gebhart/patrepeval huggingface dataset:
A Pathogen Secreted Protein as a Detection Marker for Citrus Huanglongbing (2017)

The citrus industry is facing an unprecedented crisis due to Huanglongbing (HLB, aka citrus greening disease), a bacterial disease associated with the pathogen <i>Candidatus</i> Liberibacter asiaticus (<i>C</i>Las) that affects all commercial varieties. Transmitted by the Asian citrus psyllid (ACP), <i>C</i>Las colonizes citrus phloem, leading to reduced yield and fruit quality, and eventually tree decline and death. Since adequate curative measures are not available, a key step in HLB management is to restrict the spread of the disease by identifying infected trees and removing them in a timely manner. However, uneven distribution of <i>C</i>Las cells in infected trees and the long latency for disease symptom development makes sampling of trees for <i>C</i>Las detection challenging. Here, we report that a <i>C</i>Las secreted protein can be used as a biomarker for detecting HLB infected citrus. Proteins secreted from <i>C</i>Las cells can presumably move along the phloem, beyond the site of ACP inoculation and <i>C</i>Las colonized plant cells, thereby increasing the chance of detecting infected trees. We generated a polyclonal antibody that effectively binds to the secreted protein and developed serological assays that can successfully detect <i>C</i>Las infection. This work demonstrates that antibody-based diagnosis using a <i>C</i>Las secreted protein as the detection marker for infected trees offers a high-throughput and economic approach that complements the approved quantitative polymerase chain reaction-based methods to enhance HLB management programs.
Chromatic calibration of an HDR display using 3D octree forests (2015)

High dynamic range (HDR) display prototypes have been built and used for scientific studies for nearly a decade, and they are now on the verge of entering consumer market. However, problems exist regarding the accurate color reproduction capabilities on these displays. In this paper, we first characterize the color reproduction capability of a state-of-art HDR display through a set of measurements, and present a novel calibration method that takes into account the variation of the chrominance error over HDR display's wide luminance range. Our proposed 3D octree forest data structure for representing and querying the calibration function successfully addresses the challenges in calibrating HDR displays: (i) high computational complexity due to nonlinear chromatic distortions, and (ii) huge storage space demand for a look-up table (35GB vs 100kB). We show that our method achieves high color reproduction accuracy through both objective metrics and a controlled subjective study.
Enhancing virtual colonoscopy with a new visualization measure (2018)

In this paper, a new 3D surface visualization measure is proposed. The proposed measure can be used in Virtual Colonoscopy (VC) as a caparison metric of different visualization approaches and each other. The new measure utilizes the projection direction of the camera axis and surface normal as well as the camera focal length to the surface distance ratio, thus, providing a more realistic interpretation of the actual visible surface projected. These enhancements avoid many of the shortcomings of older metrics. The Virtual Fly-Through and Fly-Over visualization approaches used in VC are compared. Result show the advantages of using the proposed measure using color coding Heat-maps to enhance the visualization process.
Nanostructured Sapphire Optical Fiber for Evanescent-Field Sensing (2015)

We report an innovative and scalable strategy of transforming a commercial unclad sapphire optical fiber to an all-alumina nanostructured sapphire optical fiber (NSOF). The strategy entails fiber coating with metal aluminum followed by anodization to form alumina cladding of highly organized pore channel structure. We experimentally demonstrated Ag nanoparticles (NPs)-enabled NSOF for SERS sensing of 10−6 M Rhodamine 6G (R6G) after thermal treatment at 500 °C for 6 hours. We numerically show that AAO cladding significantly increases the evanescent-field overlap, lower porosity of AAO results in higher evanescent-field overlap.
Amine Linked Flavonoid Dimers as Modulators for P-Glycoprotein-Based Multidrug Resistance: Structure–Activity Relationship and Mechanism of Modulation (2012)

