gebhart/patrepeval huggingface dataset:
Outer-Membrane Antigens of Gram-Negative Pathogens: Summary of Session (1988)

Outer-membrane antigens and other surface structures of selected gram-negative pathogens were explored in the papers presented in this session. Although varied experimental approaches were employed to address individual problems, common themes emerged among the papers. The universal application of immunochemistry and molecular biological techniques clearly has opened new vistas in the study of the role of the bacterial surface in the pathogenesis of gram-negative bacterial infections. Neisseria gonorrhoeae protein (P) IIs are a series of related but antigenically heterogeneous proteins. An individual isolate may express none, one, or more than one PII protein on its surface either in vitro or during infection. A subset of the PIIs is associated with colony opacity in vitro; these PIIs are not expressed in strains isolated from patients during menstruation or from strains isolated from patients with invasive gonococcal disease. However, since no good animal model for gonococcal disease is available, the role of the PII proteins in virulence or pathogenesis cannot be addressed directly. Thus, recent studies have been directed toward understanding the structure and genetic organization of these proteins. The PII proteins contain conserved and hypervariable domains. The mechanisms for control of protein II and pilin expression are different, indicating that gonococci have evolved at least two mechanisms for the regulation of the expression of antigenically variable surface structures. Variable expression of these antigens may enhance the ability of the gonococcus to evade the host's immune system. The role of Ca` in the modulation of the invasiveness of Salmonella and in the expression of a set of outer-membrane proteins produced by Yersinia species was discussed by Peterson and Niesel and by Straley, respectively. Several Salmonella species ex-
Interplay of Adaptive Th2 Immunity with Eotaxin‐3/C‐C Chemokine Receptor 3 in Eosinophilic Esophagitis (2007)

Collectively, these studies demonstrate cooperation between systemic CD4+ Th2-cell-mediated immunity and an enhanced eosinophil-CCR3/eotaxin-3 pathway in EE pathogenesis. Furthermore, the imbalanced Th2 immunity and increased CCR3 expression are reversible with disease remission.
Frequent Coinfection of Cells Explains Functional In Vivo Complementation between Cytomegalovirus Variants in the Multiply Infected Host (2005)

In contrast to many other virus infections, primary cytomegalovirus (CMV) infection does not fully protect against reinfection. Accordingly, clinical data have revealed a coexistence of multiple human CMV variants/strains in individual patients. Notably, the phenomenon of multiple infection was found to correlate with increased virus load and severity of CMV disease. Although of obvious medical relevance, the mechanism underlying this correlation is unknown. A weak immune response in an individual could be responsible for a more severe disease and for multiple infections. Alternatively, synergistic contributions of variants that differ in their biological properties can lead to qualitative changes in viral fitness by direct interactions such as genetic recombination or functional complementation within coinfected host cells. We have addressed this important question paradigmatically with the murine model by differently designed combinations of two viruses employed for experimental coinfection of mice. Specifically, a murine cytomegalovirus (MCMV) mutant expressing Cre recombinase was combined for coinfection with a mutant carrying Cre-inducible green fluorescent protein gene, and attenuated mutants were combined for coinfection with wild-type virus followed by two-color in situ hybridization studies visualizing the replication of the two viruses in infected host organs. These different approaches concurred in the conclusion that coinfection of host cells is more frequent than statistically predicted and that this coinfection alters virus fitness by functional trans-complementation rather than by genetic recombination. The reported findings make a major contribution to our molecular understanding of enhanced CMV pathogenicity in the multiply infected host.
Superconductivity in the Tl-Sr-Ca-Cu-O system (1988)

Superconductivity at 20 K has been unambiguously observed in the Tl-Sr-Ca-Cu-O system. Superconductivity at 70 K was also observed in the same system. These observations may provide a new insight into the mechanism of oxide superconductivity.
Nanocomposite Electrolytes with Fumed Silica and Hectorite Clay Networks: Passive versus Active Fillers (2003)

