gebhart/patrepeval huggingface dataset:
Metal-dependent folding of a single zinc finger from transcription factor IIIA. (1987)

A 30-amino acid peptide, which corresponds to the second "zinc finger" domain of transcription factor IIIA, has been synthesized and purified. This peptide folds in the presence of zinc: adding Zn2+ significantly changes the circular dichroism spectrum, and Zn2+ protects the peptide from tryptic digestion. The peptide also binds Co2+, and the absorption spectrum of the Co2+ complex suggests that a tetrahedral binding site is formed by two cysteines and two histidines. Experiments at higher temperatures (60-75 degrees C) suggest that these folded metal-peptide complexes are quite thermostable. The peptide shows some sequence-specific effects in DNase and methylation protection experiments. However, it does not give a clear "footprint," and some effects are observed in the absence of added zinc.
Autologous Islet Transplantation to Prevent Diabetes After Pancreatic Resection (1995)

Pancreatectomy can relieve intractable pain caused by chronic pancreatitis. Islet autotransplantation is safe and can prevent long-term diabetes in more than 33% of patients and should be an adjunct to any pancreatic resection. A given patient's probability of success can be predicted by the morphologic features of the pancreas.
Single molecule detection of intermediates during botulinum neurotoxin translocation across membranes (2007)

The dynamics of Clostridium botulinum neurotoxins (BoNTs) protein-translocation across membranes was investigated by using a single molecule assay with millisecond resolution on excised patches of neuronal cells. Translocation of BoNT/A light chain (LC) by heavy chain (HC) was observed in real time as an increase of channel conductance: the HC channel is occluded by the LC during transit, then unoccluded after completion of translocation and release of LC-cargo. We identified an entirely unknown succession of intermediate conductance stages during LC translocation. For the single-chain BoNT/E, by contrast to the di-chain BoNT/A, we demonstrate that productive translocation requires proteolysis of the LC cargo from the HC chaperone. We propose a model for the set of protein-protein interactions between translocase and cargo at each step of translocation that supports the notion of an interdependent, tight interplay between the HC chaperone and the LC cargo preventing LC aggregation and dictating the outcome of translocation: productive passage of cargo or abortive channel occlusion by cargo.
A conserved double-stranded RNA-binding domain. (1992)

We have identified a double-stranded (ds)RNA-binding domain in each of two proteins: the product of the Drosophila gene staufen, which is required for the localization of maternal mRNAs, and a protein of unknown function, Xlrbpa, from Xenopus. The amino acid sequences of the binding domains are similar to each other and to additional domains in each protein. Database searches identified similar domains in several other proteins known or thought to bind dsRNA, including human dsRNA-activated inhibitor (DAI), human trans-activating region (TAR)-binding protein, and Escherichia coli RNase III. By analyzing in detail one domain in staufen and one in Xlrbpa, we delimited the minimal region that binds dsRNA. On the basis of the binding studies and computer analysis, we have derived a consensus sequence that defines a 65- to 68-amino acid dsRNA-binding domain.
Biosynthesis of salicylic acid in plants (2009)

Salicylic acid (SA) is an important signal molecule in plants. Two pathways of SA biosynthesis have been proposed in plants. Biochemical studies using isotope feeding have suggested that plants synthesize SA from cinnamate produced by the activity of phenylalanine ammonia lyase (PAL). Silencing of PAL genes in tobacco or chemical inhibition of PAL activity in Arabidopsis, cucumber and potato reduces pathogen-induced SA accumulation. Genetic studies, on the other hand, indicate that the bulk of SA is produced from isochorismate. In bacteria, SA is synthesized from chorismate through two reactions catalyzed by isochorismate synthase (ICS) and isochorismate pyruvate lyase (IPL). Arabidopsis contains two ICS genes but has no gene encoding proteins similar to the bacterial IPL. Thus, how SA is synthesized in plants is not fully elucidated. Two recently identified Arabidopsis genes, PBS3 and EPS1, are important for pathogen-induced SA accumulation. PBS3 encodes a member of the acyl-adenylate/thioester-forming enzyme family and EPS1 encodes a member of the BAHD acyltransferase superfamily. PBS3 and EPS1 may be directly involved in the synthesis of an important precursor or regulatory molecule for SA biosynthesis. The pathways and regulation of SA biosynthesis in plants may be more complicated than previously thought.
WHITE-LIGHT VIEWING OF SURFACE HOLOGRAMS BY SIMPLE DISPERSION COMPENSATION (1966)

