gebhart/patrepeval huggingface dataset:
Natural Shape-Retaining Microcapsules With Shells Made of Chitosan-Coated Colloidal Lignin Particles (2019)

Thin film coating of charged nanoparticles with oppositely charged polymers is an efficient and straightforward way for surface modification, but synthetic polyelectrolytes should be replaced by abundant biopolymers. In this study a thin film of chitosan was adsorbed onto colloidal lignin particles (CLPs) that were then systematically studied for olive oil stabilization with an objective to develop shape-retaining microcapsules that comprised of only renewable biomaterials. Full surface coverage was achieved with merely 5 wt% of chitosan relative to the dry weight of CLPs, reversing their surface charge from negative to positive. Such modification rendered the chitosan-coated particles excellent stabilizers for forming Pickering emulsions with olive oil. The emulsion droplets could be further stabilized by sodium triphosphate that provided ionic intra- and inter-particle cross-linking of the chitosan corona on the CLPs. Following the optimum conditions, the non-cross-linked microcapsules exhibited a strong stability against coalescence and the electrostatically stabilized ones additionally retained their shape upon drying and rewetting. Non-cross-linked microcapsules were used to demonstrate encapsulation and rapid release of ciprofloxacin as a model lipophilic drug in aqueous media. Overall, the combination of antimicrobial chitosan and antioxidative lignin nanoparticles hold unprecedented opportunities as biocompatible and biodegradable materials for controlled drug delivery.
A Scalable and High-Yielding Synthesis of 2-(2-Furyl)-1,3-dioxolane from Biomass Derived Furfural and Ethylene Glycol Using Heteropoly Acids as Green Catalyst (2019)

In present work, Keggin-type commercial heteropoly acids have been employed as efficient solid acid catalysts in the acetalization of biomass-derived furfural with ethylene glycol. The reaction was optimized on parameters such as the type and loading of catalyst, duration of reaction and the relative ratio of reagents. The reaction was scaled up and the cyclic acetal 2-(furan-2-yl)-1,3-dioxolane was isolated in 92 % yield within 4 h using only 2 wt % of phosphotungstic acid in refluxing benzene.
Effect of ramping up rate on end of range defect in multielement molecular-ion (CH3O)-implanted silicon wafers (2019)

The dependence of the density of CH3O ion-implantation defects on ramping up rate after annealing at 1100 °C for 300 s have been investigated using rapid thermal annealing. We found that the density of defects after annealing was highest at a ramping up rate of 15 °C s−1. Furthermore, we also found that the diffusion behavior of implanted carbon and oxygen which were gettered by the CH3O ion-implantation defects, was dependent on the annealing temperature. Therefore, the ramping up rate dependence of the density of CH3O ion-implantation defects was considered to be caused by the difference between the formation behavior of CH3O ion-implantation defects and the dissociative adsorption behavior of carbon and oxygen. An increase in the defect density led to an increase in the density of gettering sinks. The gettering capability of the CH3O ion-implantation region is expected to be improved by optimizing the ramping up rate.
Grid Faults Impact on the Mechanical Loads of Active Stall Wind Turbine (2008)

Abstract — Emphasis in this paper is on the fault ride-through operation impact on the wind turbines structural loads. Grid faults are typically simulated in power system simulation tools using simplified drive train mechanical model, approach which doesn’t allow a thorough investigation of structural loads. This paper presents a two-steps simulation procedure, where two complimentary tools are combined, i.e. power system simulation tool and advanced aeroelastic simulation code. The goal is to investigate the whole integrated wind turbine design and to provide insight both into the structural as well as the electrical design of the wind turbine response during grid faults. The two-step simulation procedure is assessed by means of a simulation example. The effect of a grid fault on the structural part of a typical fixed speed wind turbine, equipped with an induction generator, is assessed. Index Terms — grid fault, mechanical loads, aeroelastic computer code, fault-ride trough.
Fimbriation of Haemophilus Species Isolated from the Respiratory Tract of Adults (1984)

Twenty-two clinical isolates of Haemophilus species were studied within two passages of their original isolation for the presence of fimbriae by negative-staining electron microscopy. Six isolates were identified as fimbriated, including three strains of nontypable Haemophilus influenzae, one strain of Haemophilus parainfluenzae, and two strains of Haemophilus haemolyticus. In fresh isolates of fimbriated strains of nontypable H. influenzae, approximately 40%-50% of cells had fimbriae; after five passages in vitro, less than 1% of the cells had fimbriae. Thus, a variety of Haemophilus species that colonize the human respiratory tract can be fimbriated, and this fimbriation is rapidly lost on passage in vitro.
Quantum Communications in Reconfigurable Optical Networks: DWDM QKD through a ROADM (2010)

