gebhart/patrepeval huggingface dataset:
Combined Bioinformatic and Rational Design Approach To Develop Antimicrobial Peptides against Mycobacterium tuberculosis (2016)

Drug-resistant pathogens are a growing problem, and novel strategies are needed to combat this threat. Among the most significant of these resistant pathogens is Mycobacterium tuberculosis, which is an unusually difficult microbial target due to its complex membrane. Here, we design peptides for specific activity against M. tuberculosis using a combination of "database filtering" bioinformatics, protein engineering, and de novo design. Several variants of these peptides are structurally characterized to validate the design process. The designed peptides exhibit potent activity (MIC values as low as 4 μM) against M. tuberculosis and also exhibit broad activity against a host of other clinically relevant pathogenic bacteria such as Gram-positive bacteria (Streptococcus) and Gram-negative bacteria (Escherichia coli). They also display excellent selectivity, with low cytotoxicity against cultured macrophages and lung epithelial cells. These first-generation antimicrobial peptides serve as a platform for the design of antibiotics and for investigating structure-activity relationships in the context of the M. tuberculosis membrane. The antimicrobial peptide design strategy is expected to be generalizable for any pathogen for which an activity database can be created.
A Novel Solid State Ultracapacitor (2017)

Novel dielectric materials were researched to develop an internal barrier layer capacitor that is fully solid state. These materials included reduced nanoparticles of barium titanate that were coated with various atomic layer deposited oxides. The nanoparticle powders were then densified into pellets and characterized using a dielectric test fixture over a frequency range of 20 Hz to 2 MHz. Densification and sintering were evaluated using scanning electron microscopic techniques. Ultimately, the samples showing the most promising electrical characteristics of permittivity, dissipation factor and equivalent series resistance were chosen to manufacture devices for subsequent testing.
Interleukin-22 Drives Endogenous Thymic Regeneration in Mice (2012)

Endogenous thymic regeneration is a crucial function that allows for renewal of immune competence after stress, infection, or immunodepletion. However, the mechanisms governing this regeneration remain poorly understood. We detail such a mechanism, centered on interleukin-22 (IL-22) and triggered by the depletion of CD4(+)CD8(+) double-positive thymocytes. Intrathymic levels of IL-22 were increased after thymic insult, and thymic recovery was impaired in IL-22-deficient mice. IL-22, which signaled through thymic epithelial cells and promoted their proliferation and survival, was up-regulated by radio-resistant RORγ(t)(+)CCR6(+)NKp46(-) lymphoid tissue inducer cells after thymic injury in an IL-23-dependent manner. Administration of IL-22 enhanced thymic recovery after total body irradiation. These studies reveal mechanisms of endogenous thymic repair and offer innovative regenerative strategies for improving immune competence.
Investigating the Increase in Energy Storage Density of Subsea Hydro-Pneumatic Accumulators Using a Compressible Fluid Undergoing Phase Change (2022)

Abstract The integration of energy storage systems (ESS) on a large-scale is becoming essential to mitigate intermittency issues in power supply from offshore wind farms. This paper deals with an offshore Hydro-Pneumatic Energy Storage (HPES) system comprising of a subsea accumulator pre-charged with a compressed gas. The paper applies a simplified thermodynamic model to investigate the potential increase in the energy storage density of the proposed HPES system by replacing air with carbon dioxide (CO2) that is able to undergo a phase change (gas-liquid-gas) during the storage cycle when limiting the peak operating pressure below the critical point. The study is based on a numerical model for simulating the thermodynamics of the entire storage cycle. A sensitivity study is conducted to examine the influence of main operational parameters, primarily the seawater temperature, peak working pressure and sea depth, on the storage density of the HPES system operating with a dual phase fluid. It is shown that the storage density of HPES accumulators can be increased substantially by using CO2 in lieu of air. The increase in density is found to depend considerably on the seawater temperature and sea depth.
Oxygen ratio control in critical care ventilation using compressed oxygen and blower gas sources (2020)

