gebhart/patrepeval huggingface dataset:
Optimized RNA Targets of Two Closely Related Triple KH Domain Proteins, Heterogeneous Nuclear Ribonucleoprotein K and αCP-2KL, Suggest Distinct Modes of RNA Recognition (2001)

The KH domain mediates RNA binding in a wide range of proteins. Here we investigate the RNA-binding properties of two abundant RNA-binding proteins, alphaCP-2KL and heterogeneous nuclear ribonucleoprotein (hnRNP) K. These proteins constitute the major poly(C) binding activity in mammalian cells, are closely related on the basis of the structures and positioning of their respective triplicated KH domains, and have been implicated in a variety of post-transcriptional controls. By using SELEX, we have obtained sets of high affinity RNA targets for both proteins. The primary and secondary structures necessary for optimal protein binding were inferred in each case from SELEX RNA sequence comparisons and confirmed by mutagenesis and structural mapping. The target sites for alphaCP-2KL and hnRNP K were both enriched for cytosine bases and were presented in a single-stranded conformation. In contrast to these shared characteristics, the optimal target sequence for hnRNP K is composed of a single short "C-patch" compatible with recognition by a single KH domain whereas that for alphaCP-2KL encompassed three such C-patches suggesting more extensive interactions. The binding specificities of the respective SELEX RNAs were confirmed by testing their interactions with native proteins in cell extracts, and the importance of the secondary structure in establishing an optimized alphaCP-2KL-binding site was supported by comparison of SELEX target structure with that of the native human alpha-globin 3'-untranslated region. These data indicate that modes of macromolecular interactions of arrayed KH domains can differ even among closely related KH proteins and that binding affinities are substantially dependent on the presentation of the target site within the RNA secondary structure.
Novel double-ring optical-guided-wave Vernier resonator (1997)

A theoretical study of a novel optical-guided-wave Vernier resonator is presented. The resonator is a compound configuration of two triple-coupler ring-based resonators (CTCRR) with different radii. Transmittance characteristics of the CTCRR are derived by using a combination of transfer-matrix and chain-matrix formulations. The dependence of the transmittance characteristics of the CTCRR on the amplitude-coupling ratios of the directional couplers are studied, and optimum design relationships are determined. An extensive comparison between the CTCRR and two double-ring-resonator (DRR) configurations reported in the literature is carried out. It is shown that the CTCRR features double free spectral range (FSR), higher transmission at resonance, and better crosstalk than DRRs with the same radii of curvature, waveguide propagation loss and finesse. These advantages make the CTCRR particularly attractive for those applications, such as frequency-selective filtering in high-density multichannel optical FDM systems, where conflicting requirements of wide FSR and low insertion loss have to be satisfied.
Studies on the constituents of Xanthoceras sorbifolia Bunge. IV. Structures of the minor prosapogenins. (1985)

The prosapogenins from the partial hydrolysate of fruit saponin of Xanthoceras sorbifolia BUNGE (Sapindaceae) were examined. On the basis of chemical and spectral analyses, compound G was identified as protoaescigenin (1). Two new prosapogenins were characterized as 16-O-acetyl-21-O-(3', 4'-di-O-angeloyl)-β-D-fucopyranosylprotoaescigenin (5) and 22-O-acetyl-21-O-(3', 4'-di-O-angeloyl)-β-D-fucopyranosylprotoaescigenin 3-O-β-D-glucuronopyranoside (7).
On the Capacity Achieving Covariance Matrix for Frequency Selective MIMO Channels Using the Asymptotic Approach (2011)

In this contribution, an algorithm for evaluating the capacity-achieving input covariance matrices for frequency selective Rayleigh MIMO channels is proposed. In contrast with the flat fading Rayleigh case, no closed-form expressions for the eigenvectors of the optimum input covariance matrix are available. Classically, both the eigenvectors and eigenvalues are computed numerically and the corresponding optimization algorithms remain computationally very demanding. In this paper, it is proposed to optimize (w.r.t. the input covariance matrix) a large system approximation of the average mutual information derived by Moustakas and Simon. The validity of this asymptotic approximation is clarified thanks to Gaussian large random matrices methods. It is shown that the approximation is a strictly concave function of the input covariance matrix and that the average mutual information evaluated at the argmax of the approximation is equal to the capacity of the channel up to a <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">O</i> ( <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> / <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">t</sub> ) term, where <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">t</i> is the number of transmit antennas. An algorithm based on an iterative waterfilling scheme is proposed to maximize the average mutual information approximation, and its convergence studied. Numerical simulation results show that, even for a moderate number of transmit and receive antennas, the new approach provides the same results as direct maximization approaches of the average mutual information.
Herpes Simplex Virus Vectors for the Nervous System (2001)

