gebhart/patrepeval huggingface dataset:
HIV Sequence Compendium 2010 (2010)

This compendium is an annual printed summary of the data contained in the HIV sequence database. In these compendia we try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2010. Hence, though it is called the 2010 Compendium, its contents correspond to the 2009 curated alignments on our website. The number of sequences in the HIV database is still increasing exponentially. In total, at the time of printing, there were 339,306 sequences in the HIV Sequence Database, an increase of 45% since last year. The number of near complete genomes (>7000 nucleotides) increased to 2576 by end of 2009, reflecting a smaller increase than in previous years. However, as in previous years, the compendium alignments contain only a small fraction of these. Included in the alignments are a small number of sequences representing each of the subtypes and the more prevalent circulating recombinant forms (CRFs) such as 01 and 02, as well as a few outgroup sequences (group O and N and SIV-CPZ). Of the rarer CRFs we included one representative each. A more complete version of all alignments is available on our website, http://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html. Reprints are available from our website in the form of both HTML and PDF files. As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to seq-info@lanl.gov.
Diagnosis and Treatment of Perianal Fistulas in Crohn Disease (2001)

Perianal fistulas occur in up to 43% of patients with Crohn disease. Diagnostic evaluation to determine the location and type of fistulas and the presence or absence of rectal inflammation is required. A combined medical and surgical approach to the management of such patients is the optimal treatment plan. Perianal abscesses must be drained. Superficial, low transsphincteric, and low intersphincteric fistulas are usually treated with fistulotomy and antibiotics. High transsphincteric, suprasphincteric, and extrasphincteric fistulas are usually treated with noncutting setons, antibiotics, and azathioprine or 6-mercaptopurine and, in many cases, infliximab.
Room-temperature Single-photon Emitters in Silicon Nitride (2021)

We report the discovery of room-temperature quantum emitters in silicon nitride. Photophysical analysis reveals bright (&gt;10 5 counts/s), stable, and pure single-photon emission with an average of g (2) (0) of about 0.25 collected from a hundred emitters.
On the Delay Advantage of Coding in Packet Erasure Networks (2012)

We consider the delay of network coding compared to routing with retransmissions in packet erasure networks with probabilistic erasures. We investigate the sub-linear term in the block delay required for unicasting $n$ packets and show that there is an unbounded gap between network coding and routing. In particular, we show that delay benefit of network coding scales at least as $\sqrt{n}$. Our analysis of the delay function for the routing strategy involves a major technical challenge of computing the expectation of the maximum of two negative binomial random variables. This problem has been studied previously and we derive the first exact characterization which may be of independent interest. We also use a martingale bounded differences argument to show that the actual coding delay is tightly concentrated around its expectation.
1P169 Over-expression of Recombinant Human Hemoglobin(5. Heme protein,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006) (2006)

Development of anificial and safe biooti substitutes has been attracting much attention
Acceleration of Calcite Kinetics by Abalone Nacre Proteins (2005)

Abalone shell nacre proteins act as surfactants to promote ion attachment at calcite steps, causing acceleration of the molecular-scale kinetics of calcite crystal growth. The proteins modify the shape of growing calcite (see Figure) through step-specific interactions, even though the proteins are larger than the atomic-scale steps. Understanding of crystal-growth control by interactions with proteins may give better control of new crystalline materials.
Adsorption of poly(vinyl formamide‐co‐vinyl amine) onto silica particle surfaces and stability of the formed hybrid materials (2004)

Abstract In order to produce silica/polyelectrolyte hybrid materials the adsorption of the polyelectrolyte poly(vinyl formamide‐ co ‐vinyl amine), P(VFA‐ co ‐VAm) was investigated. The adsorption of the P(VFA‐ co ‐VAm) from an aqueous solution onto silica surface is strongly influenced by the pH value and ionic strength of the aqueous solution, as well as the concentration of polyelectrolyte. The adsorption of the positively charged P(VFA‐ co ‐VAm) molecules on the negatively charged silica particles offers a way to control the surface charge properties of the formed hybrid material. Changes in surface charges during the polyelectrolyte adsorption were studied by potentiometric titration and electrokinetic measurements. X‐ray photoelectron spectroscopy (XPS) was employed to obtain information about the amount of the adsorbed polyelectrolyte and its chemical structure. The stability of the adsorbed P(VFA‐ co ‐VAm) was investigated by extraction experiments and streaming potential measurements. It was shown, that polyelectrolyte layer is instable in an acidic environment. At a low pH value a high number of amino groups are protonated that increases the solubility of the polyelectrolyte chains. The solvatation process is able to overcompensate the attractive electrostatic forces fixing the polyelectrolyte molecules on the substrate material surface. Hence, the polyelectrolyte layer partially undergoes dissolving process.
Optimised virtual loudspeaker reproduction (2010)

