gebhart/patrepeval huggingface dataset:
Anaerobic degradation of veratrylglycerol-beta-guaiacyl ether and guaiacoxyacetic acid by mixed rumen bacteria (1985)

Veratrylglycerol-beta-guaiacyl ether (0.2 g/liter), a lignin model compound, was found to be degraded by mixed rumen bacteria in a yeast extract medium under strictly anaerobic conditions to the extent of 19% within 24 h. Guaiacoxyacetic acid, 2-(o-methoxyphenoxy)ethanol, vanillic acid, and vanillin were detected as degradation products of veratrylglycerol-beta-guaiacyl ether by thin-layer chromatography, gas chromatography, and gas chromatography-mass spectrometry. Guaiacoxyacetic acid (0.25 g/liter), when added into the medium as a substrate, was entirely degraded within 36 h, resulting in the formation of phenoxyacetic acid, guaiacol, and phenol. These results suggest that the beta-arylether bond, an important intermonomer linkage in lignin, can be cleaved completely by these rumen anaerobes.
A two-dimensional particle-in-cell simulation of an electron-cyclotron-resonance etching tool (1995)

A particle-in-cell (PIC) simulation of an axisymmetric electron-cyclotron-resonance (ECR) etching tool is developed in which up to 2×106 particles per species are loaded in a two-dimensional spatial computational mesh (r,z), along with three velocity components (vr,vθ,vz). An ECR heating scheme based on single-particle trajectories in the resonance zone generates the simulated plasma. Electron- and ion-neutral elastic and inelastic collisions are treated by a null Monte Carlo collision method. The code generates the electron and ion-velocity distributions, plasma potentials, and densities in a CF+3/CF4 etching plasma. In addition, a novel scaling technique which bridges the gap between the ion and electron-time scales and accelerates the rate of convergence of the code is introduced for a PIC code. The predictions of the code show that microwaves are completely absorbed before reaching the exact location of resonance.
Dysprosium-Modified Tobacco Mosaic Virus Nanoparticles for Ultra-High-Field Magnetic Resonance and Near-Infrared Fluorescence Imaging of Prostate Cancer (2017)

The increasing prevalence of ultra-high-field magnetic resonance imaging (UHFMRI) in biomedical research and clinical settings will improve the resolution and diagnostic accuracy of MRI scans. However, better contrast agents are needed to achieve a satisfactory signal-to-noise ratio. Here, we report the synthesis of a bimodal contrast agent prepared by loading the internal cavity of tobacco mosaic virus (TMV) nanoparticles with a dysprosium (Dy<sup>3+</sup>) complex and the near-infrared fluorescence (NIRF) dye Cy7.5. The external surface of TMV was conjugated with an Asp-Gly-Glu-Ala (DGEA) peptide via a polyethylene glycol linker to target integrin α<sub>2</sub>β<sub>1</sub>. The resulting nanoparticle (Dy-Cy7.5-TMV-DGEA) was stable and achieved a high transverse relaxivity in ultra-high-strength magnetic fields (326 and 399 mM<sup>-1</sup> s<sup>-1</sup> at 7 and 9.4 T, respectively). The contrast agent was also biocompatible (low cytotoxicity) and targeted PC-3 prostate cancer cells and tumors in vitro and in vivo as confirmed by bimodal NIRF imaging and T<sub>2</sub>-mapping UHFMRI. Our results show that Dy-Cy7.5-TMV-DGEA is suitable for multiscale MRI scanning from the cellular level to the whole body, particularly in the context of UHFMRI applications.
Comparison of Several Multi-Cylinder Paper Drying Simulation Models (1995)

ABSTRACT Many models for simulation of paper drying in multi-cylinder dryer sections exist. In this work. three independently developed models are directly compared using the same reference data The models consired are the Texas A&M model, the Kuiosa model, and the VTT model. Predicted moisture contents plus cylinder and avenge web temperatures along the dryer section are presentcd for the different models. Predicted average evaporation rates during drying are also shown. Three major differences in the model details are highlighted. The effects of these differences on model accuracy evaluated by considering two different paper grades dried with two different machine geometries. This work is the first published direct comparison of different simulation models. The reference machine data provided can be used for comparison of these three models to other models.
Critical chemical features in trans-acting-responsive RNA are required for interaction with human immunodeficiency virus type 1 Tat protein (1991)

