gebhart/patrepeval huggingface dataset:
Tailoring in vitro evolution for protein affinity or stability (2000)

We describe a rapid and general technology working entirely in vitro to evolve either the affinity or the stability of ligand-binding proteins, depending on the chosen selection pressure. Tailored in vitro selection strategies based on ribosome display were combined with in vitro diversification by DNA shuffling to evolve either the off-rate or thermodynamic stability of single-chain Fv antibody fragments (scFvs). To demonstrate the potential of this method, we chose to optimize two proteins already possessing favorable properties. A scFv with an initial affinity of 1.1 nM (koff at 4°C of 10−4 s−1) was improved 30-fold by the use of off-rate selections over a period of several days. As a second example, a generic selection strategy for improved stability exploited the property of ribosome display that the conditions can be altered under which the folding of the displayed protein occurs. We used decreasing redox potentials in the selection step to select for molecules stable in the absence of disulfide bonds. They could be functionally expressed in the reducing cytoplasm, and, when allowed to form disulfides again, their stability had increased to 54 kJ/mol from an initial value of 24 kJ/mol. Sequencing revealed that the evolved mutant proteins had used different strategies of residue changes to adapt to the selection pressure. Therefore, by a combination of randomization and appropriate selection strategies, an in vitro evolution of protein properties in a predictable direction is possible.
Targeting a Pneumocystis carinii Group I Intron with Methylphosphonate Oligonucleotides:  Backbone Charge Is Not Required for Binding or Reactivity (2000)

Pneumocystis carinii is a mammalian pathogen that contains a self-splicing group I intron in its large subunit rRNA precursor. We report the binding of methylphosphonate/DNA chimeras and neutral methylphosphonate oligonucleotides to a ribozyme that is a truncated form of the intron. At 15 mM Mg(2+), the nuclease-resistant all-methylphosphonate hexamer, d(AmTmGmAmCm)rU, with a sequence that mimics the 3' end of the precursor's 5' exon, binds with a dissociation constant of 272 nM. The hexamer's dissociation constant for binding by base-pairing alone to the ribozyme's binding site sequence is 8.3 mM. Thus there is a 30 000-fold binding enhancement by tertiary interactions (BETI), which is close to the 60 000-fold enhancement previously observed with the all-ribo hexamer, r(AUGACU). Evidently, backbone charge and 2' hydroxyl groups are not required for BETI. At 3-15 mM Mg(2+), the all-methylphosphonate and DNA oligonucleotides trans-splice to a truncated form of the rRNA precursor, but do not compete with cis-splicing when pG is present. These results suggest that uncharged or partially charged backbones may be used to design therapeutics to target RNAs through binding enhancement by tertiary interactions and suicide inhibition strategies.
Cationic iridium(iii) complexes for phosphorescence staining in the cytoplasm of living cells (2008)

Two cationic iridium(III) complexes with bright green and red emissions were demonstrated as phosphorescent dyes for living cell imaging. In particular, their exclusive staining in cytoplasm, low cytotoxicity and reduced photobleaching, as well as cell membrane permeability, make the two complexes promising candidates for the design of specific bioimaging agents.
Reliability of preparation procedure for sphingosomal vincristine (2005)

The recommended constitution procedure of sphingosomal vincristine from a three-vial kit can be reliably performed in pharmacies with a high degree of confidence. Small variations in temperature and incubation time had no effects on the quality of the product.
Using speech recognition in a personal communications system (2003)

The authors give an overview of speech recognition systems and discuss design strategies for their use in portable communications. State-of-the-art speech recognition systems can recognize continuously spoken speech from a large vocabulary in real time. In the future, portable speech recognition systems will be made possible by advances in integrated circuit technology, by optimizing system architectures, and by exploiting the special features of personal communications systems. Types of speech recognizers are discussed. Current speech recognition systems are outlined. Personal communication systems with speech recognition are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
ON THE BINDING OF CONGO RED BY AMYLOID (1962)