In this paper we present a method for spatial audio reproduction over headphones using Head-Related Impulse Response (HRIR) simplification and Ambisonic decoding. The method is shown to significantly reduce computational complexity for real-time audio based rendering by decomposing the directional component of HRIRs into spherical harmonic basis functions. Localisation distortion due to reduced filter lengths is assessed through psychoacoustic evaluation criteria and a minimum phase approach is shown to be optimal.
Measurements and Modeling of Wetting Efficiency in Trickle-Bed Reactors: Liquid Viscosity and Bed Packing Effects (2009)

An experimental parametric study on wetting efficiency is reported which evaluates the influence of liquid viscosity, as well as the effect of particle size(/shape) and bed porosity (εB), separately. A 10-fold increase of liquid viscosity improves slightly catalyst wetting (by about 10%), while an increase of either bed porosity or particle size has the opposite effect. Wetting efficiency is reduced by about 0.1 for an increase of εB from 0.38 and 0.40 due to a change of particle size from 1.8 to 7 × 10−3 m while the decrease is only 0.05 for a similar variation of εB (0.38−0.41) with the same particles. The effect of particle shape (cylindrical/trilobe extrudates or spheres) appears very small in the investigated conditions. A new correlation for wetting efficiency is proposed, using a bounded function and only three dimensionless groups (liquid Froude and Morton numbers and bed porosity). This correlation is able to predict wetting efficiency with a very good precision on a large database, provided wetting liquids are used. Adding fines in the fixed bed is also examined, and its positive effect can be correlated with the size ratio between catalyst particles and fines.
Designed PKC-targeting bryostatin analogs modulate innate immunity and neuroinflammation (2020)

SUMMARY Neuroinflammation characterizes multiple neurologic diseases, including primary inflammatory conditions such as multiple sclerosis (MS) and classical neurodegenerative diseases. Aberrant activation of the innate immune system contributes to disease progression in these conditions, but drugs that modulate innate immunity, particularly within the central nervous system (CNS), are lacking. The CNS-pene-trant natural product bryostatin-1 (bryo-1) attenuates neuroinflammation by targeting innate myeloid cells. Supplies of natural bryo-1 are limited but a recent scalable synthesis has enabled access to it and its analogs (termed bryologs), the latter providing a path to more efficacious, better tolerated, and more accessible agents. Here, we show that multiple synthetically accessible bryologs replicate the anti-inflammatory effects of bryo-1 on innate immune cells in vitro , and a lead bryolog attenuates neuroinflammation in vivo – actions mechanistically dependent on PKC binding. Our findings identify bryologs as promising drug candidates for targeting innate immunity in neuroinflammation and create a platform for evaluation of synthetic PKC modulators in neuroinflammatory diseases such as MS. Graphical Abstract
Supplementary Figure 2 from Cancer-Induced Immunosuppression: IL-18–Elicited Immunoablative NK Cells (2023)

&lt;p&gt;PDF file - 105K, IL-18 does not promote the proliferation of Kit+ NK cells in vivo&lt;/p&gt;
Design of a digital IP for 3D-IC die-to-die clock synchronization (2017)

In this paper the design of a novel IP for 3D IC die-to-die clock synchronization is presented. The proposed design offers notable benefits over the conventional dual DLL based architectures for 3D IC clock synchronization. Simulation results of the IP are presented with GLOBALFOUNDRIES 14nm finFET library, and Through-Silicon Via (TSV) technology.
Rho-Kinase Signaling Regulates Pulmonary Infiltration of Neutrophils in Abdominal Sepsis Via Attenuation of CXC Chemokine Formation and Mac-1 Expression on Neutrophils (2012)

