gebhart/patrepeval huggingface dataset:
Transgenic Plants with Enhanced Resistance to the Fungal Pathogen Rhizoctonia solani (1991)

The production of enzymes capable of degrading the cell walls of invading phytopathogenic fungi is an important component of the defense response of plants. The timing of this natural host defense mechanism was modified to produce fungal-resistant plants. Transgenic tobacco seedlings constitutively expressing a bean chitinase gene under control of the cauliflower mosaic virus 35S promoter showed an increased ability to survive in soil infested with the fungal pathogen Rhizoctonia solani and delayed development of disease symptoms.
Physiological and metabolic correlations in human sepsis. Invited commentary. (1979)

The septic response in man appears to be a disease in which the infecting agent induces a state of disordered metabolic control in the host. The abnormal regulation of metabolic pathways causes a diversion of substrate utilization toward gluconeogenesis and ketone body formation and a reduction in oxidative energy-producing metabolism. This state of metabolic insufficiency is reflected in the pattern of cardiorespiratory, vascular, and physiological compensation. The precise magnitude of the resultant physiological compensation and its rate and direction of change can be quantified by the use of physiological state trajectories which also reflect the magnitude of underlying metabolic derrangements. The prognostic and therapeutic implications of these changes are discussed.
A new Double Two-Way Ranging algorithm for ranging system (2010)

For wireless positioning system, a study on two-way ranging algorithms has been progressed to improve the accuracy of position estimates. In this paper, we propose an asynchronous Double Two-Way Ranging (D-TWR) algorithm, executing an overlapped Two-Way Ranging (TWR) effectively. In this way, the D-TWR algorithm can reduce the number of the required packets in the ranging algorithm as compared with that of the Symmetric Double Sided Two-Way Ranging (SDS-TWR) algorithm. Moreover, D-TWR can achieve more robust Time-of-Arrival (TOA) estimation than SDS-TWR by reducing the TOA estimation errors caused by clock crystal drift between two nodes.
Development and Application of a upp -Based Counterselective Gene Replacement System for the Study of the S-Layer Protein SlpX of Lactobacillus acidophilus NCFM (2009)

In silico genome analysis of Lactobacillus acidophilus NCFM coupled with gene expression studies have identified putative genes and regulatory networks that are potentially important to this organism's survival, persistence, and activities in the gastrointestinal tract. Correlation of key genotypes to phenotypes requires an efficient gene replacement system. In this study, use of the upp-encoded uracil phosphoribosyltransferase (UPRTase) of L. acidophilus NCFM was explored as a counterselection marker to positively select for recombinants that have resolved from chromosomal integration of pORI-based plasmids. An isogenic mutant carrying a upp gene deletion was constructed and was resistant to 5-fluorouracil (5-FU), a toxic uracil analog that is also a substrate for UPRTase. A 3.0-kb pORI-based counterselectable integration vector bearing a upp expression cassette, pTRK935, was constructed and introduced into the Deltaupp host harboring the pTRK669 helper plasmid. Extrachromosomal replication of pTRK935 complemented the mutated chromosomal upp allele and restored sensitivity to 5-FU. This host background provides a platform for a two-step plasmid integration and excision strategy that can select for plasmid-free recombinants with either the wild-type or mutated allele of the targeted gene in the presence of 5-FU. The efficacy of the system was demonstrated by in-frame deletion of the slpX gene (LBA0512) encoding a novel 51-kDa secreted protein associated with the S-layer complex of L. acidophilus. The resulting DeltaslpX mutant exhibited lower growth rates, increased sensitivity to sodium dodecyl sulfate, and greater resistance to bile. Overall, this improved gene replacement system represents a valuable tool for investigating the mechanisms underlying the probiotic functionality of L. acidophilus.
Downregulation of proinflammatory cytokine release in whole blood from septic patients (1995)