Herpes simplex virus type 1 (HSV1) has a number of properties which could potentially be exploited in the development of vectors for the delivery of genes to the nervous system. These include a natural tropism for neurons, a large viral genome allowing the insertion of multiple exogenous genes, and the ability to establish asymptomatic life-long latent infections. Despite these inherent advantages, the development of HSV vectors successfully exploiting all these properties has been problematical. This has mainly been due to either vector toxicity or an inability to maintain transgene expression in the long term. Recent progress towards overcoming these problems and several applications of the technology are discussed.
Structure-Based Thermodynamic Analysis of a Coupled Metal Binding−Protein Folding Reaction Involving a Zinc Finger Peptide (2002)

The thermodynamics of metal binding by the prototypical Cys(2)His(2) zinc finger peptide CP-1 has been examined through the use of isothermal titration calorimetry. In cholamine buffer at pH 7.0, the binding of zinc(II) to CP-1 shows an enthalpy change of DeltaH degrees (obs) = -33.7 +/- 0.8 kcal/mol. Between one and two protons appear to be released accompanying the metal binding process. The heat of protonation of the cholamine buffer used is quite large (-11.5 kcal/mol), indicating that a portion of the observed metal binding enthalpy is due to buffer protonation. Structure-based thermodynamic analysis including the effect of water release from zinc(II) appears to account for the entropy associated with the coupled metal binding-protein folding process semiquantitatively. The strongest driving force for the reaction is the enthalpy associated with the four bonds from zinc(II) to cysteinate and histidine residues, compared with the bonds from zinc(II) to water. The binding of cobalt(II) to CP-1 is less enthalpically driven than the binding of zinc(II) by -7.6 kcal/mol. This value is approximately equal to, but slightly larger than, the expectation based on considerations of ligand field stabilization energy.
A hydroxylapatite micromethod for measuring estrogen receptor in human breast cancer. (1978)

A novel Quantum Dot monolithically integrated 1×8 switch is shown to provide robust routing of data at 10Gb/s modulation rates. Two cascaded switches providing, 1×64 functionality, operate with a power penalty of only 0.9dB.
Recombinant Adenovirus Serotype 26 (Ad26) and Ad35 Vaccine Vectors Bypass Immunity to Ad5 and Protect Nonhuman Primates against Ebolavirus Challenge (2011)

The use of adenoviruses (Ad) as vaccine vectors against a variety of pathogens has demonstrated their capacity to elicit strong antibody and cell-mediated immune responses. Adenovirus serotype C vectors, such as Ad serotype 5 (Ad5), expressing Ebolavirus (EBOV) glycoprotein (GP), protect completely after a single inoculation at a dose of 10(10) viral particles. However, the clinical application of a vaccine based on Ad5 vectors may be hampered, since impairment of Ad5 vaccine efficacy has been demonstrated for humans and nonhuman primates with high levels of preexisting immunity to the vector. Ad26 and Ad35 segregate genetically from Ad5 and exhibit lower seroprevalence in humans, making them attractive vaccine vector alternatives. In the series of studies presented, we show that Ad26 and Ad35 vectors generate robust antigen-specific cell-mediated and humoral immune responses against EBOV GP and that Ad5 immune status does not affect the generation of GP-specific immune responses by these vaccines. We demonstrate partial protection against EBOV by a single-shot Ad26 vaccine and complete protection when this vaccine is boosted by Ad35 1 month later. Increases in efficacy are paralleled by substantial increases in T- and B-cell responses to EBOV GP. These results suggest that Ad26 and Ad35 vectors warrant further development as candidate vaccines for EBOV.
Lean and mean: network coding for commercial devices (2013)

