gebhart/patrepeval huggingface dataset:
Tryptophan-rich antimicrobial peptides: comparative properties and membrane interactions (2002)

The interaction of several tryptophan (Trp)-rich cationic antimicrobial peptides with membranes was investigated. These peptides included tritrpticin, indolicidin, lactoferricin B (Lfcin B), and a shorter fragment of lactoferricin (LfcinB4-9). The average environment of the Trp residues of these peptides was assessed from their fluorescence properties, both the wavelength of maximal emission as well as the red edge effect. The insertion of the peptides into vesicles of differing composition was examined using quenching of the Trp fluorescence, with both soluble acrylamide and nitroxide-labelled phospholipids as well as by chemical modification of the Trp residues with N-bromosuccinimide. The results were consistent with the Trp side chains positioned mostly near the membrane-water interface. The extent of burial of the Trp side chains appears to be greater in vesicles containing phospholipids with the anionic phosphatidylglycerol headgroup. Leakage of the aqueous contents of liposomes was also measured using the 8-aminonaphthalene-1,3,6-trisulfonic acid--p-xylene-bis-pyridinium bromide assay. Tritrpticin, which demonstrated the greatest red edge shift, also displayed the largest amount of leakage from liposomes. Taken together, the results illustrate that cationic Trp-rich antimicrobial peptides preferentially disrupt large unilamellar vesicles with a net negative charge following their insertion into the interfacial region of the phospholipid bilayer.
Chip-level area routing (1998)

We present a chip-level area router for modern VLSI technologies. The gridless area router can handle any number of layers, as well as rectilinear blockage areas on any layer. A two-stage divide-and-conquer strategy is applied so that the area router can handle very large chips. The first stage includes an area-minimization loop by using an efficient and accurate multi-layer global router. The global router minimizes the chip area while performing the global routing. According to the global routing results, switchboxes are generated for the whole chip area. Then the switchboxes are sent to the second stage for detailed routing, in which a tile-expansion based switchbox router is used. With multi-level rip-up and re-route techniques, the detailed router is shown to be able to complete many difficult switchboxes. The router was tested on the MCNC building block circuits. Our results show better chip areas than the best previously published results.
Scrubbers with a level head (1997)

The available methods for removing pollutants from a gas stream are numerous, to say the least. A popular method, scrubbers allow users to separate gases and solids by allowing the gas to come into contact with a liquid stream. In the end, the pollutants are washed away in the effluent, and the gas exits the system to be used in later processes or to be released into the atmosphere. For many years, counter-flow scrubber methods have been used for the lion`s share of the work in industries such as phosphate fertilizer and semiconductor chemicals manufacturing. Now these industries are exploring the use of cross-flow scrubber design, which offers consistently high efficiency and low operating costs. In addition, the unit`s horizontal orientation makes maintenance easier than typical tower scrubbers. For certain classes of unit operations, cross-flow is now being recognized as a strong alternative to conventional counterflow technology.
The development of a segment-based musculoskeletal model of the lower limb: introducing F <scp>ree</scp> B <scp>ody</scp> (2015)

Traditional approaches to the biomechanical analysis of movement are joint-based; that is the mechanics of the body are described in terms of the forces and moments acting at the joints, and that muscular forces are considered to create moments about the joints. We have recently shown that segment-based approaches, where the mechanics of the body are described by considering the effect of the muscle, ligament and joint contact forces on the segments themselves, can also prove insightful. We have also previously described a simultaneous, optimization-based, musculoskeletal model of the lower limb. However, this prior model incorporates both joint- and segment-based assumptions. The purpose of this study was therefore to develop an entirely segment-based model of the lower limb and to compare its performance to our previous work. The segment-based model was used to estimate the muscle forces found during vertical jumping, which were in turn compared with the muscular activations that have been found in vertical jumping, by using a Geers' metric to quantify the magnitude and phase errors. The segment-based model was shown to have a similar ability to estimate muscle forces as a model based upon our previous work. In the future, we will evaluate the ability of the segment-based model to be used to provide results with clinical relevance, and compare its performance to joint-based approaches. The segment-based model described in this article is publicly available as a GUI-based Matlab® application and in the original source code (at www.msksoftware.org.uk).
Digital camera zooming based on unified CFA image processing steps (2004)