Using animal models or healthy volunteers, injection of lipopolysaccharide (LPS) or bacteria causes activation of macrophages with excessive synthesis and secretion of proinflammatory cytokines. Although these models mimic the effects of LPS in the host, they may represent more of an experimental expression of endotoxemia than natural infection itself. Therefore, as an ex vivo model of sepsis, whole blood from 15 patients with severe sepsis and 20 control patients without infection was stimulated with LPS to study the kinetics of mRNA expression and release of proinflammatory cytokines, tumor necrosis factor (TNF)-alpha, interleukin (IL)-1 beta, and IL-6. Stimulation of whole blood with 1 microgram/mL LPS resulted in a maximum increase of cytokine secretion in the control group, while a marked (P < .01) depression of TNF-alpha, IL-1 beta, and IL-6 release was observed in the septic group, which persisted up to 10 days after study enrollment. While IL-1 beta mRNA expression was similar in peripheral blood mononuclear cells (PBMCs) harvested from LPS-stimulated whole blood in septic and control patients, the half-life and consequently the expression of TNF-alpha and IL-6 mRNA were strongly reduced in the septic group. These data indicate a downregulatory mechanism of cytokine release in whole blood from patients with severe sepsis that occurs on different levels. Although excessive secretion of proinflammatory cytokines has been considered deleterious for the host, the reduced capacity of PBMCs in whole blood from septic patients to synthesize and secrete proinflammatory cytokines to an inflammatory stimulus may result in immunodeficiency, because these cytokines in low concentrations are involved in the upregulation of essential cellular and humoral immune functions.
Reactions with 2,3,4,5‐Tetrahydro‐benzo[b]thiepin‐5‐one and its Derivatives (1974)

Abstract 2,3,4,5‐Tetrahydro‐benzo[b]thiepin‐5‐one, its 7‐methyl derivative, and their S, S‐dioxides condense with aromatic aldehydes to give the corresponding 4‐arylidene derivatives 3 and 4 . Compounds 4 react with hydrazine and phenylhydrazine to yield 3, 3a, 4, 5‐tetrahydro‐2 H‐benzo‐[b]thiepino[4, 5‐c]pyrazole S, S‐dioxide derivatives 5 and 6 . Some of the arylidene derivatives 4 add G RIGNARD reagents to give 7 . The IR spectra of representative examples are discussed.
Hijacking the Supplies: Metabolism as a Novel Facet of Virus-Host Interaction (2019)

Viral replication is a process that involves an extremely high turnover of cellular molecules. Since viruses depend on the host cell to obtain the macromolecules needed for their proper replication, they have evolved numerous strategies to shape cellular metabolism and the biosynthesis machinery of the host according to their specific needs. Technologies for the rigorous analysis of metabolic alterations in cells have recently become widely available and have greatly expanded our knowledge of these crucial host-pathogen interactions. We have learned that most viruses enhance specific anabolic pathways and are highly dependent on these alterations. Since uninfected cells are far more plastic in their metabolism, targeting of the virus-induced metabolic alterations is a promising strategy for specific antiviral therapy and has gained great interest recently. In this review, we summarize the current advances in our understanding of metabolic adaptations during viral infections, with a particular focus on the utilization of this information for therapeutic application.
Molecular basis of cranial suture biology and disease: Osteoblastic and osteoclastic perspectives (2014)

The normal growth and development of the skull is a tightly regulated process that occurs along the osteogenic interfaces of the cranial sutures. Here, the borders of the calvarial bones and neighboring tissues above and below, function as a complex. Through coordinated remodeling efforts of bone deposition and resorption, the cranial sutures maintain a state of patency from infancy through early adulthood as the skull continues to grow and accommodate the developing brain's demands for expansion. However, when this delicate balance is disturbed, a number of pathologic conditions ensue; and if left uncorrected, may result in visual and neurocognitive impairments. A prime example includes craniosynostosis, or premature fusion of one or more cranial and/or facial suture(s). At the present time, the only therapeutic measure for craniosynostosis is surgical correction by cranial vault reconstruction. However, elegant studies performed over the past decade have identified several genes critical for the maintenance of suture patency and induction of suture fusion. Such deeper understandings of the pathogenesis and molecular mechanisms that regulate suture biology may provide necessary insights toward the development of non-surgical therapeutic alternatives for patients with cranial suture defects. In this review, we discuss the intricate cellular and molecular interplay that exists within the suture among its three major components: dura mater, osteoblastic related molecular pathways and osteoclastic related molecular pathways.
Brain-to-Brain (mind-to-mind) interaction at distance: a confirmatory study (2014)