The human immunodeficiency virus type 1 Tat protein binds to an RNA stem-loop structure called TAR which is present at the 5' end of all human immunodeficiency virus type 1 transcripts. This binding is centered on a bulge within the stem of TAR and is an essential step in the trans-activation process which results in a dramatic increase in viral gene expression. By analysis of a series of TAR derivatives produced by transcription or direct chemical synthesis, we determined the structural and chemical requirements for Tat binding. Tat binds well to structures which have a bulge of two to at least five unpaired bases bounded on both sides by a double-stranded RNA stem. This apparent flexibility in bulge size is in contrast to an absolute requirement for an unpaired uridine (U) in the 5'-most position of the bulge (+23). Substitution of the U with either natural bases or chemical analogs demonstrated that the imido group at the N-3 position and, possibly, the carbonyl group at the C-4 position of U are critical for Tat binding. Cytosine (C), which differs from U at only these positions, is not an acceptable substitute. Furthermore, methylation at N-3 abolishes binding. While methylation of U at the C-5 position has little effect on binding, fluorination reduces it, possibly because of its effects on relative tautomer stability at the N-3 and C-4 positions. Thus, we have identified key moieties in the U residue that are of importance for the binding of Tat to TAR RNA. We hypothesize that the invariant U is involved in hydrogen bond interactions with either another part of TAR or the TAR-binding domain in Tat.
Radiotherapy and cGAS/STING signaling: Impact on MDSCs in the tumor microenvironment (2021)

Myeloid derived suppressor cells (MDSCs) are a highly heterogeneous population of immature immune cells with immunosuppressive functions that are recruited to the tumor microenvironment (TME). MDSCs promote tumor growth and progression by inhibiting immune effector cell proliferation and function. MDSCs are affected by both novel anti-cancer therapies targeting the immune system to promote anti-tumor immunity, as well as by conventional treatments such as radiotherapy. Following radiotherapy, cytoplasmic double stranded DNA stimulates the cyclic GMP-AMP synthase (cGAS)/stimulator of interferon genes (STING) pathway, resulting in type I interferon production. Effectiveness of radiotherapy and cGAS/STING signaling are closely intertwined: activation of cGAS and STING is key to generate systemic anti-tumor immunity after irradiation. This review focuses on how radiotherapy and cGAS/STING signaling in MDSCs and/or tumor cells impact MDSC recruitment, expansion and function. The influence of conventional and ablative radiotherapy treatment schedules, inflammatory response following radiotherapy, and hypoxia are discussed as MDSC modulators.
Recognition on The Freedom of Culture (2020)

문화는 우리 인간들이 지니고 있는 고유한 속성을 실현하는 장이고, 우리가 공유하는 가치와 행동양식이 과거로부터 현재까지 영속되어 다음 세대에 전하여 가치를 인정을 받는 의미와 기능을 지니고 있다. 오늘날에 이러한 문화의 의미에 커다란 새로운 변수로 등장한 것이 정보매체의 출현으로 새로운 문화를 창조하고 한계성을 극복할 수 있는 내용과 동시에 그것이 잘못 왜곡 전달되는 결과도 초래하기도 한다. 문화는 우리생활의 정신적, 물질적 영역에서 자신의 지니고 있는 고유한 정신적 가치를 자유롭게 표출하고 내재화 하는 실천방식을 가지고 있다. 우리가 사는 세대는 과연 문화가 어떻게 우리들에게 자유로움을 표출시켜는 그 무엇가에 대하여 이를 탐색하고, 호기심 있게 느끼고, 보는 것을 마음에 담아 잔잔히 고민해 보는 것도 문화의 자유로움이 주는 흥미로움과 친밀감을 보여주는 첫걸음이라고 여긴다. 이 글에서는 우선, 문화의 의미를 다양한 측면에서 알아보고, 이어, 이러한 문화 속에서 진정한 자유로움이 무엇인지를 출발하는 수준에서 모색해 보는 것에 이 글의 의미를 두고 있다.
Preserving privacy in environments with location-based applications (2003)

The increase in location-based applications makes protecting personal location information a major challenge. Addressing this challenge requires a mechanism that lets users automate control of their location information, thereby minimizing the extent to which the system intrudes on their lives.
Utility of 5‐aminolaevulinic acid fluorescence‐guided endoscopic biopsy for malignant mesothelioma in a cat and dog (2022)

