gebhart/patrepeval huggingface dataset:
Is protein context responsible for peptide-mediated interactions? (2019)

Many cell signaling pathways are orchestrated by the weak, transient, and reversible protein-protein interactions that are mediated by the binding of a short peptide segment in one protein (parent protein) to a globular domain in another (partner protein), known as peptide-mediated interactions (PMIs). Previous studies normally had an implicit hypothesis that a PMI is functionally equivalent or analogous to the protein-peptide interaction (PTI) involved in the PMI system, while ignoring parent context contribution to the peptide binding. Here, we perform a systematic investigation on the reasonability and applicability of the hypothesis at structural, energetic and dynamic levels. It is revealed that the context impacts PMIs primarily through conformational constraint of the peptide segments, which can (i) reduce the peptide flexibility and disorder in an unbound state, (ii) help the peptide conformational selection to fit the active pocket of partner proteins, and (iii) enhance the peptide packing tightness against the partners. Long, unstructured and/or middle-located peptide segments seem to be more vulnerable to their context than short, structured and/or terminal ones. The context is found to moderately or considerably improve both the binding affinity and specificity of PMIs as compared to their PTI counterparts; with the context support a peptide segment can contribute to ∼30-60% total binding energy of the whole PMI system, whereas the contribution is reduced to ∼5-50% when the context constraint is released. In addition, we also observe that peptide selectivity is largely impaired or even reversed upon stripping of their parent context (global selectivity decreases from 34.2 to 1.7-fold), by examining the crystal structures of full-length Src family kinases in an autoinhibitory state. Instead of the direct interaction and desolvation that are primarily concerned in traditional studies, peptide flexibility and the entropy penalty should also play a crucial role in the context effect on PMIs. Overall, we suggest that the context factor should not be ignored in most cases, particularly those with peptide segments that are long, highly disordered, and/or located at the middle region of their parent proteins.
Isolation and Functional Characterization of Pluripotent Stem Cell–Derived Cardiac Progenitor Cells (2010)

The use of transgenic markers in pluripotent stem cells allows the facile isolation of transient cell populations that appear at certain phases of embryonic development. Here, we describe a procedure for deriving cardiac progenitors from mouse pluripotent stem cells carrying a GFP reporter under the control of an Nkx2.5 enhancer sequence. The cells are propagated under standard conditions and are differentiated using the hanging-droplet method with medium optimized for commitment to the cardiac lineage. Cardiac progenitors are isolated from the differentiation culture using fluorescence-activated cell sorting (FACS) and can be cultured further for functional characterization and experimentation. The protocols described here can be applied to both embryonic and induced pluripotent stem cells and can easily be adapted to transgenic lines carrying other cardiac cell lineage reporters.
DECL: A circular inference method for indoor pedestrian localization using phone inertial sensors (2014)

Pedestrian dead reckoning plays an important role in indoor pedestrian localization applications. Although this approach has a notable advantage that no extra infrastructure is required, it also suffers an issue known as the drift, which means the estimation errors accumulate and ultimately may make the result unreliable. In this paper, we propose a circular inference method applying online learning in order to reduce such drift errors. Map information is used as prior knowledge and identified land marks are used as triggers for learning processing. A multidimensional optimization algorithm is designed and used in learning phase to efficiently tune the estimation parameters. On the basis of the design we implement an end system running on smartphones and use it in the evaluation experiments. The results show that the proposed method can effectively improve the accuracy and reliability of the localization system.
Expression profiling of CD34 <sup>+</sup> hematopoietic stem/ progenitor cells reveals distinct subtypes of therapy-related acute myeloid leukemia (2002)