With its ability to reduce the number of transmissions in lossy networks as well as its potential to simplify the design and required signaling of communication protocols, network coding has emerged as an attractive solution to harness the power of wireless and cooperative networks in order to provide higher throughput and lower energy expenditure. This article shows that network coding's complexity is not an issue for current mobile devices even without hardware acceleration. We provide real-life measurements of energy savings gains of two design styles of network coding, namely, inter- and intra-session network coding using commercial platforms, including Open-Mesh routers and various mobile phones. We demonstrate that the energy per bit invested in coding/decoding operations can be several orders of magnitude smaller than that used for transmission/reception, while also maintaining processing speeds as high as several hundreds of Mb/s or even several Gb/s depending on the device and coding configuration used.
Vaccination of recurrent glioma patients with tumour lysate-pulsed dendritic cells elicits immune responses: results of a clinical phase I/II trial (2003)

In this Phase I/II trial, the patient's peripheral blood dendritic cells were pulsed with an autologous tumour lysate of the glioma. Seven patients with glioblastoma and three patients with anaplastic glioma, ranging in age from 20 to 69 years, participated in this study. The mean numbers of vaccinations of tumour lysate-pulsed dendritic cells were 3.7 times intradermally close to a cervical lymph node, and 3.2 times intratumorally via an Ommaya reservoir. The percentage of CD56-positive cells in the peripheral blood lymphocytes increased after immunisation. There were two minor responses and four no-change cases evaluated by radiological findings. Dendritic cell vaccination elicited T-cell-mediated antitumour activity, as evaluated by the ELISPOT assay after vaccination in two of five tested patients. Three patients showed delayed-type hypersensitivity reactivity to the autologous tumour lysate, two of these had a minor clinical response, and two had an increased ELISPOT result. Intratumoral CD4+ and CD8+ T-cell infiltration was detected in two patients who underwent reoperation after vaccination. This study demonstrated the safety and antitumour effects of autologous tumour lysate-pulsed dendritic cell therapy for patients with malignant glioma.
The Transcriptional Repressor ZEB1 Promotes Metastasis and Loss of Cell Polarity in Cancer (2008)

Invasion and metastasis are the hallmarks of malignant tumor progression and the main cause of death in cancer. The embryonic program "epithelial-mesenchymal transition" (EMT) is thought to trigger invasion by allowing tumor cell dissemination. Here, we describe that the EMT-inducing transcriptional repressor ZEB1 promotes colorectal cancer cell metastasis and loss of cell polarity. Thereby, ZEB1 suppresses the expression of cell polarity factors, in particular of Lgl2, which we found reduced in colorectal and breast cancers. We further show that retention of Lgl2 expression is critical for the epithelial phenotype and that its loss might be involved in metastasis. Thus, by linking EMT, loss of polarity, and metastasis, ZEB1 is a crucial promoter of malignant tumor progression.
THE RENAL HANDLING OF HEMOGLOBIN (1969)

The glomerular filtration of hemoglobin (α2ß2) was studied under conditions in which its dissociation into αß dimers was experimentally altered. Rats receiving hemoglobin treated with the sulfhydryl reagent bis(N-maleimidomethyl) ether (BME) showed a much lower renal excretion and prolonged plasma survival as compared with animals injected with untreated hemoglobin. Plasma disappearance was also prolonged in dogs receiving BME hemoglobin. Gel filtration data indicated that under physiological conditions, BME hemoglobin had impaired subunit dissociation. In addition, BME hemoglobin showed a very high oxygen affinity and a decreased rate of auto-oxidation. Glomerular filtration was enhanced under conditions which favor the dissociation of hemoglobin into dimers. Cat hemoglobin, which forms subunits much more extensively than canine hemoglobin, was excreted more readily by the rat kidney. The renal uptake of 59Fe hemoglobin injected intra-arterially into rabbits varied inversely with the concentration of the injected dose.
Structural basis for Rab11-dependent membrane recruitment of a family of Rab11-interacting protein 3 (FIP3)/Arfophilin-1 (2006)

