gebhart/patrepeval huggingface dataset:
Direct real-time detection of the actin-activated power stroke within the myosin catalytic domain (2013)

We have used transient kinetics, nanosecond time-resolved fluorescence resonance energy transfer (FRET), and kinetics simulations to resolve a structural transition in the Dictyostelium myosin II relay helix during the actin-activated power stroke. The relay helix plays a critical role in force generation in myosin, coupling biochemical changes in the ATPase site with the force-transducing rotation of the myosin light-chain domain. Previous research in the absence of actin showed that ATP binding to myosin induces a dynamic equilibrium between a bent prepower stroke state of the relay helix and a straight postpower stroke state, which dominates in the absence of ATP or when ADP is bound. We now ask whether actin binding reverses this transition and if so, how this reversal is coordinated with actin-activated phosphate release. We labeled a Cys-lite Dictyostelium myosin II motor domain with donor and acceptor probes at two engineered Cys residues designed to detect relay helix bending. We then performed transient time-resolved FRET following stopped-flow mixing of actin with labeled myosin, preincubated with ATP. We determined the kinetics of actin-activated phosphate release, using fluorescent phosphate-binding protein. The results show that actin binding to the myosin.ADP.P complex straightens the relay helix before phosphate dissociation. This actin-activated relay helix straightening is reversible, but phosphate irreversibly dissociates from the postpower stroke state, preventing reversal of the power stroke. Thus, relay helix straightening gates phosphate dissociation, whereas phosphate dissociation provides the thermodynamic driving force underlying force production.
Autophagy Protects the Retina from Light-induced Degeneration (2013)

Autophagy is a conserved feature of lysosome-mediated intracellular degradation. Dysregulated autophagy is implicated as a contributor in neurodegenerative diseases; however, the role of autophagy in retinal degeneration remains largely unknown. Here, we report that the photo-activated visual chromophore, all-trans-retinal, modulated autophagosome formation in ARPE19 retinal cells. Increased formation of autophagosomes in these cells was observed when incubated with 2.5 μM all-trans-retinal, a condition that did not cause cell death after 24 h in culture. However, autophagosome formation was decreased at concentrations, which caused cell death. Increased expression of activating transcription factor 4 (Atf4), which indicates the activation of oxidative stress, was recorded in response to light illumination in retinas of Abca4(-/-)Rdh8(-/-) mice, which showed delayed clearance of all-trans-retinal after light exposure. Expression of autophagosome marker LC3B-II and mitochondria-specific autophagy, mitophagy, regulator Park2, were significantly increased in the retinas of Abca4(-/-)Rdh8(-/-) mice after light exposure, suggesting involvement of autophagy and mitophagy in the pathogenesis of light-induced retinal degeneration. Deletion of essential genes required for autophagy, including Beclin1 systemically or Atg7 in only rod photoreceptors resulted in increased susceptibility to light-induced retinal damage. Increased photoreceptor cell death was observed when retinas lacking the rod photoreceptor-specific Atg7 gene were coincubated with 20 μM all-trans-retinal. Park2(-/-) mice also displayed light-induced retinal degeneration. Ultra-structural analyses showed mitochondrial and endoplasmic reticulum impairment in retinas of these model animals after light exposure. Taken together, these observations provide novel evidence implicating an important role of autophagy and mitophagy in protecting the retina from all-trans-retinal- and light-induced degeneration.
The human acrosome reaction. (2000)