We demonstrate coexistence of classical and quantum signals for quantum key distribution in a DWDM reconfigurable networking environment using a ROADM. We show how the limiting noise mechanism can depend on the link configuration.
Therapeutic Proteins (2012)

Protein-based therapeutics are highly successful in clinic and currently enjoy unprecedented recognition of their potential. More than 100 genuine and similar number of modified therapeutic proteins are approved for clinical use in the European Union and the USA with 2010 sales of US$108 bln; monoclonal antibodies (mAbs) accounted for almost half (48%) of the sales. Based on their pharmacological activity, they can be divided into five groups: (a) replacing a protein that is deficient or abnormal; (b) augmenting an existing pathway; (c) providing a novel function or activity; (d) interfering with a molecule or organism; and (e) delivering other compounds or proteins, such as a radionuclide, cytotoxic drug, or effector proteins. Therapeutic proteins can also be grouped based on their molecular types that include antibody-based drugs, Fc fusion proteins, anticoagulants, blood factors, bone morphogenetic proteins, engineered protein scaffolds, enzymes, growth factors, hormones, interferons, interleukins, and thrombolytics. They can also be classified based on their molecular mechanism of activity as (a) binding non-covalently to target, e.g., mAbs; (b) affecting covalent bonds, e.g., enzymes; and (c) exerting activity without specific interactions, e.g., serum albumin. Most protein therapeutics currently on the market are recombinant and hundreds of them are in clinical trials for therapy of cancers, immune disorders, infections, and other diseases. New engineered proteins, including bispecific mAbs and multispecific fusion proteins, mAbs conjugated with small molecule drugs, and proteins with optimized pharmacokinetics, are currently under development. However, in the last several decades, there are no conceptually new methodological developments comparable, e.g., to genetic engineering leading to the development of recombinant therapeutic proteins. It appears that a paradigm change in methodologies and understanding of mechanisms is needed to overcome major challenges, including resistance to therapy, access to targets, complexity of biological systems, and individual variations.
Monte Carlo investigation of the characteristics of radioactive beams for heavy ion therapy (2019)

This work presents a simulation study evaluating relative biological effectiveness at 10% survival fraction (RBE10) of several different positron-emitting radionuclides in heavy ion treatment systems, and comparing these to the RBE10s of their non-radioactive counterparts. RBE10 is evaluated as a function of depth for three positron-emitting radioactive ion beams (<sup>10</sup>C, <sup>11</sup>C and <sup>15</sup>O) and two stable ion beams (<sup>12</sup>C and <sup>16</sup>O) using the modified microdosimetric kinetic model (MKM) in a heterogeneous skull phantom subject to a rectangular 50 mm × 50 mm × 60 mm spread out Bragg peak. We demonstrate that the RBE10 of the positron-emitting radioactive beams is almost identical to the corresponding stable isotopes. The potential improvement in PET quality assurance image quality which is obtained when using radioactive beams is evaluated by comparing the signal to background ratios of positron annihilations at different intra- and post-irradiation time points. Finally, the incidental dose to the patient resulting from the use of radioactive beams is also quantified and shown to be negligible.
Alzheimer’s disease brain-derived tau-containing extracellular vesicles: Pathobiology and GABAergic neuronal transmission (2020)