Excessive neutrophil infiltration is a major component in septic lung injury, although the signaling mechanisms behind pulmonary recruitment of neutrophils in polymicrobial sepsis remain elusive. Herein, we hypothesized that Rho-kinase activity may play a significant role in pulmonary neutrophil recruitment and tissue damage in abdominal sepsis. Male C57BL/6 mice were treated with the Rho-kinase inhibitor Y-27632 (0.5 or 5 mg/kg) before cecal ligation and puncture (CLP). Bronchoalveolar lavage fluid and lung tissue were harvested for analysis of neutrophil infiltration, as well as edema and CXC chemokine formation. Blood was collected for analysis of Mac-1 on neutrophils and CD40L on platelets as well as soluble CD40L and matrix metalloproteinase 9 (MMP-9) in plasma. Cecal ligation and puncture triggered significant pulmonary damage characterized by neutrophil infiltration, increased levels of CXC chemokines, and edema formation in the lung. Furthermore, CLP upregulated Mac-1 expression on neutrophils, decreased CD40L on platelets, and increased soluble CD40L and MMP-9 in the circulation. Interestingly, inhibition of Rho-kinase dose-dependently decreased CLP-induced neutrophil expression of Mac-1, formation of CXC chemokines and edema, as well as neutrophil infiltration and tissue damage in the lung. Moreover, Rho-kinase inhibition significantly reduced sepsis-provoked gene expression of CXC chemokines in alveolar macrophages. In contrast, Rho-kinase inhibition had no effect on platelet shedding of CD40L or plasma levels of MMP-9 in septic mice. In conclusion, these data demonstrate that the Rho-kinase signaling pathway plays a key role in regulating pulmonary infiltration of neutrophils and tissue injury via regulation of CXC chemokine production in the lung and Mac-1 expression on neutrophils in abdominal sepsis.
Roaming Nairobi Roads: Instrumenting Roads under Resource Constraints (2017)

Many intelligent transportation systems (ITS) in cities with developed economies are making use of mobile technology as data sources (e.g., many crowd-sourced traffic-related applications) to improve the quality and efficiency of transportation networks. Often, these data sources are used to supplement existing traffic monitoring equipment (e.g., ground-loop detectors, traffic cameras), to provide greater insights into roadway infrastructure and traffic dynamics. For cities with emerging economies where traditional traffic monitoring equipment is cost prohibitive, the rise in mobile technology presents a unique opportunity to leverage smartphone sensors as an alternative data source for ITS. There are, however, challenges to using these sensors particularly with the cost of mobile data, network consistency, and on-device resources. In this paper, we present a mobile system that instruments roads under resource constraint while a vehicle is in motion. It determines when and what data to collect and/or upload using a number of on-device valuation and optimisation functions, by prioritising data collection over uploading or vis-versa. We deployed our mobile system on a fleet of heavy-duty waste-collection trucks in Nairobi, Kenya to collect a large volume of real-word road infrastructure and mobility data. Results show that a 42 % reduction in wireless transmissions costs can be achieved with minimal impact to the time in which important data are collected, uploaded and harmonized into a frequently updated map of road infrastructure and traffic.
Low resistance Al/Ti/n-GaN ohmic contacts with improved surface morphology and thermal stability (2000)

The Al/Ti/n-GaN ohmic contact and multilayer variations on this contact are widely used because of the low contact resistivities they provide to n-GaN. However, there are few reports that reveal the influence of the atomic ratio of Al to Ti on the contact resistivity, thermal stability and surface morphology of the contacts. This study reveals that the ratio of Al to Ti strongly influences all of these characteristics. All contacts in this study had atomic ratios of Al to Ti higher than 1. Those contacts with ratios of Al to Ti less than 3 required higher annealing temperatures or longer annealing times to reach comparable contact resistivities compared to the more Al-rich contacts. On the other hand, the less Al-rich contacts provided several advantages. They exhibited smooth surface morphologies even after they were annealed at temperatures near 1000 °C, and they suffered much less severe degradation during long-term aging at 600 °C. These findings are explained by differences in the phases formed after annealing.
Immunohistochemical Analysis of Interleukin-1β–Converting Enzyme/Ced-3 Family Protease, CPP32/Yama/Caspase-3, in Hodgkin's Disease (1997)

