gebhart/patrepeval huggingface dataset:
Extracytoplasmic proteins of Mycobacterium tuberculosis – mature secreted proteins often start with aspartic acid and proline (2000)

A surrogate expression system, based on fusions to the phoA bacterial reporter gene, was used to identify Mycobacterium tuberculosis genes that encode exported proteins and the promoter regions required for their expression in the heterologous host Mycobacterium smegmatis. To assess these results in the context of the complete M. tuberculosis genome sequence, the corresponding genes were identified and computational algorithms were employed to identify signal peptide (SP), transmembrane domain and membrane lipoprotein attachment motifs. This information was used to predict the subset of M. tuberculosis genes that encode exported proteins. Of the 34 genes identified by the phoA method, 22 were classified to encode potential soluble secreted proteins. Among these, 14 genes may encode novel secreted proteins. Six of the remaining 12 genes were predicted to encode membrane lipoproteins and an additional six to encode integral membrane proteins. Published observations of proteins proven to be secreted into M. tuberculosis culture filtrates were reviewed to further characterize the mycobacterial SP motif. It was concluded that mycobacterial SPs are comparable in size to Gram-positive SPs, but certain features are different. In particular, arginine was the predominant N-terminally positively charged amino acid in contrast to lysine in the Gram-positives. The hydrophobic transmembrane segment of the SP was dominated by alanine, in contrast to leucine. At the C-terminal end of the SPs, the (-3, -1) rule (AXA motif) holds, with alanine as the dominant amino acid in both positions, being most dominant in the (-1) position. A high proportion of mature sequences start with aspartic acid in the (+1) position and proline in the (+2) position - the DP motif. The authors propose that the DP sequence serves as a sorting signal, following translocation and cleavage by signal peptidase I. Alternatively, the DP motif may be part of the recognition site for the signal peptidase.
Molecular systems for ultrafast optical switching: Controlling electron transfer reactions with femtosecond laser pulses (1994)

Rapid, reversible photoinduced electron transfer reactions are a class of photophysical phenomena that can be exploited to develop schemes for optical switching. Molecular electronic switches, wires, micro-sensors for chemical analysis, and opto-electronic components for use in optical computing are currently under active investigation. The principal advantages of using molecules in these applications are high component density, increased response speeds, and high energy efficiency. Since photoinduced electron transfer processes within molecules can take place on a picosecond time scale, it should be possible to produce efficient devices that respond very rapidly. Molecules that employ reversible electron transfer reactions for optical switching should possess both speed and photostability advantages over molecular switches based on photochemical changes in molecular structure. For this purpose the authors recently designed several molecular systems that display properties that may be exploited for optical switching. In this paper, two or more laser pulses are used to manipulate photochromic ion pairs that results from rapid reversible photoinduced electron transfer in complex donor-acceptor molecules.
Numerical analysis of percolation formation in carbon nanotube based nanofluids (2013)

SUMMARY The intriguing behaviour of carbon nanotube suspensions shows that thermal conduction cannot be described by conventional approaches. These results led the researchers on the percolation and the interfacial layer resistance (also known as Kapitza resistance) as the main mechanisms governing the effective thermal conductivity enhancement for these nanoparticles suspensions. A numerical simulation on the behaviour of these suspensions, when subjected to a Brownian force field, was conducted to characterize the main factors affecting the dynamic interactions and percolation structures formation. To this end, three different numerical models based on continuum mechanics were developed. The obtained results suggest that the size, shape and aspect ratio of the nanoparticles are main factors controlling the dynamic network formation. On the other hand, the influence of the Brownian motion and the structural flexibility of the nanotubes seem to have a rather negligible effect on the results. The numerical model developed and proposed here may assist in understanding and correlating the experimental thermal conductivity data of nanofluids, contributing to demystify some of the intriguing behaviours reported. Copyright © 2013 John Wiley & Sons, Ltd.
Cardiovascular Magnetic Resonance: Basic Principles, Methods, and Techniques (2010)