Abstract Extracellular vesicles (EVs) propagate tau pathology for Alzheimer’s disease (AD). How EV transmission influences AD are, nonetheless, poorly understood. To these ends, the physicochemical and molecular structure-function relationships of human brain-derived EVs, from AD and prodromal AD (pAD), were compared to non-demented controls (CTRL). AD EVs were shown to be significantly enriched in epitope-specific tau oligomers versus pAD or CTRL EVs assayed by dot-blot and atomic force microscopy tests. AD EVs were efficiently internalized by murine cortical neurons and transferred tau with higher aggregation potency than pAD and CTRL EVs. Strikingly, inoculation of tau-containing AD EVs into the outer molecular layer of the dentate gyrus induced tau propagation throughout the hippocampus. This was seen in 22 months-old C57BL/6 mice at 4.5 months post-injection by semiquantitative brain-wide immunohistochemistry tests with multiple anti-phospho-tau (p-tau) antibodies. Inoculation of the equal amount of tau from CTRL EVs or as oligomer or fibril-enriched fraction from the same AD donor showed little propagation. AD EVs induced tau accumulation in the hippocampus as oligomers or sarkosyl-insoluble proteins. Unexpectedly, p-tau cells were mostly GAD67 + GABAergic neurons and to a lesser extent, GluR2/3 + excitatory mossy cells, showing preferential EV-mediated GABAergic neuronal tau propagation. Whole-cell patch clamp recording of Cornu Ammonis (CA1) pyramidal cells showed significant reduction in the amplitude of spontaneous inhibitory post-synaptic currents. This was accompanied by reductions in c-fos + GAD67 + GABAergic neurons and GAD67 + GABAergic neuronal puncta surrounding pyramidal neurons in the CA1 region confirming reduced interneuronal projections. Our study posits a novel tau-associated pathological mechanism for brain-derived EVs.
A Wideband Sliding Correlator-Based Channel Sounder with Synchronization in 65 nm CMOS (2019)

A programmable ultra-wideband sliding correlator-based channel sounder with high temporal and spatial resolution is designed in standard 65 nm CMOS. The baseband chip can be configured either as a baseband transmitter to generate a pseudorandom spread spectrum signal with flexible sequence lengths, or as a baseband receiver with sliding correlator having an absolute timing reference to obtain power delay profiles of the multipath components of the wireless channel. The sequence achieved a chip rate of one Giga-bit-per-second, resulting in a multipath delay resolution of 1 ns. The baseband chip occupies an area of 0.66 mm x 1 mm with a power dissipation of 6 mA at 1.1 V in 65 nm CMOS. The sliding correlator-based channel sounder in this work is a critical block for future low-cost, miniaturized channel sounding systems used in accurate and efficient channel propagation measurements at millimeter-wave frequencies.
Sequence-specific resonance assignments of the proton NMR spectra of a synthetic, biologically active EIAV-Tat Protein (1993)

The equine infectious anemia virus (EIAV) trans-activating (Tat) protein is a close homologue of the human immunodeficiency virus (HIV) Tat protein. Both of these proteins bind to an RNA trans-activation responsive element (TAR). We synthesized chemically a protein with the sequence of the 75 amino acid Tat protein from EIAV. The chemically synthesized protein was shown to be biologically active. Circular dichroism (CD) and 1H nuclear magnetic resonance (NMR) spectroscopy were used to structurally characterize the synthetic protein. We obtained nearly complete resonance assignments in the 2D-NMR spectra of the protein at pH 3.0. There is at least some evidence from the experimental data that the basic TAR binding domain of the synthetic protein has a tendency to form a helix, but our experiments also indicate that the protein probably does not have an overall stable tertiary structure in aqueous solution at this pH. CD spectroscopy suggested that the protein adopts a more stable, predominantly alpha-helical structure in a trifluoroethanol/water solution.
Chimie des matériaux hybrides (2011)

En chimie, le terme d’hybridation est associé au modèle des orbitales hybrides dont les plus simples, nommées sp3, sp2, sp, sont générées par la combinaison des orbitales atomiques 2s et 2p de la couche de valence du carbone. C’est sur cette base que Linus Pauling, prix Nobel en 1954, proposa le modèle de l’hybridation pour décrire les liaisons chimiques entre atomes. Pour un chimiste, cette dénomination spn se traduit par l’image d’un tétraèdre, d’une molécule plane ou linéaire – les plus si...
PET Chemistry: The Driving Force in Molecular Imaging (2007)

PET Chemistry: The Driving Force in Molecular Imaging describes the development of radiochemicals as concepts move from bench work to clinical products. Molecular targets have been applied as tools for personalized medicine in the areas of disease imaging, therapy assessment, selection of patients
Genomic DNA Copy Number Alterations Present in AML Bone Marrow Samples with Normal Cytogenetics. (2004)

