gebhart/patrepeval huggingface dataset:
Comparative Analysis of H&E and Prussian Blue Staining in a Mouse Model of Cerebral Microbleeds (2014)

Cerebral microbleeds are microscopic hemorrhages with deposits of blood products in the brain, which can be visualized with MRI and are implicated in cerebrovascular diseases. Hematoxylin and eosin (H&E) and Perl's Prussian blue are popular staining methods used to localize cerebral microbleeds in pathology. This paper compared these two staining techniques in a mouse model of cerebral microbleeds. We used lipopolysaccharide (LPS) to induce cerebral microhemorrhages. C57B6 mice were treated with LPS (5 mg/kg, i.p.) or vehicle at baseline and at 24 hr. The brains were extracted 48 hr after the first injection and adjacent coronal sections were stained with H&E and Prussian blue to compare the effectiveness of the two staining techniques. H&E-positive stains were increased with LPS treatment and were correlated with grossly visible microhemorrhages on the brain surface; Prussian blue-positive stains, by comparison, showed no significant increase with LPS treatment and did not correlate with either H&E-positive stains or surface microhemorrhages. H&E staining is thus a more reliable indicator of acute bleeding events induced by LPS in this model within a short time span.
RGD‐modified anti‐CD3 antibodies redirect cytolytic capacity of cytotoxic T lymphocytes toward α<sub>v</sub>β<sub>3</sub>‐expressing endothelial cells (2004)

To redirect the lytic activity of cytotoxic T lymphocytes (CTL) toward tumor vascular endothelial cells, we prepared bifunctional proteins with specificity for both alphavbeta3 and CD3. Monocyclic RGD peptides (cRGDfK) were covalently coupled to an anti-CD3 monoclonal antibody at different peptide:protein ratios. The resulting RGDpep-anti-CD3 conjugates bound specifically to alphavbeta3-expressing endothelial cells. Displacement studies with radiolabeled alphavbeta3 ligand demonstrated that the alphavbeta3 binding affinity of RGDpep-anti-CD3 conjugates was elevated as compared to the non-conjugated RGDpep. IC50 values ranged from 150-1.1 nM, depending on the amount of coupled RGDpep molecules per antibody molecule. RGD modification did not affect the ability of anti-CD3 antibodies to bind to CTL. Furthermore, RGDpep-anti-CD3 was fully capable of activating T cells upon CD3 binding as was shown in a Jurkat/NFAT reporter-gene activation assay. All RGDpep-anti-CD3 conjugates were able to induce RGDpep, CD3-dependent lysis of human primary endothelial cells by anti-CD3/IL-2 activated human peripheral blood mononuclear cells (PBMC), with a significant induction of cytotoxicity observed at an E/T ratio as low as 10. Redirecting cytolytic activity reached up to 50% cytotoxicity using the conjugate with the highest RGD peptide load. Combining the good accessibility of tumor blood vessel endothelium for CTL with the efficiency of target cell killing warrants further investigations on anti-tumor effects of this type of conjugates in vivo.
<i>Ab initio</i>molecular-dynamics simulation of the liquid-metal–amorphous-semiconductor transition in germanium (1994)

We present ab initio quantum-mechanical molecular-dynamics simulations of the liquid-metal--amorphous-semiconductor transition in Ge. Our simulations are based on (a) finite-temperature density-functional theory of the one-electron states, (b) exact energy minimization and hence calculation of the exact Hellmann-Feynman forces after each molecular-dynamics step using preconditioned conjugate-gradient techniques, (c) accurate nonlocal pseudopotentials, and (d) Nos\'e dynamics for generating a canonical ensemble. This method gives perfect control of the adiabaticity of the electron-ion ensemble and allows us to perform simulations over more than 30 ps. The computer-generated ensemble describes the structural, dynamic, and electronic properties of liquid and amorphous Ge in very good agreement with experiment. The simulation allows us to study in detail the changes in the structure-property relationship through the metal-semiconductor transition. We report a detailed analysis of the local structural properties and their changes induced by an annealing process. The geometrical, bonding, and spectral properties of defects in the disordered tetrahedral network are investigated and compared with experiment.
Identification of a transcription factor, an 80-kDa protein that interacts with the HLH recognition motif of the rat p53 promoter (2001)

