gebhart/patrepeval huggingface dataset:
Potential of endophytic fungi as biocontrol agents of Duponchelia fovealis (Zeller) (Lepidoptera:Crambidae) (2017)

This study reports the first assessment of endophytic fungi isolated from strawberry leaves and selection of isolates for the control of Duponchelia fovealis, a new pest of strawberries. A total of 400 strawberry leaves of the cultivar 'Albion' were collected in four commercial farms. Leaves were disinfected, cut in fragments, and placed on Petri dishes containing potato dextrose agar media with tetracycline and incubated for 30 days. Following this time, 517 fungal colonies were isolated, and thirteen genera were identified: Cladosporium, Aspergillus, Nigrospora, Fusarium, Trichoderma, Chaetomium, Alternaria, Paecilomyces, Penicillium, Ulocladium, Bipolaris, Diaporthe, and Phoma. Eight isolates belonging to the genera Aspergillus, Diaporthe, Paecilomyces, and Cladosporium were selected for pathogenicity bioassays against third instar larvae of D. fovealis. Isolates of Paecilomyces induced the highest mortality rates.
Thousandfold signal increase using field‐amplified sample stacking for on‐chip electrophoresis (2003)

Field-amplified sample stacking (FASS) leverages conductivity gradients between a volume of injected sample and the background buffer to increase sample concentration. A major challenge in applying FASS to on-chip assays is the initial setup of high-conductivity gradient boundaries in the region of the injected sample volume. We have designed, fabricated, and characterized a novel FASS-capillary electrophoresis (CE) chip design that uses a photoinitiated porous polymer structure to facilitate sample injection and flow control for high-gradient FASS. This polymer structure provides a region of high flow resistance that allows the electromigration of sample ions. We have demonstrated an electropherogram signal increase by a factor of 1100 in electrophoretic separations of fluorescein and Bodipy with, respectively, 2 microM and 1 microM initial concentrations.
Identification of Conserved Regions and Residues within Hedgehog Acyltransferase Critical for Palmitoylation of Sonic Hedgehog (2010)

This study has pinpointed specific regions and multiple residues that regulate Hhat stability and catalysis. Our findings should be applicable to other MBOAT proteins that mediate lipid modification of Wnt proteins and ghrelin, and should serve as a model for understanding how secreted morphogens are modified by palmitoyl acyltransferases.
Recognition of Stage-Specific Mycobacterial Antigens Differentiates between Acute and Latent Infections with Mycobacterium tuberculosis (2006)

Mycobacterium tuberculosis is estimated to infect 80 to 100 million people annually, the majority of whom do not develop clinical tuberculosis (TB) but instead maintain the infection in a latent state. These individuals generally become positive in response to a tuberculin skin test and may develop clinical TB at a later date, particularly if their immune systems are compromised. Latently infected individuals are interesting for two reasons. First, they are an important reservoir of M. tuberculosis, which needs to be considered for TB control. Second, if detected prior to recrudescence of the disease, they represent a human population that is making a protective immune response to M. tuberculosis, which is very important for defining correlates of protective immunity. In this study, we show that while responsiveness to early secretory antigenic target 6 is a good marker for M. tuberculosis infection, a strong response to the 16-kDa Rv2031c antigen (HspX or alpha-crystallin) is largely restricted to latently infected individuals, offering the possibility of differential immunodiagnosis of, or therapeutic vaccination against, TB.
Native Escherichia coli SufA, Coexpressed with SufBCDSE, Purifies as a [2Fe−2S] Protein and Acts as an Fe−S Transporter to Fe−S Target Enzymes (2009)

