostatin. When inoculated into athymic mice, vasostatin significantly reduced growth of human Burkitt lymphoma and human colon carcinoma. Compared with other inhibitors of angiogenesis, vasostatin is a small, soluble, and stable molecule that is easy to produce and deliver. As an angiogenesis inhibitor that specifically targets proliferating endothelial cells, vasostatin has a unique potential for cancer treatment.
Content versus Label Claims in Cannabidiol (CBD)-Containing Products Obtained from Commercial Outlets in the State of Mississippi (2020)

Products containing cannabidiol (CBD) are now available throughout the United States, but their quality is oftentimes questionable. The CBD and Δ<sup>9</sup>-tetrahydrocannabinol (THC) content of 25 commercially available hemp oil products, obtained throughout the state of Mississippi, was determined <i>via</i> gas chromatography/flame ionization detection (GC/FID). These products were also analyzed for the presence of synthetic cannabinoids using full scan gas chromatography/mass spectrometry (GC/MS). Analytical findings were compared to label claims for CBD content. Product label claims for CBD ranged from no claim to 500<b> </b>mg per serving; however, marked variability was observed between actual CBD content and claimed quantities. Of the 25 products, only three were within ±20% of label claim. Fifteen were well below the stated claim for CBD; two exceed claims in excess of 50%; and 5 made no claims. In addition, THC content for three products exceeded the 0.3% legal limit. Furthermore, four products-primarily marketed for vaping-were adulterated with synthetic cannabinoids. From this small, but diverse, sampling of hemp-derived merchandise, it appears that most product label claims do not accurately reflect actual CBD content and are fraudulent in that regard. Moreover, products that exceed legal THC levels may jeopardize a consumer's employment status (i.e. failed "drug test"), while those adulterated with synthetic cannabinoids may subject them to serious adverse health effects. These findings argue strongly for further development of current good manufacturing practices for CBD-containing products and their stringent enforcement.
Ultra-sensitive NO<inf>2</inf> detection with AlGaN/GaN 2DEG channels for air quality monitoring (2012)

Low-ppb room temperature NO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> detection is demonstrated for the first time using ultra-thin AlGaN/GaN heterostructures fabricated on silicon substrates. AlGaN/GaN shows great promise as a generic platform for (bio-)chemical sensing because of its robustness and intrinsic sensitivity to surface charges and dipoles. Here, we employ the two-dimensional electron gas (2DEG) formed at the interface of the AlGaN/GaN heterostructure for the monitoring of low-ppb NO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> concentrations in ambient air. We find that in the presence of humidity, the interaction of NO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> with the open gate area reversibly changes 2DEG conductivity. The dynamic range of these structures can be tuned to that of interest for air quality monitoring (0-100 ppb) by precisely back etching the open gate areas. A slope-based detection scheme in combination with periodic heating-induced gas desorption enables continuous air quality (NO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> ) monitoring.
Synthesis of Non-PGM ORR Catalysts: Control of Chemical, Morphological and Catalytic Properties (2015)

Development of non-platinum catalysts for both the anode [1] and cathode [2] attracts significant attention from researchers around the globe. Catalysts consisting of transition metal, nitrogen and carbon (M-N-C) where M=Fe, Co, Ni etc)framework possess reasonable stability and activity in both acidic and alkaline media. The use of inexpensive organic precursors doped with low molecular weight metal salts is proposed in the present research to provide a high surface area framework consisting of C-N decorated with M species. All catalysts presented in this work were synthesized using a modified sacrificial silica support method which has been widely adopted in our research group [4]. Appropriate amounts of metal precursor (iron nitrate or cobalt nitrate) and nitrogen-containing, precursors ( e.g. polyethyleneimine (PEI)) were deposited on the surface of fumed silica (surface area ~380 m -2 g -1 ) by Mechanochemical approach. The composite material was pyrolyzed in a nitrogen atmosphere at various temperatures, to form the M-N-C-SiO 2 framework. The pyrolysis conditions were determined from a MS-TGA analysis, where MS was used to identify the precursor’s decomposition products as a function of thermal treatment. After heat treatment, the fumed silica was removed by etching in HF acid and washed appropriately, revealing a high surface area M-N-C matrix The catalysts were comprehensively characterized by BET, SEM, TEM, XRD and XPS. Catalytic activity for ORR was measured in acidic media (0.5M H 2 SO 4 ) using the RRDE method and fuel cell test. Figure 1. Mechanochemical synthesis The broad XRD peak for Fe indicates small metallic iron particles exist on the order of several nanometers ( Fig. 1 ). It can be assumed that the homogeneous distribution of precursors on the high surface of fumed silica prevents metal particles from agglomeration. Analysis of material morphology by SEM reveals that the Fe-DAAPyr catalyst yields a highly porous surface structure. BET analysis of the adsorption isotherm reveals a surface area of ~700m -2 g -1 . Synthesized materials were found to be active in ORR in both RRDE and MEA fuel cell tests conditions. We would like to acknowledge funding support from DOE-EERE Fuel Cell Technology Program: “Development of Novel Non Pt Group Metal Electrocatalysts for PEM Fuel Cell Applications” (S. Mukerjee, NEU, PI). References: M. Min, C. Park, H. Kim, C. Kwak, A. A. Serov, H. Kweon, S. Lee, Electrochimica Acta, 52, (2006) 1670-1675. A. Serov, K. Artyushkova, P. Atanassov, Adv. Energy Mater., 4: 1301735 (2014). doi: 10.1002/aenm.201301735.. U. Tylus, Q. Jia, K. Strickland, N. Ramaswamy, A. Serov, P. Atanassov, S. Mukerjee, J. Phys. Chem. C, 118 (17) (2014) pp 8999–9008. A. Serov,A. Aziznia, P. H. Benhangi, K. Artyushkova, P. Atanassov, E. Gyenge J. Mater. Chem. A 1 (2013) 14384-14391. Figure 1
Assessing neuromuscular disease with multifrequency electrical impedance myography (2006)

