gebhart/patrepeval huggingface dataset:
A mouse model of pneumonitis induced by Chlamydia trachomatis: morphologic, microbiologic, and immunologic studies. (1980)

Swiss-Webster white mice were infected with Chlamydia trachomatis organisms through intranasal inoculation. It was found that a typical interstitial pneumonitis could be induced. Histopathologic findings showed that the lung infiltration was predominantly polymorphonuclear cells and was most prominant on Day 2. The cellular infiltrate gradually changed to mononuclear cells after Day 3. Intracytoplasmic inclusions were frequently found in the interstitial cells and occasionally in the bronchial epithelial cells. Typical chlamydial bodies (elementary, intermediate, and reticulate forms) were identified by electron microscopy. The organisms were recovered from mouse lungs on Days 1--7, with the highest yields on Day 2. This correlated with the peak of lung infiltration seen by histologic examination. Antibodies specific to the infecting immunotype began to appear between Day 7 and Day 10 after inoculation and lasted until Day 35 without a decline in titers. A delayed hypersensitivity reaction was observed by footpad test from Day 5 to Day 21, with the peak reaction at Day 7. This study showed that the mouse model could be used to study the immunopathogenesis of C trachomatis infection.
New 5-HT3 (Serotonin-3) Receptor Antagonists. IV. Synthesis and Structure-Activity Relationships of Azabicycloalkaneacetamide Derivatives. (1995)

The synthesis and structure-activity relationships of a series of new azabicycloalkanes as 5-HT3 (serotonin-3) receptor antagonists are described. Our study on the azabicycloalkaneacetamide derivatives showed that 2,3-dihydroindole as the aromatic ring moiety afforded potent 5-HT3 receptor antagonist activity, as judged by blockade of bradycardia induced by i.v. injection of 2-methylserotonin in anesthetized rats. 7-Azaindole as the aromatic moiety afforded weak 5-HT3 receptor antagonists activity. The best 5-HT3 antagonists in this study were endo-3,3-diethyl- (9k) and 3,3-dimethyl-2,3-dihydro-1-[(8-methyl-8-azabicyclo[3.2.1]oct-3-yl) acetyl-1H-indole (9d), being approximately 10-fold more potent than ondansetron (1). This study shows that the azabicycloalkaneacetyl group is a new pharmacophoric element as a basic nitrogen and a linking carbonyl moiety.
Methods for Prediction of Peptide Binding to MHC Molecules: A Comparative Study (2002)

A variety of methods for prediction of peptide binding to major histocompatibility complex (MHC) have been proposed. These methods are based on binding motifs, binding matrices, hidden Markov models (HMM), or artificial neural networks (ANN). There has been little prior work on the comparative analysis of these methods. We performed a comparison of the performance of six methods applied to the prediction of two human MHC class I molecules, including binding matrices and motifs, ANNs, and HMMs. The selection of the optimal prediction method depends on the amount of available data (the number of peptides of known binding affinity to the MHC molecule of interest), the biases in the data set and the intended purpose of the prediction (screening of a single protein versus mass screening). When little or no peptide data are available, binding motifs are the most useful alternative to random guessing or use of a complete overlapping set of peptides for selection of candidate binders. As the number of known peptide binders increases, binding matrices and HMM become more useful predictors. ANN and HMM are the predictive methods of choice for MHC alleles with more than 100 known binding peptides. The ability of bioinformatic methods to reliably predict MHC binding peptides, and thereby potential T-cell epitopes, has major implications for clinical immunology, particularly in the area of vaccine design.
Effect of the Molecular Weight of AB Diblock Copolymers on the Lamellar Orientation in Thin Films: Theory and Experiment (2007)

Abstract We propose a theoretical explanation of the parallel and perpendicular lamellar orientations in free surface films of symmetric polystyrene‐ block ‐polybutadiene diblock copolymers on silicon substrates (with a native SiO x layer). Two approaches are developed: A correction to the strong segregation theory and a qualitative analysis of the intermediate segregation regime. We show that the perpendicular orientation of the lamellae formed by the molecules of high molecular weight is stabilized by A–B interfacial interactions. They are weaker in the case of the perpendicular orientation of the lamellae, whereas the surface tension coefficient of the A–B interface decreases with the increase of the molecular weight. magnified image
DNA cross-linking responses of human malignant glioma cell strains to chloroethylnitrosoureas, cisplatin, and diaziquone. (1987)