Two successful methods are reported for achromatizing the white-light reconstruction of a 2-beam surface hologram. One method uses prisms for dispersion compensation. The other uses a single-plane diffraction grating as the correcting element.
Dynamics of oralrespiratory coordination in full‐term and preterm infants: II. Continuing effects at 3 months post term (1999)

Thirty‐two infants participating in a longitudinal study of the effects of premature birth on sucking and breathing were tested at 3 months post term. They were assigned at a previous test to either a healthy full‐term, healthy preterm, or high risk preterm group on the basis of birth weight, postconceptional age at birth, and perinatal medical status. Positive and negative sucking pressure as well as chest and abdominal breathing movements were recorded during nutritive sucking. The high risk preterms used a simpler and more stable pattern of coordination between sucking and breathing, were more likely to interrupt breathing at milk onset, and produced longer phase lags between positive and negative sucking pressure.
Leaf senescence in rice plants: cloning and characterization of senescence up‐regulated genes (2001)

To identify senescence-associated genes (SAGs) in rice leaves, senescence was induced by transferring rice seedlings into darkness. Senescence up-regulated cDNAs were obtained by PCR-based subtractive hybridization. Among 14 SAG clones characterized, 11 were found to be associated with both dark-induced and natural leaf senescence. Three clones were associated only with dark-induced leaf senescence. The possible physiological roles of these SAGs during rice leaf senescence are discussed.
HMGB1, an innate alarmin, in the pathogenesis of type 1 diabetes. (2009)

HMGB1, an evolutionarily conserved chromosomal protein, was recently re-discovered to act as a "danger signal" (alarmin) to alert the innate immune system for the initiation of host defense or tissue repair. Extracellular HMGB1 can be either passively released from damaged/necrotic cells or secreted by activated immune cells. Upon stimulation, dendritic cells (DCs), macrophages and natural killer (NK) cells secrete high levels of HMGB1 into the intercellular milieu. HMGB1 is potent to target DCs, macrophages, neutrophils and CD4(+) T cells. It also upregulates the expression of BCL-XL by which it may prevent the elimination of activated immune cells. As a result, HMGB1 has been suggested to be implicated in the pathogenesis of autoimmune disorders such as systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), and experimental allergic encephalomyelitis (EAE). Given the similarities of autoimmune response against beta cell self-antigens in type 1 diabetes (T1D), in this view we will discuss the possible implications of HMGB1 in T1D pathogenesis. Specifically, we will summarize and update the advancement of HMGB1 in the pathogenesis of autoimmune initiation and progression during T1D development, as well as islet allograft rejection of diabetic patients after islet transplantation. Elucidation of the role for HMGB1 in T1D pathogenesis would not only enhance the understanding of disease etiology, but also have the potential to shed new insight into the development of therapeutic strategies for prevention or intervention of this disorder.
Paradoxical Psychometric Functions (“Swan Functions”) are Explained by Dilution Masking in Four Stimulus Dimensions (2013)

The visual system dissects the retinal image into millions of local analyses along numerous visual dimensions. However, our perceptions of the world are not fragmentary, so further processes must be involved in stitching it all back together. Simply summing up the responses would not work because this would convey an increase in image contrast with an increase in the number of mechanisms stimulated. Here, we consider a generic model of signal combination and counter-suppression designed to address this problem. The model is derived and tested for simple stimulus pairings (e.g. A + B), but is readily extended over multiple analysers. The model can account for nonlinear contrast transduction, dilution masking, and signal combination at threshold and above. It also predicts nonmonotonic psychometric functions where sensitivity to signal A in the presence of pedestal B first declines with increasing signal strength (paradoxically dropping below 50% correct in two-interval forced choice), but then rises back up again, producing a contour that follows the wings and neck of a swan. We looked for and found these "swan" functions in four different stimulus dimensions (ocularity, space, orientation, and time), providing some support for our proposal.
Small-Animal PET of Tumors with 64Cu-Labeled RGD-Bombesin Heterodimer (2009)

