gebhart/patrepeval huggingface dataset:
A Novel Cyanophage with a Cyanobacterial Nonbleaching Protein A Gene in the Genome (2011)

A cyanophage, PaV-LD, has been isolated from harmful filamentous cyanobacterium Planktothrix agardhii in Lake Donghu, a shallow freshwater lake in China. Here, we present the cyanophage's genomic organization and major structural proteins. The genome is a 95,299-bp-long, linear double-stranded DNA and contains 142 potential genes. BLAST searches revealed 29 proteins of known function in cyanophages, cyanobacteria, or bacteria. Thirteen major structural proteins ranging in size from 27 kDa to 172 kDa were identified by SDS-PAGE and mass-spectrometric analysis. The genome lacks major genes that are necessary to the tail structure, and the tailless PaV-LD has been confirmed by an electron microscopy comparison with other tail cyanophages and phages. Phylogenetic analysis of the major capsid proteins also reveals an independent branch of PaV-LD that is quite different from other known tail cyanophages and phages. Moreover, the unique genome carries a nonbleaching protein A (NblA) gene (open reading frame [ORF] 022L), which is present in all phycobilisome-containing organisms and mediates phycobilisome degradation. Western blot detection confirmed that 022L was expressed after PaV-LD infection in the host filamentous cyanobacterium. In addition, its appearance was companied by a significant decline of phycocyanobilin content and a color change of the cyanobacterial cells from blue-green to yellow-green. The biological function of PaV-LD nblA was further confirmed by expression in a model cyanobacterium via an integration platform, by spectroscopic analysis and electron microscopy observation. The data indicate that PaV-LD is an exceptional cyanophage of filamentous cyanobacteria, and this novel cyanophage will also provide us with a new vision of the cyanophage-host interactions.
Phosphoinositide-3-OH kinase-dependent regulation of glycogen synthase kinase 3 and protein kinase B/AKT by the integrin-linked kinase (1998)

Integrin-linked kinase (ILK) is an ankyrin-repeat containing serine-threonine protein kinase capable of interacting with the cytoplasmic domains of integrin beta1, beta2, and beta3 subunits. Overexpression of ILK in epithelial cells disrupts cell-extracellular matrix as well as cell-cell interactions, suppresses suspension-induced apoptosis (also called Anoikis), and stimulates anchorage-independent cell cycle progression. In addition, ILK induces nuclear translocation of beta-catenin, where the latter associates with a T cell factor/lymphocyte enhancer-binding factor 1 (TCF/LEF-1) to form an activated transcription factor. We now demonstrate that ILK activity is rapidly, but transiently, stimulated upon attachment of cells to fibronectin, as well as by insulin, in a phosphoinositide-3-OH kinase [Pi(3)K]-dependent manner. Furthermore, phosphatidylinositol(3,4,5)trisphosphate specifically stimulates the activity of ILK in vitro, and in addition, membrane targetted constitutively active Pi(3)K activates ILK in vivo. We also demonstrate here that ILK is an upstream effector of the Pi(3)K-dependent regulation of both protein kinase B (PKB/AKT) and glycogen synthase kinase 3 (GSK-3). Specifically, ILK can directly phosphorylate GSK-3 in vitro and when stably, or transiently, overexpressed in cells can inhibit GSK-3 activity, whereas the overexpression of kinase-deficient ILK enhances GSK-3 activity. In addition, kinase-active ILK can phosphorylate PKB/AKT on serine-473, whereas kinase-deficient ILK severely inhibits endogenous phosphorylation of PKB/AKT on serine-473, demonstrating that ILK is involved in agonist stimulated, Pi(3)K-dependent, PKB/AKT activation. ILK is thus a receptor-proximal effector for the Pi(3)K-dependent, extracellular matrix and growth factor mediated, activation of PKB/AKT, and inhibition of GSK-3.
Multiplicity of §‐endotoxin genes with different insecticidal specificities in Bacillus thuringiensis aizawai 7.29 (1988)