The p53 promoter has been shown to contain a number of potential regulatory motifs. It was previously reported that the upstream stimulating factor (USF) played a central role in regulating the p53 expression. The USF binding site, E-box, is located around 40 bp upstream of the major transcription start site. In this study, it was confirmed that the E-box binds to proteins by DNase I footprinting assay. In the electrophoretic mobility shift assay (EMSA), two retarded bands were detected. One band was abolished by the competition of USF consensus oligonucleotide, but the other band was not. This result indicated that a factor, other than USF, was bound to the E-box. The molecular masses of the binding proteins were determined by a Southwestern-blotting assay. As a result, 46- and 80-kDa proteins were detected. The 46-kDa protein was eliminated by the competition of USF consensus oligonucleotide. Also, the Southwestern-blotting assay with 32P-labeled USF consensus oligonucleotide showed only a 46-kDa protein. Therefore, the 46-kDa protein was USF. These results showed that USF and the 80-kDa protein were bound to the E-box. In addition, it was proved by in vitro transcription assay that this 80-kDa protein had a basal transcriptional activity.Key words: E-box, HLH, rat p53 promoter, transcription factor, upstream stimulating factor (USF).
On the development of a case‐based supplier management tool for multi‐national manufacturers (2002)

The rapid globalization in markets for manufactured goods and the growth of information technology has led to the demand for delivering superior value to international customers. Knowledge‐based systems, such as the case‐based reasoning (CBR) technique, have the potential to play a significant role in managing customer and supplier relationships under the dispersed network production systems model. The characteristic of the CBR technique in case retrieval, reuse, revision and retaining was used in solving a purchasing problem. However, there is a lack of literature in using a case‐based tool when comparing supplier bidding for the same order on a global basis. Proposes a case‐based supplier management tool (CBSMT) using the CBR technique in the areas of intelligent supplier selection and management that will enhance performance as compared to using the traditional approach. This CBSMT was first proposed as a task allocation tool, it was also used as a tool in a multi‐agent based virtual enterprise architecture. Describes an overview of the foundational issues related to CBR which provides some methodological approaches and exemplifies the current state through supplier management. Then defines a general supplier selection workflow, followed by the application of the case‐based technique to manage the problem of supplier selection. Finally, discusses an application case study of applying this supplier management tool to Honeywell Consumer Products (Hong Kong) Limited to help the selection of suppliers in their daily operations.
Anomalous Diffusion of Hydrogen in Fused Quartz (1977)

A mass spectrometer was used to measure diffusion coefficionts, permeabilities and solubilities of hydrogen in some kinds of fused quartz tubes, which are now used for newly developed lamps.The values obtained for diffusion coefficient at 800°C is 2-3×10-6cm2/sec, and the activation energy of diffusion at 400-800°C is 11.6 Kcal/mol. These values are in good agreement with other reported values.Precise measurements at elevated temperatures exceeding 800°C generally showed an unusual fall off of diffusion coefficient, while permeabilities showed monotonical increasing, and solubilities, which were calculated from diffusion coefficient and permeability, displayed abrupt rise.
Eye Movements in Alzheimer's Disease (2015)

A growing body of literature has investigated changes in eye movements as a result of Alzheimer's disease (AD). When compared to healthy, age-matched controls, patients display a number of remarkable alterations to oculomotor function and viewing behavior. In this article, we review AD-related changes to fundamental eye movements, such as saccades and smooth pursuit motion, in addition to changes to eye movement patterns during more complex tasks like visual search and scene exploration. We discuss the cognitive mechanisms that underlie these changes and consider the clinical significance of eye movement behavior, with a focus on eye movements in mild cognitive impairment. We conclude with directions for future research.
An Insect‐Specific Toxin from <i>Centruroides noxius</i> Hoffmann (1996)