Compared with other tracers, (64)Cu-NOTA-RGD-bombesin showed favorable in vivo kinetics and enhanced tumor uptake, which warrants its further investigation for targeting tumors that express integrin or GRPR or that coexpress integrin and GRPR for imaging and therapeutic applications. The synergistic effect of RGD-bombesin heterodimers observed in this study also encourages further investigations of novel heterodimers recognizing other cell surface receptors for tumor targeting.
Photoinduced Electron-Transfer Processes between [C60]Fullerene and Triphenylamine Moieties Tethered by Rotaxane Structures. Through-Space Electron Transfer via Excited Triplet States of [60]Fullerene (2004)

Two rotaxanes tethering [60]fullerene (C60) and triphenylamine (TPA) moieties were synthesized in good yields by the urethane end-capping method using a crown ether−secondary amine motif. In these rotaxanes, the C60 group serving as electron acceptor is attached to the crown ether wheel through which the axle with a TPA group acting as electron donor on its terminal penetrates. One rotaxane has an ammonium moiety, whereas the other has a neutral amide moiety in the center of the axle. The corresponding reference compounds without rotaxane structures were also prepared. The intra-rotaxane photoinduced electron-transfer processes of C60 and TPA have been investigated by time-resolved transient absorption and fluorescence measurements with changing solvent polarity and temperature. Nanosecond transient absorption measurements of these rotaxanes demonstrated that the long-lived charge-separated state (C60•-,TPA•+)rotaxane is formed via the excited triplet state of C60 (3C60*) in polar solvents. The rate constants for the charge separation process were in the range of (5−8) × 107 s-1, while the rate constants of charge recombination were in the range of (3−6) × 106 s-1, corresponding to the lifetimes of the charge-separated states of 170−300 ns. Both rate constants depended on rotaxane structure, solvent polarity, and temperature. The activation free energy changes of charge separation and recombination processes were evaluated to be 0.01−0.03 and 0.03−0.06 eV by temperature dependences, respectively. Such low activation energies may be related to through-space electron transfer in these rotaxanes. On the other hand, in a covalently connected TPA−C60 dyad, fast charge separation from the excited singlet state and fast charge recombination were observed through bonds in polar solvents.
Homocysteine-Mediated Reactivity and Assembly of Gold Nanoparticles (2006)

This paper reports the findings of an investigation of the reactivity and assembly of gold nanoparticles mediated by homocysteine (Hcys), a thiol-containing amino acid found in plasma. The aim is to gain insight into the interparticle interaction and reactivity, which has potential application for the detection of thiol-containing amino acids. By monitoring the evolution of the surface plasmon resonance absorption and the dynamic light scattering of gold nanoparticles in the presence of Hcys, the assembly was shown to be dependent on the nature and concentration of the electrolytes, reflecting an effective screening of the diffuse layer around the initial citrate-capped nanoparticles that decreases the barrier to the Hcys adsorption onto the surface, and around the subsequent Hcys-capped nanoparticles that facilitate the zwitterion-type electrostatic interactions between amino acid groups of Hcys bound to different nanoparticles. A key element of the finding is that the interparticle zwitterion interaction of the Hcys-Au system is much stronger than the expectation for a simple Hcys or Au solution, a new phenomenon originating from the unique nanoscale interparticle interaction. The strength and reversibility of the interparticle zwitterion-type electrostatic interactions between amino acid groups are evidenced by the slow disassembly upon increasing pH at ambient temperatures and its acceleration at elevated temperature. These findings provide new insight into the precise control of interfacial interactions and reactivities between amino acids anchored to nanoparticles and have broad implications in the development of colorimetric nanoprobes for amino acids.
Intra-abdominal Pressure Measurements Using a Wireless Radio Pressure Pill and Two Wire Connected Pressure Transducers: A Comparison (1984)