The hypothesis according to which multiple and different delta-endotoxin genes could determine the host-range specificity of the lepidopteran strains of Bacillus thuringiensis is being checked in the case of strains aizawai 7.29 (serotype 7) and entomocidus 601 (serotype 6). From these strains, several crystal protein genes, belonging to different structural types, have been isolated. One of the cloned genes that is not present in strain entomocidus 601 is duplicated in strain aizawai 7.29. This gene belongs to a previously characterized type of crystal protein gene and encodes a protein preferentially active against Pieris brassicae. Two other genes, of presumed chromosomal location, are present in both strains and each displays a unique physical map. In both strains the two genes are in close proximity and in the same orientation. The first, which belongs to a new type of crystal protein gene, encodes a 130-140 kD protein that is not significantly active against the two insect species tested. The other new type of crystal protein gene directs the synthesis of a polypeptide preferentially active against Spodoptera littoralis.
Diastolic chamber properties of the left ventricle assessed by global fitting of pressure-volume data: improving the gold standard of diastolic function (2013)

In cardiovascular research, relaxation and stiffness are calculated from pressure-volume (PV) curves by separately fitting the data during the isovolumic and end-diastolic phases (end-diastolic PV relationship), respectively. This method is limited because it assumes uncoupled active and passive properties during these phases, it penalizes statistical power, and it cannot account for elastic restoring forces. We aimed to improve this analysis by implementing a method based on global optimization of all PV diastolic data. In 1,000 Monte Carlo experiments, the optimization algorithm recovered entered parameters of diastolic properties below and above the equilibrium volume (intraclass correlation coefficients = 0.99). Inotropic modulation experiments in 26 pigs modified passive pressure generated by restoring forces due to changes in the operative and/or equilibrium volumes. Volume overload and coronary microembolization caused incomplete relaxation at end diastole (active pressure > 0.5 mmHg), rendering the end-diastolic PV relationship method ill-posed. In 28 patients undergoing PV cardiac catheterization, the new algorithm reduced the confidence intervals of stiffness parameters by one-fifth. The Jacobian matrix allowed visualizing the contribution of each property to instantaneous diastolic pressure on a per-patient basis. The algorithm allowed estimating stiffness from single-beat PV data (derivative of left ventricular pressure with respect to volume at end-diastolic volume intraclass correlation coefficient = 0.65, error = 0.07 ± 0.24 mmHg/ml). Thus, in clinical and preclinical research, global optimization algorithms provide the most complete, accurate, and reproducible assessment of global left ventricular diastolic chamber properties from PV data. Using global optimization, we were able to fully uncouple relaxation and passive PV curves for the first time in the intact heart.
Anti‐interferon immunoglobulins can improve the trisomy 16 mouse phenotype (1995)

Mouse trisomy 16 is a well-studied model for human chromosome 21 trisomy (Down's syndrome). The late stage trisomy 16 mouse fetus exhibits significant growth retardation, inappropriately opened eyes, and convex rather than concave back curvature. The interferons (alpha, beta, and gamma) have potent growth retarding activity, and sensitivity to these cytokines is controlled by genes that map to mouse chromosome 16 and human chromosome 21. In experiments designed to determine if the interferons induce or aggravate the trisomy phenotype, mice pregnant with trisomy 16 fetuses were injected with a combination of anti-alpha, -beta, and -gamma interferon IgG. This maternal anti-interferon treatment was found to provide measurable benefit to the development and growth of the trisomic fetuses with significant return-toward-normal values observed for overall fetal growth, eye opening, and back curvature.
Internet congestion control (2002)

This article reviews the current transmission control protocol (TCP) congestion control protocols and overviews recent advances that have brought analytical tools to this problem. We describe an optimization-based framework that provides an interpretation of various flow control mechanisms, in particular, the utility being optimized by the protocol's equilibrium structure. We also look at the dynamics of TCP and employ linear models to exhibit stability limitations in the predominant TCP versions, despite certain built-in compensations for delay. Finally, we present a new protocol that overcomes these limitations and provides stability in a way that is scalable to arbitrary networks, link capacities, and delays.
Automating Failure Testing Research at Internet Scale (2016)