Congo red in alkaline 80% ethyl alcohol solution saturated with NaCl stains amyloid selectively. The distribution of the dye is very similar to that observed in serial sections stained with Highman's Congo red method. In sections stained with Congo red in aqueous or alcoholic solutions without differentiation all tissue structures are intensely colored, but only amyloid is dichroic. The rapid removal of dye by alkaline solutions from structures other than amyloid suggests ionic or salt-type bonds between Congo red and these structures. In contrast, the binding of Congo red by amyloid from alkaline alcoholic solutions and the increase in intensity of staining upon addition of NaCl indicate a non-ionic type linkage between amyloid and dye. The effects of deamination, acetylation and various oxidation procedures on the binding of Congo red indicate interaction of the dye with hydroxyl groups of amyloid. According to data on the direct dyeing of cellulose in textile dyeing, Congo red is adsorbed by hydrogen bonding between hydroxyl groups of the polysaccharide chains and the amino groups of the dye. It seems probable that a similar mechanism is involved in the binding of Congo red by amyloid. It is suggested that the selective staining of amyloid with Congo red is due to steric configurations of amyloid or one of its components which favor non-ionic binding of the eye.
Putative roles of hepatitis B x antigen in the pathogenesis of chronic liver disease (2009)

Under most circumstances, hepatitis B virus (HBV) is noncytopathic. However, hepatocellular regeneration that accompanies each bout of hepatitis appears to be associated with increased integration of HBV DNA fragments expressing the virus encoded hepatitis B x antigen (HBxAg). Intrahepatic HBxAg staining correlates with the intensity and progression of chronic liver disease (CLD), and additional work has shown that HBxAg blocks immune mediated killing by Fas and by tumor necrosis factor alpha (TNFalpha). This is not only associated with the blockage of caspase activities by HBxAg, but also by the constitutive stimulation of hepatoprotective pathways, such as nuclear factor kappa B (NF-kappaB), phosphoinositol 3-kinase (PI3K), and beta-catenin (beta-catenin). HBxAg also appears to promote fibrogenesis, by stimulating the production of fibronectin. HBxAg also stimulates the production and activity of transforming growth factor beta1 (TGFbeta1) by several mechanisms, thereby promoting the profibrogenic and tumorigenic properties of this important cytokine. In addition, HBxAg appears to remodel the extracellular matrix (ECM) by altering the expression of several matrix metalloproteinases (MMPs), which may promote tumor metastasis. Hence, HBxAg appears to promote chronic infection by preventing immune mediated apoptosis of infected hepatocytes, by promoting the establishment and persistence of fibrosis and cirrhosis preceding the development of HCC, and by promoting the remodeling of EMC during tumor progression.
Synthesis of the C45–C53 tetrahydropyran domain of norhalichondrins and the C14–C22 tetrahydrofuran domain of the halichondrin family (2012)

Sequential asymmetric α-aminoxylation of aldehydes and Horner–Wadsworth–Emmons olefination has been used as the key reaction for the synthesis of the C45–C53 tetrahydropyran domain of norhalichondrins and C14–C22 tetrahydrofuran domain of halichondrin family.
Dual-Functionalized Nanostructured Biointerfaces by Click Chemistry (2014)

The presentation of biologically active molecules at interfaces has made it possible to investigate the responses of cells to individual molecules in their matrix at a given density and spacing. However, more sophisticated methods are needed to create model surfaces that present more than one molecule in a controlled manner in order to mimic at least partially the complexity given in natural environments. Herein, we present dual-functionalized surfaces combining quasi-hexagonally arranged gold nanoparticles with defined spacings and a newly developed PEG-alkyne coating to functionalize the glass in the intermediate space. The PEG-alkyne coating provides an inert background for cell interactions but can be modified orthogonally to the gold nanoparticles with numerous azides, including spectroscopically active molecules, peptides, and biotin at controlled densities by the copper(I)-catalyzed azide alkyne click reaction. The simultaneous presentation of cRGD on the gold nanoparticles with 100 nm spacing and synergy peptide PHSRN in the space between has a striking effect on REF cell adhesion; cells adhere, spread, and form mature focal adhesions on the dual-functionalized surfaces, whereas cells cannot adhere on either monofunctional surface. Combining these orthogonal functionalization methods creates a new platform to study precisely the crosstalk and synergy between different signaling molecules and clustering effects in ligand-receptor interactions.
Electron Microscopic Analysis of the Bone-Titanium Interface (1983)