A unified camera image processing system that performs zooming and full color image reconstruction for single-sensor digital cameras is introduced. Compact and low-cost single-sensor solutions often lack optical zooming capabilities and thus depend on digital techniques. However, the computational power required for high-quality output using traditional techniques is generally too prohibitive to implement in such devices. The proposed scheme employs a small number of reusable, low-complexity operations and a consistent color model throughout to achieve high-quality zoomed output that is practical for hardware implementation. The high-level system components are color filter array (CFA) zooming, CFA interpolation (demosaicking) and demosaicked image postprocessing. The resulting output is consistently superior to other methods.
Voltage Tunable Radio Frequency Microelectromechanical Resonators And Filters (2009)

Advanced radio technology demands for low power consumption and compact ar-chitecture that operate at the global range of frequency standards. Using discrete components based on traditional surface acoustic wave (SAW) or thin film bulk acoustic resonator (TFBAR) technology to manufacture quad-band and 7-band ra-dios presently requires an enormous number of power-hungry and large-size filters fabricated on different substrates. On the other hand, employment of Micro Elec-tromechanical Systems (MEMS) technology to create radio front-ends facilitates reductions in size, weight, cost, and power in radio communications. Several research groups from academia and industry have recently demon-strated electrostatically and ferroelectrically transduced microelectromechanical resonators and filters that operate at high frequency and exhibit low insertion loss as potential substitutes for conventional quartz and ceramic devices. However, the modern radio architecture today also requires the ability to discern bandwidths be-tween 0.1 MHz and 5 MHz. This requires frequency-agile intermediate-frequency filters, generating a strong demand for narrow-bandwidth channel-select filters
Determination of plasma membrane lipid mass and composition in cultured Chinese hamster ovary cells using high gradient magnetic affinity chromatography (1993)

We have utilized wheat germ agglutinin conjugated to iron/dextran particles in conjunction with high gradient magnetic affinity chromatography (HIMAC) to prepare plasma membranes from cultured cells. Membrane-impermeable succinimidyl esters inactivate alkaline phosphodiesterase 1 (APDE-1) and were used to establish the proportion of APDE-1 expressed at the cell surface. The yield of inhibitable APDE-1 provides an accurate indication of plasma membrane yield, which was > 90% for Chinese hamster ovary (CHO) cells. Plasma membranes prepared by HIMAC contained < 5-13% of endoplasmic reticulum, Golgi, mitochondria, lysosomes, or endosomes. Pulse-chase experiments performed with the alpha 5 beta 1 integrin receptor confirmed the high yield of plasma membrane and demonstrated the utility of this procedure for examining trafficking of proteins to and from the plasma membrane. We determined the lipid content of plasma membranes prepared by HIMAC. CHO plasma membranes contain 49% of total cellular phospholipid, 69% of sphingomyelin, and 64% of cholesterol. Phosphatidylserine was the only glycerophospholipid highly enriched (71%) in the retained fraction. The glycosphingolipids lactosylceramide and ganglioside GM3 were enriched in the plasma membrane fraction to the same extent as sphingomyelin. The major fraction of the glycosphingolipid precursors glucosylceramide and ceramide was localized to intracellular membranes. These findings indicate that the plasma membrane of CHO cells contains approximately half of the total cellular phospholipids and an even higher percentage of sphingomyelin and cholesterol. The high efficiency and rapidity of this isolation procedure should aid the analysis of plasma membrane components significantly.
Unusual Activity Analysis Using Video Epitomes and pLSA (2008)

In this paper, we address the problem of unsupervised learning of usual patterns of activities in an area under surveillance and detecting deviant patterns. We use video epitomes for segmenting foreground objects from background and obtain an approximate shape, trajectory and temporal information in the form of space-time patches. We apply pLSA for finding correlations among these patches to learn usual activities in the scene. We also extend pLSA to classify a novel video as usual or unusual.
CARAT-ARC: a scalable and reliable digital media archiving system (2002)