Abstract The use of nanocomposites constitutes a versatile and robust approach in the development of novel electrolytes with tailored electrochemical and mechanical characteristics. In this study, we examine the morphology, rheology, and ion‐transport properties of two types of nanocomposite electrolyte gels, one consisting of branched silica nanoparticles and the other composed of hectorite clay. In the first system with hydrophobic (fumed) silica, oligomers of poly(ethylene oxide) (PEO), and lithium salt, the silica acts as a passive filler and does not participate in ion transport. The electrochemical properties are controlled by the salt–PEO electrolyte, allowing for ionic conductivities greater than 10 –3 S cm –1 at ambient temperature. At sufficiently high concentrations, the silica forms an elastic gel possessing a large open network structure that provides for unimpeded ion mobility. In the second system composed of lithium‐exchanged hectorite filler, the nanoscale platelets serve as the anion. This active filler yields ionic conductivities in excess of 10 –4 S cm –1 and lithium transference numbers approaching unity. Similar to fumed silica, the hectorite clay also forms an elastic gel network. However, the morphologies of the two systems are distinctively different both in terms of network structure and characteristic length scale. These morphological differences manifest themselves in different rheological responses with regard to gel modulus and yield stress.
Novor: Real-Time Peptide de Novo Sequencing Software (2015)

De novo sequencing software has been widely used in proteomics to sequence new peptides from tandem mass spectrometry data. This study presents a new software tool, Novor, to greatly improve both the speed and accuracy of today's peptide de novo sequencing analyses. To improve the accuracy, Novor's scoring functions are based on two large decision trees built from a peptide spectral library with more than 300,000 spectra with machine learning. Important knowledge about peptide fragmentation is extracted automatically from the library and incorporated into the scoring functions. The decision tree model also enables efficient score calculation and contributes to the speed improvement. To further improve the speed, a two-stage algorithmic approach, namely dynamic programming and refinement, is used. The software program was also carefully optimized. On the testing datasets, Novor sequenced 7%-37% more correct residues than the state-of-the-art de novo sequencing tool, PEAKS, while being an order of magnitude faster. Novor can de novo sequence more than 300 MS/MS spectra per second on a laptop computer. The speed surpasses the acquisition speed of today's mass spectrometer and, therefore, opens a new possibility to de novo sequence in real time while the spectrometer is acquiring the spectral data. Graphical Abstract ᅟ.
Multi-Surface and Multi-Field Co-Segmentation of 3-D Retinal Optical Coherence Tomography (2014)

When segmenting intraretinal layers from multiple optical coherence tomography (OCT) images forming a mosaic or a set of repeated scans, it is attractive to exploit the additional information from the overlapping areas rather than discarding it as redundant, especially in low contrast and noisy images. However, it is currently not clear how to effectively combine the multiple information sources available in the areas of overlap. In this paper, we propose a novel graph-theoretic method for multi-surface multi-field co-segmentation of intraretinal layers, assuring consistent segmentation of the fields across the overlapped areas. After 2-D en-face alignment, all the fields are segmented simultaneously, imposing a priori soft interfield-intrasurface constraints for each pair of overlapping fields. The constraints penalize deviations from the expected surface height differences, taken to be the depth-axis shifts that produce the maximum cross-correlation of pairwise-overlapped areas. The method's accuracy and reproducibility are evaluated qualitatively and quantitatively on 212 OCT images (20 nine-field, 32 single-field acquisitions) from 26 patients with glaucoma. Qualitatively, the obtained thickness maps show no stitching artifacts, compared to pronounced stitches when the fields are segmented independently. Quantitatively, two ophthalmologists manually traced four intraretinal layers on 10 patients, and the average error ( 4.58 ±1.46 μm) was comparable to the average difference between the observers ( 5.86±1.72 μm). Furthermore, we show the benefit of the proposed approach in co-segmenting longitudinal scans. As opposed to segmenting layers in each of the fields independently, the proposed co-segmentation method obtains consistent segmentations across the overlapped areas, producing accurate, reproducible, and artifact-free results.
Optical Guided Waves and Devices (1992)