Scorpion toxins acting on sodium channels differ in their specificity. Toxic peptides specific towards mammals and arthropods (insects and/or crustaceans) have been described. Because of the similar three-dimensional fold of these peptides, the molecular base of their specificity is thought to reside in certain differences at the level of amino acid residues especially within or near the binding site of the toxin to the particular ion channel. The cDNA, amino acid sequence and biological activity of an insect-specific toxin, Cn10, from the scorpion Centruroides noxius Hoffmann is reported. The electrostatic potential surface around a three-dimensional model of Cn10 was calculated. It revealed that residues Tyr4, Lys13, Ile18, Leu19, Gly20, Lys43, Leu44, Thr57, Tyr58, Pro59, Thr64 and Cys65, situated at the side of the toxin proposed in the literature to bind to the sodium channel, constitute a positive surface region. Therefore, they may form the site that binds to the channel. Cn10 was included in a comparative analysis of two groups of natural variants, highly similar peptides of the genus Centruroides with specificities towards mammals or arthropods. A number of surface-accessible residues, consistently different between the two groups and situated near the putative binding site, may be of importance for the specificity of the analyzed toxins.
Functional analysis of cloned macrophage hybridomas. IV. Induction and inhibition of mixed lymphocyte responses. (1985)

A series of macrophage (M phi) hybridomas were generated by fusion of drug-marked P388D1 (H-2d) tumor cells with CKB (H-2k) splenic adherent cells. The ability of this panel of cloned M phi hybridomas expressing various levels of surface Ia antigens to induce allogeneic mixed lymphocytes responses (MLR) was examined. All MLR stimulatory M phi hybridomas expressed surface Ia antigens. However, some Ia+ and all Ia- M phi hybridomas were unable to induce vigorous MLR responses. Furthermore, even after induction of surface Ia antigen expression with Con A supernatants (Con A Sn) or purified interferon-gamma, the nonstimulatory M phi hybridomas remained ineffective at inducing strong MLR proliferative responses. Furthermore, addition of the latter M phi hybridoma clones (both with and without Con A Sn treatment) to conventional MLR cultures resulted in inhibition of MLR responses. The series of inhibitory M phi hybridomas secreted normal levels of IL 1 upon stimulation with lipopolysaccharide. After surface Ia induction with Con A Sn, the inhibitory M phi hybridomas could stimulate secretion of IL 2 and expression of IL 2 receptors. Moreover, although they inhibited conventional MLR responses, IL 2 production and IL 2 receptor expression were not significantly inhibited. Addition of these M phi hybridomas 24 to 48 hr after initiation of MLR response also inhibited MLR proliferation. The results indicated that the group of inhibitory M phi hybridomas can inhibit MLR responses after IL 2 secretion and acquisition of IL 2 receptors. Finally, this inhibitory activity has been maintained during 1 yr of continuous in vitro culture, and the hybridomas represent a stable "homogeneous" subpopulation of inhibitory macrophages. Thus, the inhibitory phenotype appears to reflect arrest at a distinct differentiation stage.
Memristor Logic Operation Gate With Share Contact RRAM Cell (2011)

In this letter, we proposed a novel operation of a share contact resistive random access memory (CRRAM) structure to realize a nonvolatile latch (NV latch) with a single transistor. With a share CRRAM structure and sequential input operations, the NV latch as well as and/ or functions have been successfully demonstrated. The new mixing approach of combining memory and logic in a single unit projects the possibility of new applications for VLSI circuits.
Acoustic modelling for speech recognition: Hidden Markov models and beyond? (2009)

Hidden Markov models (HMMs) are still the dominant form of acoustic model used in automatic speech recognition (ASR) systems. However over the years the form, and training, of the HMM for ASR have been extended and modified, so that the current forms used in state-of-the-art speech recognition systems are very different to those originally proposed thirty years ago. This talk will review two of the more important extensions that have been proposed over the years: discriminative training; and speaker and environment adaptation. The use of discriminative training is now common with forms based on minimum Bayes' training and minimum classification error being applied to systems trained on many hundreds of hours of speech data. The talk will describe these current approaches, as well as discussing the current trends towards schemes based on large-margin training approaches. Linear transform based speaker adaptation is the dominant form for speaker adaptation. Current approaches, including extensions to linear transforms and model-based noise robustness techniques, and trends will also be described. Details of the various forms of the adaptation/noise transformation, training criterion and approaches for adaptive training will be given. The final part of the talk will discuss research beyond the current HMM framework. Schemes based on both discriminative models and functions, as well as non-parametric approaches will be described.
Thermonuclease test for same-day identification of Staphylococcus aureus in blood cultures (1985)