This paper introduces the CARAT-ARC digital multimedia archiving system. CARAT-ARC is an open system for indexing, storing and searching multimedia documents (audio, video, graphics, text, etc.) It uses a hybrid approach to multimedia indexing and retrieval by combining automatic feature extraction with advanced multimedia browsing and logging tools. The motivation for such a hybrid approach as well as a description of the main parts of the systems are presented.
Mitochondrial Dysfunction Contributes to Oncogene-Induced Senescence (2009)

The expression of oncogenic ras in normal human cells quickly induces an aberrant proliferation response that later is curtailed by a cell cycle arrest known as cellular senescence. Here, we show that cells expressing oncogenic ras display an increase in the mitochondrial mass, the mitochondrial DNA, and the mitochondrial production of reactive oxygen species (ROS) prior to the senescent cell cycle arrest. By the time the cells entered senescence, dysfunctional mitochondria accumulated around the nucleus. The mitochondrial dysfunction was accompanied by oxidative DNA damage, a drop in ATP levels, and the activation of AMPK. The increase in mitochondrial mass and ROS in response to oncogenic ras depended on intact p53 and Rb tumor suppression pathways. In addition, direct interference with mitochondrial functions by inhibiting the expression of the Rieske iron sulfur protein of complex III or the use of pharmacological inhibitors of the electron transport chain and oxidative phosphorylation was sufficient to trigger senescence. Taking these results together, this work suggests that mitochondrial dysfunction is an effector pathway of oncogene-induced senescence.
Rational Synthesis of Covalently Bonded Organic–Inorganic Hybrids (2004)

Hybrid materials based on covalently linked inorganic polyoxometalates (POMs) and organic species containing a delocalized pi system have drawn increasing attention. These hybrids, traditionally prepared by cluster assembly approaches that lack predictability and controllability, can now be synthesized through common organic reactions by using organically functionalized POM clusters as building blocks. This minireview highlights some of the most recent advances on a particular type of hybrids where the organic and inorganic components are connected by an imido linkage.
Hepatocellular Carcinoma (2002)

Hepatocellular carcinoma (HCC) is the fifth most common malignancy in the world and is estimated to cause approximately half a million deaths annually. Because of its high fatality rates, the incidence and mortality rates are almost equal. The major risk factors for HCC are chronic hepatitis B virus infection, chronic hepatitis C virus (HCV) infection, and alcoholic cirrhosis. The epidemiology of HCC is characterized by marked demographic (age, gender, race/ethnicity) and geographic variations. Hepatitis B virus infection, with and without aflatoxin exposure, is responsible for most cases in developing countries; better control of these risk factors has resulted in a recent decline in HCC in some places like Taiwan and China. Recently, however, a trend of rising rates of HCC has been reported from several developed countries in Europe and North America. These new trends are associated with "new" risk factors such as HCV and, possibly, diabetes. In the United States, the incidence of HCC has approximately doubled over the past 3 decades. White individuals are two to three times less often affected than African Americans, who in turn are two to three times less often affected than Asians, Pacific Islanders, or Native Americans. Men are two to three times more often affected than women. Concomitant with the rising rates of HCC, there has been a shift of incidence from typically elderly patients to relatively younger patients between ages of 40 to 60 years. An increase in HCV-related HCC accounts for at least half of the witnessed increase in HCC in the United States. Hepatocellular carcinoma continues to carry an overall dismal survival rate (close to 5%); very few patients qualify for and receive potentially curative therapy. The future incidence trends of HCC will be determined to a large extent by the clinical course of HCV-infected people.
Nasopharyngeal carcinoma: presenting symptoms and duration before diagnosis. (1997)

This is a retrospective analysis of 4768 patients with undifferentiated or non-keratinising carcinoma of the nasopharynx who were treated during 1 January 1976 to 31 December 1985. The mean duration of symptoms before diagnosis was 8 months (range, 1-36 months for 95% of patients). A significant association between the duration of symptoms and the presenting stage was observed (P<0.001); 58% and 39% of stage I and stage V patients, respectively, reported as having had symptoms for less than 6 months. Of the later presenters (those having had symptoms for 6 months or longer), 89% were given a full course of radical megavoltage radiotherapy, but 6% were too advanced for any irradiation attempt. Consequently, the 10-year actuarial disease-specific survival was significantly higher among the early presenters: 48% versus 42% (P<0.001). The importance of early detection is emphasised.
Aerodynamic size distribution of metered-dose bronchodilator aerosols. (1978)

