gebhart/patrepeval huggingface dataset:
Fluorescent nanodiamonds encapsulated by <i>Cowpea Chlorotic Mottle Virus</i> (CCMV) proteins for intracellular 3D-trajectory analysis (2021)

Long-term tracking of nanoparticles to resolve intracellular structures and motions is essential to elucidate fundamental parameters as well as transport processes within living cells. Fluorescent nanodiamond (ND) emitters provide cell compatibility and very high photostability. However, high stability, biocompatibility, and cellular uptake of these fluorescent NDs under physiological conditions are required for intracellular applications. Herein, highly stable NDs encapsulated with Cowpea chlorotic mottle virus capsid proteins (ND-CP) are prepared. A thin capsid protein layer is obtained around the NDs, which imparts reactive groups and high colloidal stability, while retaining the opto-magnetic properties of the coated NDs as well as the secondary structure of CPs adsorbed on the surface of NDs. In addition, the ND-CP shows excellent biocompatibility both in vitro and in vivo. Long-term 3D trajectories of the ND-CP with fine spatiotemporal resolutions are recorded; their intracellular motions are analyzed by different models, and the diffusion coefficients are calculated. The ND-CP with its brilliant optical properties and stability under physiological conditions provides us with a new tool to advance the understanding of cell biology, e.g., endocytosis, exocytosis, and active transport processes in living cells as well as intracellular dynamic parameters.
P1‐447: Time‐course effects of amyloid toxicity induced by a single icv injection of Aβ(25–35) on the glucocorticoids system in rats (2008)

Alzheimer's disease (AD) is a neurodegenerative pathology characterized by the presence of senile plaques and neurofibrillary tangles, accompanied by synaptic and neuronal loss. The major component of senile plaques is a β-amyloid protein (Aβ). Intracerebral injection of Aβ to rodents induces learning and memory impairments as well as neurodegeneration in brain area related to cognitive functions. In AD patients, it was also observed some endocrine modifications and more particularly changes in the hypothalamo-pituitary-adrenocortical (HPA) axis activity, which are characterized by an hyper-secretion of glucocorticoids. In this study, we assessed the time-course effects (during 6 weeks) of a single intracerebroventricular (icv) injection of aggregated Aβ fragment (25–35) at a dose of 10 μg/rat on the glucocorticoids system. The hippocampal, amygdala, frontal cortex and hypothalamic mRNA and protein levels (RT-PCR and western blot) of glucocorticoids receptors (MR and GR) were evaluated before and 1, 2, 3 and 6 weeks after the single icv injection of Aβ(25–35). The effects of Aβ icv injection on the subcellular localization of glucocorticoids receptors were also evaluated by immunohistochemistry. Plasmatic concentrations of ACTH and corticosterone (CORT) were determined (RIA) before and after Aβ(25–35) injection. The eventual modification of glucocorticoids feedback following the single icv injection of Aβ(25–35) was estimated with the dexamethasone (DEX) suppression test. The icv injection of scrambled Aβ(25–35) peptide was used as sham control. The results show that aggregated Aβ(25–35) affects differentially the expression of GR and MR over the time and the cerebral region considered. It seems that amyloid peptide induces a progressive localization of GR in the nucleolus over the time, which is more pronounced in the frontal cortex, the amygdala and the hippocampus than in the hypothalamus. Plasma concentrations of ACTH are significantly increased only 3 and 6 weeks after the single injection of Aβ(25–35), while the plasma concentrations of CORT are significantly increased after 1, 2, 3 and 6 weeks. In conclusion, this study shows that Aβ(25–35) seems to induce a glucocorticoids resistance that could initiate and/or contribute to cognitive and physiological deficits at an early stage of Alzheimer's disease.
Biomarker analysis from a phase III trial (GOLD) of dovitinib (Dov) versus sorafenib (Sor) in patients with metastatic renal cell carcinoma after one prior VEGF pathway–targeted therapy and one prior mTOR inhibitor therapy. (2014)