Cell strains derived by culture of malignant glioma (astrocytoma grade III-IV) surgical specimens were tested for the production of DNA interstrand cross-links (ISC) and DNA-protein cross-links following treatment in vitro with 1-(2-chloroethyl)-1-nitrosourea, 1,3-bis(2-chloroethyl)-1-nitrosourea (BCNU, carmustine), 1-(2-chloroethyl)-3-(2,6-dioxo-1-piperidyl)-1-nitrosourea (PCNU), cis-dichlorodiammineplatinum(II) (cisplatin), and 3,6-diaziridinyl-2,5-bis(carboethoxyamino)-1,4-benzoquinone (diaziquone). ISC and DNA-protein crosslinks were measured by means of the DNA alkaline elution technique. Large differences among the cell strains were observed in DNA cross-linking responses to individual agents. The DNA responses to the chloroethylnitrosoureas, cisplatin, and diaziquone were largely independent of each other, except for a weak correlation between ISC responses to chloroethylnitrosoureas were distributed bimodally, in accord with a phenotypic distinction between Mer+ and Mer- cells. ISC responses to cisplatin and diaziquone showed significant variation among cell strains, but the distributions were not bimodal. The results demonstrate the existence of diverse DNA cross-linking response patterns among cell strains from different tumors of a given histological type.
UDP-Galactopyranose Mutase in Nematodes (2013)

Nematodes represent a diverse phylum of both free living and parasitic species. While the species Caenorhabditis elegans is a valuable model organism, parasitic nematodes or helminths pose a serious threat to human health. Indeed, helminths cause many neglected tropical diseases that afflict humans. Nematode glycoconjugates have been implicated in evasive immunomodulation, a hallmark of nematode infections. One monosaccharide residue present in the glycoconjugates of several human pathogens is galactofuranose (Galf). This five-membered ring isomer of galactose has not been detected in mammals, making Galf metabolic enzymes attractive therapeutic targets. The only known pathway for biosynthetic incorporation of Galf into glycoconjugates depends upon generation of the glycosyl donor UDP-Galf by the flavoenzyme uridine 5'-diphosphate (UDP) galactopyranose mutase (UGM or Glf). A putative UGM encoding gene (glf-1) was recently identified in C. elegans. We sought to assess the catalytic activity of the corresponding gene product (CeUGM). CeUGM catalyzes the isomerization of UDP-Galf and UDP-galactopyranose (UDP-Galp). In the presence of enzyme, substrate, and a hydride source, a galactose-N5-FAD adduct was isolated, suggesting the CeUGM flavin adenine dinucleotide (FAD) cofactor serves as a nucleophile in covalent catalysis. Homology modeling and protein variants indicate that CeUGM possesses an active site similar to that of prokaryotic enzymes, despite the low sequence identity (∼15%) between eukaryotic and prokaryotic UGM proteins. Even with the primary sequence differences, heterocyclic UGM inhibitors developed against prokaryotic proteins also inhibit CeUGM activity. We postulate that inhibitors of CeUGM can serve as chemical probes of Galf in nematodes and as anthelmintic leads. The available data suggest that CeUGM facilitates the biosynthetic incorporation of Galf into nematode glycoconjugates through generation of the glycosyl donor UDP-Galf.
Sparse deep belief net model for visual area V2 (2007)

Motivated in part by the hierarchical organization of the cortex, a number of al-gorithms have recently been proposed that try to learn hierarchical, or “deep,” structure from unlabeled data. While several authors have formally or informally compared their algorithms to computations performed in visual area V1 (and the cochlea), little attempt has been made thus far to evaluate these algorithms in terms of their fidelity for mimicking computations at deeper levels in the cortical hier-archy. This paper presents an unsupervised learning model that faithfully mimics certain properties of visual area V2. Specifically, we develop a sparse variant of the deep belief networks of Hinton et al. (2006). We learn two layers of nodes in the network, and demonstrate that the first layer, similar to prior work on sparse coding and ICA, results in localized, oriented, edge filters, similar to the Gabor functions known to model V1 cell receptive fields. Further, the second layer in our model encodes correlations of the first layer responses in the data. Specifically, it picks up both colinear (“contour”) features as well as corners and junctions. More interestingly, in a quantitative comparison, the encoding of these more complex “corner ” features matches well with the results from the Ito &amp;amp; Komatsu’s study of biological V2 responses. This suggests that our sparse variant of deep belief networks holds promise for modeling more higher-order features. 1
Immunoreactive myelin proteolipid protein—like activity in cerebrospinal fluid and serum of neurologically impaired patients (1983)