Malignant mesothelioma (MM) is uncommon in cats and dogs and can be challenging to diagnose. Adequate tissue sampling is required for superior diagnostic accuracy. Protoporphyrin IX, a metabolite of 5-aminolaevulinic acid (5-ALA), is a photosensitiser for photodynamic diagnosis (PDD). To the best of our knowledge, no study has reported the use of 5-ALA-PDD to detect MM in veterinary medicine. The present study describes the use of 5-ALA-PDD for MM diagnosis in a cat and dog, as well as the effectiveness of intracavitary chemotherapy. We evaluated the use of PDD with 5-ALA hydrochloride (5-ALA-PDD) in two cases of MM. A 12-year-old cat presented with a 1-month history of respiratory distress, and a 9-year-old dog presented with a 3-month history of mild abdominal distention. We endoscopically biopsied lesions in both the cases using 5-ALA-PDD. Histopathological examination revealed mesothelioma, and immunohistochemical staining was positive for calretinin. Both patients were treated with carboplatin. The cat died of respiratory failure. Although, the dog's condition improved 21 days after the first chemotherapeutic drug administration, the dog died on day 684 owing to cardiac-related issues. 5-ALA-PDD is thus, safe and feasible for the diagnosis of MM in veterinary medicine.
On krypton-doped capsule implosion experiments at the National Ignition Facility (2017)

This paper presents the spectroscopic aspects of using Krypton as a dopant in NIF capsule implosions through simulation studies and the first set of NIF experiments. Using a combination of 2D hohlraum and 1D capsule simulations with comprehensive spectroscopic modeling, the calculations focused on the effect of dopant concentration on the implosion, and the impact of gradients in the electron density and temperature to the Kr line features and plasma opacity. Experimental data were obtained from three NIF Kr-dopant experiments, performed with varying Kr dopant concentrations between 0.01% and 0.03%. The implosion performance, hotspot images, and detailed Kr spectral analysis are summarized relative to the predictions. Data show that fuel-dopant spectroscopy can serve as a powerful and viable diagnostic for inertial confinement fusion implosions.
Detecting Qubit-coupling Faults in Ion-trap Quantum Computers (2022)

Ion-trap quantum computers offer a large number of possible qubit couplings, each of which requires individual calibration and can be misconfigured. To enhance the duty cycle of an ion trap, we develop a strategy that diagnoses individual miscalibrated couplings using only log-many tests. This strategy is validated on a commercial ion-trap quantum computer, where we illustrate the process of debugging faulty quantum gates. Our methodology provides a scalable pathway towards fault detections on a larger scale ion-trap quantum computers, confirmed by simulations up to 32 qubits.
O3‐06‐01: Oral treatment with an Aβ42 oligomer modulating D‐amino acid peptide improves cognitive behavior of APP/ PS1 double transgenic mice (2009)

Alzheimer's disease (AD) is a progressive neurodegenerative disorder, affecting more than 20 million people world-wide. Today, only palliative therapies for AD are available. Several lines of evidence, including genetics, have provided strong evidence for a central role of amyloid-β-peptide (Aβ) in the pathogenesis of AD. Recents studies indicate that soluble Aβ oligomers instead of fibrillar forms are the major toxic species. We successfully tested Aβ binding D-peptides in AD transgenic mouse models regarding their therapeutic properties. Additionally, we used several biophysical methods for the elucidation of the mechanism thereof. We report on a novel D-enantiomeric amino acid peptide which reduces amyloid plaque load and cerebral damage of transgenic mouse models of AD after direct brain application. Additionally, we show that next to plaque load and inflammation reduction, oral application of the peptide improves cognitive performance. We are providing in vitro data suggesting an Aβ42 oligomer modulating activity of D3. The D-enantiomeric peptide D3 is able to modulate Aβ42 oligomers in vitro. Regardless of its in vivo mechanism of action, D3 exerts therapeutically interesting activities.
Bayesian spectrum estimation of harmonic signals (1995)

A Bayesian spectrum estimator of harmonic signals in Gaussian noise is derived. It is based on the expected value of the theoretical signal spectrum over the joint posterior density function of the signal and noise parameters. Simulation results are provided that show its performance and comparison with MUSIC.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Nanofiber composites containing N-heterocyclic carbene complexes with antimicrobial activity (2012)

