gebhart/patrepeval huggingface dataset:
The microbial community composition of anaerobic digesters is strongly influenced by immigration (2016)

Anaerobic digestion (AD) is globally applied for bioenergy production. Although its widespread application, improved understanding of the underlying microbial ecology is needed to provide solutions for optimised process performance. In this study, we investigated the impact of immigration on the microbial community and conducted detailed investigations of bacteria from the hitherto undescribed phylum Hyd24-12, which’s role in AD has been overlooked so far.<br/>A total of 32 AD reactors at 18 Danish full-scale wastewater treatment plants were sampled during five years of operation. The bacterial and archaeal community were analysed separately using 16S rRNA gene amplicon sequencing in all 300+ samples. In addition, the microbial composition in the feed were analysed to investigate the effect of immigrating microbes. Full-scale AD reactors applying thermal hydrolysis based pre-treatment served as controls without influent microbes. <br/>The immigrating microorganisms had a notable influence on community structure. Comparing the abundance in the feed and AD reactors, we were able to classify 10 of the 20 most abundant genera as heavily influenced by immigration and potentially inactive. Hence, not taking immigration into account, would highly bias the conclusions. One of the most abundant non-immigrating bacteria belonged to candidate phylum Hyd24-12. Using differential coverage binning of multiple AD metagenomes, we retrieved the first genome of Hyd24-12. The genome allowed for detailed metabolic reconstruction, which revealed a strictly fermentative metabolism. In addition, FISH probes were designed for visualization and further in-situ studies to elucidate the microbial ecology of this, so far, overlooked group of bacteria in AD.<br/>
Plastic Deformation and Computer Simulations of Equal Channel Angular Pressing (2014)

Severe Plastic Deformation (SPD) is a generic designation of a group of metal-working techniques involving very large shear strains which are imposed, in combination with hydrostatic pressure, without any significant change in the overall dimensions of a specimen or a workpiece. This technique can produce miraculously fine grained structures below submicron scale. Equal channel angular pressing (ECAP) is a unique and relatively simple metal forming process to the other metal forming processes, but still complex under coupled effects with multi-factors, such as geometric factors, material factors and processing conditions.\nInvestigating the plastic deformation behavior in the deformation zone during ECAP is crucial for predicting the metal flow, microstructural evolution, controlling the quality of deformed workpiece and optimizing the ECAP process. In this review, modelling of ECAP using various numerical methods are reviewed. The papers from literature analyzing ECAP processing by the FEM are summarized and compared by software, mesh size, dimension, and analyzed results. It can be found that not only stress, strain, velocity, and fracture tendency but also their distributions in terms of the effects of the processing variables (speed, size, friction, die geometries, etc.) can be predicted.
Self-consistent simulation of VCSELs using MINILASE (1999)

The simulation method presented above will be applied to various VCSEL design configurations in order to obtain comparative information about the utility of certain design features. We show the three dimensional fundamental mode pattern of a standard oxide confined VCSEL with a l /spl mu/m diameter oxide aperture which occupies the first DBR layer. Design parameters which will be tested include oxide placement, oxide thickness, tapering of the oxide tip, and DBR design, amongst others.
Identification of agthi1, whose product is involved in biosynthesis of the thiamine precursor thiazole, in actinorhizal nodules of Alnus glutinosa (1996)

A cDNA clone, pAgthi1, encoding a homologue of yeast Thi4, which is involved in thiazole biosynthesis, was isolated from a library made from poly(A) RNA from actinorhizal nodules of Alnus glutinosa by differential screening with nodule and root cDNA, respectively. The corresponding gene, agthi1, was shown to be expressed at high levels in nodules and shoot tips of A. glutinosa, while having low expression levels in roots, flowers, and developing fruits. The function of AgThi1 was demonstrated by yeast complementation studies, in which AgThi1 was able to rescue a yeast thi4 mutant when fused to the yeast Thi4 signal peptide. In A. glutinosa nodules, high levels of agthi1 mRNA were detected in the infected cortical cells and in the pericycle of the nodule vascular system. A homologue of this cDNA, ara6/tz, was identified in Arabidopsis thaliana. ara6 maps in a region of chromosome 5 of Arabidopsis containing the tz locus which is consistent with the fact that ara6 transcription is disturbed in two tz mutant lines. ara6/tz is expressed at high levels in chloroplast-containing parenchymatic cells of leaves, inflorescence shoots and flowers of Arabidopsis, and at lower levels in the vascular system.
Science to Practice: Molecular-targeted Drug Delivery in Combination with Radiofrequency Ablation of Liver Cancer: A Magic Bullet? (2017)