Two hundred seventy-eight samples of cerebrospinal fluid and 273 samples of sera from a variety of neurological patients were examined by radioimmunoassay for myelin proteolipid protein-like reactivity as an index of structural damage to myelin. Groups of patients with active central nervous system damage could be distinguished easily, although there was a small percentage of false positive reactions. The reactivity was most marked in the demyelinative, encephalitic, and stroke categories. A radioimmunoassay for proteolipid protein of proper sensitivity and specificity may prove to be a useful objective clinical measure of the presence and degree of disease activity in multiple sclerosis and other diseases.
Direct inactivation of viruses by MCP-1 and MCP-2, natural peptide antibiotics from rabbit leukocytes (1985)

Six homologous peptides were purified to homogeneity from rabbit granulocytes or alveolar macrophages and tested for their ability to inactivate herpes simplex virus type 1 (HSV-1). Two of the peptides, MCP-1 and MCP-2, showed considerable in vitro neutralizing activity, whereas four structurally homologous peptides (NP-3a, NP-3b, NP-4, and NP-5) were relatively ineffective. Inactivation of HSV-1 by MCP-1 or MCP-2 depended on peptide concentration and on the time, temperature, and pH of the incubation. HSV-2, vesicular stomatitis virus, and influenza virus A/WSN were also susceptible to direct neutralization by MCP-1 or MCP-2, whereas cytomegalovirus, echovirus type 11, and reovirus type 3 were not. We speculate that MCP-1 and MCP-2, peptides that are abundant in rabbit granulocytes and lung macrophages, may contribute to antiviral defenses by mediating the direct inactivation of HSV-1 and selected other viruses.
Bipolar Host Materials: A Chemical Approach for Highly Efficient Electrophosphorescent Devices (2011)

The future of organic light-emitting devices (OLEDs) is drifting from electrofluorescence toward electrophosphorescence due to the feasibility of realizing 100% internal quantum efficiency. There is limited availability of transition metals (TMs) such as Ir, Os, and Pt, which are used for color-tunable phosphorescent emitters, and the use of the host-guest strategy is necessary for suppressing the detrimental triplet-triplet annihilation inherently imparted by the TM-centered emitters. The inevitable demands of organic host materials provide organic chemists with tremendous opportunities to contribute their expertise to this technology. With suitable molecular design and judicious selection of chemical structures featured with different electronic nature, the incorporation of hole-transporting (HT) and electron-transporting (ET) moieties combines the advantages of both functional units into bipolar host materials, which perform balanced injection/transportation/recombination of charge carriers and consequentially lead the OLEDs to have higher performances and low roll-off efficiencies. This review highlights recently developed bipolar host materials with the focus on molecular design strategies and the structure-property-performance relationships of various classes of bipolar host materials, which are classified into several categories according to the structural features of their constituents (HT/ET blocks and spacers).
The phagocytic process and the role of complement in host defense. (1991)

Three lines of defense play an integral role in host defense. The mechanical barrier (skin and mucous membrane: first line), non-specific defense (phagocytic cells non-specific humoral factors) and the specific line of defense. Phagocytic cells act in phases: chemotaxis, attachment of the bacteria to the membrane of the phagocytic cells, ingestion, killing and digestion. Attachment of the particle to receptors is only optimal when the bacteria are loaded with antibodies (IgG) and/or activated complement factors (C3b, C3Bbi), because the phagocyte has receptors for these opsonins (Fc, and C receptors). The late complement factors are also able to kill and lyse certain bacteria without phagocytes. The killing mechanism of the phagocyte is complex. It is oxygen dependent and oxygen independent. Presumably toxic oxygen species are most important to kill bacteria by phagocytes.
Autologous Fat Grafts Harvested and Refined by the Coleman Technique: A Comparative Study (2008)