This report concerns nanofiber composites that incorporate N-heterocyclic carbenes and the use of such composites for testing antimicrobial and antifungal activities. The nanofiber composites were produced by electrospinning mixtures of the gold chloride or gold acetate complexes of a bis(imino)acenaphthene (BIAN)-supported NHC with aqueous solutions of polyvinyl alcohol (PVA). The products were characterized by scanning-electron microscopy, which revealed that nanofibers in the range of 250-300 nm had been produced. The biological activities of the nanofiber composites were tested against two Gram-positive bacteria, six Gram-negative bacteria, and two fungal strains. No activity was evident against the fungal strains. However, the gold chloride complex was found to be active against all the Gram-positive pathogens and one of the Gram-negative pathogens. It was also found that the activity of the produced nanofibers was localized and that no release of the bioactive compound from the nanofibers was evident. The demonstrated antimicrobial activities of these novel nanofiber composites render them potentially useful as wound dressings.
True (2000)

Molecular charge is one of the main determinants of transvascular transport. There are, however, no data available on the effect of molecular charge on microvascular permeability of macromolecules in solid tumours. To this end, we measured tumour microvascular permeability to different proteins having similar size but different charge. Measurements were performed in the human colon adenocarcinoma LS174T transplanted in transparent dorsal skinfold chambers in severe combined immunodeficient (SCID) mice. Bovine serum albumin (BSA) and IgG were fluorescently labelled and were either cationized by conjugation with hexamethylenediamine or anionized by succinylation. The molecules were injected i.v. and the fluorescence in tumour tissue was quantified by intravital fluorescence microscopy. The fluorescence intensity and pharmacokinetic data were used to calculate the microvascular permeability. We found that tumour vascular permeability of cationized BSA (pI-range: 8.6-9.1) and IgG (pI: 8.6-9.3) was more than two-fold higher (4.25 and 4.65x10(-7) cm s(-1)) than that of the anionized BSA (pI approximately 2.0) and IgG (pI: 3.0-3.9; 1.11 and 1.93x10(-7) cm s(-1), respectively). Our results indicate that positively charged molecules extravasate faster in solid tumours compared to the similar-sized compounds with neutral or negative charges. However, the plasma clearance of cationic molecules was approximately 2x faster than that of anionic ones, indicating that the modification of proteins enhances drug delivery to normal organs as well. Therefore, caution should be exercised when such a strategy is used to improve drug and gene delivery to solid tumours.
A Study of the Fischer–Tropsch Synthesis in a Batch Reactor: Rate, Phase of Water, and Catalyst Oxidation (2017)

We used a batch reactor to conduct the Fischer–Tropsch reaction on a Co/TiO2 catalyst without charging any liquid in the reactor tank. The catalyst was loaded in a fixed catalyst basket, and the reactor was operated as a “gas–solid” reaction system. Before entering the batch operation for the reactor, it was initially operated under CSTR mode. The reactor was controlled under 210 °C and 20 bar (g) of pressure with a 2:1 H2/CO ratio in the feed gas when it was under CSTR mode. The time for the batch operations was varied between 20 min and 22.5 h. After each batch operation, the reactor was resumed to the CSTR mode for building up the same starting conditions for different batch operations. Both the selectivity to the olefinic and paraffinic products and the reaction rate were observed to increase when changing the operation from CSTR to batch mode. The reactor pressure was monitored and the comparison of the reading pressure and the pressure derived from the mass balance suggested that part of the product water was in the liquid phase in the reactor. Oxidation of Co might have happened when approaching the end of the batch operation.
L-shaped tibial condylar valgus osteotomy for advanced medial knee osteoarthritis: A case report (2017)

Case: A 63 year-old woman with bilateral severe medial knee osteoarthritis, huge cartilaginous defects, and severe varus-valgus instability was treated by tibial condylar valgus (TCV) osteotomy. Her preoperative point of the weight-bearing (mechanical) axis was right -19% and left -20%. After surgery, the mechanical axis was right 60% and left 61% with a high degree of patient satisfaction.
Conclusion: The TCV osteotomy technique consists of an L-shape osteotomy from the medial aspect of the proximal tibia to the intercondylar eminence. Corrected limb alignment and improved joint congruity can distribute the weight bearing force, stabilize the joint, and relieve pain of advanced medial knee osteoarthritis.
The influence of quality of primers on the formation of primer dimers in PCR (2020)