Overview electromagnetic fields and plane waves material effects the optics of beams reflection and refraction at a single interface the slab waveguide planar waveguide integrated optics optical fibres and fibre devices coupled mode devices optoelectronic interactions in semiconductors optoelectronic devices optic device fabrication systems and applications.
Cloning and Characterization of a Novel Human Class I Histone Deacetylase That Functions as a Transcription Repressor (2000)

Histone acetylation alters chromatin state by modifying lysines on histone and plays an important role in modulating gene transcription. A dynamic balance of histone acetylation/deacetylation is maintained by histone acetyltransferases and histone deacetylases. Emerging evidence suggests that a family of histone deacetylases may exist to regulate diverse cellular functions, including chromatin structure, gene expression, cell cycle progression, and oncogenesis. We describe here a novel human histone deacetylase, named HDAC8, cloned from human kidney. HDAC8 encodes 377 amino acid residues and shares extensive homology to several known HDACs, in particular a histone deacetylase from Arabidopsis thaliana. Northern blot analyses revealed that HDAC8 expression pattern for HDAC8 is distinct from that for HDAC1 and HDAC3, and expression of HDAC8 mRNA occurs in multiple organs including heart, lung, kidney, and pancreas. HDAC8 mRNA was also observed in several cell lines derived from cancerous tissues. When expressed in HEK293 cells, HDAC8 exhibited deacetylase activity toward acetylated histone, indicating that this protein is a bona fide histone deacetylase. Its histone deacetylase activity was inhibited by trichostatin and other known histone deacetylase inhibitors. Furthermore, active recombinant HDAC8 was expressed and purified from Escherichia coli. When ectopically expressed in cells, HDAC8 was found to be localized to the nucleus. Co-transfection experiments demonstrated that expression of HDAC8 repressed a viral SV40 early promoter activity. These results indicate that HDAC8 is a novel member of the histone deacetylase family, which may play a role in the development of a broad range of tissues and potentially in the etiology of cancer.
"La Paidología" de Domingo Barnés: estudio de su tesis doctoral y la evolución de su obra publicada (1989)

Ankle sprain is reported to be among the most common recurrent injuries. About 20% of acute ankle sprain patients develop chronic ankle instability. The failure of functional rehabilitation after acute ankle sprain leads to the development of chronic ankle instability. Differentiation between functional and anatomical ankle instability is very essential to guide the proper treatment. Stability testing by varus stress test and anterior drawer test should be carried out. Subtalar instability is an important pathology that is commonly by passed during the assessment of chronic ankle instability. Unlike acute ankle sprain, chronic ankle instability might require surgical intervention. The surgical and conservative management options can be very much developed by in-depth knowledge of the ankle anatomy, biomechanics, and pathology. Anatomical repair, augmentation by tendon, or both are the basic methods of surgical intervention. Arthroscopy is becoming more popular in the management of chronic ankle instability.
Synthesis and bioassay of improved mosquito repellents predicted from chemical structure (2008)

Mosquito repellency data on acylpiperidines derived from the U.S. Department of Agriculture archives were modeled by using molecular descriptors calculated by CODESSA PRO software. An artificial neural network model was developed for the correlation of these archival results and used to predict the repellent activity of novel compounds of similar structures. A series of 34 promising N-acylpiperidine mosquito repellent candidates (4a-4q') were synthesized by reactions of acylbenzotriazoles 2a-2p with piperidines 3a-3f. Compounds (4a-4q') were screened as topically applied mosquito repellents by measuring the duration of repellency after application to cloth patches worn on the arms of human volunteers. Some compounds that were evaluated repelled mosquitoes as much as three times longer than N,N-diethyl-m-toluamide (DEET), the most widely used repellent throughout the world. The newly measured durations of repellency were used to obtain a superior correlation equation relating mosquito repellency to molecular structure.
Therapeutic efficacy of OX-40 receptor antibody depends on tumor immunogenicity and anatomic site of tumor growth. (2000)