<ns4:p>This study reports the results of a confirmatory experiment testing the hypothesis that it is possible to detect coincidences of a sequence of events (silence-signal) of different length, by analyzing the EEG activity of two human partners spatially separated when one member of the pair receives the stimulation and the second one is connected only mentally with the first.</ns4:p> <ns4:p>Seven selected participants with a long friendship and a capacity to maintain focused mental concentration, were divided into two groups located in two different laboratories approximately 190 km apart. Each participant acted both as a “stimulated” and as a “mentally connected” member of the pair for a total of twenty sessions overall.</ns4:p> <ns4:p>The offline analysis of EEG activity using a special classification algorithm based on a support vector machine, detected the coincidences in the sequence of events of the stimulation protocol between the EEG activity of the “stimulated” and the “mentally connected” pairs.</ns4:p> <ns4:p>Furthermore the correlation of the power spectra of the five EEG frequency bands between each of the twenty pairs of data was analyzed using a bootstrap procedure.</ns4:p> <ns4:p>The overall percentage of coincidences out of 88 events was 78.4% and the statistically significant average correlations between the EEG alpha and gamma bands among the pairs of participants, confirmed the results observed in a pilot study. The examination of potential internal, external and statistical artifacts which might have caused these results, ruled out external and internal artifacts. However, the examination of potential statistical artifacts revealed a good level of coincidences in only four pairs using a new procedure to detect the sequences of silence and signal between the EEG activity of the pairs of participants, giving a mild support to the hypothesis that two brains and hence two minds can be connected at distance.</ns4:p>
Tumor Infarction in Mice by Antibody-Directed Targeting of Tissue Factor to Tumor Vasculature (1997)

Selective occlusion of tumor vasculature was tested as a therapy for solid tumors in a mouse model. The formation of blood clots (thrombosis) within the tumor vessels was initiated by targeting the cell surface domain of human tissue factor, by means of a bispecific antibody, to an experimentally induced marker on tumor vascular endothelial cells. This truncated form of tissue factor (tTF) had limited ability to initiate thrombosis when free in the circulation, but became an effective and selective thrombogen when targeted to tumor endothelial cells. Intravenous administration of the antibody-tTF complex to mice with large neuroblastomas resulted in complete tumor regressions in 38 percent of the mice.
Spatial Geometry of the Human Pelvis (1982)

This report presents a three-dimensional description of adult female and male pelvis from the Hamann-Todd skeletal collection, Cleveland Museum of Natural History. Based on a linear height/weight matching strategy and the 1961- 1964 U.S. Health and Examination Survey (HES) data, specimens were selected to represent the small female, medium male, and large male pelvic sizes. One hundred and twenty-three anatomically defined points are used to describe the spatial pelvic geometry in a pelvic-anatomical axis system. A statistical summary of means and standard deviations is presented as X, Y, and Z coordinate value sets to identify each point in three-dimensional space. Full-scale models for each size category were produced for design modeling of anthropomorphic test devices. These data will also be useful as comparative standards for forensic investigations of air crashes and quantitative information on size and shape variability of adult human pelvis.
Plasma proteome changes in cardiovascular disease patients: novel isoforms of apolipoprotein A1 (2011)

The reported data show plasma proteome changes in patients with AMI, UAP, and SAP. We propose some apolipoprotein A1 fractions as a possible new disease-associated marker of cardiovascular disorders.
A novel classification system for evolutionary aging theories (2013)