This chapter contains sections titled: Introduction Physical Principles Underlying MRI CMR Imaging Techniques Cardiac Magnetic Resonance Spectroscopy Safety and Contraindications Acknowledgement References
Flash X-Ray (FXR) Accelerator Optimization - Beam-induced Voltage Simulation and TDR Measurements (2004)

Lawrence Livermore National Laboratory (LLNL) is evaluating design alternatives to improve the voltage regulation in our Flash X-Ray (FXR) accelerator cell and pulse-power system. The goal is to create a more mono-energetic electron beam that will create an x-ray source with a smaller spot-size. Studying the interaction of the beam and accelerator cell will generate improved designs for high-current accelerators at Livermore and elsewhere. When an electron beam crosses the energized gap of an accelerator cell, the electron energy is increased. However, the beam with the associated electromagnetic wave also looses a small amount of energy because of the increased impedance seen across the gap. The phenomenon is sometimes called beam loading. It can also be described as a beam-induced voltage at the gap which is time varying. This creates beam energy variations that we need to understand and control. A high-fidelity computer simulation of the beam and cell interaction has been completed to quantify the time varying induced voltage at the gap. The cell and pulse-power system was characterized using a Time-domain Reflectometry (TDR) measurement technique with a coaxial air-line to drive the cell gap. The beam-induced cell voltage is computed by convoluting the cell impedance with measured beam current. The voltage was checked against other measurements to validate the accuracy. The simulation results predicted that there are significant beam-induced gap voltage variations. Beam-induced voltages from different current profiles and cell impedances were simulated and compared. This allows us to predict the effect on voltage regulation for different design alternatives before making hardware changes and high-voltage testing. The beam-induced voltages are incorporated into a larger accelerator system-model to quantify their effect on total beam energy variations.
Characterization of superoxide dismutases purified from either anaerobically maintained or aerated Bacteroides gingivalis (1990)

Superoxide dismutases (SODs) were purified from extracts of either anaerobically maintained or aerated Bacteroides gingivalis. Each purified enzyme (molecular weight, 46,000) was a dimer composed of two subunits of equal sizes. SOD from anaerobically maintained cells (anaero-SOD) contained 1.79 g-atom of Fe and 0.28 g-atom of Mn, and SOD from aerated cells (aero-SOD) contained 1.08 g-atom of Mn and 0.36 g-atom of Fe. Spectral analysis showed that anaero-SOD had the characteristic of Fe-SOD and that aero-SOD had that of Mn-SOD. Both enzyme preparations contained three isozymes with identical isoelectric points. On the basis of inactivation of SOD by H2O2, it was found that aero-SOD consisted of one Mn-SOD and a small quantity of two Fe-SODs, whereas anaero-SOD contained only Fe-SOD. However, each apoprotein from anaero-SOD and aero-SOD, prepared by dialysis in guanidinium chloride plus 8-hydroxyquinoline, showed only one protein band each with the same isoelectric point on an isoelectric focusing gel. Subsequent dialysis of both apoenzymes with either MnCl2 or Fe(NH4)2(SO4)2 restored the activity. These reconstituted SODs showed only one protein band with SOD activity on native polyacrylamide gel electrophoresis. Furthermore, the two enzymes had similar amino acid compositions, and their amino-terminal sequences were identical through the first 12 amino acids. These results suggest that the three isozymes of anaero-SOD and aero-SOD in B. gingivalis are formed from a single apoprotein.
An analysis of electro-optic measurement of electric fields using Jones matrix formulation (2011)

We present an analysis of polarization sensitive electro-optic measurement using Jones matrix formulation. Based on our formulation, we present an optimisation of the angle of incidence within the electro-optic probe and its ability to measure electric-fields in a three dimensional Cartesian coordinate system.
Gastrointestinale Blutung (2018)

Gastrointestinale Blutungen sind insgesamt häufig – in ihrem klinischen Erscheinungsbild sind sie jedoch sehr unterschiedlich und sie bedürfen einer differenzierten Diagnostik und Therapie. Der folgende Artikel befasst sich mit dem Management, der Diagnostik und der Therapie gastrointestinaler Blutungen [1].
Lack of evidence for PERV expression after apoptosis‐mediated horizontal gene transfer between porcine and human cells (2007)