The OX-40 receptor (OX-40R) is a cell surface glycoprotein of the tumor necrosis factor receptor family that is expressed primarily on activated CD4 T cells. Engagement of OX-40R by the OX-40 ligand (OX-40L) is known to costimulate the production of cytokines by activated T lymphocytes and to rescue effector T cells from activation-induced cell death. It was previously reported that in vivo ligation of OX-40R by administration of OX-40L:immunoglobulin fusion protein or OX-40R monoclonal antibody (mAb) resulted in a significant prolongation of survival of tumor-bearing mice in four histologically distinct solid tumors. In this study, we demonstrate that the therapeutic efficacy of OX-40R mAb was influenced by the tumor burden, the intrinsic immunogenicity of the tumor as well as by the histological site of tumor growth. Whereas subdermal and intracranial growth of weakly immunogenic MCA 203 and MCA 205 sarcomas and GL261 glioma were susceptible to the mAb treatment, established pulmonary MCA 205 metastases were refractory to the same regimen of treatment. Furthermore, the mAb administration had no impact on the growth of the poorly immunogenic B16/D5 mela noma. Tumor regression mediated by OX-40R mAb was dependent on the participation of both CD4 and CD8 T cells and as a result of tumor rejection, a long-term tumor-specific immunity was established. Analysis of tumor-infiltrating T cells revealed the presence of a far greater number of OX-40R+ T cells of both CD4 and CD8 phenotypes in the intracranial immunogenic GL261 glioma than that in the poorly immunogenic B16/D5 melanoma. These results suggest that ligation of OX-40R on activated T cells in situ in the tumor may provide a necessary costimulatory signal to augment immune responses leading to tumor regression and immunological memory.
Identification of a Novel Stat3 Recruitment and Activation Motif Within the Granulocyte Colony-Stimulating Factor Receptor (1999)

Stat3 is essential for early embryonic development and for myeloid differentiation induced by the cytokines granulocyte colony-stimulating factor (G-CSF) and interleukin-6 (IL-6). Two isoforms of Stat3 have been identified, (p92) and beta (p83), which have distinct transcriptional and biological functions. Activation of both Stat3 and Stat3beta requires the distal cytoplasmic domain of the G-CSFR, which contains four Tyr at positions 704, 729, 744, and 764. The studies reported here were undertaken to determine which, if any, of these tyrosine residues participated in Stat3/beta recruitment and activation. We showed that Stat3 and Stat3beta were affinity purified using phosphopeptides containing Y704 and Y744 but not by nonphosphorylated peptide analogues or by phosphopeptides containing Y729 and Y764. Complementary results were obtained in studies examining the ability of these peptides to destabilize and inhibit DNA binding of activated Stat3. Both Y704 and Y744 contributed to optimal activation of Stat3/beta in M1 murine myeloid leukemia cells containing wild-type and Y-to-F mutant G-CSFR constructs. Carboxy-terminal to Y704 at the +3 position is Gln; YXXQ represents a consensus Stat3 recruitment and activation motif. Y744 is followed at the +3 position by Cys (C); YXXC, represents a novel motif implicated in the recruitment and activation of Stat3. Modeling of the SH2 domain of Stat3 based on homologous SH2 domains of known structure revealed polar residues whose side chains contact the +3 position. This substitution may confer specificity for the Y704- and Y744-based ligands by allowing H-bond formation between the binding surface and the Gln or Cys found at the respective +3 position.
Interaction of drugs with apomorphine, tryptamine and norepinephrine. A new 'in vivo' approach: the ATN-test in rats. (1977)

A new experimental test procedure is described for the 'in vivo' study of drug interactions with dopamine (DA), 5 hydroxy-tryptamine (5-HT) and norepinephrine (NE). The ultimate aim of this study is to provide an empirical evaluation of the relative specificity with which drugs may affect particular neurotransmitter systems, and to allow a classification of new drugs in this respect. The data indicate that, within certain dosage limits, compounds may modulate specifically a single component of the test procedure and may thus be considered as interacting specifically to modify one neurotransmitter system: i.e. DA in the apomorphine-test (e.g. pimozide), 5-HT in the tryptamine-test (e.g. pizotifen) and NE in the norepinephrine-test (e.g. phenoxy-benzamine). Higher doses of the same compounds may, however, excert effects on other neurotransmitter systems as well, and these actions may be classified as nonspecific. Thus the concept of drug specificity as applied in the present study, is not exclusive, but refers to the dissociation, in terms of doses, which exists between a drug's effect on one neurotransmitter system and its possible effects on other systems. The ATN-test separates and delineates, in terms of doses, the specific and nonspecific effects of drugs.
Hierarchical chamfer matching: a parametric edge matching algorithm (1988)