Polymerase chain reaction (PCR) is the most commonly used method for nucleic acids amplification. PCR performance depends on several causes, among which the quality of primers is one of the main determinants affecting specificity, sensitivity and reliability of the reaction. Here, we report on the results of the detailed study devoted to the dimerization of the primers during PCR. The course and specificity of the reaction were studied on the model DNA templates as well as genomic DNA using primers that form amplifiable heterodimeric structures with different thermodynamic stability. It was confirmed that more than two 3'-overlapping nucleotides cause a considerable accumulation of primer dimers. It turned out that the presence of any DNA promotes the formation of dimers even for primers, which do not tend to nonspecific amplification in the absence of DNA. It was shown that dimerization could not be eliminated by commonly used techniques. Even the use of hot-start DNA polymerases does not prevent PD formation if primers with stable 3'-overlapping are employed. Despite several advantages of PCR with abutting primers, their close disposition has no benefits regarding the formation of PD if low-quality primers are utilized.
Investigations on the three theoretical models of permittivity measurement for biological tissues (2010)

Comparative studies of three theoretical models relating the coaxial line end reflection to the permittivity of sample under test (SUT) are presented, including capacitance model, virtual line model and impedance model. The basic principles of these three models are introduced briefly at first; then their accuracies in measuring lossy biological materials are then tested. In our work, the porcine liver is used as a sample of biological tissue with relatively high permittivity, while porcine fat representing the biological tissue with low permittivity. The permittivity for the two biological tissues is extracted respectively using the three models and compared with known reference data. The validity of the three models in different frequencies and permittivity range are discussed.
Delayed effects of chronic variable stress during peripubertal‐juvenile period on hippocampal morphology and on cognitive and stress axis functions in rats (2004)

Animal studies on the effects of chronic variable stress during the peripubertal-juvenile period on hippocampal structure and function are lacking. Twenty-eight-day-old Sprague-Dawley rats were subjected to random, variable physical or social stress regimens for 4 weeks. Hippocampal volume was found to continue to grow in all lamina examined during the transition into young adulthood. Our variable physical stress paradigm led to inhibition of this growth in the CA1 pyramidal cell layer (PCL) and in the dentate gyrus-granular cell layer (DG-GCL), which reached full arrest in the CA3-PCL. Volume deficits were first observed after chronic stress exposure when 3 weeks, but not 24 h, of recovery had elapsed. Moreover, these volume deficits were associated with impairments in the Morris water-maze navigation, sustained down-regulation in the basal hippocampal glucocorticoid receptor gene expression, and deficits in the shutdown of acute stress-induced corticosterone secretion. Volume changes both due to normal maturation and after chronic stress exposure were independent of neuron number. Thus, a peripubertal-juvenile chronic stress paradigm that leads to significant alterations in the limbic-hypothalamic-pituitary-adrenal axis can produce robust effects in hippocampal structure and cognitive ability, lasting into adulthood.
Intracellular responses of onset neurones in the ventral cochlear nucleus to acoustic stimulation [Abstract] (1998)

This is an abstract of a poster presentation from the Proceedings of the Australian Neuroscience Society 1998. This version is reproduced with the permission of the publisher.
Neprilysin Is Suppressed by Dual-Specificity Tyrosine-Phosphorylation Regulated Kinase 1A (DYRK1A) in Down-Syndrome-Derived Fibroblasts (2017)

Amyloid-β peptide (Aβ) accumulation is a triggering event leading to the Alzheimer's disease (AD) pathological cascade. Almost all familial AD-linked gene mutations increase Aβ production and accelerate the onset of AD. The Swedish mutation of amyloid precursor protein (APP) affects β-secretase activity and increases Aβ production up to ca. 6-fold in cultured cells; the onset age is around 50. Down syndrome (DS) patients with chromosome 21 trisomy present AD-like pathologies at earlier ages (40s) compared with sporadic AD patients, because APP gene expression is 1.5-fold higher than that in healthy people, thus causing a 1.5-fold increase in Aβ production. However, when comparing the causal relationship of Aβ accumulation with the onset age between the above two populations, early DS pathogenesis does not appear to be accounted for by the increased Aβ production alone. In this study, we found that neprilysin, a major Aβ-degrading enzyme, was downregulated in DS patient-derived fibroblasts, compared with healthy people-derived fibroblasts. Treatment with harmine, an inhibitor of dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A), which is located in the DS critical region of chromosome 21, and gene knockdown of DYRK1A, upregulated neprilysin in fibroblasts. These results suggest that a decrease in the Aβ catabolic rate may be, at least in part, one of the causes for accelerated AD-like pathogenesis in DS patients if a similar event occurs in the brains, and that neprilysin activity may be regulated directly or indirectly by DYRK1A-mediated phosphorylation. DYRK1A inhibition may be a promising disease-modifying therapy for AD via neprilysin upregulation.