We used a thermonuclease test to presumptively identify Staphylococcus aureus directly in blood cultures on the same day that a smear of the broth showed gram-positive cocci in clusters. There were no discrepancies between the identification of S. aureus directly from 250 blood cultures and identification by the tube coagulase test which was performed on the 18- to 24-h subculture isolates. These rapid results were clinically relevant and enabled physicians to make more timely and cost-effective decisions about antibiotic therapy.
Targeting the proteasome: partial inhibition of the proteasome by bortezomib or deletion of the immunosubunit LMP7 attenuates experimental colitis (2010)

It was demonstrated that modulation of the proteasome activity is effective in attenuating experimental colitis. The results reveal that reduction of the proteasome activity either by partial inhibition with bortezomib or by specifically targeting the immunoproteasome subunit LMP7 is a suitable treatment of intestinal inflammation.
A distributed QoS routing architecture for scalable video streaming over multi-domain OpenFlow networks (2012)

This paper proposes a new Quality of Service (QoS) optimized routing architecture for video streaming over large-scale multi-domain OpenFlow networks managed by a distributed control plane, where each controller performs optimal routing within its domain and shares summarized intra-domain routing data with other controllers to reduce problem dimensionality for calculating inter-domain routing. We apply the proposed architecture to streaming of scalable (layered) videos, where the base layer routes are dynamically optimized to fulfill a required QoS level, while enhancement layers follow traditional shortest path. We show that the proposed solution approaches the expensive non-scalable globally optimal solution (single controller for the whole network) in terms of received video quality under various congestion scenarios.
Disrupting the association of hepatitis C virus core protein with lipid droplets correlates with a loss in production of infectious virus (2007)

In infected cells, hepatitis C virus (HCV) core protein is targeted to lipid droplets, which serve as intracellular storage organelles. Using a tissue culture system to generate infectious HCV, we have shown that the coating of lipid droplets by the core protein occurs in a time-dependent manner and coincides with higher rates of virus production. At earlier times, the protein was located at punctate sites in close proximity to the edge of lipid droplets. Investigations by using Z-stack analysis have shown that many lipid droplets contained a single punctate site that could represent positions where core transfers from the endoplasmic reticulum membrane to droplets. The effects of lipid droplet association on virus production were studied by introducing mutations into the domain D2, the C-terminal region of the core protein necessary for droplet attachment. Alteration of a phenylalanine residue that was crucial for lipid droplet association generated an unstable form of the protein that could only be detected in the presence of a proteasome inhibitor. Moreover, converting two proline residues in D2 to alanines blocked coating of lipid droplets by core, although the protein was directed to punctate sites that were indistinguishable from those observed at early times for wild-type core protein. Neither of these virus mutants gave rise to virus progeny. By contrast, mutation at a cysteine residue positioned 2 aa upstream of the phenylalanine residue did not affect lipid droplet localization and produced wild-type levels of infectious progeny. Taken together, our findings indicate that lipid droplet association by core is connected to virus production.
Erratum: Spin-Orbit Coupling, Quantum Dots, and Qubits in Monolayer Transition Metal Dichalcogenides [Phys. Rev. X 4, 011034 (2014)] (2014)

Received 19 May 2014DOI:https://doi.org/10.1103/PhysRevX.4.039901This article is available under the terms of the Creative Commons Attribution 3.0 License. Further distribution of this work must maintain attribution to the author(s) and the published article’s title, journal citation, and DOI.Published by the American Physical Society
EFFECTS OF ACTIVE COMPRESSION-DECOMPRESSION RESUSCITATION ON MYOCAR-DIAL AND CEREBRAL BLOOD FLOW IN PIGS (1993)

Lindner, Karl; Pfenninger, Ernst; Lurie, Keith‡; Lindner, Ingrid; Ahnefeld, FriedrichAuthor Information
Cell-penetrating peptides and antimicrobial peptides: how different are they? (2006)