Abstract Cytogenetics and comparative genomic hybridization (CGH) have been used to identify large genomic amplifications and deletions in all subtypes of acute myeloid leukemia (AML). Up to 15–20% of AML patients have a normal karyotype at diagnosis. While cytogenetic abnormalities confer important prognostic information for patients with AML, there remain differences in the therapeutic response and outcome among patients with the same cytogenetic profile, implying that other, more subtle, genetic abnormalities may exist. We hypothesized that a subset of AML patients with normal cytogenetics may contain genomic DNA copy number changes that are too small to be detected using standard cytogenetic techniques. To address this possibility, we used high-resolution bacterial artificial chromosome (BAC) array CGH technology to examine 31 AML patients with normal cytogenetics. The BAC arrays contain 2,464 BAC clones spotted in triplicate on glass slides, and provide a 1 Mb resolution of the entire human genome. Technical generation of the arrays, hybridization parameters, and analysis were similar to that reported for murine BAC array CGH (Nat Genet. 2001 Dec;29(4):459–64). The 31 AML samples included 4 M0, 8 M1, 10 M2, and 9 M4 patients. Array CGH experiments were performed using 500 nanograms of Cyanine 5 labeled genomic DNA from unmanipulated AML bone marrow, mixed with an equal amount of control DNA (a pool of DNA from 4 cancer-free individuals) labeled with Cyanine 3. Using the human 1 Mb BAC arrays, we identified amplifications and deletions from multiple samples that were confirmed with G-banding cytogenetics [del(7)(q31), del(7)(p11.2), +8, del(11)(q13q23), +21, add(21)(q22), −X, −Y, +Y]. In addition, BAC arrays robustly detected copy number alterations that were identified in as few as 4/21 metaphases. We identified 5/31 (16%) patients with normal cytogenetics that contained altered genomic DNA copy numbers using BAC array CGH. Copy number changes were confirmed for several of these genomic loci using a dye-swap experiment, where the AML DNA was labeled with Cyanine 3, and the control DNA with Cyanine 5. Two of the 5 patients with abnormalities detected using array CGH would be reclassified from “intermediate” to “unfavorable” cytogenetics [del(7)(q31.31q34), add(11)(q23.3qter), and 17(p12pter)]. These results suggest that a subset of AML patients with normal cytogenetics contain genomic copy number alterations that may effect treatment and outcome. Patient # FAB subtype Genomic location Gain or loss Size (Megabase) Dye-Swap confirmed 1 M0 7(q31.31q34) loss 2.0 Not done 1 11(q23.3qter) gain 16.5 Not done 2 M1 11(p14) loss 7.4 Yes 3 M1 11(q13.2q14.1) gain 15.8 Yes 3 19(p) gain 64.0 Yes 4 M2 17(p12pter) gain 8.6 Not Done 5 M2 19(p13.1pter) loss 14.8 Yes 5 12(q13) loss 5.0 Yes
Rapid Detection and Typing of Actinobacillus pleuropneumoniae Serovars Directly From Clinical Samples: Combining FTA® Card Technology With Multiplex PCR (2021)

<i>Actinobacillus pleuropneumoniae</i> (APP), the causative agent of porcine pleuropneumonia, is highly contagious and responsible for high morbidity, mortality, and economic losses in the swine industry worldwide, but quick serotyping and diagnosis are still not widely available. In this study, we sought to validate the use of Whatman FTA<sup>®</sup> cards for collection and processing of <i>A. pleuropneumoniae</i> isolates, or porcine lung tissue samples, for direct use in diagnostic multiplex PCRs. We have optimized the processing of 3-mm discs punched from FTA<sup>®</sup> cards loaded with cultured <i>A. pleuropneumoniae</i>, or imprinted on lesioned regions of lung tissue, with only three distilled water washes before addition into our APP-multiplex PCR (mPCR) assay for rapid, low-cost identification and serotyping. DNA captured on FTA<sup>®</sup> cards generated the same diagnostic PCR results as DNA extracted using commercial kits for 85 <i>A. pleuropneumoniae</i> clinical isolate cultures and 22 lung samples. Additionally, bacterial DNA bound to FTA<sup>®</sup> cards was detectable by PCR after 6 months of storage at 37°C. This study provides simple, efficient, rapid, and practical sample processing for detection and molecular serotyping of <i>A. pleuropneumoniae</i>.
Bicarbonate Ion Stimulates the Expression of Locus of Enterocyte Effacement-Encoded Genes in Enterohemorrhagic Escherichia coli O157:H7 (2002)