Electrical impedance myography (EIM) is a noninvasive technique for neuromuscular assessment in which low-intensity alternating current is applied to a muscle and the consequent surface voltage patterns are evaluated. Previous work using a single frequency of 50 kHZ has demonstrated quantitative correlation of EIM parameters with disease status. In this investigation we examined the use of multifrequency EIM, studying a prototypical neurogenic disease (amyotrophic lateral sclerosis, ALS) and myopathic disorder (inflammatory myopathy, IM). Eleven ALS patients, 7 IM patients, and 46 normal subjects participated in the study. Although disease-specific patterns were not identified such that IM could be differentiated from ALS, impedance vs. frequency patterns for diseased subjects differed substantially from those of the age-matched normal subjects, with the greatest alterations occurring in the most severe cases. Multifrequency EIM may be well-suited to serve as an easily applied technique to assess disease severity in a variety of neuromuscular conditions.
Electronic nanotechnology and reconfigurable computing (2002)

Chemically assembled electronic nanotechnology (CAEN) is a promising alternative to CMOS for constructing circuits with feature sizes in the tens of nanometers range. In this paper we describe some of the recent advances in CAEN and how they influence the design of digital circuits. We show how reconfigurability supports inexpensive manufacturing. Finally, we describe a molecular latch that overcomes the lack of a viable CAEN-based transistor.
Methods for controlling positions of guided modes of photonic-crystal waveguides (2001)

We analyze different methods for controlling positions of guided modes of planar photonic-crystal waveguides. Methods based both on rearrangements of holes in the photonic-crystal lattice and on changes of hole sizes are presented. The ability to tune frequencies of guided modes within a frequency bandgap is necessary to achieve efficient guiding of light within a waveguide, as well as to match frequencies of eigenmodes of different photonic-crystal-based devices for the purpose of good coupling between them. We observe and explain the appearance of acceptor-type modes in donor-type waveguides.
Experimental investigation of membrane distillation with bubble column dehumidifier system for water desalination (2022)

The performance of a new integrated system of single-stage sweeping gas membrane distillation module and a bubble column dehumidifier (SGMD-BCD) was experimentally investigated. The productivity and energy consumption of the system is evaluated under different operating conditions. The SGMD module acts as a humidifier to produce high-quality distilled and the bubble column dehumidifier is an effective condenser for improved performance. The sweeping air stream is created in two different ways; using a vacuum pump and compressed air. Results showed that the integrated system yields higher permeate flux, better gained output ratio (GOR), and lower specific thermal energy consumption (SEC) when the vacuum pump is used. Increasing the feed temperature from 50 to 80 °C increased the flux by 175%, on average. Doubling the sweeping air flow rate from 1 to 2 SCFM resulted in flux enhancement of 49% and 25% for the vacuum pump and the compressed air supply, respectively. Operating the system with the vacuum pump and without cooling the bubble column dehumidifier showed a marginal reduction in flux but resulted in significant improvements in GOR and SEC values of 0.76 and 909 kWh/m3, respectively, at an optimum dehumidifier water column height of 9.5 cm.