473 Background: In the GOLD trial, Dov did not improve progression-free survival (PFS) or overall survival (OS) over Sor. An exploratory objective of the study was to investigate plasma and tumor biomarkers to predict outcome. Methods: Plasma samples were obtained longitudinally throughout the study, and biomarkers were assessed by immunoassay. Primary archival tumor samples were assessed by immunohistochemistry. Log-rank tests, stratified by baseline MSKCC risk group, for difference in Kaplan-Meier curves between biomarker category (low/high based on &lt;/≥ median baseline values) within treatment arm were performed. Hazard ratios (HRs) were estimated from Cox proportional hazards models. Results: Plasma samples were available from 561 patients (Dov, n = 281; Sor, n = 280), and tumor samples were available from 341 patients (Dov, n = 181; Sor, n = 160). Baseline plasma biomarker levels were not predictive of Dov or Sor PFS or OS. However, strong prognostic effects, particularly for OS, were observed. High baseline cKIT and low baseline FGF2, HGF, PlGF, sVEGFR1, VEGFA, and VEGFD were associated with better OS for both Dov and Sor (Table). Changes from baseline in a number of plasma biomarkers were observed following treatment with Dov and Sor, consistent with VEGFR/FGFR inhibitory effects. Prognostic effects were also observed for low FGFR2 (PFS) and low FGF2 (OS) expression in archival tumors. Conclusions: Baseline plasma biomarkers are prognostic but not predictive in the third-line setting. Clinical trial information: NCT01223027. [Table: see text]
Operation methods of rapid load changes for integrated coal gasification combined cycle power plants (2014)

The IGCC (integrated gasification combined cycle) is emerging as one of the most advanced and effective systems for electric energy generation. The IGCC consists of pressure vessels such as a gasifier, syngas cooler and gas cleanup unit with the large time constants, so dynamic response of the power plant is delayed. On the other hand, the fluctuating power generation of renewable energies creates the need for flexible operations (e.g. fast start-up and rapid load change) of thermal power plants including IGCC power plants. This paper describes: (1) two new control methods for IGCC power plants that are combined as the proposed control method to reduce the gasifier pressure rise when rapid load changes are required; and (2) a plant-wide dynamic simulation to consider the operability and controllability of the plants. Simulation results showed the gasifier pressure rise rate was reduced from 7.4% to 3.6% due to the new proposed control method, recycle gas flow rate and steam flow rate control, with load change from 100% to 65% at 20%/min. In the case of 15%/min load change, the gasifier pressure rise rate was 2.8% and less than the maximum permissible value of 3.0%.
Flow cytometry measurement of the DNA contents of G0/G1 diploid cells from three different teleost fish species (2002)

The methodology used in this study provides an accurate and easy measurement of the genome size of a species.
Genes for the CPE Receptor (CPETR1) and the Human Homolog of RVP1 (CPETR2) Are Localized within the Williams–Beuren Syndrome Deletion (1998)

Williams-Beuren syndrome (WBS) is a neurodevelopmental disorder affecting multiple systems. Haploinsufficiency of genes deleted in chromosomal region 7q11.23 is the likely cause for this syndrome. We now report the localization of the genes for the CPE-R (Clostridium perfringens enterotoxin receptor, CPETR1) and the human homolog of RVP1 (rat ventral prostate 1 protein, CPETR2), both previously mapped to 7q11, to the WBS critical region. A single nucleotide polymorphism (SNP) present in CPETR1 has been identified and was used to determine parental origin of the deleted allele in five informative families. The mouse homologs Cpetr1 and Cpetr2 were identified and mapped to the conserved syntenic region on mouse chromosome 5. Northern blot analysis of CPETR1 demonstrates tissue specificity, with expression in kidney, lung, thyroid, and gastrointestinal tissues. In mouse, Cpetr1 is expressed in the early embryo, appears to be developmentally upregulated during gestation, and is present in adult tissues. Our results suggest a role for CPE-R in internal organ development and function during pre- and postnatal life.
Hierarchical Genetic Algorithm Approach to Determine Pulse Sequences in NMR (2009)