Here we report a great improvement in reversal potency of cancer drug resistance when flavonoid dimers possess a functionally substituted aminopolyethylene glycol linker. The most potent compound, 18, contains a N-benzyl group at the linker. It has many advantages including (1) high potencies in reversing P-glycoprotein (P-gp) mediated resistance in LCC6MDR cells to various anticancer drugs with EC(50) in the nanomolar range, (2) low toxicity and high therapeutic index, and (3) preferential inhibition of P-gp over multidrug resistance protein 1 and breast cancer resistance protein. Compound 18 stimulates P-gp-ATPase activity by 2.7-fold and mediates a dose-dependent inhibition of doxorubicin (DOX) transport activity. Lineweaver-Burk and Dixon plots suggest that 18 is a competitive inhibitor to DOX in binding to P-gp with a K(i) of 0.28-0.34 μM and a Hill coefficient of 1.17. Moreover, the LCC6MDR cell displays about 2.1-fold lower intracellular accumulation of 18 compared to the wild type, suggesting that 18 is a P-gp substrate as well.
Multiple memristor read and write circuit for neuromorphic applications (2011)

A memristor based write circuit is presented that can update multiple memristors using a neuron spike generated by the Izhikevich model. A memristor read circuit is also presented that is capable of quantizing the resistance into 5 discrete values that could be digitally decoded. Together, these circuits provide the basic block for a memristor based neuromorphic architecture. The memristors were modeled using published device characterization data.
Identification of a Polymyxin Synthetase Gene Cluster of <i>Paenibacillus polymyxa</i> and Heterologous Expression of the Gene in <i>Bacillus subtilis</i> (2009)

Polymyxin, a long-known peptide antibiotic, has recently been reintroduced in clinical practice because it is sometimes the only available antibiotic for the treatment of multidrug-resistant gram-negative pathogenic bacteria. Lack of information on the biosynthetic genes of polymyxin, however, has limited the study of structure-function relationships and the development of improved polymyxins. During whole genome sequencing of Paenibacillus polymyxa E681, a plant growth-promoting rhizobacterium, we identified a gene cluster encoding polymyxin synthetase. Here, we report the complete sequence of the gene cluster and its function in polymyxin biosynthesis. The gene cluster spanning the 40.6-kb region consists of five open reading frames, designated pmxA, pmxB, pmxC, pmxD, and pmxE. The pmxC and pmxD genes are similar to genes that encode transport proteins, while pmxA, pmxB, and pmxE encode polymyxin synthetases. The insertional disruption of pmxE led to a loss of the ability to produce polymyxin. Introduction of the pmx gene cluster into the amyE locus of the Bacillus subtilis chromosome resulted in the production of polymyxin in the presence of extracellularly added L-2,4-diaminobutyric acid. Taken together, our findings demonstrate that the pmx gene cluster is responsible for polymyxin biosynthesis.
Glucagon receptor inhibition normalizes blood glucose in severe insulin-resistant mice (2017)

Inactivating mutations in the insulin receptor results in extreme insulin resistance. The resulting hyperglycemia is very difficult to treat, and patients are at risk for early morbidity and mortality from complications of diabetes. We used the insulin receptor antagonist S961 to induce severe insulin resistance, hyperglycemia, and ketonemia in mice. Using this model, we show that glucagon receptor (GCGR) inhibition with a monoclonal antibody normalized blood glucose and β-hydroxybutyrate levels. Insulin receptor antagonism increased pancreatic β-cell mass threefold. Normalization of blood glucose levels with GCGR-blocking antibody unexpectedly doubled β-cell mass relative to that observed with S961 alone and 5.8-fold over control. GCGR antibody blockage expanded α-cell mass 5.7-fold, and S961 had no additional effects. Collectively, these data show that GCGR antibody inhibition represents a potential therapeutic option for treatment of patients with extreme insulin-resistance syndromes.
Bistetracene: An Air-Stable, High-Mobility Organic Semiconductor with Extended Conjugation (2014)