Ten cylindrical implants, made of polycarbonate and covered with a 120-250-nm-thick layer of pure titanium, were implanted into each tibial metaphysis of five rabbits. Observation time was 12 weeks. The implants were surrounded by mature, living bone. No soft tissue intervened between bone and implant at any point. With TEM microscopy the titanium was shown to be bordered by a 20-nm-thick layer of proteoglycans, showing the characteristics of ground substance, and separating the collagen from the implant surface. Cells at the interface were likewise separated from the titanium by such a layer. Hydroxyapatite crystals were observed within the ground substance layer, occasionally seemingly in direct contact with the titanium. Normal mineralization was present 100-500 nm from the implant surface. While this study aims at defining interface anatomy, it also shows that macroscopically smooth-surfaced titanium can readily heal into bone without a soft tissue envelope. This could be of help for materials' choice and design of permanently fixed implants.
Spinning-sideband-free and spinning-sideband-only NMR spectra in spinning samples (1982)

NMR spectra are needlessly confusing when spinning sidebands and isotropic peaks lie on the same curve. Qualitative analysis is impossible if these spinning sidebands cannot be distinguished from isotropic peaks and quantitative measurement is frustrated whenever any sideband overlaps any other peak. Resolving a spectrum into several curves, one containing only isotropic peaks, another only first higher frequency sidebands, still another only first lower, etc., eliminates these problems. These extra curves, which can be generated by an echo technique, do not require extra acquisition time. An ordinary echo spectrum refocused after two revolutions has the same S/N ratio as each curve in a separated spectrum which is made with the same total number of acquisitions.
No-Reference Perceptual Quality Assessment Of Colour Image (2006)

Publication in the conference proceedings of EUSIPCO, Florence, Italy, 2006
Secure PC Platform Based on Dual-Bus Architecture (2012)

The emergence of single CPU dual bus architecture provided a new kind of architecture that aimed at preventing intruders from accessing valuable information stored in the computer system. Security in Von Neumann architecture is currently poorly considered, and it does not reduce significant vulnerabilities. Separating the network communication components from the data processing ones is our concern in this paper. Many proposed schemes were presented recently, but none of which, employing separate system bus, have been proven experimentally as a potentially effective method for protecting the data stored in hard drives and removable disks. In our scheme, the system does not need to maintain any authentication mechanism or data integrity for the packets sent by any node, with a well-received attention towards threatening our valuable stored data. In this paper we implemented a model for a dual bus architecture system based on a bus bridge which controls the data transferred between the two system buses, as well as preventing all spy ware programs. The experiment is done and the result has proven that the dual bus architecture is reasonable and effective. The analysis also showed that the entire computer system, including peripherals is well protected from outside intruders.
Closed-Chest Decannulation of Transthoracically Inserted Aortic Balloon Catheter without Grafting (1987)

A method is presented which allows removal of a balloon assist catheter inserted directly (without a graft) through the ascending aorta in the course of heart surgery without the need for reopening the sternotomy incision. The catheter is inserted through the aortic wall under the protection of two purse string sutures which are temporarily tightened using implantable grade silastic rubber tourniquet. The end of the tourniquet is placed subcutaneously in a subxiphoid position. At the time of discontinuation of balloon assist, the balloon can be removed using local anesthesia without reopening the sternum by exposing the end of the tourniquet substernally, removing the catheter, and plugging the tourniquet. The silastic tourniquet may be left in indefinitely or removed through a similar exposure six to eight weeks after the procedure.
Small intestinal bacterial overgrowth in systemic sclerosis (2009)

Our study underscores that SIBO often occurs in SSc patients. We further suggest that GSS may be systematically performed in SSc patients; since we found a correlation between GSS of digestive symptoms > or =5 and SIBO, we suggest that glucose H(2)/CH(4) breath test may be performed in the subgroup of SSc patients exhibiting GSS > or =5.
Down‐regulation of a morphogen (sonic hedgehog) gradient in the gastric epithelium of Helicobacter pylori‐infected Mongolian gerbils (2005)