One of the most serious consequences of cytotoxic cancer therapy is the development of therapy-related acute myeloid leukemia (t-AML), a neoplastic disorder arising from a multipotential hematopoietic stem cell. To gain insights into the molecular basis of this disease, we performed gene expression profiling of CD34(+) hematopoietic progenitor cells from t-AML patients. Our analysis revealed that there are distinct subtypes of t-AML that have a characteristic gene expression pattern. Common to each of the subgroups are gene expression patterns typical of arrested differentiation in early progenitor cells. Leukemias with a -5/del(5q) have a higher expression of genes involved in cell cycle control (CCNA2, CCNE2, CDC2), checkpoints (BUB1), or growth (MYC), and loss of expression of the gene encoding IFN consensus sequence-binding protein (ICSBP). A second subgroup of t-AML is characterized by down-regulation of transcription factors involved in early hematopoiesis (TAL1, GATA1, and EKLF) and overexpression of proteins involved in signaling pathways in myeloid cells (FLT3) and cell survival (BCL2). Establishing the molecular pathways involved in t-AML may facilitate the identification of selectively expressed genes that can be exploited for the development of urgently needed targeted therapies.
Degradation of Chlorinated Dibenzofurans and Dibenzo-p-Dioxins by Sphingomonas sp. Strain RW1 (1996)

The ability of the dibenzofuran- and dibenzo-p-dioxin-mineralizing bacterium Sphingomonas sp. strain RW1 (R.-M. Wittich, H. Wilkes, V. Sinnwell, W. Francke, and P. Fortnagel, Appl. Environ. Microbiol. 58:1005-1010, 1992) to oxidize chlorinated derivatives of dibenzofuran and dibenzo-p-dioxin was analyzed. Strain RW1 degraded several mono- and dichlorinated dibenzofurans and dibenzo-p-dioxins, but it did not degrade more highly chlorinated congeners. Most mono- and dichlorinated dibenzofurans and dibenzo-p-dioxins investigated in this study were degraded to the corresponding mono- and dichlorinated salicylates and catechols, respectively, together with salicylate and catechol. This indicates an initial dioxygenolytic attack on the substituted as well as on the nonsubstituted aromatic nucleus of most of the target compounds. Strain RW1 could not grow at the expense of monochlorinated dibenzo-p-dioxins and dibenzofurans as carbon sources, with the exception of 4-chlorodibenzofuran, which was stoichiometrically converted to 3-chlorosalicylate.
Chitosan-Coated Mesoporous Silica Nanoparticle Treatment of <i>Citrullus lanatus</i> (Watermelon): Enhanced Fungal Disease Suppression and Modulated Expression of Stress-Related Genes (2019)

This work assesses the potential of mesoporous silica nanoparticles with or without a chitosan coating to suppress Fusarium wilt (Fusarium oxysporum f. sp. niveum) in watermelon (Citrullus lanatus) by virtue of dissolution to release silicic acid. Plant health was assessed by monitoring the total biomass and fruit production in both healthy and pathogen-infected plants up to 100 days after a single nanoparticle application (500 mg/L) was applied at the seedling stage. Both types of mesoporous silica nanoparticles enhanced the innate defense mechanisms of watermelon, with mesoporous silica nanoparticles (MSNs) and chitosan-coated mesoporous silica nanoparticles (CTS-MSNs) reducing disease severity by ∼40% and ∼27%, respectively, as measured by the area-under-the-disease-progress curve. Changes in gene expression measured several weeks after nanoparticle application demonstrated reduced expression of several stress-related genes after CTS-MSN and MSN treatments, indicating a reduced disease burden on the plant. Although treatment did not impact fruit production from diseased plants, a single application of chitosan-coated mesoporous silica nanoparticles at the seedling stage led to a 70% increase in the fruit yield of uninfected watermelon. Monitoring plant biomass revealed that MSNs and CTS-MSNs had no significant impact on the biomass reductions in diseased plants, likely because seedlings were treated and biomass was measured weeks later in the fully grown plants. These findings demonstrate the utility of a single application of mesoporous silica nanoparticles with or without a chitosan coating as a nanoenabled agricultural amendment, and current work is focused on optimizing the material synthesis and treatment regimens for maximum benefit.
Transplantation of Neuronal and Glial Restricted Precursors into Contused Spinal Cord Improves Bladder and Motor Functions, Decreases Thermal Hypersensitivity, and Modifies Intraspinal Circuitry (2005)