Although fat grafts obtained by both methods maintain normal histologic structure, the Coleman technique yields a greater number of viable adipocytes and sustains a more optimal level of cellular function within fat grafts and should be considered superior to conventional liposuction as a preferred method of choice for fat graft harvesting.
Activation or anergy: NKT cells are stunned by -galactosylceramide (2005)

Invariant natural killer T (iNKT) cells are T lymphocytes that behave similarly to cells of the innate immune system. The glycolipid alpha-galactosylceramide (alpha-GalCer) is a potent and specific activator of mouse and human iNKT cells and has been used in cancer clinical trials to drive NKT cell-mediated immune responses. However, little is known about the dynamics of the iNKT cell response to alpha-GalCer in vivo. In this issue of the JCI, Parekh and colleagues demonstrate that administration of alpha-GalCer causes iNKT cells to become unresponsive, for at least 1 month, in mice. This leads us to ask, should sequential administration of alpha-GalCer still be used to activate iNKT cells given the anergic state it has been shown here to induce? This intriguing article raises the issue of the avoidance of anergy induction in the design of treatment regimens that use alpha-GalCer as a specific activator of iNKT cells.
Stem cells in human neurodegenerative disorders — time for clinical translation? (2010)

Stem cell-based approaches have received much hype as potential treatments for neurodegenerative disorders. Indeed, transplantation of stem cells or their derivatives in animal models of neurodegenerative diseases can improve function by replacing the lost neurons and glial cells and by mediating remyelination, trophic actions, and modulation of inflammation. Endogenous neural stem cells are also potential therapeutic targets because they produce neurons and glial cells in response to injury and could be affected by the degenerative process. As we discuss here, however, significant hurdles remain before these findings can be responsibly translated to novel therapies. In particular, we need to better understand the mechanisms of action of stem cells after transplantation and learn how to control stem cell proliferation, survival, migration, and differentiation in the pathological environment.
High-Resolution Multiwavelength Surface Plasmon Resonance Spectroscopy for Probing Conformational and Electronic Changes in Redox Proteins (1999)

To date, surface plasmon resonance (SPR) spectroscopy identifies molecules via specific bindings with their ligands immobilized on a surface. We demonstrate here that a high-resolution multiwavelength SPR technique can measure the electronic states of the molecules and thus allow direct identification of the molecules. Using this new capability, we have studied the electronic and conformational differences between the oxidized and reduced states of cytochrome c immobilized on a modified gold electrode. When the wavelength of the incident light is far away from the optical absorption bands of the protein, a approximately 0.008 degree decrease in the resonance angle, due to a conformational change, occurs as the protein is switched from the oxidized to reduced states. When the wavelength is tuned to the absorption bands, the resonance angle oscillates at the wavelengths of the absorption peaks, which provides electronic signatures of the protein.
Scene retrieval method using temporal condition changes (1993)

Abstract This paper proposes a method that retrieves a required scene with such dynamic changes as the motion of the object in the scene as the key from the dynamic images stored as the database. In the traditional database, scenes are retrieved using the keyword for each scene, for example. By contrast, in the proposed system the object of retrieval is an arbitrary interval represented by the dynamic images, and the images are retrieved based on the content represented by the dynamic images. The retrieval request from the user is transformed into the functional format, which describes the time‐course of changes of the object in the image. The retrieval is based on the primitive characteristic data (PCD) as the management data for the video images, and the condition description factor (CDF) obtained by the transformation of the retrieval request from the user. An experiment is attempted where the two‐dimensional position coordinate of the object on the scene is used as PCD, and the motion of the object in the scene or the relative motion of more than one object is used as the key to retrieve the desired scene. The effectiveness of the method is verified.
Dose-response of chronic beta-blocker treatment in heart failure from either idiopathic dilated or ischemic cardiomyopathy. Bucindolol Investigators. (1994)

In heart failure from systolic dysfunction, beta-blockade with bucindolol produces a dose-related improvement in and prevents deterioration of left ventricular function.
Expression of human decay accelerating factor or membrane cofactor protein genes on mouse cells inhibits lysis by human complement (1992)