Iron-sulfur (Fe-S) clusters are versatile biological cofactors that require biosynthetic systems in vivo to be assembled. In Escherichia coli, the Isc (iscRSUA-hscBA-fdx-iscX) and Suf (sufABCDSE) pathways fulfill this function. Despite extensive biochemical and genetic analysis of these two pathways, the physiological function of the A-type proteins of each pathway (IscA and SufA) is still unclear. Studies conducted in vitro suggest two possible functions for A-type proteins, as Fe-S scaffold/transfer proteins or as iron donors during cluster assembly. To resolve this issue, SufA was coexpressed in vivo with its cognate partner proteins from the suf operon, SufBCDSE. Native SufA purified anaerobically using this approach was unambiguously demonstrated to be a [2Fe-2S] protein by biochemical analysis and UV-vis, Mossbauer, resonance Raman, and EPR spectroscopy. Furthermore, native [2Fe-2S] SufA can transfer its Fe-S cluster to both [2Fe-2S] and [4Fe-4S] apoproteins. These results clearly show that A-type proteins form Fe-S clusters in vivo and are competent to function as Fe-S transfer proteins as purified. This study resolves the contradictory results from previous in vitro studies and demonstrates the critical importance of providing in vivo partner proteins during protein overexpression to allow correct biochemical maturation of metalloproteins.
Brain opioid peptides may participate in the reversal of pentylenetetrazol-induced amnesia. (1990)

Post-training administration of pentylenetetrazol (PTZ, 45 mg/kg, i.p.) disrupted 48-h retention, in mice, of an inhibitory avoidance response. The effect was reversed by any of the following treatments given 1 h prior to testing: a) a beta-endorphin injection (0.1 microgram/kg, i.p.), b) PTZ injection, or c) exposure to a novel experience (10 min in a stainless steel box with a wire mesh top). All treatments had a similar time course of effectiveness (up to at least 3 h) and their effects were blocked by naltrexone (0.1 mg/kg, i.p.) but not by naltrexone methyl bromide (10 mg/kg, i.p.). These findings suggest that the recovery of memory is probably due to an activation of central opioid mechanisms and, as a consequence, to the reinstatement of the neurohumoral conditions which were present during the post-training period. These results are consistent with previous evidence indicating that naltrexone given after training prevents the effects of PTZ on memory, and can be interpreted as showing that PTZ did not affect memory storage.
Lagrangian Texture Advection: Preserving both Spectrum and Velocity Field (2010)

Texturing an animated fluid is a useful way to augment the visual complexity of pictures without increasing the simulation time. But texturing flowing fluids is a complex issue, as it creates conflicting requirements: we want to keep the key texture properties (features, spectrum) while advecting the texture with the underlying flow-which distorts it. In this paper, we present a new, Lagrangian, method for advecting textures: the advected texture is computed only locally and follows the velocity field at each pixel. The texture retains its local properties, including its Fourier spectrum, even though it is accurately advected. Due to its Lagrangian nature, our algorithm can perform on very large, potentially infinite scenes in real time. Our experiments show that it is well suited for a wide range of input textures, including, but not limited to, noise textures.
Scanning force microscopy of chromatin. (1995)

Scanning force microscopy (SFM) is a new method to obtain the topography of surfaces with nanometer-resolution. The ability to image under liquids makes the technique attractive for biological applications, especially for the determination of the ultrastructure of biomolecules under native conditions. One growing field of interest is the investigation of chromatin and chromatin-related structures. Different levels of chromatin condensation were the subject of several previous SFM investigations, from the nucleosomal chain, to the 30-nm fiber, ending with the metaphase chromosome. The SFM yielded new information on such fundamental problems as the core spacing of the nucleosomal chain, the internal structure of the 30-nm fiber and the banding mechanism of metaphase chromosomes. Other investigations dealt with the SFM characterization of polytene chromosomes. This paper reviews the state-of-the-art in SFM chromatin research and discusses future developments in this field.
Use of real-time PCR to monitor human herpesvirus 6 reactivation after allogeneic bone marrow transplantation. (2000)

Reactivation of human herpesvirus 6 (HHV-6) is common following allogeneic marrow transplantation, however, little is known about the immune control and pathogenic potential of HHV-6 infection after transplantation. In order to determine whether reactivation of HHV-6 plays an important role in the development of complications in patients undergoing allogeneic bone marrow transplantation or not, we developed a very rapid quantification of viral DNA using a LightCycler. The amount of viral DNA was determined using a supernatant of a chronically infected cell line [TaY(OK)] which contains a known amount of viral DNA. Peripheral blood cells were collected from 5 patients undergoing allogeneic bone marrow transplantation once before transplant and once per week after transplant for 8-24 weeks. The real-time PCR system revealed that there was a linear correlation in the range of 101 to 105 molecules of reference. Using this system, we have found the presence of non-diagnosed HHV-6 reactivation as well as symptomatic infection, indicating the potential for routine implementation of this technology for laboratory diagnosis of HHV-6 infection. Our study shows that this method of rapid quantification of HHV-6 genomes by the real-time PCR using a LightCycler may be useful not only to understand the reconstitution of the immune system following marrow transplantation but also to manage the care of patients.
The correlation of serum estrogens and androgens with bone density in the late postmenopause (1987)