We develop a new class of genetic algorithm that computationally determines efficient pulse sequences to implement a quantum gate U in a three-qubit system. The method is shown to be quite general, and the same algorithm can be used to derive efficient sequences for a variety of target matrices. We demonstrate this by implementing the inversion-on-equality gate efficiently when the spin-spin coupling constants $J_{12}=J_{23}=J$ and $J_{13}=0$. We also propose new pulse sequences to implement the Parity gate and Fanout gate, which are about 50% more efficient than the previous best efforts. Moreover, these sequences are shown to require significantly less RF power for their implementation. The proposed algorithm introduces several new features in the conventional genetic algorithm framework. We use matrices instead of linear chains, and the columns of these matrices have a well defined hierarchy. The algorithm is a genetic algorithm coupled to a fast local optimizer, and is hence a hybrid GA. It shows fast convergence, and running on a MATLAB platform takes about 20 minutes on a standard personal computer to derive efficient pulse sequences for any target 8X8 matrix $U$.
Gastric epithelial cell death caused by Helicobacter suis and Helicobacter pylori γ-glutamyl transpeptidase is mainly glutathione degradation-dependent (2011)

Helicobacter (H.) suis is the most prevalent non-H. pylori Helicobacter species colonizing the stomach of humans suffering from gastric disease. In the present study, we aimed to unravel the mechanism used by H. suis to induce gastric epithelial cell damage. H. suis lysate induced mainly apoptotic death of human gastric epithelial cells. Inhibition of γ-glutamyl transpeptidase (GGT) activity present in H. suis lysate and incubation of AGS cells with purified native and recombinant H. suis GGT showed that this enzyme was partly responsible for the observed apoptosis. Supplementation of H. suis or H. pylori GGT-treated cells with glutathione strongly enhanced the harmful effect of both enzymes and resulted in the induction of oncosis/necrosis, demonstrating that H. suis and H. pylori GGT-mediated degradation of glutathione and the resulting formation of glutathione degradation products play a direct and active role in the induction of gastric epithelial cell death. This was preceded by an increase of extracellular H(2)O(2) concentrations, generated in a cell-independent manner and causing lipid peroxidation. In conclusion, H. suis and H. pylori GGT-mediated generation of pro-oxidant glutathione degradation products brings on cell damage and causes apoptosis or necrosis, dependent on the amount of extracellular glutathione available as a GGT substrate.
Supplementary Figure 1 from Preclinical Analysis of the γ-Secretase Inhibitor PF-03084014 in Combination with Glucocorticoids in T-cell Acute Lymphoblastic Leukemia (2023)

&lt;p&gt;PDF file, 252KB, PF-03084014 reverses glucocorticoid resistance in T-ALL cell lines.&lt;/p&gt;
Service Object Request Management Architecture: SORMA Concepts and Examples (1996)

We report on SORMA, the Service Object Request Management Architecture, its concept, developement, and implementation examples. SORMA provides an intelligent\n“object-bus” for distributed computing and inter-operation of robotics hardware. It is a software framework for rapid development of object-oriented software modules and their integration into stand-alone and distributed applications.\nSORMA was designed to meet the requirements arising from a large set of spcialized robotics components in a university research institution (see also SFB360-TR-96-4). Our experiences show,(i) that many robotics experiments and applications typically have been a “one-of-a-kind” process, where often the software was developed from scratch, even though much of the code is similar to code written for other applications; (ii) due to the short life-time of single-usage code, extensive, robust, and verbose exception handling is often sacrificed; (iii)\nearly sharing and integration of several complex application components, concurently developed by\na team of programmers, needs strong tool support.\nSORMA encourages the re-use of components by interactive test, exploration,and usage throughout the life span of a software component. At the same time this\nuser-friendlyness does not impair its real-time capabilities. After describing the SORMA concept, we report on two hybrid integration examples: The “Bielefeld Robot Checkers Player” and a realtime 3 D tracking\napplication combining vision and force commands.
Decision making through stochastic maneuver validation for overtaking on country roads (2020)

Driver assistance systems have become more and more important in recent years due to the increasing degree of automation in road traffic - especially with regard to safety. Often a driver's perception of a situation is prone to inaccuracy, particularly on country roads. Consequently, there is a high mortality rate due to frontal collisions with oncoming traffic (among others). One of the most dangerous maneuvers that leads to such conflicts is overtaking. Overtaking involves other traffic participants and therefore uncertainties exist. We cope with this challenge by introducing a system that evaluates the options a vehicle has during overtaking (completing or aborting the maneuver) using stochastic models of the surrounding traffic. The stochastic models are used to predict the movements of surrounding road users. As a next step, the general feasibility of the possible maneuvers is checked and rated. The results of this analysis can either be directly used for longitudinal control, be forwarded to a low level controller, or serve as a guideline for the decision-making process of a human driver.
Effects of the blended fibroin/aloe gel film on wound healing in streptozotocin-induced diabetic rats (2012)