In an effort to improve the technical success rates and clinical outcomes of radiofrequency (RF) ablation, Yan et al validated the use of a tumor-penetrating peptide and thermosensitive doxorubicin (DOX)-loaded nanoparticles in combination with RF ablation in a hepatocellular carcinoma mouse model. By achieving higher chemotherapeutic drug concentrations in target lesions, fewer toxic effects, and improved survival end points in an animal tumor model, the authors conclude that superior tumor treatment with RF ablation is possible when combined with molecular-targeted drug delivery systems.
Supplementary Table 9 from <i>TP53</i> Cancerous Mutations Exhibit Selection for Translation Efficiency (2023)

Supplementary Table 9 from &lt;i&gt;TP53&lt;/i&gt; Cancerous Mutations Exhibit Selection for Translation Efficiency
Beyond Cancer Vaccines (2011)

Despite significant scientific knowledge in the field of cancer immunology, therapeutic strategies using cancer vaccines to generate anti-tumor immunity have historically resulted in only modest clinical benefit. Disappointing results from prior cancer vaccine trials are likely due to multifactorial causes. Perhaps the most important is the role of inherent tumor-induced immune suppression and enhanced immunologic tolerance. Current research directed toward understanding the mechanisms of immunologic tolerance has led to the development of promising therapeutic immune regulatory antibodies that inhibit immunologic checkpoints and subsequently enhance immunologic anti-tumor activity. This review discusses the prior challenges associated with cancer vaccines and describes how, by breaking immune inhibition and facilitating immune stimulation, immune regulatory antibodies show great promise in the treatment of a variety of tumors.
The Heat‐Shock Protein HslVU from Escherichia Coli is a Protein‐Activated ATPase as well as an ATP‐Dependent Proteinase (1997)

HslVU in Escherichia coli a new two-component ATP-dependent protease composed of two heat-shock proteins, the HslU ATPase and the HslV peptidase which is related to proteasome beta-type subunits. Here we show that the reconstituted HslVU enzyme degrades not only certain hydrophobic peptides but also various polypeptides, including insulin B-chain, casein, and carboxymethylated lactalbumin. Maximal proteolytic activity was obtained with a 1:2 molar ratio of HslV (a 250-kDa complex) to HslU (a 450-kDa complex). By itself, HslV could slowly hydrolyze these polypeptides, but its activity was stimulated 20-fold by HslU in the presence of ATP. The ATPase activity of HslU was stimulated up to 50% by the protein substrates, but not by nonhydrolyzed proteins, and this stimulation further increased 2-3-fold in the presence of HslV. Concentrations of insulin B-chain that maximally stimulated the ATPase allowed maximal rates of the B-chain hydrolysis. Furthermore, addition of increasing amounts of ADP or N-ethylmaleimide reduced ATP and protein or peptide hydrolysis in parallel. Thus, HslVU is a protein-activated ATPase as well as an ATP-dependent proteinase, and these processes appear linked. Surprisingly, the protein and peptide substrates do not compete with each other for hydrolysis. Lactacystin strongly inhibits protein degradation, but has little effect on peptide hydrolysis, while the peptide aldehydes are potent inhibitors of hydrolysis of small peptides, but have little effect on proteins. Thus, the functional requirements for ATP-dependent hydrolysis of peptides and proteins appear different.
Axon termination conditions for electrical stimulation (1993)

The cable model for electrical stimulation near the terminal of a passive fiber is derived for excitation by an arbitrary, time-varying, applied extracellular field. Unless the termination impedance is comparable to that of mammalian node of Ranvier, the end-conditions require the longitudinal intracellular current at the fiber terminal to be negligibly small. This requirement substantially alters the membrane potential profile from that obtained with a fiber of infinite length. Stimulation near the end of a fiber may result in lower thresholds and may reverse the anodal/cathodal threshold ratio obtained with stimulation in the mid-portion of the fiber. Chronaxie for stimulation near the terminal may be much smaller than at a distance from the terminal and the strength-duration curve may be nonmonotonic. These differences may have significant implications for any application of electrical stimulation where fiber terminations may play a role in the excitatory process.
Molecular Barbells (1998)