We report the synthesis and characterization of "bistetracene", an unconventional, linearly extended conjugated core with eight fused rings. The annellation mode of the system allows for increased stability of the conjugated system relative to linear analogues due to the increased number of Clar aromatic sextets. By attaching the appropriate solubilizing substituents, efficient molecular packing with large transfer integrals can be obtained. The electronic structure calculations suggest these large polycyclic aromatic hydrocarbons (PAHs) exhibit excellent intrinsic charge transport properties. Charge carrier mobilities as large as 6.1 cm(2) V(-1) s(-1) and current on/off ratios of 10(7) were determined experimentally for one of our compounds. Our study provides valuable insight into the design of unconventional semiconductor compounds based on higher PAHs for use in high-performance devices.
Enhanced Geosteering With While-Drilling Productivity Evaluation: A Methodology to Optimize Horizontal Well Productivity (2016)

Abstract Geosteering is a proven concept which enables the delivery of productive wells by ensuring such wells stay within the target reservoir and sweet spot, and are precisely placed relative to fluid contacts. When reservoir engineering concepts are combined with Geosteering, quantitative estimates of the well's productivity can be determined to further evaluate the performance of the Geosteering and aid in decision-making. This workflow, applied in real-time, is called Real-Time Productivity Steering (RTPS). This paper describes the application of RTPS to a horizontal well placed in a thin layer of oil reservoir. Prior to performing the real time productivity estimates while drilling, a prejob model was built, using offset well data, to estimate productivity from the planned well. Sensitivity analysis was performed on the trajectory, well length and some rock and fluid properties, to determine the plan that would result in optimum productivity for the well. While the well was drilled, Logging While Drilling (LWD) information was used to update the existing model, geosteer, and perform productivity prediction while drilling. Productivity was predicted at three target depths: 8400 ft MD, 8800 ft MD, and at Total Depth (TD). The increasing liquid productivity index (PI) at the selected target depths were further justification to continue drilling until the predetermined TD. The results at TD showed that the open hole liquid PI of the well in the sand of interest was about 63.8 stb/d/psi for a stable production rate of 1200 blpd. When completions were imposed on this single well reservoir model, it was predicted that the well will produce at a stable rate of 750 bopd. This was compared with a preliminary test done on the well where for the same well and reservoir conditions, the well produced 800 bopd. This paper demonstrates that quantitative estimates of productivity can be made while drilling to complement geosteering. In addition to complementing and enhancing geosteering, RTPS provides a reliable dynamic model for subsequent completion design. The RTPS workflow of complementing geosteering with reservoir engineering will enhance the ability to drill more productive wells as it will enable wells to be steered in the direction of maximum productivity, and also provide operators with sufficient information while drilling to make informed decisions for completions and for future wells.
Optical clearing of skin enhanced with hyaluronic acid for increased contrast of optoacoustic imaging (2016)

Enhanced delivery of optical clearing agents (OCA) through skin may improve sensitivity of optical and optoacoustic (OA) methods of imaging, sensing, and monitoring. This report describes a two-step method for enhancement of light penetration through skin. Here, we demonstrate that topical application of hyaluronic acid (HA) improves skin penetration of hydrophilic and lipophilic OCA and thus enhances their performance. We examined the OC effect of 100% polyethylene and polypropylene glycols (PPGs) and their mixture after pretreatment by HA, and demonstrated significant increase in efficiency of light penetration through skin. Increased light transmission resulted in a significant increase of OA image contrast in vitro. Topical pretreatment of skin for about 30 min with 0.5% HA in aqueous solution offers effective delivery of low molecular weight OCA such as a mixture of PPG-425 and polyethylene glycol (PEG)-400. The developed approach of pretreatment by HA prior to application of clearing agents (PEG and PPG) resulted in a ∼ 47-fold increase in transmission of red and near-infrared light and significantly enhanced contrast of OA images.
Preparation and Characterization of Membranes with Adjustable Sep Aration Performance Using Polyphosphazene Membranes (1997)