Transplanting neuronal and glial restricted precursors (NRP/GRP) into a midthoracic injury 9 d after contusion improved bladder and motor function, diminished thermal hypersensitivity, and modified lumbosacral circuitry compared with operated controls (OP-controls). Histological analysis showed that NRP/GRP survived, filled the lesion site, differentiated into neurons and glia, and migrated selectively. Volume of spinal cord spared was increased in NRP/GRP recipients, suggesting local protection. Bladder areflexia developed in both operated groups, but NRP/GRP recipients exhibited an accelerated recovery, with decreased micturition pressure and fewer episodes of detrusor hyperreflexia. Because noradrenergic receptors proliferate after spinal injury and descending noradrenergic pathways contribute to regulation of bladder control, we examined the effects of administering an alpha-1A-adrenergic antagonist, Tamsulosin, on urodynamics. This improved all cystometric parameters in both operated groups, and micturition pressure in NRP/GRP rats recovered to normal levels. Both operated groups initially showed increased sensitivity to a thermal stimulus applied to the tail; the NRP/GRP rats showed significant improvement over time. NRP/GRP grafts also produced greater recovery of hindlimb function in several tests, although both groups showed persistent and similar deficits in locomotion on a grid. Because bladder, hindlimb, and tail sensory and motor functions are organized through lumbosacral cord, we examined descending and primary afferent projections at L6-S1. The density of serotonergic, noradrenergic, and corticotrophin releasing factor-positive fibers increased in the NRP/GRP group compared with OP-controls, suggesting some sparing and/or sprouting of these modulatory pathways. Immunocytochemical staining density of dorsal root axons in the dorsal horn increased in the OP-controls but appeared normal in the NRP/GRP group. Synaptophysin immunoreactivity in the lumbosacral dorsal horn was similar among groups, consistent with restoration of synaptic density in both groups of operated animals but by different pathways. We suggest that local protection provided by NRP/GRP resulted in increased sparing/sprouting of descending pathways, which prevented sprouting by dorsal root axons, and that this modification in lumbosacral circuitry contributes to the recovery of function.
Viscoelastic coagulation testing: technology, applications, and limitations (2011)

Use of viscoelastic point-of-care (POC) coagulation instrumentation is relatively new to veterinary medicine. In human medicine, this technology has recently undergone resurgence owing to its capacity to detect hypercoagulability. The lack of sensitive tests for detecting hypercoagulable states, along with our current understanding of in vivo coagulation, highlights the deficiencies of standard coagulation tests, such as prothrombin and partial thromboplastin times, which are performed on platelet-poor plasma. Viscoelastic coagulation analyzers can provide an assessment of global coagulation, from the beginning of clot formation to fibrinolysis, utilizing whole blood. In people, use of this technology has been reported to improve management of hemostasis during surgery and decrease usage of blood products and is being used as a rapid screen for hypercoagulability. In veterinary medicine, clinical use of viscoelastic technology has been reported in dogs, cats, foals, and adult horses. This article will provide an overview of the technology, reagents and assays, applications in human and veterinary medicine, and limitations of the 3 viscoelastic POC analyzers in clinical use.
Solar cells on porcelain stoneware tiles (2006)

Porcelain stoneware tilesare getting a prominent role on the market offering excellent solution either for interiors or for exteriors construction for flooring and coverings. This ceramic material meets the basic requirements to be compatible with different semiconductor deposition technique. Based on these consideration we investigated the possibility of using porcelain stoneware tiles as solar cells substrates for built-integrated photovoltaic applications. The compatibility of the commercial tiles with the solar cell fabrication process was successful proved and a conversion efficiency of more than 4% has been obtained on a small area devices as a preliminary result.
Improved soft-switching ZVT converters with active snubber (2002)

A new family of improved soft-switching ZVT power converters with an active snubber is developed in order to improve the efficiency of conventional ZVT power converters using a feedback inductor. Besides the ZVT turn-on performance of the main switch, the improved ZVT soft-switching power converters have less turn-off switching loss of the main switch than do conventional ZVT converters using a feedback inductor. With this new technique, an improved single-phase CCM ZVT soft-switching PFC power converter prototype has been implemented to show higher efficiency improvement than the conventional ZVT converters using a feedback inductor.
Mitochondrial Targeting of Human<i>O</i>6-Methylguanine DNA Methyltransferase Protects against Cell Killing by Chemotherapeutic Alkylating Agents (2005)