We developed tests of sperm-oocyte interaction: sperm-zona binding, zona-induced acrosome reaction, spermzona penetration and sperm-oolemma binding, using oocytes which failed to fertilise in clinical in vitro fertilization (IVF). Although oocyte defects contribute to failure of sperm oocyte interaction, rarely are all oocytes from one woman affected. Low or zero fertilization in standard IVF was usually caused by sperm abnormalities. Poor sperm-zona pellucida binding was frequently associated with failure of standard IVF and obvious defects of sperm motility or morphology. The size and shape of the acrosome is particularly important for sperm binding to the oocyte. The proportion of acrosome intact sperm in the insemination medium was related to the IVF rate. Inducing the acrosome reaction with a calcium ionophore reduced sperm-zona binding. Blocking acrosome dispersal with an acrosin inhibitor prevented spermzona penetration. Sperm-zona penetration was even more highly related to IVF rates than was sperm-zona binding. Some patients had low or zero fertilization rates with standard IVF but normal sperm by conventional tests and normal sperm-zona binding. Few of their sperm underwent the acrosome reaction on the surface of the zona and none penetrated the zona. In contrast, fertilization and pregnancy rates were high with intracytoplasmic sperm injection. We call this condition defective zona pellucida induced acrosome reaction. Discovery of the nature of the abnormalities in the signal transduction and effector pathways of the human zona pellucida induced acrosome reaction should result in simpler tests and treatments for the patients and also provide new leads for contraceptive development.
Infrared Spectra of Substituted Phenanthrolines in the Out-of-plane CH Deformation Region (1962)

Detailed interpretation of vibrational spectra is impossible for complex molecules but information of value may be obtained from an empirical study of the spectra of series of related substances.The dependence of band pattern on molecular substitution has been demonstrated for several regions in the infrared spectra of aromatic compounds, for example, the out-of-plane CH deformation region, 900-650 cm-l.
Leukemia Inhibitory Factor, Oncostatin M, IL-6, and Stem Cell Factor mRNA Expression in Human Thymus Increases with Age and Is Associated with Thymic Atrophy (2000)

The roles that thymus cytokines might play in regulating thymic atrophy are not known. Reversing thymic atrophy is important for immune reconstitution in adults. We have studied cytokine mRNA steady-state levels in 45 normal human (aged 3 days to 78 years) and 34 myasthenia gravis thymuses (aged 4 to 75 years) during aging, and correlated cytokine mRNA levels with thymic signal joint (sj) TCR delta excision circle (TREC) levels, a molecular marker for active thymopoiesis. LIF, oncostatin M (OSM), IL-6, M-CSF, and stem cell factor (SCF) mRNA were elevated in normal and myasthenia gravis-aged thymuses, and correlated with decreased levels of thymopoiesis, as determined by either decreased keratin-positive thymic epithelial space or decreased thymic sjTRECs. IL-7 is a key cytokine required during the early stages of thymocyte development. Interestingly, IL-7 mRNA expression did not fall with aging in either normal or myasthenia gravis thymuses. In vivo administration of LIF, OSM, IL-6, or SCF, but not M-CSF, i.p. to mice over 3 days induced thymic atrophy with loss of CD4+, CD8+ cortical thymocytes. Taken together, these data suggest a role for thymic cytokines in the process of thymic atrophy.
Carbon Overcoat Oxidation in Heat-Assisted Magnetic Recording (2013)

Due to the ever increasing demand for higher storage capacity in disk drives, novel techniques to read and write information, such as heat-assisted magnetic recording are being developed. However, the recording temperatures impact not only the media but also the carbon overcoat that is used to protect both the media and writing head. In this paper, we discuss the effect of thermal annealing on the rate of carbon erosion on overcoats deposited using two different techniques, viz. filtered-cathodic arc and plasma-enhanced chemical vapor deposition.
Developing the Blacksburg electronic village (1996)

article Free Access Share on Developing the Blacksburg electronic village Authors: John M. Carroll Department of Computer Science, Virginia Tech., Blacksburg, Va. Department of Computer Science, Virginia Tech., Blacksburg, Va.View Profile , Mary Beth Rosson Department of Computer Science, Virginia Tech. Department of Computer Science, Virginia Tech.Search about this author Authors Info & Claims Communications of the ACMVolume 39Issue 12Dec. 1996pp 69–74https://doi.org/10.1145/240483.240498Published:01 December 1996Publication History 135citation1,068DownloadsMetricsTotal Citations135Total Downloads1,068Last 12 Months112Last 6 weeks13 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
TRAIL signals to apoptosis in chronic lymphocytic leukaemia cells primarily through TRAIL‐R1 whereas cross‐linked agonistic TRAIL‐R2 antibodies facilitate signalling via TRAIL‐R2 (2007)