Enterohemorrhagic Escherichia coli (EHEC) strains adhere to the intestinal mucosa and produce an attaching and effacing (A/E) lesion. Most of the genes required to produce A/E lesions are thought to be encoded by the 36-kb pathogenicity island termed the locus for enterocyte effacement (LEE). Although the mechanisms underlying the bacterial adherence, including the genes involved, are still poorly understood, the preferential adherence phenotype of EHEC is thought to depend on the nature of the genes and/or the response of these genes to changes in environmental conditions. To explore the environmental factors affecting EHEC adherence, we used an O157:H7 strain and investigated the optimal growth conditions for its adherence to Caco-2 cells. We observed that EHEC grown in Dulbecco's modified Eagle's medium (DMEM) adhered more efficiently to Caco-2 cells than EHEC grown in Luria-Bertani (LB) broth. Among the components of DMEM, only NaHCO(3) was found to remarkably stimulate bacterial adherence. When bacteria were grown in LB broth containing NaHCO(3), the production of intimin, Tir, EspA, and EspB was greatly enhanced compared with the production in LB broth. Indeed, the transcription of ler required for LEE-encoded gene expression was promoted in response to the concentration of NaHCO(3) in LB broth. Since the concentration of NaHCO(3) in the lower intestinal tract has been shown to be relatively high compared with that in the upper small intestine, our results may imply that NaHCO(3) is an important signaling factor for promoting colonization of EHEC in the lower intestinal tract in humans.
Mapping of the interface between leptin and the leptin receptor CRH2 domain (2005)

Despite the impact of the leptin system on body weight and other physiologic processes, little is known about the binding of leptin to its receptor. The extracellular domain of the leptin receptor consists of two cytokine receptor homology (CRH) domains separated by an immunoglobulin-like domain, and followed by two juxtamembrane fibronectin type III modules. The CRH2 domain functions as a high-affinity binding site for leptin, and we previously demonstrated interaction with helices A and C of leptin. In this work, we constructed a homology model for the leptin/CRH2 complex and performed a detailed mutation analysis of the CRH2/leptin interface. Using both cell-based and in vitro binding assays using the isolated CRH2 domain, we show the critical role of hydrophobic interactions between Leu 13 and Leu 86 of leptin and Leu 504 in CRH2 in leptin binding and signalling. This binding pattern closely resembles the interaction of other four-helix bundle long chain cytokines with the CRH domain of their cognate receptors.
Abstract 9374: The Attenuation of Blood Pressure Lability Assessed by Frequency Analysis of Very Short-Term Continuous Blood Pressure Recording Reflects the Hemodynamic Aggravation in Heart Failure Patients with Reduced Ejection Fraction (2021)

Introduction: The lower blood pressure variability (BPV) assessed by 24-hour ambulatory bloop pressure (BP) monitoring predicts cardiac events in heart failure with reduced ejection fraction (HFrEF) patients. However, the trends of BPV assessed by short-term continuous BP recording in HFrEF patients remains unknown. Hypothesis: We recently reported a novel method of BPV analysis which is focused on the power spectral density (PSD) of 30-min continuous BP recording. In the PSD, we defined the integrated area of PSD from 0.01Hz to 0.1Hz as an index of short-term BPV (BP lability index: BLI) (Figure 1). Since the worsening of cardiac function decreases the dynamic variability of BP, we hypothesized that reduced cardiac function lowers BLI. In this study, we investigated how the worsening of cardiac function alters BLI. Methods: We compared 33 HFrEF patients with 15 hypertensive (HT) patients as a normal cardiac function. We assessed baseline characteristics, the value of brain natriuretic peptide (BNP), echocardiography and 30-min continuous BP in those patients. BP time series in each subject was converted to PSD by the Fourier transform. Results: Compared to HT, HFrEF patients showed lower left ventricular ejection fraction (LVEF) (33.8±11.8 vs. 68.9±6.8 %, p&lt;0.001) and higher E/e’ (17.5±10.8 vs. 10.5±2.7, p=0.002), indicating the hemodynamic aggravation. In continuous BP, HFrEF reduced both averaged systolic BP (122.0±18.1 vs. 137.9±19.7 mmHg, p=0.006) and pulse pressure (50.1±13.9 vs. 59.2±14.9 mmHg, p=0.037). BLI was significantly lower in HFrEF patients than that in HT (2.07±0.98 vs. 2.64±0.95, p=0.010]. Interestingly, the patients with reduced LVEF and high E/e’ showed lower BLI (Figure 2). Furthermore, BLI negatively associated with BNP (r=-0.38, p=0.012) (Figure 3). Conclusions: BLI was lower in HFrEF patients than that in HT patients with normal cardiac function. BLI has a potential to develop a novel marker of hemodynamic assessment in HFrEF patients.