Some proteins have multiple ligand-binding sites. For instance, ligand-gated ion channels, transport proteins, and many allosteric enzymes have two or more binding sites. To design new drugs that can bind to these proteins, one would ideally want to know the targets' structure. Another approach is to use combinatorial chemistry, by screening a large number of random combinations of chemical groups as potential ligands. Yet another alternative just published in the journal Nature consists of taking an existing ligand and creating a dimer by linking the two units with a polymer molecule (1). The authors reasoned that once one ligand unit has bound to a site on the target, the probability of binding of the other ligand unit will increase, thus increasing the overall affinity of the dimer.
Plasmonic nano-imprinting by photo-doping (2018)

A method to directly explore the effect of electron density on the surface plasmon wave and the corresponding laser-induced structures is demonstrated by controllable doping of silver nitrate (AgNO<sub>3</sub>) into a water-soluble polymer polyvinyl alcohol (PVA). It is shown that periodic nanostructures on PVA appeared only when the electron density was more than 6×10<sup>20</sup> cm<sup>-3</sup> and became uniform when doping density corresponded to 1.2×10<sup>21</sup> cm<sup>-3</sup>. Photo-excitation of electrons in the Ag-doped PVA defined by laser fluence determined the conditions of surface plasmon wave and formation of nanostructures on the surface. The Drude-Lorentz model was used to describe the formation conditions of surface wave and to estimate the period of the structures. The demonstrated photo-electron doping brings required means to control the formation of laser-induced patterns with an optical sub-wavelength resolution.
Role of IL-1α and the Nlrp3/caspase-1/IL-1β axis in cigarette smoke-induced pulmonary inflammation and COPD (2011)

Cigarette smoke (CS), the primary risk factor of chronic obstructive pulmonary disease (COPD), leads to pulmonary inflammation through interleukin-1 receptor (IL-1R)I signalling, as determined using COPD mouse models. It is unclear whether interleukin (IL)-1α or IL-1β, activated by the Nlrp3/caspase-1 axis, is the predominant ligand for IL-1RI in CS-induced responses. We exposed wild-type mice (treated with anti-IL-1α or anti-IL-1β antibodies), and IL-1RI knockout (KO), Nlrp3 KO and caspase-1 KO mice to CS for 3 days or 4 weeks and evaluated pulmonary inflammation. Additionally, we measured the levels of IL-1α and IL-1β mRNA (in total lung tissue by RT-PCR) and protein (in induced sputum by ELISA) of never-smokers, smokers without COPD and patients with COPD. In CS-exposed mice, pulmonary inflammation was dependent on IL-1RI and could be significantly attenuated by neutralising IL-1α or IL-1β. Interestingly, CS-induced inflammation occurred independently of IL-1β activation by the Nlrp3/caspase-1 axis. In human subjects, IL-1α and IL-1β were significantly increased in total lung tissue and induced sputum of patients with COPD, respectively, compared with never-smokers. These results suggest that not only IL-1β but also IL-1α should be considered as an important mediator in CS-induced inflammation and COPD.
Active vibration control of a kitchen hood via piezoelectric patch (2009)

This paper presents a full analysis and development of a system for vibrations reduction in a kitchen hood by using piezoelectric actuators. The control system is based on a feedback controller whose action depends on a single acceleration sensor collocated with the actuator. Two different resonant control laws have been designed: the first one operates without the information of the hood motor velocity; the second one is a more sophisticated controller which exploits also the velocity information. Overall, with the information of the motor velocity the best performances are guaranteed with a reduction of 75% of the vibrations. The resonant control system without the motor velocity information provides the best compromise in terms of performances (65% of reduction) and complexity of the implemented system. Tests held in anechoic chamber have shown the influence of the reduction of vibration upon the acoustic noise.
Characteristics Associated With Differences in Survival Among Black and White Women With Breast Cancer (2013)