The Caenorhabditis elegans cell death gene, Ced-3, encodes a protein homologous to mammalian interleukin-1β–converting enzyme (ICE), a cysteine protease implicated in programmed cell death (PCD). CPP32, also known as Yama, apopain, and Caspase-3, is a member of this family, has substrate specificities similar to Ced-3, and has been shown to have an active role in PCD. Evidence suggests that these proteases act downstream of inhibitors of PCD such as Bcl-2 and Bcl-xL , which are frequently expressed in Reed-Sternberg (RS) cells of Hodgkin's disease (HD). To date there have been no studies examining the role of the ICE/Ced-3 family of proteins, in particular CPP32, in HD. We examined 24 cases of HD with a classical immunophenotype and 6 cases of nodular lymphocyte predominant HD (NLPHD) for the expression of CPP32 in the RS cells and lymphohistiocytic (L&amp;H) cells as detected by immunohistochemistry. Twenty two of 24 cases (92%) of HD expressed the protein in the RS cells, whereas the L&amp;H cells in all 6 cases of NLPHD lacked expression of CPP32. These results provide further evidence that NLPHD is a phenotypically different disease distinct from classical forms of HD. The differential expression of the cell death protein CPP32 may be an important factor contributing to the apparently different clinical behaviour of NLPHD in contrast to classical HD. The lack of expression of CPP32 in NLPHD shares similarities with low-grade B-cell non-Hodgkin's lymphomas and may explain their common clinical course. Further studies are required to elucidate the significance of CPP32 in HD.
Expression and function of α2,3‐sialyl‐ and α,3/l,4‐fucosyltransferases in colon adenocarcinoma cell lines: Role in synthesis of E‐selectin counter‐receptors (1995)

We show here that colon-carcinoma cell lines adhere to E-selectin via sialyl Lewis x and sialyl Lewis a (s(Lex) and s(Lea)) oligosaccharides and that this adhesion can be enhanced by TNF stimulation. To study in greater detail this endothelial binding, we analysed the mRNA expression and function of the enzymes participating in the generation of s(Lex) and s(Lea on cancer cells. These oligosaccharides are synthesized by sequential action of alpha 2,3 sialyl (alpha 2,3-ST) and alpha 1,3/1/4 fucosyltransferases (alpha 1,3/1,4-FT) on existing (poly)N-acetyllactosamine chains. We report here that mRNAs of 2 recently cloned alpha 2,3-STs and 4 alpha 1,3/1,4-FTs are expressed in adenocarcinoma cells. In functional assays alpha 2,3-ST and alpha 1,3- or 1,4-FT activities were observed in adenocarcinoma cell lysates to exogenous N-acetyllactosamine and lacto-N-biose acceptors and to their sialylated derivatives, leading to the synthesis of the sialyl-N-acetyllactosamine and s(Lex) or the sialyllacto-N-biose and s(Lea), respectively. Furthermore, the inflammatory cytokine TNF could enhance some alpha 2,3-ST and alpha 1,3/1,4-FT activities capable of generating E-selectin counter-receptors. Taken together, these data show that COLO 205 and HT-29 adenocarcinoma cell lines adhere to E-selectin in a TNF-inducible manner via their cell-surface s(Lex) and s(Lea). These cells also express mRNA as well as inducible enzyme activities of several alpha 2,3-STs and alpha 1,3/1,4-FTs responsible for the final steps in the synthesis of s(Lex) and s(Lea).(ABSTRACT TRUNCATED AT 250 WORDS)
Compounds which increase the permeability of the Pseudomonas aeruginosa outer membrane (1984)

Hydrolysis of the chromogenic beta-lactam nitrocefin by periplasmic beta-lactamase in intact Pseudomonas aeruginosa cells was used to assess the influence of various compounds on the permeability of the P. aeruginosa outer membrane. In addition to the five previously described outer membrane-active compounds EDTA, polymyxin B, gentamicin, poly-L-lysine, and Tris, seven other compounds were shown to increase outer membrane permeability to nitrocefin by 14- to 63-fold. These other compounds included poly-L-ornithine, neomycin, cetyltrimethylammonium bromide, nitrilotriacetate, L-ascorbate, and acetylsalicylate. In each case, Mg2+ ions antagonized, to different extents, the enhancement of outer membrane permeability. The same compounds increased the permeability of the outer membrane to the protein lysozyme and to the hydrophobic fluorescent probe 1-N-phenylnaphthylamine, although L-ascorbate and acetylsalicylate showed only very weak enhancement of uptake in these assays. In this report, we discuss the possibility that these compounds act at a common outer membrane site at which divalent cations noncovalently cross-bridge adjacent lipopolysaccharide molecules.
Abstract PR09: Macrophage promotion of anti-androgen resistance in prostate cancer bone disease (2022)