Tumour necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL), a member of the TNF family, which is being developed as an anti-tumour agent due to its selective toxicity to tumour cells, induces apoptosis by binding to two membrane-bound receptors, TRAIL-R1 and TRAIL-R2. Clinical trials have been initiated with various preparations of TRAIL as well as agonistic monoclonal antibodies to TRAIL-R1 and TRAIL-R2. Previously we reported that prior treatment of primary chronic lymphocytic leukaemia (CLL) cells with histone deacetylase inhibitors was required to sensitize CLL cells to TRAIL and, using various receptor-selective TRAIL mutant ligands, we demonstrated that CLL cells signalled to apoptosis primarily through TRAIL-R1. Some, but not all, agonistic TRAIL-receptor antibodies require cross-linking in order to induce apoptosis. The present study demonstrated that CLL cells can signal to apoptosis through the TRAIL-R2 receptor, but only after cross-linking of the agonistic TRAIL-R2 antibodies, LBY135 and lexatumumab (HGS-ETR2). In contrast, signalling through TRAIL-R1 by receptor-selective ligands or certain agonistic antibodies, such as mapatumumab (HGS-ETR1), occurs in the absence of cross-linking. These results further highlight important differences in apoptotic signalling triggered through TRAIL-R1 and TRAIL-R2 in primary tumour cells. Such information is clearly important for the rational optimisation of TRAIL therapy in primary lymphoid malignancies, such as CLL.
Microfluidic Synthesis of Highly Potent Limit-size Lipid Nanoparticles for In Vivo Delivery of siRNA (2012)

Lipid nanoparticles (LNP) are the leading systems for in vivo delivery of small interfering RNA (siRNA) for therapeutic applications. Formulation of LNP siRNA systems requires rapid mixing of solutions containing cationic lipid with solutions containing siRNA. Current formulation procedures employ macroscopic mixing processes to produce systems 70-nm diameter or larger that have variable siRNA encapsulation efficiency, homogeneity, and reproducibility. Here, we show that microfluidic mixing techniques, which permit millisecond mixing at the nanoliter scale, can reproducibly generate limit size LNP siRNA systems 20 nm and larger with essentially complete encapsulation of siRNA over a wide range of conditions with polydispersity indexes as low as 0.02. Optimized LNP siRNA systems produced by microfluidic mixing achieved 50% target gene silencing in hepatocytes at a dose level of 10 µg/kg siRNA in mice. We anticipate that microfluidic mixing, a precisely controlled and readily scalable technique, will become the preferred method for formulation of LNP siRNA delivery systems.
Effects of acceptor composition and mechanism of ABCG1-mediated cellular free cholesterol efflux (2008)

Among the known mechanisms of reverse cholesterol transport (RCT), ATP binding cassette transporter G1 (ABCG1)-mediated free cholesterol (FC) transport is the most recent and least studied. Here, we have characterized the efficiencies of different acceptors using baby hamster kidney (BHK) cells transfected with human ABCG1 cDNA, which is inducible upon treatment with mifepristone. When normalized on particle number and particle surface area, the acceptor efficiency for FC efflux was as follows: small unilamellar vesicles (SUV)>LDL>reconstituted HDL>HDL(2) = HDL(3). Based on phospholipid content, the order was reversed. ABCG1 also mediated phospholipid efflux to human serum and HDL(3). ABCG1-mediated FC efflux correlated significantly with a number of HDL subfractions and components in serum collected from 25 normolipidemic individuals: apolipoprotein A-II (apoA-II) (r(2) = 0.7), apolipoprotein A-I (apoA-I) (r(2) = 0.5), HDL-C (r(2) = 0.4), HDL-PL (r(2) = 0.4), alpha-2 HDL (r(2) = 0.4), and prebeta HDL (r(2) = 0.2). ABCG1 did not enhance influx of FC or cholesteryl oleyl ether (COE) when cells were incubated with radiolabeled HDL(3). ABCG1 expression did not increase the association of HDL(3) with cells. Compared with control cells, ABCG1 expression significantly increased the FC pool available for efflux and the rate constant for efflux. In conclusion, composition and particle size determine the acceptor efficiency for ABCG1-mediated efflux. ABCG1 increases cell membrane FC pools and changes its rate of desorption into the aqueous phase without enhancing the association with the acceptor.
Real time obstacle detection in stereovision on non flat road geometry through "v-disparity" representation (2003)