Evidence for porcine endogenous retrovirus (PERV) infection of human cells has provoked a public health debate over the proposed use of porcine xenografts to alleviate the worldwide shortage of human allografts. Nevertheless, the potential relevance of PERV transmission by apoptosis-mediated horizontal DNA transfer, a documented means of infection-independent retrovirus delivery, appears to have been overlooked in this discussion. To examine the hypothesis that apoptotic cell death during porcine xenograft rejection is capable of fostering horizontal DNA transfer, we have now assessed in vitro cocultures, consisting of phagocytic human fibroblasts and apoptotic or necrotic porcine B-lymphoblastoid cells, for evidence of cross-species PERV exchange and eventual replication. Using real-time polymerase chain reaction (PCR) assays, designed to differentiate nuclear and cytoplasmic DNA derived from either porcine or human cells, we now report evidence for the presence of porcine DNA, including PERV, in the nucleus of human fibroblasts exposed to apoptotic porcine cells. This novel demonstration of apoptosis-mediated horizontal PERV transfer is characterized by a low efficiency of transfer and a transient nature, being present in only 0.22% of the cocultured human cells and disappearing to undetectable levels within 4 weeks of exposure to apoptotic porcine cells. In contrast, using PERV-specific real-time reverse-transcriptase PCR (RT-PCR) and ultra-sensitive product-enhanced reverse transcriptase (PERT) assays, we find no evidence for human fibroblast-derived cellular PERV RNA or coculture supernatant-based RT-activity, indicating a lack of subsequent PERV replication. Together, these results suggest that apoptosis-mediated horizontal PERV transfer does not present an overt hazard within the framework of porcine xenotransplantation. However, we also present arguments against extrapolation of these in vitro observations directly to clinical circumstances.
Improvement to Foot and Skin Appearance by Using Copper Oxide Impregnated Socks - A Report of a Large Scale Internet Based User Survey (2017)

Copper has two key properties that make it an attractive component to introduce into textiles and socks in particular – it has potent biocidal properties and is an essential trace element vital for the normal function of skin. The capacity of copper oxide impregnated socks to kill fungi that causes tinea pedis (athlete’s foot) and to enhance skin elasticity has already been demonstrated. In the current study, we assessed the beneficial effect on the skin of the foot in the wider population by supplying socks impregnated with microscopic copper oxide particles to 5,000 individuals that were identified via an internet survey as people who had experienced athlete’s foot within the past 6 months or were concerned about the appearance of their feet. Each individual received 3 complementary pairs of socks and was asked to use them as they would normally use their own socks. After 90 days 3,603 paricipants answered an online questionnaire. The vast majority (82%) of responders that felt uncomfortable showing their bare feet in public before using the socks reported a meaningful improvement to their foot skin following the use of the socks for at least 5 hours a day. 61% of respondents reported elimination or reduction of their foot odor, and 60% reported stopping using a foot care regime or therapy due to using the supplied socks. 51% indicated that the socks improved the appearance of their feet and 58% indicated they were now more comfortable showing their feet in public. In view of the above, it can be concluded that the simple use of copper oxide impregnated socks for at least 5 hours a day helps improve the foot skin well-being and overall appearance of the skin.
An investigation into a micro-sized droplet impinging on a surface with sharp wettability contrast (2014)