The coupling issue between ratio (gas mix) and pressure controllers is addressed for blower based critical care ventilators. Complications can arise by how oxygen gas, supplied by a proportional flow valve, is introduced relative to the blower. A simple blower model explains why coupling effects are more sensitive when oxygen is introduced downstream of the air blower. A progressive design synthesis is described that eventually led to the solution of complementary flow actuation between blower and valve flow feedback loops. Complementary dynamic flow coupling filters connect with the pressure stage output of the feedback control cascade. The complementary coupling filters frequency response changes according to the set gas ratio helping to equalize differences in the dynamic response between blower and valve at different gas ratio settings. This design solution achieves a more uniform total flow and pressure response across all ratio settings throughout the range of expected patient load.
Apparatus for disintegrating a calculus by an underwater shock wave from outside the human body (1991)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation Kazuyoshi Takayama, Masaaki Kuwahara, Shuzo Kimura; Apparatus for disintegrating a calculus by an underwater shock wave from outside the human body. J. Acoust. Soc. Am. 1 June 1991; 89 (6): 3029. https://doi.org/10.1121/1.400785 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAcoustical Society of AmericaThe Journal of the Acoustical Society of America Search Advanced Search |Citation Search
Genetic organization, size, and complete sequence of early region 3 genes of human adenovirus type 41 (1996)

The complete nucleotide and predicted amino acid sequences for open reading frames (ORFs) of the human adenovirus type 41 (Ad41) early region 3 (E3) gene have been determined. The sequence of the Ad41 E3 gene (map units 74 to 83.9) consists of 3,373 nucleotides and has one TATA box and two polyadenylation signals (AATAAA). Analysis of the nucleotide sequence reveals that the E3 gene can encode six ORFs, designated RL1 to RL6. These are all expressed at the mRNA level, as determined by reverse transcription-PCR analysis of AD41-infected cell RNA. When compared with known E3 sequences of most other human adenoviruses deposited in GenBank, the sequences of RL1 to RL3 were found to be unique to subgroup F adenoviruses (Ad40 and Ad41). They encode putative proteins of 173 amino acids (19.4 kDa) and 276 amino acids (31.6 kDa) in one reading frame as well as a 59- amino-acid (6.7 kDa) protein in an overlapping reading frame. RL4 encodes a 90-amino-acid protein (10.1 kDa) with 40% homology to the Ad2 E3 10.4-kDa protein, which induces degradation of the epidermal growth factor receptor and functions together with the Ad2 E3 14.5-kDa protein to protect mouse cell lines against lysis. RL5 encodes a protein of 107 amino acid residues (12.3 kDa) and is analogous to the Ad E3 14.5-kDa protein. RL6 codes for a protein of 122 amino acids (14.7 kDa) that is analogous to the Ad2 14.7-kDa protein, which functions to protect Ad-infected cells from tumor necrosis factor-induced cytolysis. This finding of three unique (RL1 to RL3) E3 gene ORFs may explain why subgroup F adenoviruses differ substantially from other human adenoviruses in their host range; i.e., they replicate predominantly in the host's gastrointestinal rather than respiratory tract. A recent phylogenetic study that compared subgroup F Ad40 DNA sequences with representatives of subgroups B (Ad3), C (Ad2), and E (Ad4) reached a similar conclusion about the uniqueness of RL1 and RL2.
A comparative introduction of four fractional order controllers (2003)

Using the differentiation and integration of fractional order or non-integer order in systems control is gaining more and more interest from the systems control community. In the paper, four representative fractional-order controllers in the literature are briefly introduced, namely, TID (tilted proportional and integral) controller, CRONE controller (controle robuste d'ordre non entier), PI/sup /spl lambda//D/sup /spl mu// controller and fractional lead-lag-compensator. The basic ideas and technical formulations are presented with some comparative comments. The major purpose of the paper is to draw attention to the non-conventional method of robust control based on fractional order calculus.
An Improved Method of Back Azimuth Determination with a Multi-Arm OFIS (2007)