Abstract Metastatic castration resistant prostate cancer (mCRPC) is the final stage of prostate cancer (PC) that acquires resistance to androgen deprivation therapies (ADT). Despite many recent progresses in the mechanistic understanding of ADT resistance, the specific contribution of the metastatic microenvironment in mCRPC remains largely unknown. A novel in vivo model of androgen dependent bone metastatic PC was developed in address this question. Our identified that macrophages are the major stromal cells in bone metastatic PC. Using multiple genetic models, we demonstrated that macrophages, both monocyte-derived and bone resident populations, were critical for bone metastatic PC to develop resistance to enzalutamide, a clinically used anti-androgen. Mechanistically, macrophages drove resistance through induction of a wound healing like response in prostate cancer cells, which was strongly supported by bioinformatics analysis of multiple patient mCRPC datasets. Furthermore, macrophage depletion or SRC inhibition using a novel specific inhibitor significantly inhibited resistant growth of mCRPC. Together, our findings elucidated a novel mechanism of macrophage-induced anti-androgen resistance of metastatic PC and a promising therapeutic approach to treat this deadly disease. Citation Format: Xue-Feng Li, Cigdem Selli, Asier Unciti-Broceta, Neil O. Carragher, Hai-Yan Hu, Charles L. Sawyers, Bin-Zhi Qian. Macrophage promotion of anti-androgen resistance in prostate cancer bone disease [abstract]. In: Abstracts: AACR Virtual Special Conference: Tumor Immunology and Immunotherapy; 2021 Oct 5-6. Philadelphia (PA): AACR; Cancer Immunol Res 2022;10(1 Suppl):Abstract nr PR09.
Nanoscale Thin Film Corrosion Barriers Enabled By Multilayer Polymer Clay Nanocomposites (2020)

Ultrathin nanocomposite films fabricated by layer-by-layer (LbL) assembly are an emerging class of coatings with remarkable barrier performance. Here, we examine LBL polymer-clay nanocomposite (PCN) coatings that afford anti-corrosion properties comparable to those exhibited by more traditional films that are orders of magnitude thicker. PCN barrier thin films comprised of up to 40 bilayers of polyethyleneimine (PEI) and exfoliated laponite (LAP), montmorillonite (MMT), or vermiculite (VMT) clay platelets were coated onto steel plates using a scalable LBL dip-coating process. A combination of electrochemical impedance spectroscopy and ex-situ electron and vibrational spectroscopy were used to evaluate coating performance during exposure in 0.6 M NaCl for up to 7 days. A PEI/VMT crosslinked coating of only 250 nm thick slowed the corrosion rate of mild steel by three orders of magnitude (R ct = 10 6 vs. 10 3 Ω-cm2) after seven days in 0.6 M NaCl. This performance exceeded the reported performance of other LBL coatings along with much thicker multilayer composite coatings and several conventional pretreatments on mild steel under similar test conditions. The exceptional performance is attributed to the effective barrier properties imparted by a high loading (&gt;80 wt%) of orientated, high aspect ratio (2000:1) platelet layers in a nanobrick wall morphology. Substitution of VMT with lower aspect ratio clay platelets of either MMT (400:1) or LAP (30:1) showed that coated steel corrosion rates and apparent coating permeability scales with platelet size following LAP &gt; MMT &gt;&gt; VMT. Thus, this study has for the first time shown that platelet aspect ratio is a primary means of improving the performance LbL nanocomposite coatings which is in line with the expected behavior of conventional nanocomposites. Given film debonding from the substrate was observed as a common failure mode during exposure for all coating types, replacement of the PEI polymer component with a more debonding-resistant polymer may be an additional pathway to further improve LbL PCN anticorrosion performance.
On-board sensor failure detection of an active suspension system using the generalized likelihood ratio approach (2003)

The authors extend the application of the generalized likelihood ratio (GLR) approach for on-board sensor failure detection and identification (FDI) of an active suspension system using a half-car (bicycle) model. It is assumed that the control design allows for one accelerometer and two linear variable differential transformers. The failures considered are bias and increased sensor noise. The advantages and limitations of the GLR approach in locating the failed sensor and in detecting different types of failures are assessed. It is concluded that the application of this approach is feasible when the failure can be modeled as a deterministic additive term. In other situations the computational requirements make it less practical.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>