Delayed healing remains a major clinical problem and here we have sought to develop an improved dressing film comprising 1.95% w/v fibroin and 0.05% w/v aloe gel extract. The tensile strength of dry film was 21.1 ± 0.5 MPa and broke at 1.1 ± 0.2% elongation; corresponding values for wet film were 18.3 ± 1.3 MPa and 1.9 ± 0.1%. The film maintained its shape upon water immersion and the swelling ratio of the dry film was 0.8 ± 0.1 while the water uptake was 43.7 ± 2.6%. After 28 days of incubation in phosphate buffered saline (1 M, pH 7.4, 37 °C), the weight of film was reduced by 6.7 ± 1.1% and the tensile strength and elongation at breaking point (dry state) were 15.4 ± 0.6 MPa and 1.5 ± 0.2%, respectively. Compared to aloe-free fibroin film (2.0% fibroin extract only), the blended film enhanced the attachment and proliferation of skin fibroblasts. The bFGF immunofluorescence of fibroblasts cultured on the blended film appeared greater than those cultured on tissue culture plate or on aloe-free fibroin film while α-smooth muscle actin was maintained. In streptozotocin-induced diabetic rats, the wounds dressed with the blended film were smaller (p <0.05) by day 7 after wounding, compared to untreated diabetic wounds. Histology of repaired diabetic wounds showed the fibroblast distribution and collagen fiber organization to be similar to wounds in normal rats, and this was matched by enhanced hydroxyproline content. Thus, such accelerated wound healing by the blended fibroin/aloe gel films may find application in treatment of diabetic non-healing skin ulcers.
A continuous hydrothermolytic catalytic reactor system for the production of bio‐crude biofuels (2015)

Abstract This work describes the continuous hydrothermal conversion of free fatty acid and triglyceride‐based feedstocks to biofuel mixtures using metal oxide catalysts, supercritical water, and high temperatures (≥500 °C) in a fixed bed reactor. A brief investigation of catalyst type indicated that zirconium dioxide ( ZrO 2 ) resulted in a biofuel mixture with similar properties to petroleum fuel products and the catalyst was stable under the supercritical water conditions used. The biofuel product is comprised of alkanes, alkenes, aromatics, and ketones. A wide variety of feedstocks were investigated, as well as the effect of temperature on yield and conversion selectivity to biofuel. The temperature study led to the identification of a set of ideal conditions (515 °C, 3:1 H 2 O :soybean oil mass ratio, ZrO 2 catalyst, 60 s catalyst contact time, 3500 psi) where liquid yield (70%) and selectivity (99%) were maximized as well as making a biofuel product with a useful combination of functionalities. Finally, the biofuel mixture was distilled, first atmospherically and then under vacuum, to give a light fraction and a middle distillate fraction. The fractions were sent for ASTM D4814 or ASTM D975 quality testing to determine the similarities to their petroleum counterparts: gasoline (light distillate) and diesel (middle distillate). The ASTM results were promising as both biofuel distillates have similar properties to their petroleum counterparts, even meeting many of the ASTM testing specifications. © 2015 Society of Chemical Industry and John Wiley &amp; Sons, Ltd
Bacterial transcriptome reorganization in thermal adaptive evolution (2015)

Our results suggest that transcriptome evolution works to maintain steady-state gene expression during constrained differentiation at various evolutionary stages, while also maintaining responsiveness to environmental stimuli and transcriptome homeostasis.
Detection and Characterization of Subvisible Aggregates of Monoclonal IgG in Serum (2012)

These results show that subvisible therapeutic protein aggregates may undergo changes in number, type and size distribution upon contact with human serum. This emphasizes the importance of analytical strategies for monitoring aggregation in undiluted biological fluids.
Lichen scrofulosorum in a patient with AIDS (1994)

A patient with AIDs who presented with pulmonary tuberculosis and cervical scrofuloderma developed a widespread eruption of lichenoid papules shortly after commencing antituberculous therapy. The clinical and histological features in this case were consistent with lichen scrofulosorum even though the tuberculin test was negative. To our knowledge this is the first reported case of lichen scrofulosorum in an HIV positive patient. The lesions cleared following 8 weeks of antituberculous therapy.
Finite Element Modeling of Vasoreactivity Using COMSOL Multiphysics ® (2014)