Intra-abdominal pressures were measured simultaneously with a wireless radio pill and two wire-connected pressure transducers introduced orally and rectally respectively. Measurements were made on 8 men during common postures, simple activities and static and dynamic lifting. An acceptable correspondence was found in wave forms of the generated pressure curves in time and shape. The three systems showed, however, a less good agreement in recorded peak differences, i.e. highest and lowest pressure responses to each task. The radio pill is simple to use, but more difficult to calibrate and expensive, compared to the wire-connected methods, which however are less attractive for use in the work environment.
<title>Honeywell militarized color liquid crystal displays for the F-16</title> (1996)

A fully militarized color multifunction display for the F-16 has been completed and is in the first months of production. This high performance display is a tightly integrated ensemble of optical, electronic, mechanical, and thermal designs, Many of the elements are critically interdependent, requiring fine-tuning to achieve the exceptional performance required by the F-16 environment. With no cooling air available on the F-16, the thermal requirements, both specified and implicit, dominated the design process. The high luminance requirements, in combination with a high resolution display, concentrated a great deal of heat in the display module. As a result, thermal efficiency and management were paramount. Temperature stability and performance of the liquid crystal material itself, stability of the polarizers, optical and electronic efficiency and heat extraction design required intense scrutiny.
Comparison of Transcription-Mediated Amplification and Growth-Based Methods for the Quantitation of Enterococcus Bacteria in Environmental Waters (2008)

An assay based on transcription-mediated amplification (TMA) technology was used to quantitate Enterococcus fecal indicator bacteria in environmental water samples. The results generated by this and two growth-based methods relative to the 104 most-probable-number or CFU-per-100-ml threshold show that the three methods are in good qualitative agreement when tested against a range of water samples taken from different locations. The results demonstrate sensitive and rapid detection (approximately 4 h from sample collection to result) and quantitation of Enterococcus bacteria compared to the results with the growth-based methods.
Electrochemotherapy for the Treatment of Soft Tissue Sarcoma in a Rat Model (2003)

Each year approximately 6000 new cases of soft tissue sarcoma are diagnosed in the United States (1). The disease affects the extremities in 60% of the reported cases with the lower extremity the most likely tumor site (2,3). Management of soft tissue sarcomas is challenging but over the last 20 yr treatment has evolved from radical procedures such as amputation or compartmental resection to limb-sparing approaches (4,5). However, current limb sparing procedures are not applicable to all adult soft tissue sarcomas of the extremity. Limb sparing techniques are not employed when tumors are located close to joints, bone, or neurovascular bundles (6).
Uniform SSFLC director pattern switching (1988)

Abstract Dynamical and polarisation-dependent transmission intensity measurements on 2.0 μm SSFLC cells clarify that the director pattern profiles are uniform from top to bottom glass plate in the fully-switched, the memory and all transient states. Switching occurs by two processes: a continuous shift on the smectic C cone and a bistable multidomain transition. This behaviour is caused by tilted smectic layers. Removal of this tilt results in a true bistability in which memory and switched states arc nearly indistinguishable and possess high contrast.
Biologically inspired polymer microfibers with spatulate tips as repeatable fibrillar adhesives (2006)

Being inspired by gecko foot hairs, microfibers with flat spatulate tips are proposed as repeatable adhesives. They are fabricated by molding a master template fabricated using deep reactive ion etching and the notching effect. Fabricated polyurethane fiber arrays with 4.5μm fiber and 9μm tip diameter demonstrated macroscale adhesion pressures up to 18N∕cm2 and overall work of adhesion up to 11J∕m2 on a 6mm diameter glass hemisphere for a preload pressure of 12N∕cm2. These results show around four times higher adhesion and five times higher overall work of adhesion as compared to the flat polyurethane surface.
Achieving page-mapping FTL performance at block-mapping FTL cost by hiding address translation (2010)