The algorithm matches edges by minimizing a generalized distance between them. The matching is performed in a series of images depicting the same scene with different resolutions, i.e. in a resolution pyramid. Using this hierarchical structure reduces the computational load significantly. The algorithm is reasonably simple to implement and is insensitive to noise and other disturbances. The algorithm has been tested in several applications. Two of them are briefly presented. In the first application the outlines of common tools are matched to gray-level images of the same tools, with overlapping. In the second application lake edges from aerial photographs are matched to lake edges from a map, with translation, rotation, scale, and perspective changes. The hierarchical chamfer matching algorithm gives correct results using a reasonable amount of computational resources in all tested applications.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A muscle precursor cell-dependent pathway contributes to muscle growth after atrophy (2001)

Slow-twitch skeletal muscle atrophies greatly in response to unloading conditions. The cellular mechanisms that contribute to the restoration of muscle mass after atrophy are largely unknown. Here, we show that atrophy of the mouse soleus is associated with a 36% decrease in myonuclear number after 2 wk of hindlimb suspension. Myonuclear number is restored to control values during the 2-wk recovery period in which muscle mass returns to normal, suggesting that muscle precursor cells proliferate and fuse with myofibers. Inhibition of muscle precursor cell proliferation by local gamma-irradiation of the hindlimb completely prevents this increase in myonuclear number. Muscle growth occurs normally during the first week in irradiated muscles, but growth during the second week is inhibited, leading to a 50% attenuation in the restoration of muscle mass. Thus early muscle growth occurs independently of an increase in myonuclear number, whereas later growth requires proliferating muscle precursor cells leading to myonuclear accretion. These results suggest that increasing the proliferative capacity of muscle precursor cells may enhance restoration of muscle mass after atrophy.
Therapeutic strategies for preventing skeletal muscle fibrosis after injury (2015)

Skeletal muscle repair after injury includes a complex and well-coordinated regenerative response. However, fibrosis often manifests, leading to aberrant regeneration and incomplete functional recovery. Research efforts have focused on the use of anti-fibrotic agents aimed at reducing the fibrotic response and improving functional recovery. While there are a number of mediators involved in the development of post-injury fibrosis, TGF-β1 is the primary pro-fibrogenic growth factor and several agents that inactivate TGF-β1 signaling cascade have emerged as promising anti-fibrotic therapies. A number of these agents are FDA approved for other conditions, clearing the way for rapid translation into clinical treatment. In this article, we provide an overview of muscle's host response to injury with special emphasis on the cellular and non-cellular mediators involved in the development of fibrosis. This article also reviews the findings of several pre-clinical studies that have utilized anti-fibrotic agents to improve muscle healing following most common forms of muscle injuries. Although some studies have shown positive results with anti-fibrotic treatment, others have indicated adverse outcomes. Some concerns and questions regarding the clinical potential of these anti-fibrotic agents have also been presented.
Lethality of Drosophila lacking TSC tumor suppressor function rescued by reducing dS6K signaling (2002)

Tuberous sclerosis complex (TSC) is a genetic disorder caused by mutations in one of two tumor suppressor genes, TSC1 and TSC2. Here, we show that absence of Drosophila Tsc1/2 leads to constitutive dS6K activation and inhibition of dPKB, the latter effect being relieved by loss of dS6K. In contrast, the dPTEN tumor suppressor, a negative effector of PI3K, has little effect on dS6K, but negatively regulates dPKB. More importantly, we demonstrate that reducing dS6K signaling rescues early larval lethality associated with loss of dTsc1/2 function, arguing that the S6K pathway is a promising target for the treatment of TSC.