Abstract Preparation of polymeric membranes with dynamically adjustable separation properties is a new area of research. The approach described herein involves adjusting the permeate pressure of a swollen polymeric membrane to alter its separation properties. For example, during the separation of methylene blue from isopropyl alcohol, pressure on the permeate side was increased such that both methylene blue and alcohol were passed, resulting in no separation. The permeate pressure then was decreased and only colorless isopropyl alcohol passed through the membrane. A subsequent increase in the pressure on the permeate side results in no separation once again demonstrating that the effects were fully reversible. In a mixed dye experiment in isopropyl alcohol, methylene blue and rose bengal were separated with the lower-molecular-weight methylene blue permeating with isopropyl alcohol while the rose bengal was retained in the feed. The new membranes are distinguished by improved control of separation parameters as well as improved flux rates and have been experimentally characterized for their separation abilities using both flat sheets and tubular systems. This approach can be used for virtually any polymer which swells, but does not dissolve in the solvents which are being used.
The ERV-9 LTR enhancer is not blocked by the HS5 insulator and synthesizes through the HS5 site non-coding, long RNAs that regulate LTR enhancer function (2003)

A solitary long terminal repeat (LTR) of ERV-9 human endogenous retrovirus is located upstream of the HS5 site in the human beta-globin locus control region and possesses unique enhancer activity in erythroid K562 cells. In cells transfected with plasmid LTR-HS5-epsilonp-GFP, the LTR enhancer activates the GFP reporter gene and is not blocked by the interposed HS5 site, which has been reported to have insulator function. The LTR enhancer initiates synthesis of long RNAs from the LTR promoter through the intervening HS5 site into the epsilon-globin promoter and the GFP gene. Synthesis of the sense, long LTR RNAs is correlated with high level synthesis of GFP mRNA from the epsilon-globin promoter. Mutations of the LTR promoter and/or the epsilon-globin promoter show that (i) the LTR enhancer can autonomously initiate synthesis of LTR RNAs independent of the promoters and (ii) the LTR RNAs are not processed into GFP mRNA or translated into GFP. However, reversing the orientation of the LTR in plasmid (LTR)rev-HS5-epsilonp-GFP, thus reversing the direction of synthesis of LTR RNAs in the antisense direction away from the epsilon-globin promoter and GFP gene drastically reduces the level of GFP mRNA and thus LTR enhancer function. The results suggest that the LTR-assembled transcription machinery in synthesizing non-coding, LTR RNAs can reach the downstream epsilon-globin promoter to activate transcription of the GFP gene.
Photo-real lips synthesis with trajectory-guided sample selection. (2010)

In this paper, we propose an HMM trajectory-guided, real image sample concatenation approach to photo-real talking head synthesis. It renders a smooth and natural video of articulators in sync with given speech signals. An audio-visual database is used to train a statistical Hidden Markov Model (HMM) of lips movement first and the trained model is then used to generate a visual parameter trajectory of lips movement for given speech signals, all in the maximum likelihood sense. The HMM generated trajectory is then used as a guide to select, in the original training database, an optimal sequence of mouth images which are then stitched back to a background head video. The whole procedure is fully automatic and data driven. With an audio/video footage as short as 20 minutes from a speaker, the proposed system can synthesize a highly photo-real video in sync with the given speech signals. This system won the FIRST place in the Audio-Visual match contest in LIPS2009 Challenge, which was perceptually evaluated by recruited human subjects.
CoViCAD: Comprehensive Visualization of Coronary Artery Disease (2007)

We present novel, comprehensive visualization techniques for the diagnosis of patients with Coronary Artery Disease using segmented cardiac MRI data. We extent an accepted medical visualization technique called the bull's eye plot by removing discontinuities, preserving the volumetric nature of the left ventricular wall and adding anatomical context. The resulting volumetric bull's eye plot can be used for the assessment of transmurality. We link these visualizations to a 3D view that presents viability information in a detailed anatomical context. We combine multiple MRI scans (whole heart anatomical data, late enhancement data) and multiple segmentations (polygonal heart model, late enhancement contours, coronary artery tree). By selectively combining different rendering techniques we obtain comprehensive yet intuitive visualizations of the various data sources.
Correlative Study of Human Papillomavirus DNA, Histopathology, and Morphometry in Cervical Condyloma and Intraepithelial Neoplasia (1988)