DNA repair capacity of eukaryotic cells has been studied extensively in recent years. Mammalian cells have been engineered to overexpress recombinant nuclear DNA repair proteins from ectopic genes to assess the impact of increased DNA repair capacity on genome stability. This approach has been used in this study to specifically target O(6)-methylguanine DNA methyltransferase (MGMT) to the mitochondria and examine its impact on cell survival after exposure to DNA alkylating agents. Survival of human hematopoietic cell lines and primary hematopoietic CD34(+) committed progenitor cells was monitored because the baseline repair capacity for alkylation-induced DNA damage is typically low due to insufficient expression of MGMT. Increased DNA repair capacity was observed when K562 cells were transfected with nuclear-targeted MGMT (nucl-MGMT) or mitochondrial-targeted MGMT (mito-MGMT). Furthermore, overexpression of mito-MGMT provided greater resistance to cell killing by 1,3-bis (2-chloroethyl)-1-nitrosourea (BCNU) than overexpression of nucl-MGMT. Simultaneous overexpression of mito-MGMT and nucl-MGMT did not enhance the resistance provided by mito-MGMT alone. Overexpression of either mito-MGMT or nucl-MGMT also conferred a similar level of resistance to methyl methanesulfonate (MMS) and temozolomide (TMZ) but simultaneous overexpression in both cellular compartments was neither additive nor synergistic. When human CD34(+) cells were infected with oncoretroviral vectors that targeted O(6)-benzylguanine (6BG)-resistant MGMT (MGMT(P140K)) to the nucleus or the mitochondria, committed progenitors derived from infected cells were resistant to 6BG/BCNU or 6BG/TMZ. These studies indicate that mitochondrial or nuclear targeting of MGMT protects hematopoietic cells against cell killing by BCNU, TMZ, and MMS, which is consistent with the possibility that mitochondrial DNA damage and nuclear DNA damage contribute equally to alkylating agent-induced cell killing during chemotherapy.
Fine‐tuning the hydrophobicity of a mitochondria‐targeted antioxidant (2004)

The mitochondria-targeted antioxidant MitoQ comprises a ubiquinol moiety covalently attached through an aliphatic carbon chain to the lipophilic triphenylphosphonium cation. This cation drives the membrane potential-dependent accumulation of MitoQ into mitochondria, enabling the ubiquinol antioxidant to prevent mitochondrial oxidative damage far more effectively than untargeted antioxidants. We sought to fine-tune the hydrophobicity of MitoQ so as to control the extent of its membrane binding and penetration into the phospholipid bilayer, and thereby regulate its partitioning between the membrane and aqueous phases within mitochondria and cells. To do this, MitoQ variants with 3, 5, 10 and 15 carbon aliphatic chains were synthesised. These molecules had a wide range of hydrophobicities with octan-1-ol/phosphate buffered saline partition coefficients from 2.8 to 20000. All MitoQ variants were accumulated into mitochondria driven by the membrane potential, but their binding to phospholipid bilayers varied from negligible for MitoQ3 to essentially total for MitoQ15. Despite the span of hydrophobicites, all MitoQ variants were effective antioxidants. Therefore, it is possible to fine-tune the degree of membrane association of MitoQ and other mitochondria targeted compounds, without losing antioxidant efficacy. This indicates how the uptake and distribution of mitochondria-targeted compounds within mitochondria and cells can be controlled, thereby facilitating investigations of mitochondrial oxidative damage.
Comparative energy metabolism in cultured heart muscle and hela cells (1983)