The aerodynamic size distributions of 9 commonly used bronchodilator aerosols were determined by using a new instrument, the single-particle, aerodynamic relaxation time analyzer, which can measure the aerodynamic size of single particles and droplets in real time independent of density, shape, and other physical characteristics. The following commercial preparations were studied: Duo-Medihaler, Medihaler-Epi, Medihaler-Epi Medihaler-Iso, Norisodrine Aerotrol, Alupent, Metaprel, Isuprel Mistometer, Bronkometer, and Asthma-Meter. Count median diameters ranged from 0.62 to 0.82 micrometer, and mass median aerodynamic diameters ranged from 2.8 to 4.3 micrometer. The heterodisperse nature of the aerosols was demonstrated by the relatively large geometric standard deviations, which ranged from 1.5 to 2.1. None of these aerosols had a log-normal distribution; rather, the distribution curves were multimodal.
Antibody–Drug Conjugates: A Comprehensive Review (2019)

Antibody-drug conjugates (ADC) are one of the fastest growing anticancer drugs. This approach comprises a mAb conjugated to the cytotoxic payload via a chemical linker that directed toward a target antigen expressed on the cancer cell surface, reducing systemic exposure and therefore toxicity. ADCs are complex molecules that require careful attention to various components. Selection of an appropriate target, an mAb, cytotoxic payload, and the manner in which the antibody is linked to the payload are key determinants of the safety and efficacy of ADCs. This review provides an overview of the systemic evaluation of each component of an ADC design, improved understanding of the mechanism of action of ADC, and mechanistic pathways involved in ADC resistance and various strategies to optimize ADC design. Moreover, this review also shed light on the current status of ADCs that have gained regulatory approval from the FDA including a description of biology and chemistry, metabolic profiles, adverse events, drug interactions, and the future perspective on combination strategies with other agents, including immunotherapy.
Synthesis of enzymatically active human α‐<scp>l</scp>‐iduronidase in <i>Arabidopsis cgl</i> (complex glycan‐deficient) seeds (2005)

As an initial step to develop plants as systems to produce enzymes for the treatment of lysosomal storage disorders, Arabidopsis thaliana wild-type (Col-0) plants were transformed with a construct to express human alpha-l-iduronidase (IDUA; EC 3.2.1.76) in seeds using the promoter and other regulatory sequences of the Phaseolus vulgaris arcelin 5-I gene. IDUA protein was easily detected on Western blots of extracts from the T(2) seeds, and extracts contained IDUA activity as high as 2.9 nmol 4-methylumbelliferone (4 MU)/min/mg total soluble protein (TSP), corresponding to approximately 0.06 microg IDUA/mg TSP. The purified protein reacted with an antibody specific for xylose-containing plant complex glycans, indicating its transit through the Golgi complex. In an attempt to avoid maturation of the N-linked glycans of IDUA, the same IDUA transgene was introduced into the Arabidopsis cgl background, which is deficient in the activity of N-acetylglucosaminyl transferase I (EC 2.4.1.101), the first enzyme in the pathway of complex glycan biosynthesis. IDUA activity and protein levels were significantly higher in transgenic cgl vs. wild-type seeds (e.g. maximum levels were 820 nmol 4 MU/min/mg TSP, or 18 microg IDUA/mg TSP). Affinity-purified IDUA derived from cgl mutant seeds showed a markedly reduced reaction with the antibody specific for plant complex glycans, despite transit of the protein to the apoplast. Furthermore, gel mobility changes indicated that a greater proportion of its N-linked glycans were susceptible to digestion by Streptomyces endoglycosidase H, as compared to IDUA derived from seeds of wild-type Arabidopsis plants. The combined results indicate that IDUA produced in cgl mutant seeds contains glycans primarily in the high-mannose form. This work clearly supports the viability of using plants for the production of human therapeutics with high-mannose glycans.
DNA repair in human promyelocytic cell line, HL-60 (1987)