Theories of lifespan evolution are a source of confusion amongst aging researchers. After a century of aging research the dispute over whether the aging process is active or passive persists and a comprehensive and universally accepted theoretical model remains elusive. Evolutionary aging theories primarily dispute whether the aging process is exclusively adapted to favor the kin or exclusively non-adapted to favor the individual. Interestingly, contradictory data and theories supporting both exclusively programmed and exclusively non-programmed theories continue to grow. However, this is a false dichotomy; natural selection favors traits resulting in efficient reproduction whether they benefit the individual or the kin. Thus, to understand the evolution of aging, first we must understand the environment-dependent balance between the advantages and disadvantages of extended lifespan in the process of spreading genes. As described by distinct theories, different niches and environmental conditions confer on extended lifespan a range of fitness values varying from highly beneficial to highly detrimental. Here, we considered the range of fitness values for extended lifespan and develop a fitness-based framework for categorizing existing theories. We show that all theories can be classified into four basic types: secondary (beneficial), maladaptive (neutral), assisted death (detrimental), and senemorphic aging (varying between beneficial to detrimental). We anticipate that this classification system will assist with understanding and interpreting aging/death by providing a way of considering theories as members of one of these classes rather than consideration of their individual details.
Mechanisms of resistance to EGFR inhibitors in head and neck cancer (2009)

Epidermal growth factor receptor (EGFR), a receptor tyrosine kinase that activates multiple signaling pathways, including phosphatidylinositol-3-kinase/v-AKT murine thymoma viral oncogene homolog protein (Akt), has long been a target of novel therapies. Despite universal EGFR expression in head and neck squamous cell carcinoma (HNSCC), the majority of patients do not respond to EGFR inhibitors. This review focuses on mechanisms of resistance to these agents in HNSCC, and how these may be unique when compared with other malignancies such as non-small cell lung and colorectal cancers. Published studies and abstracts reveal that there are likely several mechanisms underlying resistance, suggesting that different strategies will be required to improve efficacy of EGFR inhibitors in HNSCC.
Import of proteins into peroxisomes and other microbodies (1992)

Research Article| September 15 1992 Import of proteins into peroxisomes and other microbodies M J de Hoop; M J de Hoop 1Laboratory of Biochemistry, Groningen University, Nijenborgh 4, 9747 AG Groningen, The Netherlands Search for other works by this author on: This Site PubMed Google Scholar G Ab G Ab 1Laboratory of Biochemistry, Groningen University, Nijenborgh 4, 9747 AG Groningen, The Netherlands Search for other works by this author on: This Site PubMed Google Scholar Biochem J (1992) 286 (3): 657–669. https://doi.org/10.1042/bj2860657 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Cite Icon Cite Get Permissions Citation M J de Hoop, G Ab; Import of proteins into peroxisomes and other microbodies. Biochem J 15 September 1992; 286 (3): 657–669. doi: https://doi.org/10.1042/bj2860657 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Journal Search Advanced Search This content is only available as a PDF. © 1992 The Biochemical Society, London1992 Article PDF first page preview Close Modal You do not currently have access to this content.
Effect of floating-body charge on SOI MOSFET design (1998)

This work presents a new method for assessing the effect of floating-body charge on a fully- and partially-depleted Silicon-on-Insulator (SOI) MOSFET device design space. Floating-body effects under transient conditions are incorporated into the device design parameters threshold voltage V/sub T/ and off-current I/sub 0FF/ using calibrated two-dimensional (2-D) device simulation. Simulation methodology which reveals the worst-case bounds of the device design parameters, from idle to switching-steady-state, is presented and applied to a CMOS inverter example. Using this methodology, the worst-case shifts in V/sub T/ and I/sub 0FF/ due to hysteretic floating-body charge are quantified for devices in L/sub eff/=0.2- and 0.1-/spl mu/m design spaces. Methods to reduce floating-body effects are discussed including a demonstration of how reducing the effective bulk carrier lifetime widens the 0.1-/spl mu/m design space.
Multifunctional Nanobiomaterials for Neural Interfaces (2009)