Mouse cells expressing the human complement regulatory proteins decay accelerating factor (DAF) or membrane cofactor protein (MCP) were produced both by hybridoma technology and by transfection with the appropriate cDNAs. The expression of either or both of these products protected the mouse cell from lysis by human (though not rabbit) complement in the presence of naturally occurring human anti-mouse antibody. This effect could be abrogated by the addition of monoclonal antibody against DAF or MCP. These data suggested that the production of animals transgenic for human complement regulatory proteins should in principle be similarly protected from hyperacute xenograft rejection.
Biofilm dispersal inXanthomonas campestrisis controlled by cell–cell signaling and is required for full virulence to plants (2003)

The rpf gene cluster of Xanthomonas campestris pathovar campestris (Xcc) is required for the pathogenesis of this bacterium to plants. Several rpf genes are involved in the coordinate positive regulation of the production of virulence factors mediated by the small diffusible molecule DSF (for diffusible signal factor). RpfF directs the synthesis of DSF, and a two-component sensory transduction system comprising RpfC and RpfG has been implicated in the perception of the DSF signal and signal transduction. In L medium, rpfF, rpfG, rpfC, and rpfGHC mutants grew as matrix-enclosed aggregates, whereas the wild type grew in a dispersed planktonic fashion. Synthesis of the extracellular polysaccharide xanthan was required for aggregate formation. Addition of DSF triggered dispersion of the aggregates formed by the rpfF strain, but not those of rpf strains defective in DSF signal transduction. An extracellular enzyme from Xcc whose synthesis was positively controlled by the DSF/rpf system could disperse the aggregates produced by all rpf strains. The enzyme was identified as the single endo-beta-1,4-mannanase encoded by the Xcc genome. This enzyme had no detectable activity against soluble xanthan. The endo-beta-1,4-mannanase was required for the full virulence of Xcc to plants. On the basis of this model system, we propose that one role of the beta-mannanase during disease is to promote transitions from an aggregated or biofilm lifestyle to a planktonic lifestyle in response to the DSF signal.
He‐Ne laser irradiation of single identified neurons (1992)

Silent (LPa2 and LPa3) and spontaneously active (V3, V5, V17) neurons of subesophageal ganglia of Helix pomatia were irradiated via a 125-mm fiber probe with a 10-mW He-Ne laser (lambda = 632.8 nm), and the rate of membrane depolarization, duration of latent period, and probability of spike activity were measured as the functions of light intensity. It was found that silent neurons can not be activated by He-Ne laser irradiation. When the spontaneously active neurons generating spikes every 7-10 min were irradiated in between their spontaneous spikes, the depolarization of membrane and generation of action potentials occurred as a function of light intensity, I. The probability of spike generation increased until the intensity reached 1 W/cm2, and when I = 4 W/cm2 was equal to 1. The depolarization of the membrane had a threshold at I = 0.1 W/cm2, then increased with increasing the intensity, and reached a plateau at I = 0.7 W/cm2 (depolarization rate 0.18 mV/s). Duration of the latent period decreased from 28 s to 17 s when the intensity was increased from 0.05 to 0.3 W/cm2. Further increase of the light intensity, from 0.3 to 1.5 W/cm2, caused a less pronounced change in the duration of the latent period (e.g., latent period equal to 11 s at I = 1.5 W/cm2).
A simple low-order adaptive optics system for near-infrared applications (1991)

It is shown that low-order wavefront compensation can significantly improve astronomical images over most of the sky. A novel approach to wavefront sensing and compensation is described. It is optimized for low-order correction and high efficiency. Computer-simulation results show it can achieve the desired performance, and preliminary laboratory tests demonstrate its feasibility.
Stereochemistry of the reductoisomerase and αβ-dihydroxyacid dehydratase-catalysed steps in valine and isoleucine biosynthesis. Observation of a novel tertiary ketol rearrangement (1974)

The reductoisomerase of Salmonella typhimurium has a requirement for the 2S-isomer of acetolactate (III, R = Me) while the αβ-dihydroxy-acid dehydratase has a requirement for the 2R configuration but is not stereoselective with respect to the configuration at C-3.