In the SEER-Medicare database, differences in breast cancer survival between black and white women did not substantially change among women diagnosed between 1991 and 2005. These differences in survival appear primarily related to presentation characteristics at diagnosis rather than treatment differences.
1H resonance assignments and secondary structure of the carbon monoxide complex of soybean leghemoglobin determined by homonuclear two‐dimensional and three‐dimensional NMR spectroscopy (1994)

Homonuclear two-dimensional and three-dimensional 1H-NMR spectroscopy has been utilized to study the 15.9-kDa protein soybean leghemoglobin. NMR experiments were performed on the diamagnetic carbon monoxide complex at two temperatures and two pH values. Sequence-specific assignments have been made for 94% of the backbone and approximately 70% of the expected side-chain resonances. The secondary structure of leghemoglobin in solution has been determined on the basis of NOE connectivity patterns, hydrogen exchange and chemical-shift analyses. Leghemoglobin consists of seven helices and, unlike mammalian myoglobins, is missing the D helix. Instead an extended loop, the CE loop, is observed which might have importance for ligand entry into and exit from the protein interior. The hydrogen exchange behavior for the F helix and at the beginning of the A helix suggests different dynamic stability compared to other helical regions in leghemoglobin. Population of a second protein conformation, in which there is perturbation at the A-G-H helix interface, is observed at low pH.
Increasing Robustness of LSB Audio Steganography by Reduced Distortion LSB Coding (2020)

Abstract: In this paper, we present a novel high bit rate LSB audio watermark-ing method that reduces embedding distortion of the host audio. Using the proposed two-step algorithm, watermark bits are embedded into higher LSB layers, resulting in increased robustness against noise addition. In addition, listening tests showed that perceptual quality of watermarked audio is higher in the case of the proposed method than in the standard LSB method. Key Words: audio steganography, LSB coding, data hiding
Hydrolysis kinetics and stability of bis(triethoxysilyl)ethane in water-ethanol solution by FTIR spectroscopy (1997)

The stability and the hydrolysis and condensation kinetics of bis(triethoxysilyl)ethane in the water-ethanol solution were investigated using FTIR spectroscopy with a transmission type cell having a very short pathlength. The pH dependence of bis(triethoxysilyl)ethane's overall stability was measured and evaluated, and a new approach was designed to calculate hydrolysis rate constants from the experimental results. Furthermore, equations involving both hydrolysis and condensation processes were solved and the calculated results were compared with experimental data.
Control of Product Formation During Glucose Fermentation by Bacillus macerans (1984)

The anaerobic fermentation of glucose by Bacillus macerans ATCC 7068 was studied in batch culture with and without pH control. The fermentation was characterized by two distinct metabolic phases. In the primary growth phase, the concentrations of ethanol and acetic acid increased exponentially, and formate was detected as a minor product. The secondary phase was marked by a slowing and eventual cessation of growth, along with the disappearance of formate and acetate, and the appearance of H2, CO2, and acetone. Exogenously-added substrates were converted with stoichiometries of 1 formate → 1 H2 + 1 CO2, and approximately 2 acetate → 1 acetone. Consumption of &gt; 8 g glucose 1−1 required exogenous pH control, and acetone formation was strongly pH-dependent. Glucose was fermented by the Embden-Meyerhof pathway. Cell extracts contained pyruvate formate-lyase and formate dehydrogenase activities, but only low pyruvate dehydrogenase activity. A balanced fermentation pathway is presented which is consistent with reaction stoichiometries and [14C]glucose labelling data in whole cultures, and with enzyme activities in extracts. The pathway is compared with those of other facultative anaerobes and the acetone-producing Clostridium acetobutylicum.
Influence of alkaline-earth substitution on structure and oxygen transport of perovskite-type oxides La0.6A0.4FeO3-δ (A = Ca, Sr, Ba) (2019)