Presents a road obstacle detection method able to cope with uphill and downhill gradients and dynamic pitching of the vehicle. Our approach is based on the construction and investigation of the "v-disparity" image which provides a good representation of the geometric content of the road scene. The advantage of this image is that it provides semi-global matching and is able to perform robust obstacle detection even in the case of partial occlusion or errors committed during the matching process. Furthermore, this detection is performed without any explicit extraction of coherent structures. This paper explains the construction of the "v-disparity" image, its main properties, and the obstacle detection method. The longitudinal profile of the road is estimated and the objects located above the road surface are then extracted as potential obstacles; subsequently, the accurate detection of road obstacles, in particular the position of tyre-road contact points is computed in a precise manner. The whole process is performed at frame rate with a current-day PC. Our experimental findings and comparisons with the results obtained using a flat geometry hypothesis show the benefits of our approach.
Microalgal oil extraction and in situ transesterification (2007)

Oil extraction from microalgae is an important process for lab analysis, the nutraceutical industry, and it will be important to growing field of algal biofuels. In this thesis, six strains of high-oil microalgae were screened for neutral lipid content and ease of culturing. One of these six, Chlorella sp., was cultured under various growth conditions to determine the settings to produce both the most cells and the highest neutral lipid content per cell. With this information, Chlorella sp. was cultured in large batches to produce sizable harvest quantities (10's of grams dry cells). During large scale culturing, cell concentration data, fluorometric (neutral lipid content) data, and pH data were collected to provide more information about the culture growth behavior and to properly time harvests. Harvested cells were centrifuged and freeze-dried for solvent extraction and in situ biodiesel production experiments. From freeze-dried cells, the total lipid mass was determined gravimetrically to be 8-10% of the dry mass, based on the solvent extraction method of Bligh and Dyer (1959). Solvent extracted lipids were derivatized to Fatty Acid Methyl Esters (FAMEs) using methanol and a base catalyst (potassium hydroxide). In situ FAME production was accomplished by adding a methanol/potassium hydroxide solution directly to freeze-dried cells and treating with high-power ultrasonication. Methanol amount, potassium hydroxide concentration, and ultrasonication time and power, were all examined for their effect on FAME production. Analysis of both solvent extraction produced FAMEs and in situ produced FAMEs was accomplished with a gas chromatograph equipped with a special FAME analysis capillary column and a Flame Ionization Detector. Pure FAME reference standards and an internal standard were used to help identify chromatographic data. For the freeze-dried cells used, the in situ FAME production was able to produce 150% of the FAMEs identified from solvent extracted lipid samples.
Selective rescue of early haematopoietic progenitors inScl–/– mice by expressingSclunder the control of a stem cell enhancer (2001)

The stem cell leukaemia gene (Scl) encodes a basic helix-loop-helix transcription factor with a pivotal role in both haematopoiesis and endothelial development. During mouse development, Scl is first expressed in extra-embryonic mesoderm, and is required for the generation of all haematopoietic lineages and normal yolk sac angiogenesis. Ectopic expression of Scl during zebrafish development specifies haemangioblast formation from early mesoderm. These results suggest that SCL is essential for establishing the transcriptional programme responsible for the formation of haematopoietic stem cells and have focused attention on the transcriptional regulation of Scl itself. Previous studies have identified a panel of Scl enhancers each of which directed expression to a subdomain of the normal Scl expression pattern. Among them, a 3' enhancer directed expression during development to vascular endothelium and haematopoietic progenitors but not to Ter119(+) erythroid cells. The expression in haematopoietic stem cells, however, remained undetermined. We demonstrate that this 3' enhancer directs lacZ expression in transgenic mice to most foetal and adult long-term repopulating haematopoietic stem cells, and therefore functions as a stem cell enhancer. Consistent with these results, expression in Scl(-/-) embryos of exogenous Scl driven by the stem cell enhancer rescued the formation of early haematopoietic progenitors and also resulted in normal yolk sac angiogenesis. By contrast, erythropoiesis remained markedly deficient in rescued embryos. This observation is consistent with the inactivity of the stem cell enhancer in erythroid cells and reveals an essential role for SCL during erythroid differentiation in vivo.
Dengue fever and dengue haemorrhagic fever: challenges of controlling an enemy still at large (2001)