A pilot group of 16 women in the late postmenopause were evaluated for bone density by computerized axial tomography (CT) scanning and for hormonal milieu. A highly statistically significant positive correlation between lumbar-3 spongiosum density and both dehydroepiandrosterone-sulfate (DHEA-S), r = 0.67; P less than 0.005 and androstenedione (A), r = 0.56; P less than 0.03 was found. No such correlations were observed with estradiol (E2), estrone (E1) or an array of other hormones. The results of this preliminary report indicate a clear association of weak androgens with bone density in the late postmenopause.
Proteases for Cell Suicide: Functions and Regulation of Caspases (2000)

Caspases are a large family of evolutionarily conserved proteases found from Caenorhabditis elegans to humans. Although the first caspase was identified as a processing enzyme for interleukin-1beta, genetic and biochemical data have converged to reveal that many caspases are key mediators of apoptosis, the intrinsic cell suicide program essential for development and tissue homeostasis. Each caspase is a cysteine aspartase; it employs a nucleophilic cysteine in its active site to cleave aspartic acid peptide bonds within proteins. Caspases are synthesized as inactive precursors termed procaspases; proteolytic processing of procaspase generates the tetrameric active caspase enzyme, composed of two repeating heterotypic subunits. Based on kinetic data, substrate specificity, and procaspase structure, caspases have been conceptually divided into initiators and effectors. Initiator caspases activate effector caspases in response to specific cell death signals, and effector caspases cleave various cellular proteins to trigger apoptosis. Adapter protein-mediated oligomerization of procaspases is now recognized as a universal mechanism of initiator caspase activation and underlies the control of both cell surface death receptor and mitochondrial cytochrome c-Apaf-1 apoptosis pathways. Caspase substrates have bene identified that induce each of the classic features of apoptosis, including membrane blebbing, cell body shrinkage, and DNA fragmentation. Mice deficient for caspase genes have highlighted tissue- and signal-specific pathways for apoptosis and demonstrated an independent function for caspase-1 and -11 in cytokine processing. Dysregulation of caspases features prominently in many human diseases, including cancer, autoimmunity, and neurodegenerative disorders, and increasing evidence shows that altering caspase activity can confer therapeutic benefits.
Neutralizing IL-12 during induction of murine acute graft-versus-host disease polarizes the cytokine profile toward a Th2-type alloimmune response and confers long term protection from disease (1997)

Injection of parental spleen cells into BDF1 mice results in a graft-vs-host disease (GVHD), the nature of which is critically dependent on the parental haplotype. B6-->BDF1 mice develop a Th1-mediated immunosuppressive lethal GVHD, whereas DBA/2-->BDF1 mice develop a Th2-dependent chronic GVHD, characterized by autoantibody production and glomerulonephritis. In this study we show that neutralizing endogenous IL-12 for a brief period during the initiation of acute GVHD in B6-->BDF1 mice not only confers long term protection from the acute disease, but also permits full repopulation of the recipient with donor B6 lymphocytes. Antibody-treated animals showed normal T cell proliferation in response to Con A stimulation and remained healthy throughout the study. Splenocytes from such mice showed reduced in vitro production of IFN-gamma and enhanced production of IL-5 and IL-10, suggesting a permanent switch from a Th1 to a Th2 cytokine response, comparable to that associated with chronic GVHD in DBA/2-->BDF1 mice. In contrast to DBA/2-->BDF1 mice, however, anti-IL-12-treated B6-->BDF1 mice displayed only mild B cell hyper-responsiveness, as evidenced by a modest increase in serum IgG and IgE levels and moderate levels of anti-dsDNA Abs. Importantly, however, anti-IL-12-treated B6-->BDF1 mice showed no evidence of immune complex-mediated glomerulonephritis. These results demonstrate that neutralizing IL-12 is an effective means of preventing acute GVHD and does not result in the development of chronic GVHD, which might otherwise limit its application.
Increase of CD4+CD25+ regulatory T cells in the peripheral blood of patients with metastatic carcinoma: a Phase I clinical trial using cyclophosphamide and immunotherapy to eliminate CD4+CD25+ T lymphocytes (2007)