Sonic hedgehog (Shh) is a morphogen involved in many aspects of patterning of the gut during embryogenesis and in gastric fundic gland homeostasis in the adult. Intestinal metaplastic change of the gastric epithelium is associated with the loss of Shh expression, and mice that lack Shh expression show intestinal transformation of the gastric mucosa. The present study was designed to investigate the alteration of Shh expression in the stomach of an experimental model of Helicobacter pylori (H. pylori) colonization. Male Mongolian gerbils were inoculated with H. pylori and examined 4 and 51 weeks later. The level of Shh mRNA expression was determined by quantitative RT-PCR and in situ hybridization. Shh protein expression was determined by immunoblotting and immunohistochemistry. Shh was expressed in the parietal cells, zymogenic cells, and mucous neck cells of the gastric fundic glands of gerbils. Prolonged colonization by H. pylori led to extension of the inflammation from the antrum to the corpus of the stomach, with loss of Shh expression. Loss of Shh expression correlated with loss of parietal cells, disturbed maturation of the mucous neck cell-zymogenic cell lineage, and increased cellular proliferation. Shh expression is significantly reduced in H. pylori-associated gastritis. These data show for the first time that H. pylori infection leads to down-regulation of the expression of a morphogen with an established role (Shh) in gastric epithelial differentiation.
Characterizing storage workloads with counter stacks (2014)

Existing techniques for identifying working set sizes based on miss ratio curves (MRCs) have large memory overheads which make them impractical for storage workloads. We present a novel data structure, the counter stack, which can produce approximate MRCs while using sublinear space. We show how counter stacks can be checkpointed to produce workload representations that are many orders of magnitude smaller than full traces, and we describe techniques for estimating MRCs of arbitrary workload combinations over arbitrary windows in time. Finally, we show how online analysis using counter stacks can provide valuable insight into live workloads.
Remarkable decrease in overpotential of oxalate formation in electrochemical CO2reduction by a metal–sulfide cluster (1995)

Triangular metal–sulfide clusters, [{Ir(C5Me5)}3(µ3-S)2]2+ and [{Co(C5H4Me)}3(µ3-S)2]2+, catalyse the electrochemical CO2 reduction to selectively produce oxalate at –1.30 and –0.70 V (vs. Ag/AgCl), respectively, in MeCN.
Effective load-balancing of peer-to-peer systems (2003)

The growing popularity of peer-to-peer (P2P) systems has necessitated the need for managing huge volumes of data e#ciently to ensure acceptable user response times. Dynamically changing popularities of data items and skewed user query patterns in P2P systems may cause some of the peers to become bottlenecks, thereby resulting in severe load imbalance and consequently increased user response times. An effective load-balancing mechanism becomes a necessity in such cases. Such load-balancing can be achieved by efficient online data migration/replication. While much work has been done to harness the huge computing resources of P2P systems for high-performance computing and scientific applications, issues concerning load-balancing with a view towards faster access to data for normal users have not received adequate attention. Notably, the sheer size of P2P networks and the inherent dynamism of the environment pose significant challenges to load-balancing. The main contributions of our proposal are three-fold. First, we view a P2P system as comprising clusters of peers and present techniques for both intra-cluster and inter-cluster load-balancing. Second, we analyze the trade-o#s between the options of migration and replication and formulate a strategy based on which the system decides at run-time which option to use. Third, we propose an e#ective strategy aimed towards automatic self-evolving clusters of peers. Our performance evaluation demonstrates that our proposed technique for inter-cluster load-balancing is indeed effective in improving the system performance significantly. To our knowledge, this work is one of the earliest attempts at addressing load-balancing via both online data migration and replication in P2P environments.
Costimulation of CD4 + T Cells via CD28 Modulates Human Immunodeficiency Virus Type 1 Infection and Replication in Vitro (1995)