Family of Rab11-interacting protein (FIP)3/Arfophlin-1 and FIP4/Arfophilin-2 are dual effectors for Rab11 and ADP ribosylation factor (ARF)5/ARF6, which are involved in membrane delivery from recycling endosomes to the plasma membrane during cytokinesis. Here, we define the distinct C-terminal binding regions of FIP3 and FIP4 for Rab11 and ARF5/ARF6. Furthermore, we determined the crystal structure of Rab11 in complex with the Rab11-binding domain (RBD) of FIP3. The long amphiphilic alpha-helix of FIP3-RBD forms a parallel coiled-coil homodimer, with two symmetric interfaces with two Rab11 molecules. The hydrophobic side of the RBD helix is involved in homodimerization and mediates the interaction with the Rab11 switch 1 region, whereas the opposite hydrophilic side interacts with the Rab11 switch 2 and is the major factor contributing to the binding specificity. The bivalent interaction of FIP3 with Rab11 at the C terminus allows FIP3 to coordinately function with other binding partners, including ARFs.
Parenteral nutrition in patients with renal failure – Guidelines on Parenteral Nutrition, Chapter 17 (2009)

Partial EN (enteral nutrition) should always be aimed for in patients with renal failure that require nutritional support. Nevertheless PN (parenteral nutrition) may be necessary in renal failure in patient groups with acute or chronic renal failure (ARF or CRF) and additional acute diseases but without extracorporeal renal replacement therapy, or in patients with ARF or CRF with additional acute diseases on extracorporeal renal replacement therapy, haemodialysis therapy (HD), peritoneal dialysis (PD) or continuous renal replacement therapy (CRRT), or in patients on HD therapy with intradialytic PN. Patients with renal failure who show marked metabolic derangements and changes in nutritional requirements require the use of specifically adapted nutrient solutions. The substrate requirements of acutely ill, non-hypercatabolic patients with CRF correspond to those of patients with ARF who are not receiving any renal replacement patients therapy (utilisation of the administered nutrients has to be monitored carefully). In ARF patients and acutely ill CRF patients on renal replacement therapy, substrate requirements depend on disease severity, type and extent/frequency of extracorporeal renal replacement therapy, nutritional status, underlying disease and complications occurring during the course of the disease. Patients under HD have a higher risk of developing malnutrition. Intradialytic PN (IDPN) should be used if causes of malnutrition cannot be eliminated and other interventions fail. IDPN should only be carried out when modifiable causes of malnutrition are excluded and enhanced oral (like i.e. additional energy drinks) or enteral supply is unsuccessful or cannot be carried out.
A review of virtual reality based training simulators for orthopaedic surgery (2015)

This review presents current virtual reality based training simulators for hip, knee and other orthopaedic surgery, including elective and trauma surgical procedures. There have not been any reviews focussing on hip and knee orthopaedic simulators. A comparison of existing simulator features is provided to identify what is missing and what is required to improve upon current simulators. In total 11 hip replacements pre-operative planning tools were analysed, plus 9 hip trauma fracture training simulators. Additionally 9 knee arthroscopy simulators and 8 other orthopaedic simulators were included for comparison. The findings are that for orthopaedic surgery simulators in general, there is increasing use of patient-specific virtual models which reduce the learning curve. Modelling is also being used for patient-specific implant design and manufacture. Simulators are being increasingly validated for assessment as well as training. There are very few training simulators available for hip replacement, yet more advanced virtual reality is being used for other procedures such as hip trauma and drilling. Training simulators for hip replacement and orthopaedic surgery in general lag behind other surgical procedures for which virtual reality has become more common. Further developments are required to bring hip replacement training simulation up to date with other procedures. This suggests there is a gap in the market for a new high fidelity hip replacement and resurfacing training simulator.
Remote physical device fingerprinting (2005)