Large-scale distributed systems must be built to anticipate and mitigate a variety of hardware and software failures. In order to build confidence that fault-tolerant systems are correctly implemented, Netflix (and similar enterprises) regularly run failure drills in which faults are deliberately injected in their production system. The combinatorial space of failure scenarios is too large to explore exhaustively. Existing failure testing approaches either randomly explore the space of potential failures randomly or exploit the "hunches" of domain experts to guide the search. Random strategies waste resources testing "uninteresting" faults, while programmer-guided approaches are only as good as human intuition and only scale with human effort.
Embryonic stem cell differentiation: emergence of a new era in biology and medicine (2005)

The discovery of mouse embryonic stem (ES) cells >20 years ago represented a major advance in biology and experimental medicine, as it enabled the routine manipulation of the mouse genome. Along with the capacity to induce genetic modifications, ES cells provided the basis for establishing an in vitro model of early mammalian development and represented a putative new source of differentiated cell types for cell replacement therapy. While ES cells have been used extensively for creating mouse mutants for more than a decade, their application as a model for developmental biology has been limited and their use in cell replacement therapy remains a goal for many in the field. Recent advances in our understanding of ES cell differentiation, detailed in this review, have provided new insights essential for establishing ES cell-based developmental models and for the generation of clinically relevant populations for cell therapy.
Synthetic Inhibitors of Cytochrome P-450 2A6:  Inhibitory Activity, Difference Spectra, Mechanism of Inhibition, and Protein Cocrystallization (2006)

A series of 3-heteroaromatic analogues of nicotine were synthesized to delineate structural and mechanistic requirements for selectively inhibiting human cytochrome P450 (CYP) 2A6. Thiophene, substituted thiophene, furan, substituted furan, acetylene, imidazole, substituted imidazole, thiazole, pyrazole, substituted pyrazole, and aliphatic and isoxazol moieties were used to replace the N-methylpyrrolidine ring of nicotine. A number of potent inhibitors were identified, and several exhibited high selectivity for CYP2A6 relative to CYP2E1, -3A4, -2B6, -2C9, -2C19, and -2D6. The majority of these inhibitors elicited type II difference spectra indicating the formation of a coordinate covalent bond to the heme iron. The majority of inhibitors were reversible inhibitors although several mechanism-based inactivators were identified. Most of the inhibitors were also relatively metabolically stable. X-ray crystal structures of CYP2A6 cocrystallized with three furan analogues bearing methanamino side chains indicated that the amine side chain coordinated to the heme iron. The pyridyl moiety was positioned to accept a hydrogen bond from Asn297, and all three inhibitors exhibited orthogonal aromatic-aromatic interactions with protein side chains. For comparison, the cocrystal structure of 4,4'-dipyridyl disulfide was also obtained and showed that the pyridine moiety could assume a different orientation than that observed for the 3-heteroaromatic pyridines examined. For the 3-heteroromatic pyridines, N-methyl and N,N-dimethyl amino groups increased the apparent Ki and distorted helix I of the protein. Substitution of a phenyl ring for the pyridyl ring also increased the apparent Ki, which is likely to reflect the loss of the hydrogen bonding interaction with Asn297. In contrast, inhibitory potency for other P450s was increased, and the selectivity of the phenyl analogues for CYP2A6 was decreased relative to the pyridyl compounds. The results suggest that inhibitors that compliment the active site features of CYP2A6 can exhibit significant selectivity for CYP2A6 relative to other human liver drug-metabolizing P450s.
Incorporation of therapeutically modified bacteria into gut microbiota inhibits obesity (2014)

Metabolic disorders, including obesity, diabetes, and cardiovascular disease, are widespread in Westernized nations. Gut microbiota composition is a contributing factor to the susceptibility of an individual to the development of these disorders; therefore, altering a person's microbiota may ameliorate disease. One potential microbiome-altering strategy is the incorporation of modified bacteria that express therapeutic factors into the gut microbiota. For example, N-acylphosphatidylethanolamines (NAPEs) are precursors to the N-acylethanolamide (NAE) family of lipids, which are synthesized in the small intestine in response to feeding and reduce food intake and obesity. Here, we demonstrated that administration of engineered NAPE-expressing E. coli Nissle 1917 bacteria in drinking water for 8 weeks reduced the levels of obesity in mice fed a high-fat diet. Mice that received modified bacteria had dramatically lower food intake, adiposity, insulin resistance, and hepatosteatosis compared with mice receiving standard water or control bacteria. The protective effects conferred by NAPE-expressing bacteria persisted for at least 4 weeks after their removal from the drinking water. Moreover, administration of NAPE-expressing bacteria to TallyHo mice, a polygenic mouse model of obesity, inhibited weight gain. Our results demonstrate that incorporation of appropriately modified bacteria into the gut microbiota has potential as an effective strategy to inhibit the development of metabolic disorders.
New insights into elastic fiber assembly (2007)