Stimulation of human immunodeficiency virus type 1 (HIV-1)-infected donor peripheral blood mononuclear cells (PBMCs) via the TCR-CD3 complex induces HIV-1 production in vitro (Zarling JM, et al.: Nature [London] 1990;347:92; Haffar OK, et al.: J Virol 1992;66:4279; Moran PM, et al.: AIDS Res Hum Retroviruses 1993;9:455). However, in addition to the primary stimulatory signal delivered through the TCR-CD3 complex, optimal T cell activation requires secondary or costimulatory signals delivered via various T cell accessory proteins (Alton A, et al.: Adv Immunol 1990;48:227). In this article we explore the role of costimulation of T cells via CD28 in HIV-1 replication. Ligation of CD28 with either a CD28-specific MAb or by coculture of PBMCs with Chinese hamster ovary (CHO) cell lines stably expressing either of the CD28 counterreceptors, B7-1 (CD80) or B7-2 (CD86), concomitant with stimulation via CD3, results in increased virus replication compared to stimulation via CD3 alone. CD28 ligation also augments de novo infection of CD3-stimulated seronegative donor PBMCs with cell-free virus. Increased virus replication following CD28 ligation is not solely attributed to increased levels of endogenous IL-2, because addition of an anti-IL-2-neutralizing antibody only partially inhibits the response. In contrast, interfering with the interaction between CD28 and its counterreceptors on antigen-presenting cells (APCs) using CTLA4Ig effectively inhibits virus replication. At high concentrations CTLA4Ig also reduces cell proliferation. These in vitro results suggest that CD28 plays a central role in HIV-1 replication and that interfering with the CD28 costimulatory pathway may modify the course of HIV-1 infection.
Motility as a virulence factor for Vibrio cholerae (1975)

The ability of motile strains of the Ogawa and Inaba serotypes of classical Vibrio cholerae and of the El Tor biotypes to kill suckling mice after oral challenge with 10-8 colony-forming units (representing at least 100 to 1,000 minimal lethal doses) was compared to that of nonmotile derivatives of the same strains. Loss of motility, in each case, resulted in a marked reduction in virulence. The mortality (at 36 h) caused by 10 of the 13 nonmotile strains was 32% or less. whereas the motile wild-type strains resulted in nearly 100% deaths. The reduced virulence of the nonmotile strains was associated with reduced capacity to adsorb to the surface of segments of mouse intestine. The mutants were tested for alterations in enterotoxin production and surface properties. The results suggest that motility may contribute to virulence by increasing the chance for association of the vibrios with the intestinal mucosa.
<title>Epidermal heating during laser-induced photothermolysis of port wine stains: modeling melanosomal heating after dynamic cooling of the skin surface</title> (1995)

The clinical objective in treatment of port wine stains is to maximize thermal damage to the abnormal blood vessels without introducing thermal damage to the normal overlying epidermis. The rationale of dynamic cooling is to protect the epidermis from thermal damage by selectively cooling this layer down immediately before delivering the laser pulse. This work discusses the thermal dynamics of epidermal cooling by milliseconds cryogen spurts and melanosomal heating by the laser pulse.
How embryos work: a comparative view of diverse modes of cell fate specification (1990)

Embryonic processes in the nematode C. elegans, the gastropod mollusc Ilyanassa, the dipteran Drosophila, the echinoid Strongylocentrotus purpuratus, the ascidian Ciona, the anuran Xenopus, the teleost Brachydanio and mouse are compared with respect to a series of parameters such as invariant or variable cleavage, the means by which the embryonic axes are set up, egg anisotropies and reliance on conditional or on autonomous specification processes. A molecular interpretation of these modes of specification of cell fate in the embryo is proposed, in terms of spatial modifications of gene regulatory factors. On this basis, classically defined phenomena such as regulative development and cytoplasmic localization can be interpreted at a mechanistic level, and the enormous differences between different forms of embryogenesis in the Animal Kingdom can be considered within a common mechanistic framework. Differential spatial expression of histospecific genes is considered in terms of the structure of the gene regulatory network that will be required in embryos that utilize cell-cell interaction, autonomous vs conditional specification and maternal spatial information to differing extents. It is concluded that the regulatory architectures according to which the programs of gene expression are organized are special to each form of development, and that common regulatory principles are to be found only at lower levels, such as those at which the control regions of histospecific structural genes operate.