We introduce the area of remote physical device fingerprinting, or fingerprinting a physical device, as opposed to an operating system or class of devices, remotely, and without the fingerprinted device's known cooperation. We accomplish this goal by exploiting small, microscopic deviations in device hardware: clock skews. Our techniques do not require any modification to the fingerprinted devices. Our techniques report consistent measurements when the measurer is thousands of miles, multiple hops, and tens of milliseconds away from the fingerprinted device, and when the fingerprinted device is connected to the Internet from different locations and via different access technologies. Further one can apply our passive and semi-passive techniques when the fingerprinted device is behind a NAT or firewall, and also when the device's system time is maintained via NTP or SNTP. One can use our techniques to obtain information about whether two devices an the Internet, possibly shifted in time or IP addresses, are actually the same physical device. Example applications include: computer forensics; tracking, with some probability, a physical device as it connects to the Internet from different public access points; counting the number of devices behind a NAT even when the devices use constant or random IP ID; remotely probing a block of addresses to determine if the addresses correspond to virtual hosts, e.g., as part of a virtual honeynet; and unanonymizing anonymized network traces.
Computational methods for the analysis of differential conservation in groups of similar DNA sequences. (2004)

Multiple sequence alignments are a powerful tool for identifying the regions of DNA which have been constrained in evolutionary divergence, presumably due to their functional role. However, such constraints rarely manifest themselves as perfect conservation of a site clearly standing out in its broader environment, as they reflect the species-specific differences in proteins, as well as the ability of some proteins to interact with multiple variants of their binding sequence. In this paper we explore the use of alignment column uncertainty as an aid in locating differential phylogenetic footprints, which refer to the sites in DNA where groups of related species exhibit sequence conservation, but where the pattern may vary between the groups. We use efficient, linear-time algorithms to locate such sites. We have performed a study of the mammalian CAV2-CAV1 gene region using our software, and we conclude with several observations concerning the differential conservation and the use of computational methods for its detection. The software developed for this project is available, free of charge, by contacting the author.
c-erbB3 protein expression in ovarian cancer (1996)

Aims-To study the prevalence of overexpression of c-erbB3 growth factor receptor in ovarian carcinomas and to analyse its relation to histological subtype, stage and grade of the tumours.Methods-Ninety eight ovarian carcinomas were evaluated immunohistochemically using the RTJ1 monoclonal antibody raised against a synthetic peptide, the sequence of which was derived from the cytoplasmic domain of the c-erbB3 protein.Results-Of the tumours, 16% (16/98) overexpressed c-erbB3 protein relative to normal ovarian epithelium, whereas 22% (22/98) were completely negative. There was a statistically significant association between overexpression and well differentiated grade.Conclusions-These findings suggest that c-erbB3 protein overexpression occurs in a significant proportion of ovarian cancers and is correlated with differentiation. Overexpression may merit further investigation as a potential prognostic indicator and as a target for new treatment.
A Three-Dimensional Flow Control Concept for Single-Cell Experiments on a Microchip. 2. Fluorescein Diacetate Metabolism and Calcium Mobilization in a Single Yeast Cell As Stimulated by Glucose and pH Changes (2004)

Using a three-dimensional flow control concept to manipulate and retain a single yeast cell in a microchip, we were able to study the kinetics of intracellular metabolism and calcium mobilization at the single-cell level, as stimulated by glucose and pH changes. As a model study, the fluorogenic substrate fluorescein diacetate (FDA) was chosen to study how the intracellular carboxylesterase metabolize it. A single yeast cell was first cultured in the microchip. Thereafter, under a constant concentration of FDA, influx of FDA into the yeast cell occurred and FDA was hydrolyzed or metabolized. It was found that changes in both pH and glucose stimulated the FDA metabolism in a yeast cell, and the stimuli can elicit multiple responses from the cell. Since it was carried out within the microchip, the whole experiment on one single yeast cell could last for as long as 10 h. The dormant cell, budding cell, and pretreated budding cell (in low-pH buffer) of yeast resulted in different responses. Experimental data provided details on the FDA metabolism at the single-cell level and revealed strong correlations between FDA metabolism and calcium mobilization. Furthermore, efflux of the FDA metabolite fluorescein could start spontaneously if there was glucose in the medium. The experiments on a single cell were of the "human cell conservation" style because the cell responded to the reagent changes implemented by the human researcher. A mathematical model was also developed to study the influx-hydrolysis-efflux processes of the FDA metabolism using single-cell fluorescent data. These long overdue single-cell experiments are now rendered possible using the three-dimensional flow control in the microchip.