The yields of energy from oxidation of fatty acids, glucose, and glutamine were compared in cultures of chick embryo heart muscle (heart) and HeLa cells. Aerobic energy production, as measured by oxygen utilization, was comparable in the two cell types. In media containing dialyzed sera, the rates of incorporation of fatty acids directly into lipids were similar in both cells and accounted for greater than 97% of fatty acid metabolism in HeLa cells. However, in heart cells only 45% ended in lipid, 42% in protein, and 13% was released as CO2; the latter two products probably reflect the oxidation of fatty acids to acetyl-coenzyme A (-CoA) and its subsequent metabolism in the citrate cycle. Increased serum concentration in the medium did not affect fatty acid metabolism in HeLa cultures, but resulted in greater oxidation by heart cells (greater than 100 times that by HeLa cells). The metabolisms of both glucose and glutamine were similar in heart and HeLa cells with greater than or equal to 60% of glucose carbon ending as medium lactate and only 3-5% converted to acetyl-CoA. About 25% of glutamine carbon ended as CO2 and increased utilizations with increasing serum concentrations was accountable in both cells by increased lactate from glucose and glutamate from glutamine. CO2 production (and energy) from glutamine was independent of glutamine concentration within a tenfold range of physiological concentrations. The yields of energy have been calculated. In 10% dialyzed calf serum, oxidation of glutamine carbon provided about half of the total energy in heart cells; glucose about 35-45%, with most coming from glycolysis; oxidation of fatty acid carbon provided only 5-10%. That greater than 90% of the aerobic energy comes from glutamine in both cells can account for the comparable rates of oxygen utilization. HeLa cells derived little or no energy from fatty acids.
Differential localization of mRNAs of collagen types I and II in chick fibroblasts, chondrocytes, and corneal cells by in situ hybridization using cDNA probes. (1986)

We have employed a highly specific in situ hybridization protocol that allows differential detection of mRNAs of collagen types I and II in paraffin sections from chick embryo tissues. All probes were cDNA restriction fragments encoding portions of the C-propeptide region of the pro alpha-chain, and some of the fragments also encoded the 3'-untranslated region of mRNAs of either type I or type II collagen. Smears of tendon fibroblasts and those of sternal chondrocytes from 17-d-old chick embryos as well as paraffin sections of 10-d-old whole embryos and of the cornea of 6.5-d-old embryos were hybridized with 3H-labeled probes for either type I or type II collagen mRNA. Autoradiographs revealed that the labeling was prominent in tendon fibroblasts with the type I collagen probe and in sternal chondrocytes with the type II collagen probe; that in the cartilage of sclera and limbs from 10-d-old embryos, the type I probe showed strong labeling of fibroblast sheets surrounding the cartilage and of a few chondrocytes in the cartilage, whereas the type II probe labeled chondrocytes intensely and only a few fibroblasts; and that in the cornea of 6.5-d-old embryos, the type I probe labeled the epithelial cells and fibroblasts in the stroma heavily, and the endothelial cells slightly, whereas the type II probe labeled almost exclusively the epithelial cells except for a slight labeling in the endothelial cells. These data indicate that embryonic tissues express these two collagen genes separately and/or simultaneously and offer new approaches to the study of the cellular regulation of extracellular matrix components.
Graphene/3C-SiC Hybrid Nanolaminate (2015)

In this work, we demonstrate a one-step approach to create graphene/3C-SiC nanolaminate structure using microwave plasma chemical vapor deposition technique. Layer-by-layer arrangement of thin 3C-SiC layers and graphene sheets is obtained with the thicknesses of the individual 3C-SiC layers and graphene sheets being 5-10 nm and 2-5 nm, respectively. An intimate contact between 3C-SiC and the graphene sheets is achieved and the nanolaminate film shows a high room temperature conductivity of 96.1 S/cm. A dedicated structural analysis of the nanolaminates by means of high-resolution transmission electron microscopy (HRTEM) reveals that the growth of the nanolaminates follows an iterative process: preferential graphene nucleation around the planar defects at the central region of the SiC layer, leading to the "splitting" of the SiC layer; and the thickening of the SiC layer after being "split". A growth mechanism based on both kinetics and thermodynamics is proposed. Following the proposed mechanism, it is possible to control the layer thickness of the graphene/3C-SiC hybrid nanolaminate by manipulating the carbon concentration in the gas phase, which is further experimentally verified. The high electrical conductivity, large surface area porous structure, feasible integration on different substrates (metal, Mo; semiconductor, Si and 2H-SiC; insulator, diamond) of the graphene/3C-SiC hybrid nanolaminate as well as other unprecedented advantages of the nanolaminate structure make it very promising for applications in mechanical, energy, and sensor-related areas.