We determined the number and functional status of CD4+ CD25(high) regulatory T cells (Treg) in blood samples from patients with metastatic carcinoma, and evaluated their sensitivity to a single intravenous infusion of cyclophosphamide. Treg numbers were significantly higher in 49 patients with metastatic cancer (9.2% of CD4+ T cells) compared to 24 healthy donors (7.1%). These cells expressed the transcription factor forkhead box P3 (FoxP3), glucocorticoid-induced tumour necrosis factor receptor family-related protein (GITR) and intracellular CD152, and demonstrated a suppressive activity in vitro against CD4+ CD25- autologous proliferation. At a single intravenous infusion, cyclophosphamide failed, in association with a non-specific immunotherapy by intratumoral bacille Calmette-Guérin (BCG), to modulate significantly Treg numbers or function. Metastatic cancer is associated with an expansion of peripheral blood CD4+ CD25(high) FoxP3+ GITR+ CD152+ Treg cells whose immunosuppressive properties do not differ from those of healthy subjects. Moreover, cyclophosphamide administration may not represent an optimal therapy to eliminate Treg, which further underlines the need to identify specific agents that would selectively deplete these cells.
Capacity analysis of a TDMA-based slow-frequency-hopped cellular system (1996)

Time-division multiple access (TDMA)-based systems have been adopted as the first generation digital cellular standards in North America, Europe, and Japan. The increasing demand for capacity motivates the study of alternate systems and enhancements to the adopted TDMA standards. In particular, CDMA techniques using direct sequence and slow frequency hopping have been suggested. We analyze the capacity of a slow-frequency-hopped TDMA-based cellular system via calculation of the outage probability. Expressions for the outage probability as a function of voice activity, power control, and antenna diversity are provided for mobile-to-base transmission. These expressions are used to evaluate the system capacity (users/MHz/cell) based on simulating mobile locations within 37 hexagonal cells. The sensitivity to power control error, voice activity factor, and soft capacity of the system is investigated.
Combined treatment of pediatric high‐grade glioma with the oncolytic viral strain MTH‐68/H and oral valproic acid (2006)

The case of a 12-year-old boy with anaplastic astrocytoma of the left thalamus is reported. Postoperative irradiation and chemotherapy could not repress tumor progression; therefore, treatment was undertaken with an oncolytic virus, MTH-68/H, an attenuated strain of Newcastle disease virus (NDV), and valproic acid (VPA), an antiepileptic drug, which also has antineoplastic properties. This treatment resulted in a far-reaching regression of the thalamic glioma, but 4 months later a new tumor manifestation, an extension of the thalamic tumor, appeared in the wall of the IVth ventricle, which required a second neurosurgical intervention. Under continuous MTH-68/H - VPA administration the thalamic tumor remained under control, but the rhombencephalic one progressed relentlessly and led to the fatal outcome. In the final stage, a third tumor manifestation appeared in the left temporal lobe. The possible reasons for the antagonistic behavior of the three manifestations of the same type of glioma to the initially most successful therapy are discussed. The comparative histological study of the thalamic and rhombencephalic tumor manifestations revealed that MTH-68/H treatment induces, similar to in vitro observations, a massive apoptotic tumor cell decline. In the rhombencephalic tumor, in and around the declining tumor cells, NDV antigen could be demonstrated immunohistochemically, and virus particles have been found in the cytoplasm of tumor cells at electron microscopic investigation. These findings document that the oncolytic effect of MTH-68/H treatment is the direct consequence of virus presence and replication in the neoplastic cells. This is the first demonstration of NDV constituents in an MTH-68/H -treated glioma.
DNA methylation in ductal carcinoma in situ related with future development of invasive breast cancer (2015)

This work contributes to the understanding of epigenetic alterations that occur in DCIS and illustrates the potential of DNA methylation as markers of DCIS progression.
[Endografting for refractory aortic dissection and dissecting aneurysm]. (2005)