Abstract : The detection of infrasound in the presence of wind is challenging. Increasing wind speeds lead to higher noise floors. While the exact nature of the noise is still a subject of investigation, several technologies and array configurations have been developed to maximize the signal to noise ratio and lower the detection threshold. Optical fiber infrasound sensors (OFIS) are long compliant tubes wrapped with two optical fibers that integrate pressure change along the length of the tube with laser interferometery. Spatially incoherent wind noise is naturally attenuated relative to spatially coherent infrasound. Because the signal pressure variation is integrated along the length of the tube, the instrument response is a function of the orientation of the OFIS arms relative to the orientation of the wavefront. We show with theory and real infrasound data recorded at Pinon Flat Observatory in southern California that this spectral property can be exploited with multiple OFIS arms in different ways to determine the phase velocity of infrasound signals. Based on these findings and unpublished results, we propose two OFIS configurations as alternatives to rosette pipe array infrasound stations.
Mechanism of Formation of Colloidal Particles of Calcium Thiophosphates in an Organic Medium (1998)

The reaction of calcium oxide, P4S10, and water in the presence of calcium alkylarylsulfonate as a surfactant and tetrahydrofuran and xylene as solvents leads to a mixture of calcium mono-, di-, and trithiophosphate as colloidal particles stabilized by the surfactant in a hydrocarbon medium. A mechanism of the formation of the colloidal particles is proposed on the basis of systematic studies of the reaction medium and the characterization of the colloidal particles performed by means of chemical analyses, 31P NMR and SAXS. The initial step is a reaction of a water-in-oil microemulsion with solid calcium oxide. The resulting reverse micelles containing water and solubilized calcium hydroxide further react with solid P4S10 to yield colloidal particles of calcium thiophosphates. The influences of the surfactant concentration, water, and THF contents have been investigated. THF acts as a cosurfactant and is absolutely required in order to obtain thiophosphates instead of phosphates.
Akinetic swept-source optical coherence tomography based on a pulse-modulated active mode locking fiber laser for human retinal imaging (2018)

Optical coherence tomography (OCT) is a noninvasive imaging modality that can provide high-resolution, cross-sectional images of tissues. Especially in retinal imaging, OCT has become one of the most valuable imaging tools for diagnosing eye diseases. Considering the scattering and absorption properties of the eye, the 1000-nm OCT system is preferred for retinal imaging. In this study, we describe the use of an akinetic swept-source OCT system based on a pulse-modulated active mode locking (AML) fiber laser at a 1080-nm wavelength for in-vivo human retinal imaging. The akinetic AML wavelength-swept fiber laser was constructed with polarization-maintaining fiber that has an average linewidth of 0.625 nm, a spectral bandwidth of 81.15 nm, and duty ratio of 90% without the buffering method. We successfully obtained in-vivo human retinal images using the proposed OCT system without the additional k-clock and the frequency shifter that provides a wide field of view of 43.1°. The main retina layers, such as the retinal pigment epithelium, can be distinguished from the OCT image with an axial resolution of 6.3 μm with this OCT system.
The Murine CD99-Related Molecule CD99-Like 2 (CD99L2) Is an Adhesion Molecule Involved in the Inflammatory Response (2007)

CD99, a glycoprotein found on the surfaces of leukocytes and concentrated at the borders of endothelial cells, plays a major role in the migration of leukocytes across endothelial cells into sites of inflammation, and has other roles in thymocyte development. The human and mouse genomes encode only two proteins related to CD99. One of these, XGA, is a red blood cell surface antigen. The function of the other, CD99-like 2 (CD99L2), is not known. We cloned mouse CD99L2 and used CD99L2 isolated from transfected cells to raise specific antibodies. Similar to human CD99, CD99L2 was expressed at the borders between transfected cells as well as on mouse leukocytes and vascular endothelial cells in situ. Transfection of L cell fibroblasts with CD99L2 imparted to them the ability to adhere to each other in a divalent cation-dependent, homophilic manner. Anti-CD99L2 antibody blocked influx of neutrophils and monocytes into a site of inflammation in vivo.
A glycoprotein inhibitor of pectin methylesterase in kiwi fruit (<i>Actinidia chinensis</i>) (1990)