Localized calcium events in the endothelial cells (EC) can modulate smooth muscle cell (SMC) calcium (Ca 2+ ) and membrane potential dynamics through release of endothelium derived hyperpolarizing and relaxing factors. Ca 2+ levels in the smooth muscle cell (SMC) determine its contractile state. The underlying complex mechanism regulating the SMC Ca 2+ levels and ultimately vessel tone remains poorly understood. We developed coupled EC-SMC continuum models to describe function at macro-scale level by integrating mechanisms at the subcellular/ molecular level. Cellular models were coupled through diffusion of ions and second messengers. The models allows introduction of spatial distribution of cellular components and micro domains. The model will provide quantification and better understanding of localized events in the EC and its modulation of the vessel tone.
O-Ethyl-S-(1,2,2,2-Tetrafluoroethyl)-Dithiocarbonate: A Convenient Reagent for the Generation and Capture of 1,2,2,2-Tetrafluoroethyl Radicals (2015)

The synthesis of a new fluorinated reagent <i>O</i>-ethyl <i>S</i>-(1,2,2,2-tetrafluoroethyl) carbonodithioate (xanthate) and its use for the generation and capture of the hitherto unexplored 1,2,2,2-tetrafluo­roethyl radicals is described. This reagent allows the convenient introduction of the rare CF<sub>3</sub>CHF motif onto various olefinic substrates with a high functional-group tolerance.
N-Heterocyclic Linkages Are Produced from Condensation of Amidines onto Graphitic Carbon (2020)

Covalent chemical modification is a powerful strategy for endowing low-cost graphitic carbon substrates with designer functionality. However, the surface chemistry of carbon is complex, making it difficult to tailor carbon materials with molecular level precision. Herein, we establish a new chemical modification strategy that generates strong aromatic linkages to carbon surfaces. In particular, we show that the condensation of amidine-containing molecules with oxidic edge defects on carbon surfaces generates well-defined pyrimidine and imidazole linkages. X-ray photoelectron and nitrogen K-edge X-ray absorption near-edge structure spectroscopies along with time-of-flight secondary ion mass spectrometry tandem mass spectrometry analysis establish the molecular structures of the surface linkages. We find that the ring structure and nucleophilicity of the precursor molecule guide the selectivity of the surface condensation reaction, with 5–5 ring strain driving selective condensation to form pyrimidine linkages on zigzag edges. This work establishes new methods for functionalizing and analyzing carbon surfaces at the molecular level.
Humoral and cell-mediated immune responses of d/d histocompatible pigs againstclassical swine fever (CSF) virus (2003)

A better understanding of cell-mediated immune responses to classical swine fever virus (CSFV) is essential for the future development of improved vaccines. We analyzed the generation of cell-mediated and humoral immune responses in d/d histocompatible pigs following CSFV infection or vaccination. Viral infection induced high T cell responses with high primary and secondary CTL activity correlated with high IFN-gamma production, whereas vaccination with a live vaccine followed by infection mainly induced neutralizing antibody but low cell-mediated responses. Moreover, high IgG1 response was associated with high IFN-gamma response following infection whereas a weak IFN-gamma response was related to a good IgG2 response but a low IgG1 production. These data could reflect Th1/Th2-like balance of immune responses depending upon immunization protocols, which has not yet been described in the pig. T-cell responses to CSFV were evidenced by CSFV-specific CD25 upregulation on CD4-CD8+, but not on CD4+CD8- cells, which further illustrated the importance of CTL responses after infection. Our results indicated that generation of cell-mediated immune responses was much higher following intranasal/oral CSFV infection than after intramuscular vaccination, which implies that the capacity of new CSFV vaccines to induce higher T-cell responses should be considered.
Microbial products. IV. X-14847, a new aminoglycoside from Micromonospora echinospora. (1980)

Micromonospora echinospora strain X-14847 produces gentamicin A as the major antibiotic together with a new aminoglycoside, termed X-14847, and identified as a 2-amino-2-deoxy-alpha-D-glucopyranosyl myo-inositol. This report describes the taxonomy of the culture, fermentation conditions, the isolation and the identification of X-14847.