This study includes 28 intraepithelial squamous lesions of the cervix associated with human papillomavirus (HPV) DNA sequences detected by the Southern blot technique. Objective analyses of the histologic features by morphometric parameters and mitotic index have demonstrated that lesions of HPV types 6 and 11 can be distinguished from types 16, 18, and 33 by stepwise discriminant functions. The latter lesions have higher mitotic and cellularity indexes and greater nuclear atypia than the former, supporting a greater degree of epithelial proliferation and abnormality seen in association with HPV types 16/18/33.
The atomic structure of baculovirus polyhedra reveals the independent emergence of infectious crystals in DNA and RNA viruses (2009)

Baculoviruses are ubiquitous insect viruses well known for their use as bioinsecticides, gene therapy vectors, and protein expression systems. Overexpression of recombinant proteins in insect cell culture utilizes the strong promoter of the polyhedrin gene. In infected larvae, the polyhedrin protein forms robust intracellular crystals called polyhedra, which protect encased virions for prolonged periods in the environment. Polyhedra are produced by two unrelated families of insect viruses, baculoviruses and cypoviruses. The atomic structure of cypovirus polyhedra revealed an intricate packing of trimers, which are interconnected by a projecting N-terminal helical arm of the polyhedrin molecule. Baculovirus and cypovirus polyhedra share nearly identical lattices, and the N-terminal region of the otherwise unrelated baculovirus polyhedrin protein sequence is also predicted to be alpha-helical. These results suggest homology between the proteins and a common structural basis for viral polyhedra. Here, we present the 2.2-A structure of baculovirus polyhedra determined by x-ray crystallography from microcrystals produced in vivo. We show that the underlying molecular organization is, in fact, very different. Although both polyhedra have nearly identical unit cell dimensions and share I23 symmetry, the polyhedrin molecules are structurally unrelated and pack differently in the crystals. In particular, disulfide bonds and domain-swapped N-terminal domains stabilize the building blocks of baculovirus polyhedra and interlocking C-terminal arms join unit cells together. We show that the N-terminal projecting helical arms have different structural roles in baculovirus and cypovirus polyhedra and conclude that there is no structural evidence for a common evolutionary origin for both classes of polyhedra.
Adsorption of Multimeric T Cell Antigens on Carbon Nanotubes: Effect on Protein Structure and Antigen‐Specific T Cell Stimulation (2012)

Antigen-specific activation of cytotoxic T cells can be enhanced up to three-fold more than soluble controls when using functionalized bundled carbon nanotube substrates ((b) CNTs). To overcome the denaturing effects of direct adsorption on (b) CNTs, a simple but robust method is demonstrated to stabilize the T cell stimulus on carbon nanotube substrates through non-covalent attachment of the linker neutravidin.
Activation of CXCL12-CXCR4 signalling induces conversion of immortalised embryonic kidney cells into cancer stem-like cells (2020)

Cancer stem cells (CSCs) have been implicated in the growth and progression of several types of human cancer. The technology to derive and establish CSCs <i>in vitro</i> could be a critical tool for understanding cancer and developing new therapeutic targets. In this study, we derived expandable CD15<sup>+</sup> induced CSCs (iCSCs) from immortalised 293FT human epithelial cells by co-culture with human bone marrow-derived mesenchymal stem cells (BM-MSCs) as feeder cells <i>in vitro</i>. The iCSCs converted through an epithelial-mesenchymal transition program acquired mesenchymal traits, the expression of stem cell markers, and epigenetic changes. Moreover, the iCSCs not only efficiently formed tumorspheres <i>in vitro</i> but also initiated tumours in immunocompromised mice injected with only 10 of the iCSCs. Furthermore, we showed that the expression of the chemokine CXCL12 and its receptor CXCR4 by the iCSCs resulted in the activation of the <i>Fut4</i> gene through CXCR4/ERK/ELK-1-signalling pathways and the maintenance of the iCSCs in the undifferentiated state through CXCR4/AKT/STAT3-signalling. These findings suggest that immortalised 293FT cells may acquire potential oncogenicity through molecular and cellular alteration processes in microenvironments using BM-MSCs, and could represent a valuable <i>in vitro</i> model as a cancer stem cell surrogate for studying the pathophysiological properties of CSCs.