Structure, oxygen-nonstoichiometry and oxygen transport properties of perovskite-type oxides La0.6A0.4FeO3-δ (A = Ca, Sr and Ba, abbreviated as LCF64, LSF64, LBF64, respectively) were investigated. Rietveld analysis of the high-temperature X-ray diffraction (XRD) patterns recorded in air show an orthorhombic-to-rhombohedral transition at 625 °C for LSF64, a rhombohedral-to-cubic transition at 850 °C for LSF64, while LBF64 remains cubic over the entire temperature range (600-1000 °C) covered by the experiments. Results from electrical conductivity relaxation (ECR) measurements in the range of temperature 650-900 °C and pO2 0.045-0.9 bar indicate that the chemical diffusion coefficients (Dchem) for the three compositions are very close (Fig. 1a). For LSF64, good agreement is noted with data reported previously [1,2]. Using data of oxygen non-stoichiometry of the materials measured by thermogravimetry, values for the oxygen self-diffusion coefficient (DS) and the diffusion coefficient (mobility) of oxygen vacancies (DV) were calculated. While DS increases in the sequence Ca &lt; Sr &lt; Ba, the opposite trend is found for DV as shown in Figs. 1b and 1c, respectively. At the conference, results of density functional theory (DFT) calculations are compared with the experimental data.
Modelling and Characterisation of a Servo Self-Piercing Riveting (SPR) System (2018)

SPR is a cold mechanical joining process in which multiple sheets of material are riveted together without the need for a predrilled hole. It works by pushing a typically semi-tubular rivet into a target stack of material, during which the plastic deformation of the material and rivet are such that a mechanical lock is formed within the material stack. The process is used extensively in the automotive industry in car body construction, and is a competing technology to more established joining techniques such as resistance spot welding. As part of the ongoing development of the technique, there is a strong need to understand and simulate the dynamics of the process. In this work, a lumped parameter model of the SPR system with a non-parametric model of the joint is presented. Simulated results are compared with experimental data for a given joint configuration. Furthermore, the model is used to highlight the significance of the compliances within the system. It is shown that during rivet insertion, the stiffness of the C-frame structure is an influential factor in determining the dynamic response of the system. The results provide the basis for a more comprehensive sensitivity analysis into the factors which affect the quality of the resulting joint.
Morphometric analysis of cardiac hypertrophy during development, maturation, and senescence in spontaneously hypertensive rats. (1987)

Hypertrophy of the mammalian heart, regardless of the initiating event, results in architectural remodeling of ventricular components that maintain structural and functional characteristics of this organ. Ventricular components that vary their morphology and morphometry in a hypertrophic state are the muscle cells, connective tissue elements, vasculature, or a combination of some or all of the above. Morphologic quantification of the progressive tissue changes occurring throughout the natural life span of the spontaneously hypertensive and normotensive Wistar-Kyoto rats has not been thoroughly documented. Using perfused-fixed tissue from both strains at 1, 6, 12, 18, and 24 months of age, we have determined the morphometric changes that occurred in the subepicardial and midwall regions of the left ventricle. Myocyte cell size, wall thickness, and arterial blood pressure were elevated in 1-month-old spontaneously hypertensive rats, reached significance by 6 months, and remained significantly greater throughout the 24 months examined. Tissue morphometry demonstrated significant tissue component volumetric differences at 6 months in the spontaneously hypertensive rat. Age-related morphometric tissue changes occurred in both strains yet were exacerbated (percent volume of myocytes) or diminished (percent volume interstitial space) in the mature and aging spontaneously hypertensive rat. Capillary density of SHR left ventricle showed a drastic decline so that 6-month-old SHR had the same density as a senescent Wistar-Kyoto. Tissue morphometry and capillary density data strongly support the hypothesis that tissue oxygenation is diminished in the spontaneously hypertensive rat, and as a result, tissue necrosis and myocyte cell death occur.
Experimental transonic flutter characteristics of two 72 deg-sweep delta-wing models (1989)

Transonic flutter boundaries are presented for two simple, 72 deg. sweep, low-aspect-ratio wing models. One model was an aspect-ratio 0.65 delta wing; the other model was an aspect-ratio 0.54 clipped-delta wing. Flutter boundaries for the delta wing are presented for the Mach number range of 0.56 to 1.22. Flutter boundaries for the clipped-delta wing are presented for the Mach number range of 0.72 to 0.95. Selected vibration characteristics of the models are also presented.
Classic Kaposi sarcoma (2000)

Many contributory factors undoubtedly have etiologic and pathogenic significance in the development of classic KS; however, the interplay between these factors has complicated the understanding of the induction and development of the disease as well as the significance of each factor. As with other cell-transforming human DNA viruses, infection with KSHV/HHV8 alone is not sufficient for the development of KS and additional cofactors are required.