Abstract Neural electrodes are designed to interface with the nervous system and provide control signals for neural prostheses. However, robust and reliable chronic recording and stimulation remains a challenge for neural electrodes. Here, a novel method for the fabrication of soft, low impedance, high charge density, and controlled releasing nanobiomaterials that can be used for the surface modification of neural microelectrodes to stabilize the electrode/tissue interface is reported. The fabrication process includes electrospinning of anti‐inflammatory drug‐incorporated biodegradable nanofibers, encapsulation of these nanofibers by an alginate hydrogel layer, followed by electrochemical polymerization of conducting polymers around the electrospun drug‐loaded nanofibers to form nanotubes and within the alginate hydrogel scaffold to form cloud‐like nanostructures. The three‐dimensional conducting polymer nanostructures significantly decrease the electrode impedance and increase the charge capacity density. Dexamethasone release profiles show that the alginate hydrogel coating slows down the release of the drug, significantly reducing the burst effect. These multifunctional materials are expected to be of interest for a variety of electrode/tissue interfaces in biomedical devices.
The homeobox gene CDX2 is aberrantly expressed in most cases of acute myeloid leukemia and promotes leukemogenesis (2007)

The homeobox transcription factor CDX2 plays an important role in embryonic development and regulates the proliferation and differentiation of intestinal epithelial cells in the adult. We have found that CDX2 is expressed in leukemic cells of 90% of patients with acute myeloid leukemia (AML) but not in hematopoietic stem and progenitor cells derived from normal individuals. Stable knockdown of CDX2 expression by RNA interference inhibited the proliferation of various human AML cell lines and strongly reduced their clonogenic potential in vitro. Primary murine hematopoietic progenitor cells transduced with Cdx2 acquired serial replating activity, were able to be continuously propagated in liquid culture, generated fully penetrant and transplantable AML in BM transplant recipients, and displayed dysregulated expression of Hox family members in vitro and in vivo. These results demonstrate that aberrant expression of the developmental regulatory gene CDX2 in the adult hematopoietic compartment is a frequent event in the pathogenesis of AML; suggest a role for CDX2 as part of a common effector pathway that promotes the proliferative capacity and self-renewal potential of myeloid progenitor cells; and support the hypothesis that CDX2 is responsible, in part, for the altered HOX gene expression that is observed in most cases of AML.
The human homologous pairing protein HPP-1 is specifically stimulated by the cognate single-stranded binding protein hRP-A. (1991)

Homologous pairing and strand exchange of DNA are catalyzed by the human homologous pairing protein HPP-1 in a magnesium-dependent, ATP-independent reaction that requires homologous DNA substrates and stoichiometric quantities of HPP-1. Here we show that the addition of the purified human single-strand binding (SSB) protein hRP-A to the reaction mixture stimulates the rate of homologous pairing 70-fold and reduces the amount of HPP-1 required for the reaction at least 10-fold. The identification of hRP-A as a stimulatory factor of HPP-1-catalyzed reaction was facilitated by its recognition as a member of a high molecular weight complex of recombination components. Neither the Escherichia coli SSB protein, bacteriophage T4 gene 32 protein, nor the highly conserved Saccharomyces cerevisiae yRP-A SSB protein could substitute for hRP-A in this stimulation. Because only the cognate SSB was capable of stimulating HPP-1, these results suggest that eukaryotes depend on unique and specific interactions between DNA recombination components.
Normalized cuts and image segmentation (2000)

We propose a novel approach for solving the perceptual grouping problem in vision. Rather than focusing on local features and their consistencies in the image data, our approach aims at extracting the global impression of an image. We treat image segmentation as a graph partitioning problem and propose a novel global criterion, the normalized cut, for segmenting the graph. The normalized cut criterion measures both the total dissimilarity between the different groups as well as the total similarity within the groups. We show that an efficient computational technique based on a generalized eigenvalue problem can be used to optimize this criterion. We applied this approach to segmenting static images, as well as motion sequences, and found the results to be very encouraging.