The human promyelocytic cell line, HL-60, shows large changes in endogenous poly(ADP-ribose) and in nuclear ADP-ribosyl transferase activity (ADPRT) during its induced myelocytic differentiation. DNA strand-breaks are an essential activator for this enzyme; and transient DNA strand breaks occur during the myelocytic differentiation of HL-60 cells. We have tested the hypothesis that these post-mitotic, terminally differentiating cells are less efficient in DNA repair, and specifically in DNA strand rejoining, than their proliferating precursor cells. We have found that this hypothesis is not tenable. We observe that there is no detectable reduction in the efficiency of DNA excision repair after exposure to either dimethyl sulphate or gamma-irradiation in HL-60 cells induced to differentiate by dimethyl sulphoxide. Moreover, the efficient excision repair of either dimethyl sulphate or gamma-irradiation induced lesions, both in the differentiated and undifferentiated HL-60 cells, is blocked by the inhibition of ADPRT activity.
Nanoscale sub-100 picosecond all-optical magnetization switching in GdFeCo microstructures (2015)

Ultrafast magnetization reversal driven by femtosecond laser pulses has been shown to be a promising way to write information. Seeking to improve the recording density has raised intriguing fundamental questions about the feasibility of combining ultrafast temporal resolution with sub-wavelength spatial resolution for magnetic recording. Here we report on the experimental demonstration of nanoscale sub-100 ps all-optical magnetization switching, providing a path to sub-wavelength magnetic recording. Using computational methods, we reveal the feasibility of nanoscale magnetic switching even for an unfocused laser pulse. This effect is achieved by structuring the sample such that the laser pulse, via both refraction and interference, focuses onto a localized region of the structure, the position of which can be controlled by the structural design. Time-resolved photo-emission electron microscopy studies reveal that nanoscale magnetic switching employing such focusing can be pushed to the sub-100 ps regime.
Mesenchymal Stem Cell Paracrine Factors in Vascular Repair and Regeneration (2014)

Mesenchymal stem cell therapy show great optimism in the treatment of several diseases. MSCs are attractive candidates for cell therapy because of easy isolation, high expansion potential giving unlimited pool of transplantable cells, low immunogenicity, amenability to ex vivo genetic modification, and multipotency. The stem cells orchestrate the repair process by various mechanisms such as transdifferentiation, cell fusion, microvesicles or exosomes and most importantly by secreting paracrine factors. The MSCs release several angiogenic, mitogenic, anti-apoptotic, anti-inflammatory and anti-oxidative factors that play fundamental role in regulating tissue repair in various vascular and cardiac diseases. The therapeutic release of these factors by the cells can be enhanced by several strategies like genetic modification, physiological and pharmacological preconditioning, improved cell culture and selection methods, and biomaterial based approaches. The current review describes the impact of paracrine factors released by MSCs on vascular repair and regeneration in myocardial infarction, restenosis and peripheral artery disease, and the various strategies adopted to enhance the release of these paracrine factors to enhance organ function.
Autologous transplantation of peripheral blood endothelial progenitor cells (CD34+) for therapeutic angiogenesis in patients with critical limb ischemia. (2003)

Satisfactory clinical improvement was achieved by using peripheral blood EPCs (CD34(+)) in the patients with CLI. No complications arose following the intramuscular administration of peripheral blood CD34(+) cells.
Automatic Discovery and Execution of Personal Applications from Shared IO Devices (2010)

Shared office information appliances such as copiers, scanners and meeting-room displays are increasingly being integrated into complex electronic document workflows. To support this new role these appliances are being designed with advanced features such as optical character recognition, networked storage, content-based routing and integration with back-end databases, yet availability of these features is often hampered by various factors. Here we present an architecture, code named Odessa, that moves all task-specific processing off the office appliance and on to a user's own device: PC / laptop, or smartphone. Key features of the architecture include a simple RESTful HTTP application interface and automatic service discovery.