The finding of a powerful inhibitor of pectin methylesterase in ripe kiwi fruit is reported. The inhibitor was revealed to be a glycoprotein. It was purified to homogeneity and found to have a molecular mass of about 28 kDa, as estimated by gel filtration chromatography, SDS/PAGE and analytical ultracentrifugation. The sugar portion is composed of galactose, arabinose and rhamnose, the latter being much less represented. The amino acid composition showed a very high content of acidic residues compared to basic ones, which is the reason for the very low isoelectric point of the protein (less than 3.5). The kind of inhibition on kiwi pectin methylesterase was found to be competitive with an apparent Ki of 0.22 microM, using citrus pectin as a substrate. Moreover, the inhibitor is effective in inhibiting pectin methylesterase in the pH range 3.5-7.5. Kiwi inhibitor appears to be specific for pectin methylesterase, inasmuch as it was found to be ineffective against other polysaccharide-degrading enzymes, such as polygalacturonase and amylase. Conversely, it appears to be completely aspecific as far as the pectin methylesterase source is concerned. In fact, it was found to inhibit this enzyme effectively from all the sources we assayed, i.e. orange, tomato, apple, banana, potato.
A low-cost, low-temperature radiometer for thermal measurements (2009)

We have developed an inexpensive, compact radiometer for in situ measurement of low levels of flux in the far infrared. It utilizes a Winston cone fabricated cheaply using a boring tool and standard commercial thermometers as sensors. Its form is similar to bolometers which have long been used for sensitive astronomical infrared measurements. By relaxing the sensitivity and response times the radiometers can be made much less costly. The sensitivity varies with the operating temperature, but at 20 K the measured resolution is better than 0.01 microwatt per cm<sup>2</sup>, equivalent to the heat from a low emissivity blanket at 30 K or a high emissivity surface at just 1 K hotter than the radiometer held at 20 K. The Winston cone provides a directional signal, excluding sources that are outside the acceptance cone (11 degree halfangle in this case) by more than a factor of 1000). The intended use is to measure the in-situ properties of aluminized Kapton at low T and to look for heat leaks and reflected flux in low temperature thermal vacuum systems.
Organic dyes containing thienylfluorene conjugation for solar cells (2005)

New organic dyes that contain variable lengths of conjugation featuring alternating thiophene and fluorene segments have been synthesized and efficient nano-crystalline TiO2 based dye-sensitized solar cells were fabricated using these molecules as light-harvesting sensitizers.
FEED‐BACK INHIBITION OF MILK SECRETION: THE EFFECT OF A FRACTION OF GOAT MILK ON MILK YIELD AND COMPOSITION (1988)

A milk fraction containing whey proteins of 10-30 kDa was injected into one mammary gland of lactating goats via the teat canal. This fraction produced a temporary dose-dependent reduction in milk yield in the treated gland; the milk yield of the other gland, which received an equal volume of carrier solution, was not affected. Injection of a second fraction, containing whey proteins of greater than 30 kDa, affected milk secretion only at high doses, and this effect was not wholly specific to the treated gland. The 10-30 kDa fraction and the greater than 30 kDa fraction produced similar transient changes in the concentrations of several ions and lactose in milk of the treated gland, but not in that of the untreated gland. These data indicate that a milk constituent present in the 10-30 kDa whey inhibits milk secretion in a temporary and reversible manner. The results are discussed in relation to regulation of milk secretion through local feedback inhibition.
Heat Treatment of Friction-Stir-Welded 7050 Aluminum Plates (2006)