Abstract Elastic fibers provide recoil to tissues that undergo repeated stretch, such as the large arteries and lung. These large extracellular matrix (ECM) structures contain numerous components, and our understanding of elastic fiber assembly is changing as we learn more about the various molecules associated with the assembly process. The main components of elastic fibers are elastin and microfibrils. Elastin makes up the bulk of the mature fiber and is encoded by a single gene. Microfibrils consist mainly of fibrillin, but also contain or associate with proteins such as microfibril associated glycoproteins (MAGPs), fibulins, and EMILIN‐1. Microfibrils were thought to facilitate alignment of elastin monomers prior to cross‐linking by lysyl oxidase (LOX). We now know that their role, as well as the overall assembly process, is more complex. Elastic fiber formation involves elaborate spatial and temporal regulation of all of the involved proteins and is difficult to recapitulate in adult tissues. This report summarizes the known interactions between elastin and the microfibrillar proteins and their role in elastic fiber assembly based on in vitro studies and evidence from knockout mice. We also propose a model of elastic fiber assembly based on the current data that incorporates interactions between elastin, LOXs, fibulins and the microfibril, as well as the pivotal role played by cells in structuring the final functional fiber. Birth Defects Research (Part C) 81:229–240, 2007. © 2008 Wiley‐Liss, Inc.
Respiratory Syncytial Virus Genetic and Antigenic Diversity (2000)

Respiratory syncytial virus (RSV) is a major cause of viral lower respiratory tract infections among infants and young children in both developing and developed countries. There are two major antigenic groups of RSV, A and B, and additional antigenic variability occurs within the groups. The most extensive antigenic and genetic diversity is found in the attachment glycoprotein, G. During individual epidemic periods, viruses of both antigenic groups may cocirculate or viruses of one group may predominate. When there are consecutive annual epidemics in which the same group predominates, the dominant viruses are genetically different from year to year. The antigenic differences that occur among these viruses may contribute to the ability of RSV to establish reinfections throughout life. The differences between the two groups have led to vaccine development strategies that should provide protection against both antigenic groups. The ability to discern intergroup and intragroup differences has increased the power of epidemiologic investigations of RSV. Future studies should expand our understanding of the molecular evolution of RSV and continue to contribute to the process of vaccine development.
Stereocontrolled Approach to Phenyl Cyclitols from (SR)-[(p-Tolylsulfinyl)methyl]-p-quinol (2009)

Reactions of enantiopure (SR)-[(p-tolylsulfinyl)methyl]-p-quinol with ArAlMe(2) reagents allowed a highly diastereoselective 1,4-addition of the aryl group with an efficient desymmetrization of the prochiral cyclohexadienone moiety. The asymmetric synthesis of phenyl-substituted polyoxygenated cyclohexane derivatives was achieved by combining this reaction with a stereoselective reduction and elimination of the beta-hydroxysulfoxide, after oxidation to sulfone, to recover a carbonyl group, and a stereoselective epoxidation.
Carriers versus Adapters in Stochastic Sensing (2005)

The perfect host: The detection of analyte-dependent changes in the conduction of individual transmembrane protein pores is demonstrated for small organic molecules, which are detected as complexes with a carrier molecule, cucurbit[6]uril (CB6). The carrier system also allows the determination of dissociation constants, and association and dissociation rate constants, for CB6⋅guest pairs (see picture; αHL=α-hemolysin, THF=tetrahydrofuran).
Laser desorption/ionization mass spectrometry for direct profiling and imaging of small molecules from raw biological materials (2008)