Endograft repair for refractory aortic dissecting aneurysm is feasible and technically successful, especially for the patients with tears in the ascending aorta or aortic arch.
Query term disambiguation for Web cross-language information retrieval using a search engine (2000)

With the worldwide growth of the Internet, research on Cross-Language Information Retrieval (CLIR) is being paid much attention. Existing CLIR approaches based on query translation require parallel corpora or comparable corpora for the disambiguation of translated query terms. However, those natural language resources are not readily available. In this paper, we propose a disambiguation method for dictionary-based query translation that is independent of the availability of such scarce language resources, while achieving adequate retrieval effectiveness by utilizing Web documents as a corpus and using co-occurrence information between terms within that corpus. In the experiments, our method achieved 97% of manual translation case in terms of the average precision.
Optical approaches to ontogeny of electrical activity and related functional organization during early heart development (1991)

Direct intracellular measurement of electrical events in the early embryonic heart is impossible because the cells are too small and frail to be impaled with microelectrodes; it is also not possible to apply conventional electrophysiological techniques to the early embryonic heart. For these reasons, complete understanding of the ontogeny of electrical activity and related physiological functions of the heart during early development has been hampered. Optical signals from voltage-sensitive dyes have provided a new powerful tool for monitoring changes in transmembrane voltage in a wide variety of living preparations. With this technique it is possible to make optical recordings from the cells that are inaccessible to microelectrodes. An additional advantage of the optical method for recording membrane potential activity is that electrical activity can be monitored simultaneously from many sites in a preparation. Thus, applying a multiple-site optical recording method with a 100- or 144-element photodiode array and voltage-sensitive dyes, we have been able to monitor, for the first time, spontaneous electrical activity in prefused cardiac primordia in the early chick embryos at the six- and the early seven-somite stages of development. We were able to determine that the time of initiation of the contraction is the middle period of the nine-somite stage. In the rat embryonic heart, the onset of spontaneous electrical activity and contraction occurs at the three-somite stage. In this review, a new view of the ontogenetic sequence of spontaneous electrical activity and related physiological functions such as ionic properties, pacemaker function, conduction, and characteristics of excitation-contraction coupling in the early embryonic heart are discussed.
Inhibition of gap junctional intercellular communication in rat liver epithelial cells with transforming RNA (2001)

Previous studies indicated that transforming RNA, derived from the 3' half of the U5 small nuclear RNA first stem structure, suppressed the secretory protein translation in vitro. Gap junctions facilitate homeostatic control of cell growth and differentiation and their dysfunction has been correlated with carcinogenesis. Here, we reported that transforming RNA directly suppressed the gap junction protein, connexin 43, translation and thereby inhibited functional gap junction function in rat epithelial cells. Together with previous data, this implies that altered expression of transforming RNA itself is a potential mechanism in inhibiting gap junction function during carcinogenesis.
Polymer Thin Films for Biomedical Applications (2010)

Abstract The sections in this article are Introduction Biocompatible Coatings Protein‐Repellant Coatings PEG ylated Thin Films Non‐ PEG ylated Hydrophilic Thin Films Thin Films of Hyperbranched Polymers Multilayer Thin Films Antithrombogenic Coatings Surface Chemistry and Blood Compatibility Membrane‐Mimetic Thin Films Heparin‐Mimetic Thin Films Clot‐Lyzing Thin Films Polyelectrolyte Multilayer Thin Films Polyurethane Coatings Vapor‐Deposited Thin Films Antimicrobial Coatings Cationic Polymers Nanocomposite Polymer Thin Films Incorporating Inorganic Biocides Antibiotic‐Conjugated Polymer Thin Films Biomimetic Antibacterial Coatings Thin Films Resistant to the Adhesion of Viable Bacteria Coatings for Tissue Engineering Substrates PEG ylated Thin Films Zwitterionic Thin Films Thin Films of Hyperbranched Polymers Polyurethane Coatings Polysaccharide‐Based Thin Films Polyelectrolyte Multilayer Thin Films Temperature‐Responsive Polymer Coatings Electroactive Thin Films Other Functional Polymer Coatings Multilayer Thin Films for Cell Encapsulation Patterned Thin Films Polymer Thin Films for Drug Delivery Polymer Thin Films for Gene Delivery Conclusions