A method of heat treatment has been developed to reverse some of the deleterious effects of friction stir welding of plates of aluminum alloy 7050. This alloy is considered unweldable by arc and high-energy-density beam fusion welding processes. The alloy can be friction stir welded, but as-welded workpieces exhibit low ductility, low tensile and yield strengths, and low resistance to stress corrosion cracking. Heat treatment according to the present method increases tensile and yield strengths, and minimizes or eliminates stress corrosion cracking. It also increases ductility. This method of heat treatment is a superior alternative to a specification-required heat treatment that caused the formation of large columnar grains, which are undesired. Workpieces subjected to the prior heat treatment exhibited elongations <2 percent, and standard three-point bend specimens shattered. The development of the present heat treatment method was guided partly by the principles that (1) by minimizing grain sizes and relieving deformation stresses, one can minimize or eliminate stress corrosion cracking and (2) the key to maximizing strength and eliminating residual stresses is to perform post-weld solution heating for as long a time as possible while incurring little or no development of large columnar grains in friction stir weld nuggets. It is necessary to perform some of the solution heat treatment (to soften the alloy and improve machine welding parameters) before welding. The following is an example of thickness- dependent pre- and post-weld heat treatments according to the present method: For plates 0.270 in. (approx.6.86 mm) thick milled from plates 4.5 in. (114.3 mm) thick, perform pre-weld solution heating at 890 F (477 C) for 1 hour, then cool in air. After friction stir welding, perform solution heating for 10 minutes, quench, hold at room temperature for 96 hours, then age at 250 F (121 C) for 5 hours followed by 325 F (163 C) for 27 hours.
Quinoline antimalarials as investigational drugs for HIV‐1/AIDS: in vitro effects on HIV‐1 replication, HIV‐1 response to antiretroviral drugs, and intracellular antiretroviral drug concentrations (2006)

Abstract In this study, the effects of the quinoline antimalarials, chloroquine and mefloquine, were tested on: (1) HIV‐1 replication; (2) virus response to existing antiretrovirals; (3) functional activity of drug efflux pumps; and (4) intracellular accumulation of antiretrovirals. Antiretroviral activity was evaluated using cells acutely infected with drug‐sensitive/resistant HIV‐1 isolates or retroviral vectors, chronically infected cell lines, and syncytium assays. Drug interactions were assessed isobolographically. Activity of efflux pumps was tested using specific fluorochromes. Antitretroviral concentrations were quantitated by HPLC. Results indicated that: (1) the antimalarials (mefloquine > chloroquine) inhibited the replication of drug‐sensitive and drug‐resistant HIV‐1 at therapeutically achievable concentrations and specifically impaired the formation of fusion‐competent viral glycoproteins; (2) anti‐HIV‐1 effects were additive to those of zidovudine and nevirapine, and synergistic to those of lopinavir; (3) the antimalarials (mefloquine > chloroquine) inhibited the P‐glycoprotein, multidrug‐resistance‐associated proteins, and breast‐cancer resistance‐associated protein; (4) Chloroquine, but not mefloquine, increased lopinavir concentrations in peripheral blood mononuclear cells (PBMCs) by approximately 5 (five)‐fold. Thus quinoline antimalarials inhibited HIV‐1 replication by a novel mechanism, resulting in additive or synergistic effects in combination with known antiretrovirals. These drugs may also have an impact on the cellular pharmacokinetics of antiretrovirals. Drug Dev. Res. 67:806–817, 2006. © 2007 Wiley‐Liss, Inc.
Novel Magnetic Tunneling Junction Memory Cell With Negative Capacitance-Amplified Voltage-Controlled Magnetic Anisotropy Effect (2017)

The high current density required by magnetic tunneling junction (MTJ) switching driven by the spin transfer torque (STT) effect leads to large power consumption and severe reliability issues, hindering the timetable for STT magnetic random access memory to mass market. By utilizing the voltage-controlled magnetic anisotropy (VCMA) effect, the MTJ can be switched by the voltage effect and is postulated to achieve ultralow power (fJ). However, the VCMA coefficient measured in experiments cannot meet the requirement for MTJ with dimensions below 100 nm. And an external in-plane magnetic field usually is demanded for precessional VCMA switching. Here, in this paper, a novel approach for the amplification of the VCMA effect, which borrows ideas from negative capacitance, is proposed. The feasibility of the proposal is proved by physical simulation and in-depth analysis. Since the amplified VCMA effect, the external magnetic field can be eliminated. A three-terminal novel MTJ memory cell is designed with which both low power and high speed can be achieved.