Flash Translation Layer (FTL) is one of the most important components of SSD, whose main purpose is to perform logical to physical address translation in a way that is suitable to the unique physical characteristics of the Flash memory technology. The pure page-mapping FTL scheme, arguably the best FTL scheme due to its ability to map any logical page number (LPN) to any physical page number (PPN) to minimize erase operations, cannot be practically deployed since it consumes a prohibitively large RAM (SRAM or DRAM) space to store the page-mapping table for an SSD of moderate to large size. Alternatives to the pure page-mapping FTL, such as block-mapping FTLs, hybrid FTLs (e.g., FAST) and the latest demand-based page-mapping FTLs (e.g., DFTL), require significantly less RAM space but suffer from a few performance issues. Block-mapping FTLs perform poorly with higher erasure counts, particularly under random write workloads. Hybrid FTL schemes incur costly merge operations that hurt performance and increase the erasure counts. Performances of demand-based FTLs heavily depend on workload characteristics such as access locality, read/write ratio and request arrival interval time. This paper proposes a new FTL scheme, called HAT, to achieve the performance of a pure page-mapping FTL at the RAM cost of a block-mapping FTL while consuming lower energy, by hiding the address translation (HAT). The basic idea behind our scheme is to create a separate access path to read/write the address mapping information to significantly Hide the Address-Translation latency by incorporating a low energy-consuming solid-state memory device that stores the entire page mapping table. We implement an SSD simulator, SSDsim, to validate our HAT design and evaluate its performance. The extensive trace-driven simulation results show that the performance of HAT is within 0.8% of the pure page-mapping FTL, while consuming about 50% of the energy.
Kinetics of O(1S) and O(1D) metastable atoms in a DC oxygen glow discharge (1991)

The concentrations of O(1D) and O(1S) metastable atoms are measured in the positive column of a DC oxygen glow discharge by vacuum ultraviolet absorption spectroscopy at 115 and 122 nm respectively. In the investigated range of pressures p=0.2-2 torr and discharge currents Id=10-80 mA, the concentrations of O(1D) and O(1S) atoms range from 1011-1012 and from 1010-1011 cm-3 respectively. In these conditions the main creation and destruction processes are discussed: the O(1D) atoms are created by electron impact dissociation of O2(X3 Sigma ) and O2(a1 Delta ), and excitation of O(3P), and lost through quenching by oxygen molecules. It is shown that it is necessary to add to the electron impact excitation another creation term of O(1S) atoms to balance the destruction through quenching by O2(X3 Sigma ), O2(a1 Delta ) and O(3P).
Structure of human platelet membrane glycoproteins IIb and IIIa as determined by electron microscopy. (1985)

The glycoprotein (GP) IIb-IIIa complex was isolated from human platelet membranes and examined for glycoprotein stoichiometry and morphology. To determine the ratio of glycoproteins in the complex, the isolated glycoproteins were solubilized with sodium dodecyl sulfate and separated by high-performance liquid chromatography. Quantitative amino acid analysis of individual glycoproteins showed that the ratio of GP IIb to GP IIIa in the Ca2+-dependent complex was 0.93:1. Morphology was determined by electron microscopy of rotary-shadowed and negatively stained specimens. Individual complexes consisted of two domains: an oblong head of approximately 8 X 10 nm with two rodlike tails extending approximately 14-17 nm from one side of the head. Treatment of the isolated complex with EDTA resulted in the appearance of a mixture of oblong and filamentous structures, which could be separated by a sucrose gradient sedimentation in Triton X-100. As seen by rotary and unidirectional shadowing, GP IIb was a compact structure, approximately 8 X 10 nm in size. Isolated GP IIIa was more heterogeneous but was most often observed in an elongated form, varying in length from 20 to 30 nm and in width from 2 to 3 nm. By comparing these structures to that of the heterodimer complex, it was determined that the oblong domain was GP IIb and the rodlike tails were GP IIIa. Each milligram of isolated GP IIb-IIIa complex bound 0.30 mg of [3H]Triton X-100, indicating that the glycoprotein complex contained limited hydrophobic domains. Upon removal of detergent, GP IIb-IIIa complexes formed aggregates that sedimented in sucrose gradients as a diffuse peak ranging from 14 to 32 s. Examination of these aggregates by electron microscopy showed that they were composed of clusters or "rosettes" of 2 to 20 or more of the GP IIb-IIIa complexes. The orientation of these rosettes was such that the tails were joined in the center, with the head portions directed away from the interacting tails. It thus appears that the primary hydrophobic domains of the GP IIb-IIIa complex exist at the tips of the GP IIIa tails. Because the GP IIb-IIIa complex is an intrinsic membrane glycoprotein, these findings indicate a potential membrane attachment site for the GP IIb-IIIa complexes.