Dengue virus infections are a serious cause of morbidity and mortality in most tropical and subtropical areas of the world: mainly Southeast and South Asia, Central and South America, and the Caribbean. Understanding the pathogenesis of dengue haemorrhagic fever (DHF), the severe form of dengue illness, is a very important and challenging research subject. Viral virulence and immune responses have been considered as two major factors responsible for the pathogenesis. Virological studies are attempting to define the molecular basis of viral virulence. The immunopathological mechanisms appear to include a complex series of immune responses. A rapid increase in the levels of cytokines and chemical mediators apparently plays a key role in inducing plasma leakage, shock and haemorrhagic manifestations. It is likely that the entire process is initiated by infection with a so-called virulent dengue virus, often with the help of enhancing antibodies in secondary infection, and then triggered by rapidly elevated cytokines and chemical mediators produced by intense immune activation. However, understanding of the DHF pathogenesis is not complete. We still have a long way to go.
A bacterial peptide acting as a plant nuclear targeting signal: the amino-terminal portion of Agrobacterium VirD2 protein directs a beta-galactosidase fusion protein into tobacco nuclei. (1990)

Agrobacterium tumefaciens is a soil bacterium capable of transferring DNA to the genome of higher plants. Of the virulence region-encoded proteins of the tumor-inducing (Ti) plasmid of A. tumefaciens, the VirD1 and VirD2 proteins are essential for T-DNA transfer to plant cells. These two proteins have been shown to be directly responsible for the formation of T-strands. VirD2 was also shown to be firmly attached to the 5' termini of T-strands; these facts have led to its postulation as a pilot protein in the T-DNA transfer process and as a nucleus-targeting signal in plants. We have constructed a chimeric gene by fusing the virD2 gene and the Escherichia coli lacZ gene. Cell fractionation and electron microscopy studies with transgenic tobacco plants containing the VirD2-LacZ fusion protein indicate that the first 292 amino acids of VirD2 are able to direct the cytoplasmic protein beta-galactosidase to the plant nucleus. This provides an example of cross-kingdom nuclear localization between two free-living organisms: a bacterial peptide is capable of acting as a eukaryotic (plant) nuclear targeting signal.
Expression of the IAP protein family acts cooperatively to predict prognosis in human bladder cancer patients (2013)

The inhibitors of apoptosis (IAPs) are a group of anti-apoptotic factors in the apoptotic pathway that render cancer cells insensitive to apoptotic stimulation. Recently, several members of the IAP family have been investigated in the context of bladder cancer, and some of these have been associated with specific clinical and pathological tumor features, and with prognosis. These data suggested that the expression of an individual nuclear IAP has an important relationship with the progression of bladder cancer. To date, there are no studies concerning the overall tendencies of IAPs and their comparative therapeutic values in bladder cancer. In this study, we investigated the overall expression trends of the five tumor-related proteins, Survivin, cIAP1, cIAP2, XIAP and Livin, in normal bladder tissues and bladder cancer tissues. We classified and compared the gene expression data of these IAPs with the corresponding clinical and pathological tumor features, and with prognosis, in the development and progression of bladder cancer. The differences in IAP expression levels between archival bladder specimens from 36 normal controls and 105 patients who underwent surgery at our facility were examined using western blot analysis. The localization and expression level of each protein in low- and high-grade bladder cancer tissues were examined through immunohistochemistry. The cytoplasmic expression levels of each protein were scored as 0 (negative), +1 (weak), +2 (medium) or +3 (strong). The nuclear expression levels of cIAP1 and Survivin were scored as 0 (0%), +1 (1-25%), +2 (26-50%) or +3 (>50%). The results demonstrated that the expression of IAPs acted cooperatively to predict prognosis in human bladder cancer patients.