Some cationic peptides, referred to as CPPs (cell-penetrating peptides), have the ability to translocate across biological membranes in a non-disruptive way and to overcome the impermeable nature of the cell membrane. They have been successfully used for drug delivery into mammalian cells; however, there is no consensus about the mechanism of cellular uptake. Both endocytic and non-endocytic pathways are supported by experimental evidence. The observation that some AMPs (antimicrobial peptides) can enter host cells without damaging their cytoplasmic membrane, as well as kill pathogenic agents, has also attracted attention. The capacity to translocate across the cell membrane has been reported for some of these AMPs. Like CPPs, AMPs are short and cationic sequences with a high affinity for membranes. Similarities between CPPs and AMPs prompted us to question if these two classes of peptides really belong to unrelated families. In this Review, a critical comparison of the mechanisms that underlie cellular uptake is undertaken. A reflection and a new perspective about CPPs and AMPs are presented.
Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential (2012)

Foxtail millet (Setaria italica), a member of the Poaceae grass family, is an important food and fodder crop in arid regions and has potential for use as a C(4) biofuel. It is a model system for other biofuel grasses, including switchgrass and pearl millet. We produced a draft genome (∼423 Mb) anchored onto nine chromosomes and annotated 38,801 genes. Key chromosome reshuffling events were detected through collinearity identification between foxtail millet, rice and sorghum including two reshuffling events fusing rice chromosomes 7 and 9, 3 and 10 to foxtail millet chromosomes 2 and 9, respectively, that occurred after the divergence of foxtail millet and rice, and a single reshuffling event fusing rice chromosome 5 and 12 to foxtail millet chromosome 3 that occurred after the divergence of millet and sorghum. Rearrangements in the C(4) photosynthesis pathway were also identified.
Size-dependent melting point depression of nanostructures: Nanocalorimetric measurements (2000)

The melting behavior of 0.1--10-nm-thick discontinuous indium films formed by evaporation on amorphous silicon nitride is investigated by an ultrasensitive thin-film scanning calorimetry technique. The films consist of ensembles of nanostructures for which the size dependence of the melting temperature and latent heat of fusion are determined. The relationship between the nanostructure radius and the corresponding melting point and latent heat is deduced solely from experimental results (i.e., with no assumed model) by comparing the calorimetric measurements to the particle size distributions obtained by transmission electron microscopy. It is shown that the melting point of the investigated indium nanostructures decreases as much as 110 K for particles with a radius of 2 nm. The experimental results are discussed in terms of existing melting point depression models. Excellent agreement with the homogeneous melting model is observed.
<i>Pisum sativum</i> and <i>Vicia faba</i> Carbohydrates: Structural Studies of Starches (1981)

ABSTRACT The fine structure of laboratory purified broadbean and smooth pea starches, with an amylose content of 32‐34%, has been studied by pullulanase debranching, before or after beta‐amylolysis, and by the properties of the chemically fractionated amylose and amylopectin. The enzymatic study has shown the presence of the three chain populations ( DP > 60, 45 and 15) observed with other starches. The linear DP 15 and 45 chains occur in a ratio of 8.5 for broadbean and 9.75 for pea, which indicates an amylopectin similar to cereal starches. The λ max , beta‐amylolysis limit and intrinsic viscosity of the two amylopectins confirm the cereal‐like nature. The two amylose components are not completely linear according to their beta‐amylolysis limit of 81.5% which corroborates the in complete debranching of the total starch. The physical structure, studied by X‐ray diffractometry, is of C‐type. By submitting legume starch granules to mild acid hydrolysis (lintnerization), a residue has been obtained from both starches, which has an increase in the crystalline fraction, with a tendency towards the A‐type pattern for broadbean and the B‐type for pea. The crystallites are mainly formed of linear chains ( CL 15) with some singly branched material ( DP 25). Gelatinization of starch granules occurs at 44‐65‐86°C for broadbean with a heat of gelatinization of 3.8 cal g −1 and at 48‐61‐80°C for pea with a heat of gelatinization of 3.2 cal g −1 .