Matrix-assisted laser desorption/ionization(MALDI) mass spectrometry(MS) has been widely used for analysis of biological molecules, especially macromolecules such as proteins. However, MALDI MS has a problem in small molecule (less than 1 kDa) analysis because of the signal saturation by organic matrixes in the low mass region. In imaging MS (IMS), inhomogeneous surface formation due to the co-crystallization process by organic MALDI matrixes limits the spatial resolution of the mass spectral image. Therefore, to make laser desorption/ionization (LDI) MS more suitable for mass spectral profiling and imaging of small molecules directly from raw biological tissues, LDI MS protocols with various alternative assisting materials were developed and applied to many biological systems of interest. Colloidal graphite was used as a matrix for IMS of small molecules for the first time and methodologies for analyses of small metabolites in rat brain tissues, fruits, and plant tissues were developed. With rat brain tissues, the signal enhancement for cerebroside species by colloidal graphite was observed and images of cerebrosides were successfully generated by IMS. In addition, separation of isobaric lipid ions was performed by imaging tandem MS. Directly from Arabidopsis flowers, flavonoids were successfully profiled and heterogeneous distribution of flavonoids in petals was observed for the first time by graphite-assisted LDI(GALDI) IMS.
EARTHQUAKE PERFORMANCE OF STEEL FRAMES WITH NITINOL BRACES (2006)

In this paper, the seismic performance of a three- and a six-storey steel frame equipped with different bracing configurations is assessed. The bracing systems consist of traditional buckling-restrained steel braces and superelastic Nitinol shape-memory alloy (SMA) braces. Background on the behaviour of SMAs is provided and a state-of-the-art review of the applications of such new materials in earthquake engineering is presented. A uniaxial constitutive model for superelastic SMAs is then implemented into the finite element platform OpenSees and nonlinear dynamic analyses are performed. Finally, the seismic performance of the structures under investigation is judged through the evaluation of several response quantities, to determine the efficacy of the new bracing system in reducing earthquake-induced vibrations.
Real-time computerized annotation of pictures (2006)

Automated annotation of digital pictures has been a highly challenging problem for computer scientists since the invention of computers. The capability of annotating pictures by computers can lead to breakthroughs in a wide range of applications including Web image search, online picture-sharing communities, and scientific experiments. In our work, by advancing statistical modeling and optimization techniques, we can train computers about hundreds of semantic concepts using example pictures from each concept. The ALIPR (Automatic Linguistic Indexing of Pictures -Real Time)system of fully automatic and high speed annotation for online pictures has been constructed. Thousands of pictures from an Internet photo-sharing site, unrelated to the source of those pictures used in the training process, have been tested. The experimental results show that a single computer processor can suggest annotation terms in real-time and with good accuracy.
Finite Element Modeling of Electric Field Effects of TASER Devices on Nerve and Muscle (2006)

TASERs deliver electrical pulses that can temporarily incapacitate subjects. The goal of this paper is to analyze the distribution of currents in muscle layers and understand the electro-muscular incapacitation safety and efficacy of TASERs. The analyses describe skeletal muscle and motor nerve activation, cell electroporation and current and electric field distributions through skin, fat and muscle layers, under worst-case assumptions for TASER electrode penetration and separation. For the muscle layer, the analysis predicts worst-case current-density and field-strength values of 94 mA/cm(2) and 47 V/cm. Both values are higher than thresholds required for neuromuscular activation but significantly lower than levels needed for permanent cellular electroporation or tissue damage. The results indicate that TASERs are safe and effective in producing temporary subject incapacitation.
A new high resolution color flow system using an eigendecomposition-based adaptive filter for clutter rejection (2002)

We present a new signal processing strategy for high frequency color flow mapping in moving tissue environments. A new application of an eigendecomposition-based clutter rejection filter is presented with modifications to deal with high blood-to-clutter ratios (BCR). Additionally, a new method for correcting blood velocity estimates with an estimated tissue motion profile is detailed. The performance of the clutter filter and velocity estimation strategies is quantified using a new swept-scan signal model. In vivo color flow images are presented to illustrate the potential of the system for mapping blood flow in the microcirculation with external tissue motion.
Prognostic factors in 1,521 melanoma patients with distant metastases. (1995)

Despite new treatment options, the survival rate of patients with metastatic melanoma has not changed significantly over the last 22 years; their prognosis remains dismal. The three prognostic variables identified in this study should be considered in the design of future clinical trials.