An experimental investigation was conducted into a micro-sized droplet jetted onto a surface with sharp wettability contrast. The dynamics of micro-sized droplet impingement on a sharp wettability contrast surface, which is critical in inkjet printing technology, has not been investigated in the literature. Hydrophilic lines with line widths ranging from 27 to 53 µm, and contact angle ranging from 17° to 77°, were patterned on a hydrophobic surface with a contact angle of 107°. Water droplets with a diameter of 81 µm were impinged at various offset distances from the centre of the hydrophilic line. The evolution of the droplet upon impingement can be divided into three distinct phases, namely the kinematic phase, the translating phase where the droplet moves towards the centre of the hydrophilic line, and the conforming phase where the droplet spreads along the line. The key parameters affecting the conformability of the droplet to the hydrophilic line pattern are the ratio of the line width to the initial droplet diameter and the contact angle of the hydrophilic line. The droplet will only conform completely to the hydrophilic pattern if the line width is not overly small relative to the droplet and the contact angle of the hydrophilic line is sufficiently low. The impact offset distance does not affect the final shape and final location of the droplet, as long as part of the droplet touches the hydrophilic line upon impingement. This process has a significant impact on inkjet printing technology as high accuracy of inkjet droplet deposition and shape control can be achieved through wettability patterning.
Impulsive stimulated thermal scattering study of α relaxation dynamics and the Debye–Waller factor anomaly in Ca0.4K0.6(NO3)1.4 (1996)

Impulsive stimulated light scattering experiments were carried out on an ionic glass former Ca0.4K0.6(NO3)1.4 to determine the temperature dependence of the Debye–Waller factor fq(T) in the q→0 limit and to investigate the structural relaxation dynamics. A square-root cusp anomaly was observed in fq→0(T) at a crossover temperature Tc of 378 K. This and the relaxation dynamics observed were consistent with predictions of the mode-coupling theory of the liquid–glass transition.
Enabling Natural Graphite in High-Voltage Aqueous Graphite || Zn Metal Dual-Ion Batteries (2020)

Graphite is regarded as a promising positive electrode (=cathode) for anion intercalation for decades due to its high operating potential (>4.50 V vs Li|Li+; > 2.22 V vs Zn|Zn2+; >1.46 V vs standard hydrogen electrode (SHE); 1.26 V vs Ag|AgCl), high abundance, low cost, low toxicity without use of any transition metals, and high overall safety. Nevertheless, due to its high operation potential, it is challenging to find suitable electrolytes, particularly in any aqueous system due to parasitic side reactions such as oxygen evolution reactions (OER) at the cathode. In this work, natural graphite (NG) is enabled as a cathode material using an aqueous system in a new “water-in-bisalt” electrolyte. We present a graphite || zinc (Zn) metal dual-ion battery (ZnG-DIB) that operates at remarkably high voltage of ˜2.3 – 2.5 V in an aqueous Zn system. Anions intercalate into a NG cathode at an on-set potential of ˜1.5 V vs Ag|AgCl (˜2.46 V vs Zn|Zn2+), delivering a reversible capacity of ˜110 mAh g–1 with high rate capability reaching a capacity of nearly 60 mAh g–1 at a charge/discharge current of 5000 mA g–1. Over 200 cycles are achieved with over 80% capacity retention in a graphite || Zn metal full-cell, showing the stability of the graphite cathode and the Zn metal negative electrode (=anode) in the electrolyte. A suite of characterization techniques collectively prove anion intercalation takes place and provide insights into the mechanism of anion intercalation into NG.
The variant<i>rpoS</i>allele of<i>S. enteritidis</i>strain 27655R does not affect virulence in a chick model nor constitutive curliation but does generate a cold-sensitive phenotype (1998)

Adherence of pathogenic Escherichia coli and Salmonella spp. to host cells is in part mediated by curli fimbriae which, along with other virulence determinants, are positively regulated by RpoS. Interested in the role and regulation of curli (SEF17) fimbriae of Salmonella enteritidis in poultry infection, we tested the virulence of naturally occurring S. enteritidis PT4 strains 27655R and 27655S which displayed constitutive and null expression of curli (SEF17) fimbriae, respectively, in a chick invasion assay and analysed their rpoS alleles. Both strains were shown to be equally invasive and as invasive as a wild-type phage type 4 strain and an isogenic derivative defective for the elaboration of curli. We showed that the rpoS allele of 27655S was intact even though this strain was non-curliated and we confirmed that a S. enteritidis rpoS::strr null mutant was unable to express curli, as anticipated. Strain 27655R, constitutively curliated, possessed a frameshift mutation at position 697 of the rpoS coding sequence which resulted in a truncated product and remained curliated even when transduced to rpoS::strr. Additionally, rpoS mutants are known to be cold-sensitive, a phenotype confirmed for strain 27655R. Collectively, these data indicated that curliation was not a significant factor for pathogenesis of S. enteritidis in this model and that curliation of strains 27655R and 27655S was independent of RpoS. Significantly, strain 27655R possessed a defective rpoS allele and remained virulent. Here was evidence that supported the concept that different naturally occurring rpoS alleles may generate varying virulence phenotypic traits.
Power and frequency bandwidth improvement of piezoelectric energy harvesting devices using phase-shifted synchronous electric charge extraction interface circuit (2017)

This article presents a new way to control the synchronous electric charge extraction interface circuit, which was formerly developed to improve the performances of piezoelectric vibration energy harvesting devices. An analytical model for energy harvesting systems including this new technique, called phase-shift synchronous electric charge extraction, is proposed. This model is then used to study the properties of this new control scheme in the cases of low and high electromechanical coupling. Contrary to the synchronous electric charge extraction technique which exhibited significant improvements in terms of harvested power for piezoelectric devices with low electromechanical coupling, the phase-shift synchronous electric charge extraction technique shows capability to increase the harvested power up to the theoretical limit for piezoelectric devices with high electromechanical coupling. In addition, the presented theoretical results show that the frequency bandwidth of piezoelectric energy harvesting devices may be substantially increased.
Immunohistochemical staining of primary-culture RA synovial cells in chamber slides: , , - phase contrast, and lightfield (2011)

<b>Copyright information:</b>Taken from "Isolation and characterization of rheumatoid arthritis synovial fibroblasts from primary culture — primary culture cells markedly differ from fourth-passage cells"Arthritis Research 2000;3(1):72-76.Published online 21 Nov 2000PMCID:PMC17827.Copyright © 2000 BioMed Central Ltd on behalf of the copyright holders While control isotype-matched mAbs (peroxidase) or rabbit serum (APAAP) showed no positive reaction, the anti-Thy-1 mAb AS02 stained large, flat, spindle-shaped or stellate-shaped cells (ie cells with FB morphology; alkaline phosphatase, purple staining) and the anti-CD14 mAb RMO52 identified small, round cells, conceivably macrophages (peroxidase, brown staining). The RA-SFB clearly expressed procollagen I and procollagen III (APAAP, red staining). The primary culture contained no endothelial cells, as documented by the lack of staining for von Willebrand factor (APAAP) and CD144 (APAAP). Original magnification: , , , and , 184 ×; - and 368 ×.
Development of Movable Machine Tool with Multi Spindles and Axes (Development of Control Software for Multi Spindles and Axes) (2006)

The study deals with the development of a movable machine tools with multi spindles and axes that can efficiently process large-sized parts to expect an additional value. The main specification of the machine tool is not having the major construction such as bed, column and saddle absolutely. Instead, the machine tool is built by only linear motor rails and beams to support. The developed machine tool can reduce the cycle time for cutting large materials by means of multi spindles and axes, equipped with 6 to 9 spindles and simultaneously control up to 40 at maximum. In addition the installation area of the machine tool is approximately 120% of area that the material occupies. The previous report explained the basic specification of the machine tool, its concept and performance evaluation. Then, this report presents the management of simultaneous movement, the division of NC program for each spindle and interference avoidance of multi axes, as well as the method of tool path generation to confirm the rapid production of large sized die and mold.
Emotional recognition with wearable EEG device (2019)

To elucidate relationships between changes in brain activity associated with emotional image presentation, EEG spectra were analyzed in the resting state and during Positive or Negative image presentation using wearable electrical encephalogram (EEG) device and custom image presentation software developed in our laboratory. When alpha band power spectra were compared between resting state and emotional image presentation conditions, power spectrum values in the resting state were found to decrease in both positive and negative image presentation conditions. In particular, alpha band attenuation was strongly observed in negative image presentation conditions. These results suggest that a wearable EEG device may be able to detect changes in brain activity associated with visual information.